diff --git a/.buildinfo b/.buildinfo index 076ec140..98e9985c 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 70805c59f5a8bfa5f658981cb4f9da62 +config: ecdef1c94c317387bf658b694c67eed4 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle index c4a70b06..64aaf67f 100644 Binary files a/.doctrees/environment.pickle and b/.doctrees/environment.pickle differ diff --git a/.doctrees/includeme.doctree b/.doctrees/includeme.doctree index da77fa04..d1f0555b 100644 Binary files a/.doctrees/includeme.doctree and b/.doctrees/includeme.doctree differ diff --git a/.doctrees/release_notes.doctree b/.doctrees/release_notes.doctree index 07dc07e5..6fab1f3c 100644 Binary files a/.doctrees/release_notes.doctree and b/.doctrees/release_notes.doctree differ diff --git a/_sources/release_notes.rst.txt b/_sources/release_notes.rst.txt index 5be83595..d7f683d4 100644 --- a/_sources/release_notes.rst.txt +++ b/_sources/release_notes.rst.txt @@ -7,6 +7,14 @@ Development Branch ------------------ `Development Branch`_ +Version 1.4.9 +------------- + +October 25, 2023 + +- Fixed deprecated numpy function impacting nasa.py and shomate.py + Conversion of an array with ndim > 0 to a scalar + Version 1.4.7 ------------- diff --git a/_static/documentation_options.js b/_static/documentation_options.js index 701da062..cc95ffd3 100644 --- a/_static/documentation_options.js +++ b/_static/documentation_options.js @@ -1,6 +1,6 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '1.4.7', + VERSION: '1.4.9', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/api/constants/constants.html b/api/constants/constants.html index 909f268f..6964c530 100644 --- a/api/constants/constants.html +++ b/api/constants/constants.html @@ -4,7 +4,7 @@ - Constants — pmutt 1.4.7 documentation + Constants — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
- 1.4.7 + 1.4.9
diff --git a/api/constants/constants/pmutt.constants.Na.html b/api/constants/constants/pmutt.constants.Na.html index 06c36401..aca1ba5a 100644 --- a/api/constants/constants/pmutt.constants.Na.html +++ b/api/constants/constants/pmutt.constants.Na.html @@ -4,7 +4,7 @@ - pmutt.constants.Na — pmutt 1.4.7 documentation + pmutt.constants.Na — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
- 1.4.7 + 1.4.9
@@ -129,7 +129,7 @@

pmutt.constants.Na
Type:
-

float

+

float

diff --git a/api/constants/constants/pmutt.constants.P0.html b/api/constants/constants/pmutt.constants.P0.html index 75fcd26e..7b24c170 100644 --- a/api/constants/constants/pmutt.constants.P0.html +++ b/api/constants/constants/pmutt.constants.P0.html @@ -4,7 +4,7 @@ - pmutt.constants.P0 — pmutt 1.4.7 documentation + pmutt.constants.P0 — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
- 1.4.7 + 1.4.9
@@ -129,7 +129,7 @@

pmutt.constants.P0
Parameters:
-

units (str) –

Units for P0. Supported units

+

units (str) –

Units for P0. Supported units

@@ -178,10 +178,10 @@

pmutt.constants.P0

P0 – Reference pressure in appropriate units

Return type:
-

float

+

float

Raises:
-

KeyError – If units is not supported.

+

KeyError – If units is not supported.

diff --git a/api/constants/constants/pmutt.constants.R.html b/api/constants/constants/pmutt.constants.R.html index 942a0d1e..8e45f59d 100644 --- a/api/constants/constants/pmutt.constants.R.html +++ b/api/constants/constants/pmutt.constants.R.html @@ -4,7 +4,7 @@ - pmutt.constants.R — pmutt 1.4.7 documentation + pmutt.constants.R — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
- 1.4.7 + 1.4.9
@@ -129,7 +129,7 @@

pmutt.constants.R
Parameters:
-

units (str) –

Units for R. Supported units

+

units (str) –

Units for R. Supported units

Unit

@@ -210,10 +210,10 @@

pmutt.constants.R

R – Universal molar gas constant in appropriate units

Return type:
-

float

+

float

Raises:
-

KeyError – If units is not supported.

+

KeyError – If units is not supported.

diff --git a/api/constants/constants/pmutt.constants.T0.html b/api/constants/constants/pmutt.constants.T0.html index 02b95790..2eaee2e8 100644 --- a/api/constants/constants/pmutt.constants.T0.html +++ b/api/constants/constants/pmutt.constants.T0.html @@ -4,7 +4,7 @@ - pmutt.constants.T0 — pmutt 1.4.7 documentation + pmutt.constants.T0 — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
- 1.4.7 + 1.4.9
@@ -129,7 +129,7 @@

pmutt.constants.T0
Parameters:
-

units (str) –

Units for T0. Supported units

+

units (str) –

Units for T0. Supported units

Unit

@@ -162,10 +162,10 @@

pmutt.constants.T0

T0 – Room temperature in appropriate units

Return type:
-

float

+

float

Raises:
-

KeyError – If units is not supported.

+

KeyError – If units is not supported.

diff --git a/api/constants/constants/pmutt.constants.V0.html b/api/constants/constants/pmutt.constants.V0.html index 1cd8e057..831ece0c 100644 --- a/api/constants/constants/pmutt.constants.V0.html +++ b/api/constants/constants/pmutt.constants.V0.html @@ -4,7 +4,7 @@ - pmutt.constants.V0 — pmutt 1.4.7 documentation + pmutt.constants.V0 — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
- 1.4.7 + 1.4.9
@@ -129,7 +129,7 @@

pmutt.constants.V0
Parameters:
-

units (str) –

Units for V0. Supported units

+

units (str) –

Units for V0. Supported units

Unit

diff --git a/api/constants/constants/pmutt.constants.c.html b/api/constants/constants/pmutt.constants.c.html index 03962a26..c3d44d12 100644 --- a/api/constants/constants/pmutt.constants.c.html +++ b/api/constants/constants/pmutt.constants.c.html @@ -4,7 +4,7 @@ - pmutt.constants.c — pmutt 1.4.7 documentation + pmutt.constants.c — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
- 1.4.7 + 1.4.9
@@ -129,7 +129,7 @@

pmutt.constants.c
Parameters:
-

units (str) –

Units for c. Supported units

+

units (str) –

Units for c. Supported units

Unit

@@ -154,10 +154,10 @@

pmutt.constants.c

c – Speed of light in appropriate units

Return type:
-

float

+

float

Raises:
-

KeyError – If units is not supported.

+

KeyError – If units is not supported.

diff --git a/api/constants/constants/pmutt.constants.e.html b/api/constants/constants/pmutt.constants.e.html index fb7eb199..5d5d329d 100644 --- a/api/constants/constants/pmutt.constants.e.html +++ b/api/constants/constants/pmutt.constants.e.html @@ -4,7 +4,7 @@ - pmutt.constants.e — pmutt 1.4.7 documentation + pmutt.constants.e — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
- 1.4.7 + 1.4.9
@@ -129,7 +129,7 @@

pmutt.constants.e
Type:
-

float

+

float

diff --git a/api/constants/constants/pmutt.constants.h.html b/api/constants/constants/pmutt.constants.h.html index 27680812..6064d964 100644 --- a/api/constants/constants/pmutt.constants.h.html +++ b/api/constants/constants/pmutt.constants.h.html @@ -4,7 +4,7 @@ - pmutt.constants.h — pmutt 1.4.7 documentation + pmutt.constants.h — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
- 1.4.7 + 1.4.9
@@ -130,7 +130,7 @@

pmutt.constants.h
Parameters:
    -
  • units (str) –

    Units for h. Supported units

    +
  • units (str) –

    Units for h. Supported units

Unit

@@ -162,17 +162,17 @@

pmutt.constants.hbool, optional) – If True, returns h/2*pi . Default is False

+
  • bar (bool, optional) – If True, returns h/2*pi . Default is False

  • Returns:

    h – Planck’s constant in appropriate units

    Return type:
    -

    float

    +

    float

    Raises:
    -

    KeyError – If units is not supported.

    +

    KeyError – If units is not supported.

    diff --git a/api/constants/constants/pmutt.constants.kb.html b/api/constants/constants/pmutt.constants.kb.html index 347bf575..b3f0a34e 100644 --- a/api/constants/constants/pmutt.constants.kb.html +++ b/api/constants/constants/pmutt.constants.kb.html @@ -4,7 +4,7 @@ - pmutt.constants.kb — pmutt 1.4.7 documentation + pmutt.constants.kb — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -129,7 +129,7 @@

    pmutt.constants.kb
    Parameters:
    -

    units (str) –

    Units for kb. Supported units

    +

    units (str) –

    Units for kb. Supported units

    Unit

    @@ -174,10 +174,10 @@

    pmutt.constants.kb

    kb – Boltzmann constant in appropriate units

    Return type:
    -

    float

    +

    float

    Raises:
    -

    KeyError – If units is not supported.

    +

    KeyError – If units is not supported.

    diff --git a/api/constants/constants/pmutt.constants.m_e.html b/api/constants/constants/pmutt.constants.m_e.html index 5f344366..888cdef9 100644 --- a/api/constants/constants/pmutt.constants.m_e.html +++ b/api/constants/constants/pmutt.constants.m_e.html @@ -4,7 +4,7 @@ - pmutt.constants.m_e — pmutt 1.4.7 documentation + pmutt.constants.m_e — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -129,7 +129,7 @@

    pmutt.constants.m_e
    Parameters:
    -

    units (str) –

    Units for m_e. Supported units

    +

    units (str) –

    Units for m_e. Supported units

    Unit

    @@ -158,10 +158,10 @@

    pmutt.constants.m_e

    m_e – Mass of electron in appropriate units

    Return type:
    -

    float

    +

    float

    Raises:
    -

    KeyError – If units is not supported.

    +

    KeyError – If units is not supported.

    diff --git a/api/constants/constants/pmutt.constants.m_p.html b/api/constants/constants/pmutt.constants.m_p.html index c213f139..497d27e5 100644 --- a/api/constants/constants/pmutt.constants.m_p.html +++ b/api/constants/constants/pmutt.constants.m_p.html @@ -4,7 +4,7 @@ - pmutt.constants.m_p — pmutt 1.4.7 documentation + pmutt.constants.m_p — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -129,7 +129,7 @@

    pmutt.constants.m_p
    Parameters:
    -

    units (str) –

    Units for m_p. Supported units

    +

    units (str) –

    Units for m_p. Supported units

    Unit

    @@ -158,10 +158,10 @@

    pmutt.constants.m_p

    m_p – Mass of proton in appropriate units

    Return type:
    -

    float

    +

    float

    Raises:
    -

    KeyError – If units is not supported.

    +

    KeyError – If units is not supported.

    diff --git a/api/constants/misc/pmutt.constants.atomic_weight.html b/api/constants/misc/pmutt.constants.atomic_weight.html index cbce76b2..d948feec 100644 --- a/api/constants/misc/pmutt.constants.atomic_weight.html +++ b/api/constants/misc/pmutt.constants.atomic_weight.html @@ -4,7 +4,7 @@ - pmutt.constants.atomic_weight — pmutt 1.4.7 documentation + pmutt.constants.atomic_weight — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -123,7 +123,7 @@

    pmutt.constants.atomic_weight
    Type:
    -

    dict

    +

    dict

    diff --git a/api/constants/misc/pmutt.constants.prefixes.html b/api/constants/misc/pmutt.constants.prefixes.html index dc565854..1013f64a 100644 --- a/api/constants/misc/pmutt.constants.prefixes.html +++ b/api/constants/misc/pmutt.constants.prefixes.html @@ -4,7 +4,7 @@ - pmutt.constants.prefixes — pmutt 1.4.7 documentation + pmutt.constants.prefixes — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -122,7 +122,7 @@

    pmutt.constants.prefixes
    Type:
    -

    dict

    +

    dict

    diff --git a/api/constants/misc/pmutt.constants.symmetry_dict.html b/api/constants/misc/pmutt.constants.symmetry_dict.html index 2c28997e..1c6cc0f1 100644 --- a/api/constants/misc/pmutt.constants.symmetry_dict.html +++ b/api/constants/misc/pmutt.constants.symmetry_dict.html @@ -4,7 +4,7 @@ - pmutt.constants.symmetry_dict — pmutt 1.4.7 documentation + pmutt.constants.symmetry_dict — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -122,7 +122,7 @@

    pmutt.constants.symmetry_dict
    Type:
    -

    dict

    +

    dict

    diff --git a/api/constants/misc/pmutt.constants.type_dict.html b/api/constants/misc/pmutt.constants.type_dict.html index 233b9291..e9de6426 100644 --- a/api/constants/misc/pmutt.constants.type_dict.html +++ b/api/constants/misc/pmutt.constants.type_dict.html @@ -4,7 +4,7 @@ - pmutt.constants.type_dict — pmutt 1.4.7 documentation + pmutt.constants.type_dict — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -122,7 +122,7 @@

    pmutt.constants.type_dict
    Type:
    -

    dict

    +

    dict

    diff --git a/api/constants/unit_conv/pmutt.constants.convert_unit.html b/api/constants/unit_conv/pmutt.constants.convert_unit.html index cf2eeb9d..88f5dbd1 100644 --- a/api/constants/unit_conv/pmutt.constants.convert_unit.html +++ b/api/constants/unit_conv/pmutt.constants.convert_unit.html @@ -4,7 +4,7 @@ - pmutt.constants.convert_unit — pmutt 1.4.7 documentation + pmutt.constants.convert_unit — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -136,20 +136,20 @@

    pmutt.constants.convert_unit
    Parameters:
      -
    • num (float, optional) – Number to convert. I not specified, will return the appropriate +

    • num (float, optional) – Number to convert. I not specified, will return the appropriate conversion factor.

    • -
    • initial (str) – Units that num is currently in

    • -
    • final (str) – Units you would like num to be in

    • +
    • initial (str) – Units that num is currently in

    • +
    • final (str) – Units you would like num to be in

    Returns:

    conversion_num – num in the appropriate units

    Return type:
    -

    float

    +

    float

    Raises:
    -

    ValueError – If unit types are not consistent or not supported

    +

    ValueError – If unit types are not consistent or not supported

    Supported Units

    diff --git a/api/constants/unit_conv/pmutt.constants.debye_to_einstein.html b/api/constants/unit_conv/pmutt.constants.debye_to_einstein.html index be64125d..5522c344 100644 --- a/api/constants/unit_conv/pmutt.constants.debye_to_einstein.html +++ b/api/constants/unit_conv/pmutt.constants.debye_to_einstein.html @@ -4,7 +4,7 @@ - pmutt.constants.debye_to_einstein — pmutt 1.4.7 documentation + pmutt.constants.debye_to_einstein — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -135,13 +135,13 @@

    pmutt.constants.debye_to_einstein
    Parameters:
    -

    debye_temperature (float) – Debye temperature in K

    +

    debye_temperature (float) – Debye temperature in K

    Returns:

    einstein_temperature – Einstein temperature in K

    Return type:
    -

    float

    +

    float

    diff --git a/api/constants/unit_conv/pmutt.constants.einstein_to_debye.html b/api/constants/unit_conv/pmutt.constants.einstein_to_debye.html index e0616037..df0292b9 100644 --- a/api/constants/unit_conv/pmutt.constants.einstein_to_debye.html +++ b/api/constants/unit_conv/pmutt.constants.einstein_to_debye.html @@ -4,7 +4,7 @@ - pmutt.constants.einstein_to_debye — pmutt 1.4.7 documentation + pmutt.constants.einstein_to_debye — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -135,13 +135,13 @@

    pmutt.constants.einstein_to_debye
    Parameters:
    -

    einstein_temperature (float) – Einstein temperature in K

    +

    einstein_temperature (float) – Einstein temperature in K

    Returns:

    debye_temperature – Debye temperature in K

    Return type:
    -

    float

    +

    float

    diff --git a/api/constants/unit_conv/pmutt.constants.energy_to_freq.html b/api/constants/unit_conv/pmutt.constants.energy_to_freq.html index fb79eac8..66c1a24e 100644 --- a/api/constants/unit_conv/pmutt.constants.energy_to_freq.html +++ b/api/constants/unit_conv/pmutt.constants.energy_to_freq.html @@ -4,7 +4,7 @@ - pmutt.constants.energy_to_freq — pmutt 1.4.7 documentation + pmutt.constants.energy_to_freq — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -135,13 +135,13 @@

    pmutt.constants.energy_to_freq
    Parameters:
    -

    energy (float) – Energy in J

    +

    energy (float) – Energy in J

    Returns:

    freq – Frequency in Hz

    Return type:
    -

    float

    +

    float

    diff --git a/api/constants/unit_conv/pmutt.constants.energy_to_temp.html b/api/constants/unit_conv/pmutt.constants.energy_to_temp.html index 48bded24..94fa90ec 100644 --- a/api/constants/unit_conv/pmutt.constants.energy_to_temp.html +++ b/api/constants/unit_conv/pmutt.constants.energy_to_temp.html @@ -4,7 +4,7 @@ - pmutt.constants.energy_to_temp — pmutt 1.4.7 documentation + pmutt.constants.energy_to_temp — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -135,13 +135,13 @@

    pmutt.constants.energy_to_temp
    Parameters:
    -

    energy (float) – Energy in J

    +

    energy (float) – Energy in J

    Returns:

    temp – Temperature in K

    Return type:
    -

    float

    +

    float

    diff --git a/api/constants/unit_conv/pmutt.constants.energy_to_wavenumber.html b/api/constants/unit_conv/pmutt.constants.energy_to_wavenumber.html index 6f15aa9b..dcfd7df7 100644 --- a/api/constants/unit_conv/pmutt.constants.energy_to_wavenumber.html +++ b/api/constants/unit_conv/pmutt.constants.energy_to_wavenumber.html @@ -4,7 +4,7 @@ - pmutt.constants.energy_to_wavenumber — pmutt 1.4.7 documentation + pmutt.constants.energy_to_wavenumber — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -135,13 +135,13 @@

    pmutt.constants.energy_to_wavenumber
    Parameters:
    -

    energy (float) – Energy in J

    +

    energy (float) – Energy in J

    Returns:

    wavenumber – Wavenumber in 1/cm

    Return type:
    -

    float

    +

    float

    diff --git a/api/constants/unit_conv/pmutt.constants.freq_to_energy.html b/api/constants/unit_conv/pmutt.constants.freq_to_energy.html index eb87178e..9feb6e08 100644 --- a/api/constants/unit_conv/pmutt.constants.freq_to_energy.html +++ b/api/constants/unit_conv/pmutt.constants.freq_to_energy.html @@ -4,7 +4,7 @@ - pmutt.constants.freq_to_energy — pmutt 1.4.7 documentation + pmutt.constants.freq_to_energy — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -135,13 +135,13 @@

    pmutt.constants.freq_to_energy
    Parameters:
    -

    freq (float) – Frequency in Hz

    +

    freq (float) – Frequency in Hz

    Returns:

    energy – Energy in J

    Return type:
    -

    float

    +

    float

    diff --git a/api/constants/unit_conv/pmutt.constants.freq_to_temp.html b/api/constants/unit_conv/pmutt.constants.freq_to_temp.html index 1e51c316..7db4b558 100644 --- a/api/constants/unit_conv/pmutt.constants.freq_to_temp.html +++ b/api/constants/unit_conv/pmutt.constants.freq_to_temp.html @@ -4,7 +4,7 @@ - pmutt.constants.freq_to_temp — pmutt 1.4.7 documentation + pmutt.constants.freq_to_temp — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -135,13 +135,13 @@

    pmutt.constants.freq_to_temp
    Parameters:
    -

    freq (float) – Frequency in Hz

    +

    freq (float) – Frequency in Hz

    Returns:

    temp – Temperature in K

    Return type:
    -

    float

    +

    float

    diff --git a/api/constants/unit_conv/pmutt.constants.freq_to_wavenumber.html b/api/constants/unit_conv/pmutt.constants.freq_to_wavenumber.html index 83b43f0a..b9705234 100644 --- a/api/constants/unit_conv/pmutt.constants.freq_to_wavenumber.html +++ b/api/constants/unit_conv/pmutt.constants.freq_to_wavenumber.html @@ -4,7 +4,7 @@ - pmutt.constants.freq_to_wavenumber — pmutt 1.4.7 documentation + pmutt.constants.freq_to_wavenumber — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -135,13 +135,13 @@

    pmutt.constants.freq_to_wavenumber
    Parameters:
    -

    freq (float) – Frequency in Hz

    +

    freq (float) – Frequency in Hz

    Returns:

    wavenumber – Wavenumber in 1/cm

    Return type:
    -

    float

    +

    float

    diff --git a/api/constants/unit_conv/pmutt.constants.inertia_to_temp.html b/api/constants/unit_conv/pmutt.constants.inertia_to_temp.html index b43ae5cd..95530d4f 100644 --- a/api/constants/unit_conv/pmutt.constants.inertia_to_temp.html +++ b/api/constants/unit_conv/pmutt.constants.inertia_to_temp.html @@ -4,7 +4,7 @@ - pmutt.constants.inertia_to_temp — pmutt 1.4.7 documentation + pmutt.constants.inertia_to_temp — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -135,13 +135,13 @@

    pmutt.constants.inertia_to_temp
    Parameters:
    -

    inertia (float) – Moment of inertia in kg*m2

    +

    inertia (float) – Moment of inertia in kg*m2

    Returns:

    rot_temperature – Rotational temperature in K

    Return type:
    -

    float

    +

    float

    diff --git a/api/constants/unit_conv/pmutt.constants.temp_to_energy.html b/api/constants/unit_conv/pmutt.constants.temp_to_energy.html index d4bda734..3429c94f 100644 --- a/api/constants/unit_conv/pmutt.constants.temp_to_energy.html +++ b/api/constants/unit_conv/pmutt.constants.temp_to_energy.html @@ -4,7 +4,7 @@ - pmutt.constants.temp_to_energy — pmutt 1.4.7 documentation + pmutt.constants.temp_to_energy — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -135,13 +135,13 @@

    pmutt.constants.temp_to_energy
    Parameters:
    -

    temp (float) – Temperature in K

    +

    temp (float) – Temperature in K

    Returns:

    energy – Energy in J

    Return type:
    -

    float

    +

    float

    diff --git a/api/constants/unit_conv/pmutt.constants.temp_to_freq.html b/api/constants/unit_conv/pmutt.constants.temp_to_freq.html index 3521b614..dbf25ea5 100644 --- a/api/constants/unit_conv/pmutt.constants.temp_to_freq.html +++ b/api/constants/unit_conv/pmutt.constants.temp_to_freq.html @@ -4,7 +4,7 @@ - pmutt.constants.temp_to_freq — pmutt 1.4.7 documentation + pmutt.constants.temp_to_freq — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -135,13 +135,13 @@

    pmutt.constants.temp_to_freq
    Parameters:
    -

    temp (float) – Temperature in K

    +

    temp (float) – Temperature in K

    Returns:

    freq – Frequency in Hz

    Return type:
    -

    float

    +

    float

    diff --git a/api/constants/unit_conv/pmutt.constants.temp_to_wavenumber.html b/api/constants/unit_conv/pmutt.constants.temp_to_wavenumber.html index ad75a16c..5d1f1c2d 100644 --- a/api/constants/unit_conv/pmutt.constants.temp_to_wavenumber.html +++ b/api/constants/unit_conv/pmutt.constants.temp_to_wavenumber.html @@ -4,7 +4,7 @@ - pmutt.constants.temp_to_wavenumber — pmutt 1.4.7 documentation + pmutt.constants.temp_to_wavenumber — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -135,13 +135,13 @@

    pmutt.constants.temp_to_wavenumber
    Parameters:
    -

    temp (float) – Temperature in K

    +

    temp (float) – Temperature in K

    Returns:

    wavenumber – Wavenumber in 1/cm

    Return type:
    -

    float

    +

    float

    diff --git a/api/constants/unit_conv/pmutt.constants.wavenumber_to_energy.html b/api/constants/unit_conv/pmutt.constants.wavenumber_to_energy.html index ac41241b..7bff3e26 100644 --- a/api/constants/unit_conv/pmutt.constants.wavenumber_to_energy.html +++ b/api/constants/unit_conv/pmutt.constants.wavenumber_to_energy.html @@ -4,7 +4,7 @@ - pmutt.constants.wavenumber_to_energy — pmutt 1.4.7 documentation + pmutt.constants.wavenumber_to_energy — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -135,13 +135,13 @@

    pmutt.constants.wavenumber_to_energy
    Parameters:
    -

    wavenumber (float) – Wavenumber in 1/cm

    +

    wavenumber (float) – Wavenumber in 1/cm

    Returns:

    energies – Corresponding temperature in J

    Return type:
    -

    float

    +

    float

    diff --git a/api/constants/unit_conv/pmutt.constants.wavenumber_to_freq.html b/api/constants/unit_conv/pmutt.constants.wavenumber_to_freq.html index d19c8208..c15fd190 100644 --- a/api/constants/unit_conv/pmutt.constants.wavenumber_to_freq.html +++ b/api/constants/unit_conv/pmutt.constants.wavenumber_to_freq.html @@ -4,7 +4,7 @@ - pmutt.constants.wavenumber_to_freq — pmutt 1.4.7 documentation + pmutt.constants.wavenumber_to_freq — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -135,13 +135,13 @@

    pmutt.constants.wavenumber_to_freq
    Parameters:
    -

    wavenumber (float) – Wavenumber in 1/cm

    +

    wavenumber (float) – Wavenumber in 1/cm

    Returns:

    freq – Frequency in Hz

    Return type:
    -

    float

    +

    float

    diff --git a/api/constants/unit_conv/pmutt.constants.wavenumber_to_inertia.html b/api/constants/unit_conv/pmutt.constants.wavenumber_to_inertia.html index bf336ab2..17554ebe 100644 --- a/api/constants/unit_conv/pmutt.constants.wavenumber_to_inertia.html +++ b/api/constants/unit_conv/pmutt.constants.wavenumber_to_inertia.html @@ -4,7 +4,7 @@ - pmutt.constants.wavenumber_to_inertia — pmutt 1.4.7 documentation + pmutt.constants.wavenumber_to_inertia — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -135,13 +135,13 @@

    pmutt.constants.wavenumber_to_inertia
    Parameters:
    -

    wavenumber (float) – Wavenumber in 1/cm

    +

    wavenumber (float) – Wavenumber in 1/cm

    Returns:

    mu – Moment of inertia in kg*m2

    Return type:
    -

    float

    +

    float

    diff --git a/api/constants/unit_conv/pmutt.constants.wavenumber_to_temp.html b/api/constants/unit_conv/pmutt.constants.wavenumber_to_temp.html index dbd2dc9f..887f765f 100644 --- a/api/constants/unit_conv/pmutt.constants.wavenumber_to_temp.html +++ b/api/constants/unit_conv/pmutt.constants.wavenumber_to_temp.html @@ -4,7 +4,7 @@ - pmutt.constants.wavenumber_to_temp — pmutt 1.4.7 documentation + pmutt.constants.wavenumber_to_temp — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -135,13 +135,13 @@

    pmutt.constants.wavenumber_to_temp
    Parameters:
    -

    wavenumber (float) – Wavenumber in 1/cm

    +

    wavenumber (float) – Wavenumber in 1/cm

    Returns:

    temperature – Corresponding temperature in K

    Return type:
    -

    float

    +

    float

    diff --git a/api/empirical/empirical.html b/api/empirical/empirical.html index 807f7e5d..4c7878b4 100644 --- a/api/empirical/empirical.html +++ b/api/empirical/empirical.html @@ -4,7 +4,7 @@ - Empirical Models — pmutt 1.4.7 documentation + Empirical Models — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    diff --git a/api/empirical/empirical_base/pmutt.empirical.EmpiricalBase.html b/api/empirical/empirical_base/pmutt.empirical.EmpiricalBase.html index 1b83fba7..3ec74266 100644 --- a/api/empirical/empirical_base/pmutt.empirical.EmpiricalBase.html +++ b/api/empirical/empirical_base/pmutt.empirical.EmpiricalBase.html @@ -4,7 +4,7 @@ - pmutt.empirical.EmpiricalBase — pmutt 1.4.7 documentation + pmutt.empirical.EmpiricalBase — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -128,7 +128,7 @@

    pmutt.empirical.EmpiricalBase
    Type:
    -

    str, optional

    +

    str, optional

    @@ -141,7 +141,7 @@

    pmutt.empirical.EmpiricalBase
    Type:
    -

    str, optional

    +

    str, optional

    @@ -156,7 +156,7 @@

    pmutt.empirical.EmpiricalBase
    Type:
    -

    dict, optional

    +

    dict, optional

    @@ -192,7 +192,7 @@

    pmutt.empirical.EmpiricalBase
    Type:
    -

    str, optional

    +

    str, optional

    @@ -204,7 +204,7 @@

    pmutt.empirical.EmpiricalBase
    Type:
    -

    str, optional

    +

    str, optional

    @@ -217,7 +217,7 @@

    pmutt.empirical.EmpiricalBase
    Type:
    -

    bool, optional

    +

    bool, optional

    @@ -397,7 +397,7 @@

    pmutt.empirical.EmpiricalBase
    Parameters:
    -

    json_obj (dict) – JSON representation

    +

    json_obj (dict) – JSON representation

    Returns:

    EmpiricalBase

    @@ -415,7 +415,7 @@

    pmutt.empirical.EmpiricalBase
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • kwargs (keyword arguments) – Parameters needed by get_CpoR

    @@ -424,7 +424,7 @@

    pmutt.empirical.EmpiricalBase

    Cp – Heat capacity (constant P) in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -439,7 +439,7 @@

    pmutt.empirical.EmpiricalBase

    CpoR – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -451,7 +451,7 @@

    pmutt.empirical.EmpiricalBase
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • kwargs (keyword arguments) – Parameters needed by get_CvoR

    @@ -460,7 +460,7 @@

    pmutt.empirical.EmpiricalBase

    Cv – Heat capacity (constant V) in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -475,7 +475,7 @@

    pmutt.empirical.EmpiricalBase

    CvoR – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -487,9 +487,9 @@

    pmutt.empirical.EmpiricalBase
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_FoRT

    @@ -497,7 +497,7 @@

    pmutt.empirical.EmpiricalBase

    F – Hemholtz energy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -514,7 +514,7 @@

    pmutt.empirical.EmpiricalBase

    FoRT – Dimensionless Helmholtz energy

    Return type:
    -

    float

    +

    float

    @@ -526,9 +526,9 @@

    pmutt.empirical.EmpiricalBase
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_GoRT

    @@ -536,7 +536,7 @@

    pmutt.empirical.EmpiricalBase

    G – Gibbs energy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -553,7 +553,7 @@

    pmutt.empirical.EmpiricalBase

    GoRT – Dimensionless Gibbs free energy

    Return type:
    -

    float

    +

    float

    @@ -565,9 +565,9 @@

    pmutt.empirical.EmpiricalBase
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_HoRT

    @@ -575,7 +575,7 @@

    pmutt.empirical.EmpiricalBase

    H – Enthalpy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -589,7 +589,7 @@

    pmutt.empirical.EmpiricalBase

    HoRT – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -601,7 +601,7 @@

    pmutt.empirical.EmpiricalBase
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • kwargs (keyword arguments) – Parameters needed by get_SoR

    @@ -610,7 +610,7 @@

    pmutt.empirical.EmpiricalBase

    S – Entropy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -624,7 +624,7 @@

    pmutt.empirical.EmpiricalBase

    SoR – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -636,9 +636,9 @@

    pmutt.empirical.EmpiricalBase
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_UoRT

    @@ -646,7 +646,7 @@

    pmutt.empirical.EmpiricalBase

    U – Internal energy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -660,7 +660,7 @@

    pmutt.empirical.EmpiricalBase

    UoRT – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -674,7 +674,7 @@

    pmutt.empirical.EmpiricalBase

    q – Returns 1

    Return type:
    -

    float

    +

    float

    @@ -687,18 +687,18 @@

    pmutt.empirical.EmpiricalBase
    Parameters:
      -
    • T_low (float) – Lower temperature in K. If not specified, +

    • T_low (float) – Lower temperature in K. If not specified, T_low attribute used.

    • -
    • T_high (float) – Upper temperature in K. If not specified, +

    • T_high (float) – Upper temperature in K. If not specified, T_high attribute used.

    • -
    • Cp_units (str) – Units to plot heat capacity. See R() +

    • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • H_units (str) – Units to plot enthalpy. See R() for +

    • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    • -
    • S_units (str) – Units to plot entropy. See R() for +

    • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • G_units (str) – Units to plot Gibbs free energy. See R() +

    • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    @@ -725,18 +725,18 @@

    pmutt.empirical.EmpiricalBase
    Parameters:
      -
    • T_low (float) – Lower temperature in K. If not specified, +

    • T_low (float) – Lower temperature in K. If not specified, T_low attribute used

    • -
    • T_high (float) – Upper temperature in K. If not specified, +

    • T_high (float) – Upper temperature in K. If not specified, T_high attribute used

    • -
    • Cp_units (str) – Units to plot heat capacity. See R() +

    • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • H_units (str) – Units to plot enthalpy. See R() for +

    • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    • -
    • S_units (str) – Units to plot entropy. See R() for +

    • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • G_units (str) – Units to plot Gibbs free energy. See R() +

    • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    @@ -763,18 +763,18 @@

    pmutt.empirical.EmpiricalBase
    Parameters:
      -
    • T_low (float) – Lower temperature in K. If not specified, T_low +

    • T_low (float) – Lower temperature in K. If not specified, T_low attribute used

    • -
    • T_high (float) – Upper temperature in K. If not specified, T_high +

    • T_high (float) – Upper temperature in K. If not specified, T_high attribute used

    • -
    • Cp_units (str) – Units to plot heat capacity. See R() for +

    • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • H_units (str) – Units to plot enthalpy. See R() for +

    • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    • -
    • S_units (str) – Units to plot entropy. See R() for +

    • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • G_units (str) – Units to plot Gibbs free energy. See R() +

    • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    @@ -802,7 +802,7 @@

    pmutt.empirical.EmpiricalBase

    obj_dict

    Return type:
    -

    dict

    +

    dict

    diff --git a/api/empirical/misc/pmutt.empirical.GasPressureAdj.html b/api/empirical/misc/pmutt.empirical.GasPressureAdj.html index 0510c4f2..dec1dcaa 100644 --- a/api/empirical/misc/pmutt.empirical.GasPressureAdj.html +++ b/api/empirical/misc/pmutt.empirical.GasPressureAdj.html @@ -4,7 +4,7 @@ - pmutt.empirical.GasPressureAdj — pmutt 1.4.7 documentation + pmutt.empirical.GasPressureAdj — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
    - 1.4.7 + 1.4.9
    @@ -198,7 +198,7 @@

    pmutt.empirical.GasPressureAdj
    Parameters:
    -

    json_obj (dict) – JSON representation

    +

    json_obj (dict) – JSON representation

    Returns:

    Obj

    @@ -216,7 +216,7 @@

    pmutt.empirical.GasPressureAdj
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • kwargs (keyword arguments) – Parameters needed by get_CpoR

    @@ -225,7 +225,7 @@

    pmutt.empirical.GasPressureAdj

    Cp – Heat capacity (constant P) in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -240,7 +240,7 @@

    pmutt.empirical.GasPressureAdj

    CpoR – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -252,7 +252,7 @@

    pmutt.empirical.GasPressureAdj
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • kwargs (keyword arguments) – Parameters needed by get_CvoR

    @@ -261,7 +261,7 @@

    pmutt.empirical.GasPressureAdj

    Cv – Heat capacity (constant V) in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -276,7 +276,7 @@

    pmutt.empirical.GasPressureAdj

    CvoR – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -288,9 +288,9 @@

    pmutt.empirical.GasPressureAdj
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_FoRT

    @@ -298,7 +298,7 @@

    pmutt.empirical.GasPressureAdj

    F – Hemholtz energy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -315,7 +315,7 @@

    pmutt.empirical.GasPressureAdj

    FoRT – Dimensionless Helmholtz energy

    Return type:
    -

    float

    +

    float

    @@ -327,9 +327,9 @@

    pmutt.empirical.GasPressureAdj
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_GoRT

    @@ -337,7 +337,7 @@

    pmutt.empirical.GasPressureAdj

    G – Gibbs energy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -354,7 +354,7 @@

    pmutt.empirical.GasPressureAdj

    GoRT – Dimensionless Gibbs free energy

    Return type:
    -

    float

    +

    float

    @@ -366,9 +366,9 @@

    pmutt.empirical.GasPressureAdj
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_HoRT

    @@ -376,7 +376,7 @@

    pmutt.empirical.GasPressureAdj

    H – Enthalpy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -390,7 +390,7 @@

    pmutt.empirical.GasPressureAdj

    HoRT – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -402,7 +402,7 @@

    pmutt.empirical.GasPressureAdj
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • kwargs (keyword arguments) – Parameters needed by get_SoR

    @@ -411,7 +411,7 @@

    pmutt.empirical.GasPressureAdj

    S – Entropy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -441,9 +441,9 @@

    pmutt.empirical.GasPressureAdj
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_UoRT

    @@ -451,7 +451,7 @@

    pmutt.empirical.GasPressureAdj

    U – Internal energy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -465,7 +465,7 @@

    pmutt.empirical.GasPressureAdj

    UoRT – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -479,7 +479,7 @@

    pmutt.empirical.GasPressureAdj

    q – Returns 1

    Return type:
    -

    float

    +

    float

    @@ -493,7 +493,7 @@

    pmutt.empirical.GasPressureAdj

    obj_dict

    Return type:
    -

    dict

    +

    dict

    diff --git a/api/empirical/nasa/pmutt.empirical.nasa.Nasa.html b/api/empirical/nasa/pmutt.empirical.nasa.Nasa.html index 877512f4..3d1b79c5 100644 --- a/api/empirical/nasa/pmutt.empirical.nasa.Nasa.html +++ b/api/empirical/nasa/pmutt.empirical.nasa.Nasa.html @@ -4,7 +4,7 @@ - pmutt.empirical.nasa.Nasa — pmutt 1.4.7 documentation + pmutt.empirical.nasa.Nasa — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
    - 1.4.7 + 1.4.9
    @@ -139,7 +139,7 @@

    pmutt.empirical.nasa.Nasa
    Type:
    -

    float

    +

    float

    @@ -150,7 +150,7 @@

    pmutt.empirical.nasa.Nasa
    Type:
    -

    float

    +

    float

    @@ -161,7 +161,7 @@

    pmutt.empirical.nasa.Nasa
    Type:
    -

    float

    +

    float

    @@ -208,7 +208,7 @@

    pmutt.empirical.nasa.Nasa
    Type:
    -

    int, optional

    +

    int, optional

    @@ -410,18 +410,18 @@

    pmutt.empirical.nasa.Nasa
    Parameters:
      -
    • name (str) – Name of the species

    • +
    • name (str) – Name of the species

    • T ((N,) numpy.ndarray) – Temperatures in K used for fitting CpoR.

    • CpoR ((N,) numpy.ndarray) – Dimensionless heat capacity corresponding to T.

    • -
    • T_ref (float) – Reference temperature in K used fitting empirical coefficients.

    • -
    • HoRT_ref (float) – Dimensionless reference enthalpy that corresponds to T_ref.

    • -
    • SoR_ref (float) – Dimensionless entropy that corresponds to T_ref.

    • -
    • elements (dict) – Composition of the species. +

    • T_ref (float) – Reference temperature in K used fitting empirical coefficients.

    • +
    • HoRT_ref (float) – Dimensionless reference enthalpy that corresponds to T_ref.

    • +
    • SoR_ref (float) – Dimensionless entropy that corresponds to T_ref.

    • +
    • elements (dict) – Composition of the species. Keys of dictionary are elements, values are stoichiometric values in a formula unit. e.g. CH3OH can be represented as: {‘C’: 1, ‘H’: 4, ‘O’: 1,}.

    • -
    • T_mid (float or iterable of float, optional) – Guess for T_mid. If float, only uses that value for T_mid. If +

    • T_mid (float or iterable of float, optional) – Guess for T_mid. If float, only uses that value for T_mid. If list, finds the best fit for each element in the list. If None, a range of T_mid values are screened between the 6th lowest and 6th highest value of T.

    • @@ -442,7 +442,7 @@

      pmutt.empirical.nasa.Nasa
      Parameters:
      -

      json_obj (dict) – JSON representation

      +

      json_obj (dict) – JSON representation

      Returns:

      Nasa

      @@ -462,21 +462,21 @@

      pmutt.empirical.nasa.Nasa
      • model (Model object or class) – Model to generate data. Must contain the methods get_CpoR, get_HoRT and get_SoR

      • -
      • name (str, optional) – Name of the species. If not passed, model.name will be used.

      • -
      • T_low (float, optional) – Lower limit temerature in K. If not passed, model.T_low will +

      • name (str, optional) – Name of the species. If not passed, model.name will be used.

      • +
      • T_low (float, optional) – Lower limit temerature in K. If not passed, model.T_low will be used.

      • -
      • T_high (float, optional) – Higher limit temperature in K. If not passed, model.T_high +

      • T_high (float, optional) – Higher limit temperature in K. If not passed, model.T_high will be used.

      • -
      • T_mid (float or iterable of float, optional) – Guess for T_mid. If float, only uses that value for T_mid. If +

      • T_mid (float or iterable of float, optional) – Guess for T_mid. If float, only uses that value for T_mid. If list, finds the best fit for each element in the list. If None, a range of T_mid values are screened between the 6th lowest and 6th highest value of T.

      • -
      • elements (dict, optional) – Composition of the species. If not passed, model.elements +

      • elements (dict, optional) – Composition of the species. If not passed, model.elements will be used. Keys of dictionary are elements, values are stoichiometric values in a formula unit. e.g. CH3OH can be represented as: {‘C’: 1, ‘H’: 4, ‘O’: 1,}.

      • -
      • n_T (int, optional) – Number of data points between T_low and T_high for fitting +

      • n_T (int, optional) – Number of data points between T_low and T_high for fitting heat capacity. Default is 50.

      • kwargs (keyword arguments) – Used to initalize model if a class is passed.

      @@ -498,16 +498,16 @@

      pmutt.empirical.nasa.Nasa
      Parameters:
        -
      • name (str) – Name of the species

      • +
      • name (str) – Name of the species

      • statmech_model (pmutt.statmech.StatMech object or class) – Statistical Mechanics model to generate data

      • -
      • T_low (float) – Lower limit temerature in K

      • -
      • T_high (float) – Higher limit temperature in K

      • -
      • T_mid (float or iterable of float, optional) – Guess for T_mid. If float, only uses that value for T_mid. If +

      • T_low (float) – Lower limit temerature in K

      • +
      • T_high (float) – Higher limit temperature in K

      • +
      • T_mid (float or iterable of float, optional) – Guess for T_mid. If float, only uses that value for T_mid. If list, finds the best fit for each element in the list. If None, a range of T_mid values are screened between the 6th lowest and 6th highest value of T.

      • references (pmutt.empirical.references.References object) – Reference to adjust enthalpy

      • -
      • elements (dict) – Composition of the species. +

      • elements (dict) – Composition of the species. Keys of dictionary are elements, values are stoichiometric values in a formula unit. e.g. CH3OH can be represented as: @@ -533,11 +533,11 @@

        pmutt.empirical.nasa.NasaParameters:
        • T (float or (N,) numpy.ndarray) – Temperature(s) in K

        • -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units.

        • -
        • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

        • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

        • -
        • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

        • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

        • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

        • @@ -560,9 +560,9 @@

          pmutt.empirical.nasa.NasaParameters:
          • T (float or (N,) numpy.ndarray) – Temperature(s) in K

          • -
          • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

          • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

          • -
          • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

          • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

          • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

          • @@ -584,7 +584,7 @@

            pmutt.empirical.nasa.Nasa
            Parameters:
              -
            • units (str) – Units as string. See R() for accepted +

            • units (str) – Units as string. See R() for accepted units.

            • kwargs (keyword arguments) – Parameters needed by get_CvoR

            @@ -593,7 +593,7 @@

            pmutt.empirical.nasa.Nasa

            Cv – Heat capacity (constant V) in appropriate units

            Return type:
            -

            float

            +

            float

          @@ -608,7 +608,7 @@

          pmutt.empirical.nasa.Nasa

          CvoR – Returns 0

        Return type:
        -

        float

        +

        float

      @@ -620,9 +620,9 @@

      pmutt.empirical.nasa.Nasa
      Parameters:
        -
      • units (str) – Units as string. See R() for accepted +

      • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

      • -
      • T (float, optional) – Temperature in K. Default is 298.15 K

      • +
      • T (float, optional) – Temperature in K. Default is 298.15 K

      • kwargs (keyword arguments) – Parameters needed by get_FoRT

      @@ -630,7 +630,7 @@

      pmutt.empirical.nasa.Nasa

      F – Hemholtz energy in appropriate units

      Return type:
      -

      float

      +

      float

    @@ -647,7 +647,7 @@

    pmutt.empirical.nasa.Nasa

    FoRT – Dimensionless Helmholtz energy

    Return type:
    -

    float

    +

    float

    @@ -660,14 +660,14 @@

    pmutt.empirical.nasa.NasaParameters:
    • T (float or (N,) numpy.ndarray) – Temperature(s) in K

    • -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

    • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

    • -
    • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

    • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

    • -
    • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of +

    • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

    • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

    @@ -689,12 +689,12 @@

    pmutt.empirical.nasa.NasaParameters:
    • T (float or (N,) numpy.ndarray) – Temperature(s) in K

    • -
    • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

    • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

    • -
    • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

    • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

    • -
    • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of +

    • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

    • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

    @@ -716,11 +716,11 @@

    pmutt.empirical.nasa.NasaParameters:
    • T (float or (N,) numpy.ndarray) – Temperature(s) in K

    • -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

    • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

    • -
    • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

    • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

    • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

    • @@ -743,9 +743,9 @@

      pmutt.empirical.nasa.NasaParameters:
      • T (float or (N,) numpy.ndarray) – Temperature(s) in K

      • -
      • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

      • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

      • -
      • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

      • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

      • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

      • @@ -768,14 +768,14 @@

        pmutt.empirical.nasa.NasaParameters:
        • T (float or (N,) numpy.ndarray) – Temperature(s) in K

        • -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units.

        • -
        • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

        • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

        • -
        • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

        • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

        • -
        • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of +

        • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

        • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

        @@ -801,7 +801,7 @@

        pmutt.empirical.nasa.Nasa

        SoR – Entropy

        Return type:
        -

        float

        +

        float

      @@ -814,12 +814,12 @@

      pmutt.empirical.nasa.NasaParameters:
      • T (float or (N,) numpy.ndarray) – Temperature(s) in K

      • -
      • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

      • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

      • -
      • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

      • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

      • -
      • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of +

      • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

      • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

      @@ -840,9 +840,9 @@

      pmutt.empirical.nasa.Nasa
      Parameters:
        -
      • units (str) – Units as string. See R() for accepted +

      • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

      • -
      • T (float, optional) – Temperature in K. Default is 298.15 K

      • +
      • T (float, optional) – Temperature in K. Default is 298.15 K

      • kwargs (keyword arguments) – Parameters needed by get_UoRT

      @@ -850,7 +850,7 @@

      pmutt.empirical.nasa.Nasa

      U – Internal energy in appropriate units

      Return type:
      -

      float

      +

      float

    @@ -864,7 +864,7 @@

    pmutt.empirical.nasa.Nasa

    UoRT – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -876,7 +876,7 @@

    pmutt.empirical.nasa.Nasa
    Parameters:
    -

    T (float) – Temperature in K

    +

    T (float) – Temperature in K

    Returns:

    a – NASA polynomial coefficients

    @@ -896,7 +896,7 @@

    pmutt.empirical.nasa.Nasa

    q – Returns 1

    Return type:
    -

    float

    +

    float

    @@ -909,18 +909,18 @@

    pmutt.empirical.nasa.Nasa
    Parameters:
      -
    • T_low (float) – Lower temperature in K. If not specified, +

    • T_low (float) – Lower temperature in K. If not specified, T_low attribute used.

    • -
    • T_high (float) – Upper temperature in K. If not specified, +

    • T_high (float) – Upper temperature in K. If not specified, T_high attribute used.

    • -
    • Cp_units (str) – Units to plot heat capacity. See R() +

    • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • H_units (str) – Units to plot enthalpy. See R() for +

    • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    • -
    • S_units (str) – Units to plot entropy. See R() for +

    • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • G_units (str) – Units to plot Gibbs free energy. See R() +

    • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    @@ -947,18 +947,18 @@

    pmutt.empirical.nasa.Nasa
    Parameters:
      -
    • T_low (float) – Lower temperature in K. If not specified, +

    • T_low (float) – Lower temperature in K. If not specified, T_low attribute used

    • -
    • T_high (float) – Upper temperature in K. If not specified, +

    • T_high (float) – Upper temperature in K. If not specified, T_high attribute used

    • -
    • Cp_units (str) – Units to plot heat capacity. See R() +

    • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • H_units (str) – Units to plot enthalpy. See R() for +

    • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    • -
    • S_units (str) – Units to plot entropy. See R() for +

    • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • G_units (str) – Units to plot Gibbs free energy. See R() +

    • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    @@ -985,18 +985,18 @@

    pmutt.empirical.nasa.Nasa
    Parameters:
      -
    • T_low (float) – Lower temperature in K. If not specified, T_low +

    • T_low (float) – Lower temperature in K. If not specified, T_low attribute used

    • -
    • T_high (float) – Upper temperature in K. If not specified, T_high +

    • T_high (float) – Upper temperature in K. If not specified, T_high attribute used

    • -
    • Cp_units (str) – Units to plot heat capacity. See R() for +

    • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • H_units (str) – Units to plot enthalpy. See R() for +

    • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    • -
    • S_units (str) – Units to plot entropy. See R() for +

    • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • G_units (str) – Units to plot Gibbs free energy. See R() +

    • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    @@ -1024,7 +1024,7 @@

    pmutt.empirical.nasa.Nasa

    CTI_str – Object represented as a CTI string.

    Return type:
    -

    str

    +

    str

    @@ -1038,7 +1038,7 @@

    pmutt.empirical.nasa.Nasa

    obj_dict

    Return type:
    -

    dict

    +

    dict

    @@ -1052,7 +1052,7 @@

    pmutt.empirical.nasa.Nasa

    yaml_dict – Dictionary compatible with Cantera’s YAML format

    Return type:
    -

    dict

    +

    dict

    diff --git a/api/empirical/nasa/pmutt.empirical.nasa.Nasa9.html b/api/empirical/nasa/pmutt.empirical.nasa.Nasa9.html index 5ebd1778..e52c1f73 100644 --- a/api/empirical/nasa/pmutt.empirical.nasa.Nasa9.html +++ b/api/empirical/nasa/pmutt.empirical.nasa.Nasa9.html @@ -4,7 +4,7 @@ - pmutt.empirical.nasa.Nasa9 — pmutt 1.4.7 documentation + pmutt.empirical.nasa.Nasa9 — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
    - 1.4.7 + 1.4.9
    @@ -150,7 +150,7 @@

    pmutt.empirical.nasa.Nasa9
    Type:
    -

    float

    +

    float

    @@ -161,7 +161,7 @@

    pmutt.empirical.nasa.Nasa9
    Type:
    -

    float

    +

    float

    @@ -381,13 +381,13 @@

    pmutt.empirical.nasa.Nasa9
    Parameters:
      -
    • name (str) – Name of the species

    • +
    • name (str) – Name of the species

    • T ((N,) numpy.ndarray) – Temperatures in K used for fitting CpoR.

    • CpoR ((N,) numpy.ndarray) – Dimensionless heat capacity corresponding to T.

    • -
    • T_ref (float) – Reference temperature in K used fitting empirical coefficients.

    • -
    • HoRT_ref (float) – Dimensionless reference enthalpy that corresponds to T_ref.

    • -
    • SoR_ref (float) – Dimensionless entropy that corresponds to T_ref.

    • -
    • elements (dict) – Composition of the species. +

    • T_ref (float) – Reference temperature in K used fitting empirical coefficients.

    • +
    • HoRT_ref (float) – Dimensionless reference enthalpy that corresponds to T_ref.

    • +
    • SoR_ref (float) – Dimensionless entropy that corresponds to T_ref.

    • +
    • elements (dict) – Composition of the species. Keys of dictionary are elements, values are stoichiometric values in a formula unit. e.g. CH3OH can be represented as: @@ -413,7 +413,7 @@

      pmutt.empirical.nasa.Nasa9
      Parameters:
      -

      json_obj (dict) – JSON representation

      +

      json_obj (dict) – JSON representation

      Returns:

      Nasa

      @@ -431,23 +431,23 @@

      pmutt.empirical.nasa.Nasa9
      Parameters:
        -
      • name (str) – Name of the species

      • +
      • name (str) – Name of the species

      • model (Model object or class) – Model to generate data. Must contain the methods get_CpoR, get_HoRT and get_SoR

      • -
      • T_low (float) – Lower limit temerature in K

      • -
      • T_high (float) – Higher limit temperature in K

      • -
      • elements (dict) – Composition of the species. +

      • T_low (float) – Lower limit temerature in K

      • +
      • T_high (float) – Higher limit temperature in K

      • +
      • elements (dict) – Composition of the species. Keys of dictionary are elements, values are stoichiometric values in a formula unit. e.g. CH3OH can be represented as: {‘C’: 1, ‘H’: 4, ‘O’: 1,}.

      • T_mid ((n_interval,) nd.ndarray) – Temperatures (in K) to use at intervals. See fit_T_mid for behavior.

      • -
      • n_interval (int, optional) – Number of NASA9 polynomials to create. Default is 2

      • -
      • n_T (int, optional) – Number of temperature values to evaluate between each interval. +

      • n_interval (int, optional) – Number of NASA9 polynomials to create. Default is 2

      • +
      • n_T (int, optional) – Number of temperature values to evaluate between each interval. Larger values result is a better fit but take longer to run. Default is 50.

      • -
      • fit_T_mid (bool, optional) – If True, T_mid values initial values and can be changed. If +

      • fit_T_mid (bool, optional) – If True, T_mid values initial values and can be changed. If False, T_mid values are not changed

      • kwargs (keyword arguments) – Used to initalize model if a class is passed.

      @@ -469,11 +469,11 @@

      pmutt.empirical.nasa.Nasa9Parameters:
      • T (float or (N,) numpy.ndarray) – Temperature(s) in K

      • -
      • units (str) – Units as string. See R() for accepted +

      • units (str) – Units as string. See R() for accepted units.

      • -
      • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

      • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

      • -
      • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

      • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

      • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

      • @@ -496,9 +496,9 @@

        pmutt.empirical.nasa.Nasa9Parameters:
        • T (float or (N,) numpy.ndarray) – Temperature(s) in K

        • -
        • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

        • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

        • -
        • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

        • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

        • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

        • @@ -520,7 +520,7 @@

          pmutt.empirical.nasa.Nasa9
          Parameters:
            -
          • units (str) – Units as string. See R() for accepted +

          • units (str) – Units as string. See R() for accepted units.

          • kwargs (keyword arguments) – Parameters needed by get_CvoR

          @@ -529,7 +529,7 @@

          pmutt.empirical.nasa.Nasa9

          Cv – Heat capacity (constant V) in appropriate units

          Return type:
          -

          float

          +

          float

        @@ -544,7 +544,7 @@

        pmutt.empirical.nasa.Nasa9

        CvoR – Returns 0

      Return type:
      -

      float

      +

      float

      @@ -556,9 +556,9 @@

      pmutt.empirical.nasa.Nasa9
      Parameters:
        -
      • units (str) – Units as string. See R() for accepted +

      • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

      • -
      • T (float, optional) – Temperature in K. Default is 298.15 K

      • +
      • T (float, optional) – Temperature in K. Default is 298.15 K

      • kwargs (keyword arguments) – Parameters needed by get_FoRT

      @@ -566,7 +566,7 @@

      pmutt.empirical.nasa.Nasa9

      F – Hemholtz energy in appropriate units

      Return type:
      -

      float

      +

      float

    @@ -583,7 +583,7 @@

    pmutt.empirical.nasa.Nasa9

    FoRT – Dimensionless Helmholtz energy

    Return type:
    -

    float

    +

    float

    @@ -596,14 +596,14 @@

    pmutt.empirical.nasa.Nasa9Parameters:
    • T (float or (N,) numpy.ndarray) – Temperature(s) in K

    • -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

    • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

    • -
    • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

    • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

    • -
    • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of +

    • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

    • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

    @@ -625,12 +625,12 @@

    pmutt.empirical.nasa.Nasa9Parameters:
    • T (float or (N,) numpy.ndarray) – Temperature(s) in K

    • -
    • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

    • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

    • -
    • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

    • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

    • -
    • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of +

    • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

    • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

    @@ -652,11 +652,11 @@

    pmutt.empirical.nasa.Nasa9Parameters:
    • T (float or (N,) numpy.ndarray) – Temperature(s) in K

    • -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

    • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

    • -
    • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

    • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

    • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

    • @@ -679,9 +679,9 @@

      pmutt.empirical.nasa.Nasa9Parameters:
      • T (float or (N,) numpy.ndarray) – Temperature(s) in K

      • -
      • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

      • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

      • -
      • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

      • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

      • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

      • @@ -704,14 +704,14 @@

        pmutt.empirical.nasa.Nasa9Parameters:
        • T (float or (N,) numpy.ndarray) – Temperature(s) in K

        • -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units.

        • -
        • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

        • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

        • -
        • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

        • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

        • -
        • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of +

        • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

        • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

        @@ -737,7 +737,7 @@

        pmutt.empirical.nasa.Nasa9

        SoR – Entropy

        Return type:
        -

        float

        +

        float

      @@ -750,12 +750,12 @@

      pmutt.empirical.nasa.Nasa9Parameters:
      • T (float or (N,) numpy.ndarray) – Temperature(s) in K

      • -
      • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

      • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

      • -
      • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

      • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

      • -
      • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of +

      • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

      • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

      @@ -776,9 +776,9 @@

      pmutt.empirical.nasa.Nasa9
      Parameters:
        -
      • units (str) – Units as string. See R() for accepted +

      • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

      • -
      • T (float, optional) – Temperature in K. Default is 298.15 K

      • +
      • T (float, optional) – Temperature in K. Default is 298.15 K

      • kwargs (keyword arguments) – Parameters needed by get_UoRT

      @@ -786,7 +786,7 @@

      pmutt.empirical.nasa.Nasa9

      U – Internal energy in appropriate units

      Return type:
      -

      float

      +

      float

    @@ -800,7 +800,7 @@

    pmutt.empirical.nasa.Nasa9

    UoRT – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -814,7 +814,7 @@

    pmutt.empirical.nasa.Nasa9

    q – Returns 1

    Return type:
    -

    float

    +

    float

    @@ -832,18 +832,18 @@

    pmutt.empirical.nasa.Nasa9
    Parameters:
      -
    • T_low (float) – Lower temperature in K. If not specified, +

    • T_low (float) – Lower temperature in K. If not specified, T_low attribute used.

    • -
    • T_high (float) – Upper temperature in K. If not specified, +

    • T_high (float) – Upper temperature in K. If not specified, T_high attribute used.

    • -
    • Cp_units (str) – Units to plot heat capacity. See R() +

    • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • H_units (str) – Units to plot enthalpy. See R() for +

    • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    • -
    • S_units (str) – Units to plot entropy. See R() for +

    • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • G_units (str) – Units to plot Gibbs free energy. See R() +

    • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    @@ -870,18 +870,18 @@

    pmutt.empirical.nasa.Nasa9
    Parameters:
      -
    • T_low (float) – Lower temperature in K. If not specified, +

    • T_low (float) – Lower temperature in K. If not specified, T_low attribute used

    • -
    • T_high (float) – Upper temperature in K. If not specified, +

    • T_high (float) – Upper temperature in K. If not specified, T_high attribute used

    • -
    • Cp_units (str) – Units to plot heat capacity. See R() +

    • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • H_units (str) – Units to plot enthalpy. See R() for +

    • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    • -
    • S_units (str) – Units to plot entropy. See R() for +

    • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • G_units (str) – Units to plot Gibbs free energy. See R() +

    • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    @@ -908,18 +908,18 @@

    pmutt.empirical.nasa.Nasa9
    Parameters:
      -
    • T_low (float) – Lower temperature in K. If not specified, T_low +

    • T_low (float) – Lower temperature in K. If not specified, T_low attribute used

    • -
    • T_high (float) – Upper temperature in K. If not specified, T_high +

    • T_high (float) – Upper temperature in K. If not specified, T_high attribute used

    • -
    • Cp_units (str) – Units to plot heat capacity. See R() for +

    • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • H_units (str) – Units to plot enthalpy. See R() for +

    • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    • -
    • S_units (str) – Units to plot entropy. See R() for +

    • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • G_units (str) – Units to plot Gibbs free energy. See R() +

    • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    @@ -947,7 +947,7 @@

    pmutt.empirical.nasa.Nasa9

    CTI_str – Object represented as a CTI string.

    Return type:
    -

    str

    +

    str

    @@ -961,7 +961,7 @@

    pmutt.empirical.nasa.Nasa9

    obj_dict

    Return type:
    -

    dict

    +

    dict

    @@ -975,7 +975,7 @@

    pmutt.empirical.nasa.Nasa9

    yaml_dict – Dictionary compatible with Cantera’s YAML format

    Return type:
    -

    dict

    +

    dict

    diff --git a/api/empirical/nasa/pmutt.empirical.nasa.SingleNasa9.html b/api/empirical/nasa/pmutt.empirical.nasa.SingleNasa9.html index 4fbf613e..b440d771 100644 --- a/api/empirical/nasa/pmutt.empirical.nasa.SingleNasa9.html +++ b/api/empirical/nasa/pmutt.empirical.nasa.SingleNasa9.html @@ -4,7 +4,7 @@ - pmutt.empirical.nasa.SingleNasa9 — pmutt 1.4.7 documentation + pmutt.empirical.nasa.SingleNasa9 — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -129,7 +129,7 @@

    pmutt.empirical.nasa.SingleNasa9
    Type:
    -

    float

    +

    float

    @@ -140,7 +140,7 @@

    pmutt.empirical.nasa.SingleNasa9
    Type:
    -

    float

    +

    float

    @@ -334,7 +334,7 @@

    pmutt.empirical.nasa.SingleNasa9
    Parameters:
    -

    json_obj (dict) – JSON representation

    +

    json_obj (dict) – JSON representation

    Returns:

    Nasa

    @@ -352,7 +352,7 @@

    pmutt.empirical.nasa.SingleNasa9
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • kwargs (keyword arguments) – Parameters needed by get_CpoR

    @@ -361,7 +361,7 @@

    pmutt.empirical.nasa.SingleNasa9

    Cp – Heat capacity (constant P) in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -390,7 +390,7 @@

    pmutt.empirical.nasa.SingleNasa9
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • kwargs (keyword arguments) – Parameters needed by get_CvoR

    @@ -399,7 +399,7 @@

    pmutt.empirical.nasa.SingleNasa9

    Cv – Heat capacity (constant V) in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -414,7 +414,7 @@

    pmutt.empirical.nasa.SingleNasa9

    CvoR – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -426,9 +426,9 @@

    pmutt.empirical.nasa.SingleNasa9
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_FoRT

    @@ -436,7 +436,7 @@

    pmutt.empirical.nasa.SingleNasa9

    F – Hemholtz energy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -453,7 +453,7 @@

    pmutt.empirical.nasa.SingleNasa9

    FoRT – Dimensionless Helmholtz energy

    Return type:
    -

    float

    +

    float

    @@ -465,9 +465,9 @@

    pmutt.empirical.nasa.SingleNasa9
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_GoRT

    @@ -475,7 +475,7 @@

    pmutt.empirical.nasa.SingleNasa9

    G – Gibbs energy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -492,7 +492,7 @@

    pmutt.empirical.nasa.SingleNasa9

    GoRT – Dimensionless Gibbs free energy

    Return type:
    -

    float

    +

    float

    @@ -504,9 +504,9 @@

    pmutt.empirical.nasa.SingleNasa9
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_HoRT

    @@ -514,7 +514,7 @@

    pmutt.empirical.nasa.SingleNasa9

    H – Enthalpy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -543,7 +543,7 @@

    pmutt.empirical.nasa.SingleNasa9
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • kwargs (keyword arguments) – Parameters needed by get_SoR

    @@ -552,7 +552,7 @@

    pmutt.empirical.nasa.SingleNasa9

    S – Entropy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -581,9 +581,9 @@

    pmutt.empirical.nasa.SingleNasa9
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_UoRT

    @@ -591,7 +591,7 @@

    pmutt.empirical.nasa.SingleNasa9

    U – Internal energy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -605,7 +605,7 @@

    pmutt.empirical.nasa.SingleNasa9

    UoRT – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -619,7 +619,7 @@

    pmutt.empirical.nasa.SingleNasa9

    q – Returns 1

    Return type:
    -

    float

    +

    float

    @@ -632,18 +632,18 @@

    pmutt.empirical.nasa.SingleNasa9
    Parameters:
      -
    • T_low (float) – Lower temperature in K. If not specified, +

    • T_low (float) – Lower temperature in K. If not specified, T_low attribute used.

    • -
    • T_high (float) – Upper temperature in K. If not specified, +

    • T_high (float) – Upper temperature in K. If not specified, T_high attribute used.

    • -
    • Cp_units (str) – Units to plot heat capacity. See R() +

    • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • H_units (str) – Units to plot enthalpy. See R() for +

    • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    • -
    • S_units (str) – Units to plot entropy. See R() for +

    • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • G_units (str) – Units to plot Gibbs free energy. See R() +

    • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    @@ -670,18 +670,18 @@

    pmutt.empirical.nasa.SingleNasa9
    Parameters:
      -
    • T_low (float) – Lower temperature in K. If not specified, +

    • T_low (float) – Lower temperature in K. If not specified, T_low attribute used

    • -
    • T_high (float) – Upper temperature in K. If not specified, +

    • T_high (float) – Upper temperature in K. If not specified, T_high attribute used

    • -
    • Cp_units (str) – Units to plot heat capacity. See R() +

    • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • H_units (str) – Units to plot enthalpy. See R() for +

    • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    • -
    • S_units (str) – Units to plot entropy. See R() for +

    • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • G_units (str) – Units to plot Gibbs free energy. See R() +

    • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    @@ -708,18 +708,18 @@

    pmutt.empirical.nasa.SingleNasa9
    Parameters:
      -
    • T_low (float) – Lower temperature in K. If not specified, T_low +

    • T_low (float) – Lower temperature in K. If not specified, T_low attribute used

    • -
    • T_high (float) – Upper temperature in K. If not specified, T_high +

    • T_high (float) – Upper temperature in K. If not specified, T_high attribute used

    • -
    • Cp_units (str) – Units to plot heat capacity. See R() for +

    • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • H_units (str) – Units to plot enthalpy. See R() for +

    • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    • -
    • S_units (str) – Units to plot entropy. See R() for +

    • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • G_units (str) – Units to plot Gibbs free energy. See R() +

    • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    @@ -744,14 +744,14 @@

    pmutt.empirical.nasa.SingleNasa9
    Parameters:
    -

    line_indent (bool, optional) – If True, the first line is indented by 16 spaces. Default is +

    line_indent (bool, optional) – If True, the first line is indented by 16 spaces. Default is False

    Returns:

    CTI_str – Object represented as a CTI string.

    Return type:
    -

    str

    +

    str

    @@ -765,7 +765,7 @@

    pmutt.empirical.nasa.SingleNasa9

    obj_dict

    Return type:
    -

    dict

    +

    dict

    diff --git a/api/empirical/references/pmutt.empirical.references.Reference.html b/api/empirical/references/pmutt.empirical.references.Reference.html index 28230300..f79405cc 100644 --- a/api/empirical/references/pmutt.empirical.references.Reference.html +++ b/api/empirical/references/pmutt.empirical.references.Reference.html @@ -4,7 +4,7 @@ - pmutt.empirical.references.Reference — pmutt 1.4.7 documentation + pmutt.empirical.references.Reference — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -128,7 +128,7 @@

    pmutt.empirical.references.Reference
    Type:
    -

    float

    +

    float

    @@ -139,7 +139,7 @@

    pmutt.empirical.references.Reference
    Type:
    -

    float

    +

    float

    @@ -319,7 +319,7 @@

    pmutt.empirical.references.Reference
    Parameters:
    -

    json_obj (dict) – JSON representation

    +

    json_obj (dict) – JSON representation

    Returns:

    EmpiricalBase

    @@ -337,7 +337,7 @@

    pmutt.empirical.references.Reference
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • kwargs (keyword arguments) – Parameters needed by get_CpoR

    @@ -346,7 +346,7 @@

    pmutt.empirical.references.Reference

    Cp – Heat capacity (constant P) in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -361,7 +361,7 @@

    pmutt.empirical.references.Reference

    CpoR – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -373,7 +373,7 @@

    pmutt.empirical.references.Reference
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • kwargs (keyword arguments) – Parameters needed by get_CvoR

    @@ -382,7 +382,7 @@

    pmutt.empirical.references.Reference

    Cv – Heat capacity (constant V) in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -397,7 +397,7 @@

    pmutt.empirical.references.Reference

    CvoR – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -409,9 +409,9 @@

    pmutt.empirical.references.Reference
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_FoRT

    @@ -419,7 +419,7 @@

    pmutt.empirical.references.Reference

    F – Hemholtz energy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -436,7 +436,7 @@

    pmutt.empirical.references.Reference

    FoRT – Dimensionless Helmholtz energy

    Return type:
    -

    float

    +

    float

    @@ -448,9 +448,9 @@

    pmutt.empirical.references.Reference
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_GoRT

    @@ -458,7 +458,7 @@

    pmutt.empirical.references.Reference

    G – Gibbs energy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -475,7 +475,7 @@

    pmutt.empirical.references.Reference

    GoRT – Dimensionless Gibbs free energy

    Return type:
    -

    float

    +

    float

    @@ -487,9 +487,9 @@

    pmutt.empirical.references.Reference
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_HoRT

    @@ -497,7 +497,7 @@

    pmutt.empirical.references.Reference

    H – Enthalpy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -511,7 +511,7 @@

    pmutt.empirical.references.Reference

    HoRT – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -523,7 +523,7 @@

    pmutt.empirical.references.Reference
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • kwargs (keyword arguments) – Parameters needed by get_SoR

    @@ -532,7 +532,7 @@

    pmutt.empirical.references.Reference

    S – Entropy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -546,7 +546,7 @@

    pmutt.empirical.references.Reference

    SoR – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -558,9 +558,9 @@

    pmutt.empirical.references.Reference
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_UoRT

    @@ -568,7 +568,7 @@

    pmutt.empirical.references.Reference

    U – Internal energy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -582,7 +582,7 @@

    pmutt.empirical.references.Reference

    UoRT – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -596,7 +596,7 @@

    pmutt.empirical.references.Reference

    q – Returns 1

    Return type:
    -

    float

    +

    float

    @@ -609,18 +609,18 @@

    pmutt.empirical.references.Reference
    Parameters:
      -
    • T_low (float) – Lower temperature in K. If not specified, +

    • T_low (float) – Lower temperature in K. If not specified, T_low attribute used.

    • -
    • T_high (float) – Upper temperature in K. If not specified, +

    • T_high (float) – Upper temperature in K. If not specified, T_high attribute used.

    • -
    • Cp_units (str) – Units to plot heat capacity. See R() +

    • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • H_units (str) – Units to plot enthalpy. See R() for +

    • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    • -
    • S_units (str) – Units to plot entropy. See R() for +

    • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • G_units (str) – Units to plot Gibbs free energy. See R() +

    • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    @@ -647,18 +647,18 @@

    pmutt.empirical.references.Reference
    Parameters:
      -
    • T_low (float) – Lower temperature in K. If not specified, +

    • T_low (float) – Lower temperature in K. If not specified, T_low attribute used

    • -
    • T_high (float) – Upper temperature in K. If not specified, +

    • T_high (float) – Upper temperature in K. If not specified, T_high attribute used

    • -
    • Cp_units (str) – Units to plot heat capacity. See R() +

    • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • H_units (str) – Units to plot enthalpy. See R() for +

    • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    • -
    • S_units (str) – Units to plot entropy. See R() for +

    • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • G_units (str) – Units to plot Gibbs free energy. See R() +

    • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    @@ -685,18 +685,18 @@

    pmutt.empirical.references.Reference
    Parameters:
      -
    • T_low (float) – Lower temperature in K. If not specified, T_low +

    • T_low (float) – Lower temperature in K. If not specified, T_low attribute used

    • -
    • T_high (float) – Upper temperature in K. If not specified, T_high +

    • T_high (float) – Upper temperature in K. If not specified, T_high attribute used

    • -
    • Cp_units (str) – Units to plot heat capacity. See R() for +

    • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • H_units (str) – Units to plot enthalpy. See R() for +

    • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    • -
    • S_units (str) – Units to plot entropy. See R() for +

    • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • G_units (str) – Units to plot Gibbs free energy. See R() +

    • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    @@ -724,7 +724,7 @@

    pmutt.empirical.references.Reference

    obj_dict

    Return type:
    -

    dict

    +

    dict

    diff --git a/api/empirical/references/pmutt.empirical.references.References.html b/api/empirical/references/pmutt.empirical.references.References.html index b5e8aa5b..a636efc0 100644 --- a/api/empirical/references/pmutt.empirical.references.References.html +++ b/api/empirical/references/pmutt.empirical.references.References.html @@ -4,7 +4,7 @@ - pmutt.empirical.references.References — pmutt 1.4.7 documentation + pmutt.empirical.references.References — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
    - 1.4.7 + 1.4.9
    @@ -128,7 +128,7 @@

    pmutt.empirical.references.References
    Type:
    -

    dict

    +

    dict

    @@ -151,7 +151,7 @@

    pmutt.empirical.references.References
    Type:
    -

    str, optional

    +

    str, optional

    @@ -162,7 +162,7 @@

    pmutt.empirical.references.References
    Type:
    -

    float, optional

    +

    float, optional

    @@ -293,7 +293,7 @@

    pmutt.empirical.references.References
    Parameters:
    -

    json_obj (dict) – JSON representation

    +

    json_obj (dict) – JSON representation

    Returns:

    References

    @@ -316,7 +316,7 @@

    pmutt.empirical.references.References
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • kwargs (keyword arguments) – Parameters needed by get_CpoR

    @@ -325,7 +325,7 @@

    pmutt.empirical.references.References

    Cp – Heat capacity (constant P) in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -340,7 +340,7 @@

    pmutt.empirical.references.References

    CpoR – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -352,7 +352,7 @@

    pmutt.empirical.references.References
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • kwargs (keyword arguments) – Parameters needed by get_CvoR

    @@ -361,7 +361,7 @@

    pmutt.empirical.references.References

    Cv – Heat capacity (constant V) in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -376,7 +376,7 @@

    pmutt.empirical.references.References

    CvoR – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -388,9 +388,9 @@

    pmutt.empirical.references.References
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_FoRT

    @@ -398,7 +398,7 @@

    pmutt.empirical.references.References

    F – Hemholtz energy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -415,7 +415,7 @@

    pmutt.empirical.references.References

    FoRT – Dimensionless Helmholtz energy

    Return type:
    -

    float

    +

    float

    @@ -427,9 +427,9 @@

    pmutt.empirical.references.References
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_GoRT

    @@ -437,7 +437,7 @@

    pmutt.empirical.references.References

    G – Gibbs energy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -454,7 +454,7 @@

    pmutt.empirical.references.References

    GoRT – Dimensionless Gibbs free energy

    Return type:
    -

    float

    +

    float

    @@ -466,9 +466,9 @@

    pmutt.empirical.references.References
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_HoRT

    @@ -476,7 +476,7 @@

    pmutt.empirical.references.References

    H – Enthalpy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -490,7 +490,7 @@

    pmutt.empirical.references.References
    Parameters:
      -
    • descriptors (dict) – Dictionary where the keys are decriptors and the values are the +

    • descriptors (dict) – Dictionary where the keys are decriptors and the values are the number of each descriptor in a formula unit

    • T (float or (N,) numpy.ndarray, optional) – Temperature in K. If not specified, adjusts using T_ref

    @@ -500,7 +500,7 @@

    pmutt.empirical.references.ReferencesReturn type: -

    float

    +

    float

    @@ -512,7 +512,7 @@

    pmutt.empirical.references.References
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • kwargs (keyword arguments) – Parameters needed by get_SoR

    @@ -521,7 +521,7 @@

    pmutt.empirical.references.References

    S – Entropy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -535,7 +535,7 @@

    pmutt.empirical.references.References

    SoR – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -547,9 +547,9 @@

    pmutt.empirical.references.References
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_UoRT

    @@ -557,7 +557,7 @@

    pmutt.empirical.references.References

    U – Internal energy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -571,7 +571,7 @@

    pmutt.empirical.references.References

    UoRT – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -585,7 +585,7 @@

    pmutt.empirical.references.References

    descriptors – Unique descriptors in reference species

    Return type:
    -

    tuple

    +

    tuple

    @@ -615,7 +615,7 @@

    pmutt.empirical.references.References

    q – Returns 1

    Return type:
    -

    float

    +

    float

    @@ -649,7 +649,7 @@

    pmutt.empirical.references.References

    obj_dict

    Return type:
    -

    dict

    +

    dict

    diff --git a/api/empirical/shomate/pmutt.empirical.shomate.Shomate.html b/api/empirical/shomate/pmutt.empirical.shomate.Shomate.html index f5f0be5a..b9ef9b4a 100644 --- a/api/empirical/shomate/pmutt.empirical.shomate.Shomate.html +++ b/api/empirical/shomate/pmutt.empirical.shomate.Shomate.html @@ -4,7 +4,7 @@ - pmutt.empirical.shomate.Shomate — pmutt 1.4.7 documentation + pmutt.empirical.shomate.Shomate — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
    - 1.4.7 + 1.4.9
    @@ -136,7 +136,7 @@

    pmutt.empirical.shomate.Shomate
    Type:
    -

    float

    +

    float

    @@ -147,7 +147,7 @@

    pmutt.empirical.shomate.Shomate
    Type:
    -

    float

    +

    float

    @@ -171,7 +171,7 @@

    pmutt.empirical.shomate.Shomate
    Type:
    -

    str, optional

    +

    str, optional

    @@ -378,13 +378,13 @@

    pmutt.empirical.shomate.Shomate
    Parameters:
      -
    • name (str) – Name of the species

    • +
    • name (str) – Name of the species

    • T ((N,) numpy.ndarray) – Temperatures in K used for fitting CpoR.

    • CpoR ((N,) numpy.ndarray) – Dimensionless heat capacity corresponding to T.

    • -
    • T_ref (float) – Reference temperature in K used fitting empirical coefficients.

    • -
    • HoRT_ref (float) – Dimensionless reference enthalpy that corresponds to T_ref.

    • -
    • SoR_ref (float) – Dimensionless entropy that corresponds to T_ref.

    • -
    • units (str, optional) – Units used to fit the Shomate polynomial. Units should be +

    • T_ref (float) – Reference temperature in K used fitting empirical coefficients.

    • +
    • HoRT_ref (float) – Dimensionless reference enthalpy that corresponds to T_ref.

    • +
    • SoR_ref (float) – Dimensionless entropy that corresponds to T_ref.

    • +
    • units (str, optional) – Units used to fit the Shomate polynomial. Units should be supported by R (e.g. J/mol/K, cal/mol/K, eV/K). Default is J/mol/K.

    @@ -404,7 +404,7 @@

    pmutt.empirical.shomate.Shomate
    Parameters:
    -

    json_obj (dict) – JSON representation

    +

    json_obj (dict) – JSON representation

    Returns:

    shomate

    @@ -424,19 +424,19 @@

    pmutt.empirical.shomate.Shomate
    • model (Model object or class) – Model to generate data. Must contain the methods get_CpoR, get_HoRT and get_SoR

    • -
    • name (str, optional) – Name of the species. If not passed, model.name will be used.

    • -
    • T_low (float, optional) – Lower limit temerature in K. If not passed, model.T_low will +

    • name (str, optional) – Name of the species. If not passed, model.name will be used.

    • +
    • T_low (float, optional) – Lower limit temerature in K. If not passed, model.T_low will be used.

    • -
    • T_high (float, optional) – Higher limit temperature in K. If not passed, model.T_high +

    • T_high (float, optional) – Higher limit temperature in K. If not passed, model.T_high will be used.

    • -
    • elements (dict, optional) – Composition of the species. If not passed, model.elements +

    • elements (dict, optional) – Composition of the species. If not passed, model.elements will be used. Keys of dictionary are elements, values are stoichiometric values in a formula unit. e.g. CH3OH can be represented as: {‘C’: 1, ‘H’: 4, ‘O’: 1,}.

    • -
    • n_T (int, optional) – Number of data points between T_low and T_high for fitting +

    • n_T (int, optional) – Number of data points between T_low and T_high for fitting heat capacity. Default is 50.

    • -
    • units (str, optional) – Units used to fit the Shomate polynomial. Units should be +

    • units (str, optional) – Units used to fit the Shomate polynomial. Units should be supported by R (e.g. J/mol/K, cal/mol/K, eV/K). Default is J/mol/K.

    • kwargs (keyword arguments) – Used to initalize model if a class is passed.

    • @@ -459,10 +459,10 @@

      pmutt.empirical.shomate.Shomate
      Parameters:
        -
      • name (str) – Name of the species

      • +
      • name (str) – Name of the species

      • statmech_model (pmutt.statmech.StatMech object or class) – Statistical Mechanics model to generate data

      • -
      • T_low (float) – Lower limit temerature in K

      • -
      • T_high (float) – Higher limit temperature in K

      • +
      • T_low (float) – Lower limit temerature in K

      • +
      • T_high (float) – Higher limit temperature in K

      • references (pmutt.empirical.references.References object) – Reference to adjust enthalpy

      • **kwargs (keyword arguments) – Used to initalize statmech_model or EmpiricalBase attributes to be stored.

      • @@ -485,11 +485,11 @@

        pmutt.empirical.shomate.ShomateParameters:
        • T (float or (N,) numpy.ndarray) – Temperature(s) in K

        • -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units.

        • -
        • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

        • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

        • -
        • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

        • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

        • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

        • @@ -512,9 +512,9 @@

          pmutt.empirical.shomate.ShomateParameters:
          • T (float or (N,) numpy.ndarray) – Temperature(s) in K

          • -
          • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

          • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

          • -
          • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

          • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

          • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

          • @@ -536,7 +536,7 @@

            pmutt.empirical.shomate.Shomate
            Parameters:
              -
            • units (str) – Units as string. See R() for accepted +

            • units (str) – Units as string. See R() for accepted units.

            • kwargs (keyword arguments) – Parameters needed by get_CvoR

            @@ -545,7 +545,7 @@

            pmutt.empirical.shomate.Shomate

            Cv – Heat capacity (constant V) in appropriate units

            Return type:
            -

            float

            +

            float

          @@ -560,7 +560,7 @@

          pmutt.empirical.shomate.Shomate

          CvoR – Returns 0

        Return type:
        -

        float

        +

        float

      @@ -572,9 +572,9 @@

      pmutt.empirical.shomate.Shomate
      Parameters:
        -
      • units (str) – Units as string. See R() for accepted +

      • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

      • -
      • T (float, optional) – Temperature in K. Default is 298.15 K

      • +
      • T (float, optional) – Temperature in K. Default is 298.15 K

      • kwargs (keyword arguments) – Parameters needed by get_FoRT

      @@ -582,7 +582,7 @@

      pmutt.empirical.shomate.Shomate

      F – Hemholtz energy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -599,7 +599,7 @@

    pmutt.empirical.shomate.Shomate

    FoRT – Dimensionless Helmholtz energy

    Return type:
    -

    float

    +

    float

    @@ -612,14 +612,14 @@

    pmutt.empirical.shomate.ShomateParameters:
    • T (float or (N,) numpy.ndarray) – Temperature(s) in K

    • -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

    • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

    • -
    • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

    • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

    • -
    • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of +

    • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

    • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

    @@ -641,12 +641,12 @@

    pmutt.empirical.shomate.ShomateParameters:
    • T (float or (N,) numpy.ndarray) – Temperature(s) in K

    • -
    • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

    • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

    • -
    • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

    • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

    • -
    • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of +

    • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

    • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

    @@ -668,11 +668,11 @@

    pmutt.empirical.shomate.ShomateParameters:
    • T (float or (N,) numpy.ndarray) – Temperature(s) in K

    • -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

    • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

    • -
    • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

    • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

    • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

    • @@ -695,9 +695,9 @@

      pmutt.empirical.shomate.ShomateParameters:
      • T (float or (N,) numpy.ndarray) – Temperature(s) in K

      • -
      • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

      • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

      • -
      • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

      • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

      • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

      • @@ -720,14 +720,14 @@

        pmutt.empirical.shomate.ShomateParameters:
        • T (float or (N,) numpy.ndarray) – Temperature(s) in K

        • -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units.

        • -
        • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

        • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

        • -
        • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

        • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

        • -
        • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of +

        • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

        • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

        @@ -753,7 +753,7 @@

        pmutt.empirical.shomate.Shomate

        SoR – Entropy

        Return type:
        -

        float

        +

        float

      @@ -766,12 +766,12 @@

      pmutt.empirical.shomate.ShomateParameters:
      • T (float or (N,) numpy.ndarray) – Temperature(s) in K

      • -
      • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

      • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

      • -
      • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

      • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

      • -
      • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of +

      • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

      • kwargs (key-word arguments) – Arguments to calculate mixture model properties, if any

      @@ -792,9 +792,9 @@

      pmutt.empirical.shomate.Shomate
      Parameters:
        -
      • units (str) – Units as string. See R() for accepted +

      • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

      • -
      • T (float, optional) – Temperature in K. Default is 298.15 K

      • +
      • T (float, optional) – Temperature in K. Default is 298.15 K

      • kwargs (keyword arguments) – Parameters needed by get_UoRT

      @@ -802,7 +802,7 @@

      pmutt.empirical.shomate.Shomate

      U – Internal energy in appropriate units

      Return type:
      -

      float

      +

      float

    @@ -816,7 +816,7 @@

    pmutt.empirical.shomate.Shomate

    UoRT – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -830,7 +830,7 @@

    pmutt.empirical.shomate.Shomate

    q – Returns 1

    Return type:
    -

    float

    +

    float

    @@ -843,18 +843,18 @@

    pmutt.empirical.shomate.Shomate
    Parameters:
      -
    • T_low (float) – Lower temperature in K. If not specified, +

    • T_low (float) – Lower temperature in K. If not specified, T_low attribute used.

    • -
    • T_high (float) – Upper temperature in K. If not specified, +

    • T_high (float) – Upper temperature in K. If not specified, T_high attribute used.

    • -
    • Cp_units (str) – Units to plot heat capacity. See R() +

    • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • H_units (str) – Units to plot enthalpy. See R() for +

    • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    • -
    • S_units (str) – Units to plot entropy. See R() for +

    • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • G_units (str) – Units to plot Gibbs free energy. See R() +

    • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    @@ -881,18 +881,18 @@

    pmutt.empirical.shomate.Shomate
    Parameters:
      -
    • T_low (float) – Lower temperature in K. If not specified, +

    • T_low (float) – Lower temperature in K. If not specified, T_low attribute used

    • -
    • T_high (float) – Upper temperature in K. If not specified, +

    • T_high (float) – Upper temperature in K. If not specified, T_high attribute used

    • -
    • Cp_units (str) – Units to plot heat capacity. See R() +

    • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • H_units (str) – Units to plot enthalpy. See R() for +

    • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    • -
    • S_units (str) – Units to plot entropy. See R() for +

    • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • G_units (str) – Units to plot Gibbs free energy. See R() +

    • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    @@ -919,18 +919,18 @@

    pmutt.empirical.shomate.Shomate
    Parameters:
      -
    • T_low (float) – Lower temperature in K. If not specified, T_low +

    • T_low (float) – Lower temperature in K. If not specified, T_low attribute used

    • -
    • T_high (float) – Upper temperature in K. If not specified, T_high +

    • T_high (float) – Upper temperature in K. If not specified, T_high attribute used

    • -
    • Cp_units (str) – Units to plot heat capacity. See R() for +

    • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • H_units (str) – Units to plot enthalpy. See R() for +

    • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    • -
    • S_units (str) – Units to plot entropy. See R() for +

    • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

    • -
    • G_units (str) – Units to plot Gibbs free energy. See R() +

    • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

    @@ -958,7 +958,7 @@

    pmutt.empirical.shomate.Shomate

    CTI_str – Object represented as a CTI string.

    Return type:
    -

    str

    +

    str

    @@ -972,7 +972,7 @@

    pmutt.empirical.shomate.Shomate

    obj_dict

    Return type:
    -

    dict

    +

    dict

    @@ -986,7 +986,7 @@

    pmutt.empirical.shomate.Shomate

    yaml_dict – Dictionary compatible with Cantera’s YAML format

    Return type:
    -

    dict

    +

    dict

    diff --git a/api/eos/eos.html b/api/eos/eos.html index 10af80c1..7ee71ae1 100644 --- a/api/eos/eos.html +++ b/api/eos/eos.html @@ -4,7 +4,7 @@ - Equations of State — pmutt 1.4.7 documentation + Equations of State — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    diff --git a/api/eos/eos/pmutt.eos.IdealGasEOS.html b/api/eos/eos/pmutt.eos.IdealGasEOS.html index 6289e02b..d50e4ccc 100644 --- a/api/eos/eos/pmutt.eos.IdealGasEOS.html +++ b/api/eos/eos/pmutt.eos.IdealGasEOS.html @@ -4,7 +4,7 @@ - pmutt.eos.IdealGasEOS — pmutt 1.4.7 documentation + pmutt.eos.IdealGasEOS — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
    - 1.4.7 + 1.4.9
    @@ -153,7 +153,7 @@

    pmutt.eos.IdealGasEOS

    Recreate an object from the JSON representation.

    Parameters:
    -

    json_obj (dict) – JSON representation

    +

    json_obj (dict) – JSON representation

    Returns:

    Obj

    @@ -171,16 +171,16 @@

    pmutt.eos.IdealGasEOS
    Parameters:
      -
    • T (float, optional) – Temperature in K. Default is standard temperature

    • -
    • V (float, optional) – Volume in m3. Default is standard volume

    • -
    • n (float, optional) – Number of moles (in mol). Default is 1 mol

    • +
    • T (float, optional) – Temperature in K. Default is standard temperature

    • +
    • V (float, optional) – Volume in m3. Default is standard volume

    • +
    • n (float, optional) – Number of moles (in mol). Default is 1 mol

    Returns:

    P – Pressure in bar

    Return type:
    -

    float

    +

    float

    @@ -192,16 +192,16 @@

    pmutt.eos.IdealGasEOS
    Parameters:
      -
    • V (float, optional) – Volume in m3. Default is standard volume

    • -
    • P (float, optional) – Pressure in bar. Default is standard pressure

    • -
    • n (float, optional) – Number of moles (in mol). Default is 1 mol

    • +
    • V (float, optional) – Volume in m3. Default is standard volume

    • +
    • P (float, optional) – Pressure in bar. Default is standard pressure

    • +
    • n (float, optional) – Number of moles (in mol). Default is 1 mol

    Returns:

    T – Temperature in K

    Return type:
    -

    float

    +

    float

    @@ -213,16 +213,16 @@

    pmutt.eos.IdealGasEOS
    Parameters:
      -
    • T (float, optional) – Temperature in K. Default is standard temperature

    • -
    • P (float, optional) – Pressure in bar. Default is standard pressure

    • -
    • n (float, optional) – Number of moles (in mol). Default is 1 mol

    • +
    • T (float, optional) – Temperature in K. Default is standard temperature

    • +
    • P (float, optional) – Pressure in bar. Default is standard pressure

    • +
    • n (float, optional) – Number of moles (in mol). Default is 1 mol

    Returns:

    V – Volume in m3

    Return type:
    -

    float

    +

    float

    @@ -234,16 +234,16 @@

    pmutt.eos.IdealGasEOS
    Parameters:
      -
    • V (float, optional) – Volume in m3. Default is standard volume

    • -
    • P (float, optional) – Pressure in bar. Default is standard pressure

    • -
    • T (float, optional) – Temperature in K. Default is standard temperature

    • +
    • V (float, optional) – Volume in m3. Default is standard volume

    • +
    • P (float, optional) – Pressure in bar. Default is standard pressure

    • +
    • T (float, optional) – Temperature in K. Default is standard temperature

    Returns:

    n – Number of moles in mol

    Return type:
    -

    float

    +

    float

    @@ -257,7 +257,7 @@

    pmutt.eos.IdealGasEOS

    obj_dict

    Return type:
    -

    dict

    +

    dict

    diff --git a/api/eos/eos/pmutt.eos.vanDerWaalsEOS.html b/api/eos/eos/pmutt.eos.vanDerWaalsEOS.html index aee8cdc8..b93650ec 100644 --- a/api/eos/eos/pmutt.eos.vanDerWaalsEOS.html +++ b/api/eos/eos/pmutt.eos.vanDerWaalsEOS.html @@ -4,7 +4,7 @@ - pmutt.eos.vanDerWaalsEOS — pmutt 1.4.7 documentation + pmutt.eos.vanDerWaalsEOS — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
    - 1.4.7 + 1.4.9
    @@ -123,7 +123,7 @@

    pmutt.eos.vanDerWaalsEOS
    Type:
    -

    float

    +

    float

    @@ -134,7 +134,7 @@

    pmutt.eos.vanDerWaalsEOS
    Type:
    -

    float

    +

    float

    @@ -193,8 +193,8 @@

    pmutt.eos.vanDerWaalsEOS
    Parameters:
      -
    • Tc (float) – Critical temperature in K

    • -
    • Pc (float) – Critical pressure in bar

    • +
    • Tc (float) – Critical temperature in K

    • +
    • Pc (float) – Critical pressure in bar

    Returns:
    @@ -212,7 +212,7 @@

    pmutt.eos.vanDerWaalsEOS
    Parameters:
    -

    json_obj (dict) – JSON representation

    +

    json_obj (dict) – JSON representation

    Returns:

    Obj

    @@ -230,16 +230,16 @@

    pmutt.eos.vanDerWaalsEOS
    Parameters:
      -
    • T (float, optional) – Temperature in K. Default is standard temperature

    • -
    • V (float, optional) – Volume in m3. Default is standard volume

    • -
    • n (float, optional) – Number of moles (in mol). Default is 1 mol

    • +
    • T (float, optional) – Temperature in K. Default is standard temperature

    • +
    • V (float, optional) – Volume in m3. Default is standard volume

    • +
    • n (float, optional) – Number of moles (in mol). Default is 1 mol

    Returns:

    P – Pressure in bar

    Return type:
    -

    float

    +

    float

    @@ -253,7 +253,7 @@

    pmutt.eos.vanDerWaalsEOS

    Pc – Critical pressure in bar

    Return type:
    -

    float

    +

    float

    @@ -265,16 +265,16 @@

    pmutt.eos.vanDerWaalsEOS
    Parameters:
      -
    • V (float, optional) – Volume in m3. Default is standard volume

    • -
    • P (float, optional) – Pressure in bar. Default is standard pressure

    • -
    • n (float, optional) – Number of moles (in mol). Default is 1 mol

    • +
    • V (float, optional) – Volume in m3. Default is standard volume

    • +
    • P (float, optional) – Pressure in bar. Default is standard pressure

    • +
    • n (float, optional) – Number of moles (in mol). Default is 1 mol

    Returns:

    T – Temperature in K

    Return type:
    -

    float

    +

    float

    @@ -288,7 +288,7 @@

    pmutt.eos.vanDerWaalsEOS

    Tc – Critcial temperature in K

    Return type:
    -

    float

    +

    float

    @@ -300,10 +300,10 @@

    pmutt.eos.vanDerWaalsEOS
    Parameters:
      -
    • T (float, optional) – Temperature in K. Default is standard temperature

    • -
    • P (float, optional) – Pressure in bar. Default is standard pressure

    • -
    • n (float, optional) – Number of moles (in mol). Default is 1 mol

    • -
    • gas_phase (bool, optional) – Relevant if system is in vapor-liquid equilibrium. If True, +

    • T (float, optional) – Temperature in K. Default is standard temperature

    • +
    • P (float, optional) – Pressure in bar. Default is standard pressure

    • +
    • n (float, optional) – Number of moles (in mol). Default is 1 mol

    • +
    • gas_phase (bool, optional) – Relevant if system is in vapor-liquid equilibrium. If True, return the larger volume (gas phase). If False, returns the smaller volume (liquid phase).

    @@ -312,7 +312,7 @@

    pmutt.eos.vanDerWaalsEOS

    V – Volume in m3

    Return type:
    -

    float

    +

    float

    @@ -323,13 +323,13 @@

    pmutt.eos.vanDerWaalsEOS
    Parameters:
    -

    n (float, optional) – Number of moles in mol. Default is 1 mol

    +

    n (float, optional) – Number of moles in mol. Default is 1 mol

    Returns:

    Vc – Critical volume in m3

    Return type:
    -

    float

    +

    float

    @@ -341,9 +341,9 @@

    pmutt.eos.vanDerWaalsEOS
    Parameters:
      -
    • T (float, optional) – Temperature in K. Default is standard temperature

    • -
    • P (float, optional) – Pressure in bar. Default is standard pressure

    • -
    • gas_phase (bool, optional) – Relevant if system is in vapor-liquid equilibrium. If True, +

    • T (float, optional) – Temperature in K. Default is standard temperature

    • +
    • P (float, optional) – Pressure in bar. Default is standard pressure

    • +
    • gas_phase (bool, optional) – Relevant if system is in vapor-liquid equilibrium. If True, return the larger volume (gas phase). If False, returns the smaller volume (liquid phase).

    @@ -352,7 +352,7 @@

    pmutt.eos.vanDerWaalsEOS

    Vm – Volume in m3

    Return type:
    -

    float

    +

    float

    @@ -364,10 +364,10 @@

    pmutt.eos.vanDerWaalsEOS
    Parameters:
      -
    • V (float, optional) – Volume in m3. Default is standard volume

    • -
    • P (float, optional) – Pressure in bar. Default is standard pressure

    • -
    • T (float, optional) – Temperature in K. Default is standard temperature

    • -
    • gas_phase (bool, optional) – Relevant if system is in vapor-liquid equilibrium. If True, +

    • V (float, optional) – Volume in m3. Default is standard volume

    • +
    • P (float, optional) – Pressure in bar. Default is standard pressure

    • +
    • T (float, optional) – Temperature in K. Default is standard temperature

    • +
    • gas_phase (bool, optional) – Relevant if system is in vapor-liquid equilibrium. If True, return the smaller moles (gas phase). If False, returns the larger moles (liquid phase).

    @@ -376,7 +376,7 @@

    pmutt.eos.vanDerWaalsEOS

    n – Number of moles in mol

    Return type:
    -

    float

    +

    float

    @@ -390,7 +390,7 @@

    pmutt.eos.vanDerWaalsEOS

    obj_dict

    Return type:
    -

    dict

    +

    dict

    diff --git a/api/equilibrium/Equilibrium/pmutt.equilibrium.Equilibrium.html b/api/equilibrium/Equilibrium/pmutt.equilibrium.Equilibrium.html index 5f084078..1486a725 100644 --- a/api/equilibrium/Equilibrium/pmutt.equilibrium.Equilibrium.html +++ b/api/equilibrium/Equilibrium/pmutt.equilibrium.Equilibrium.html @@ -4,7 +4,7 @@ - pmutt.equilibrium.Equilibrium — pmutt 1.4.7 documentation + pmutt.equilibrium.Equilibrium — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -114,7 +114,7 @@

    pmutt.equilibrium.Equilibrium
    class pmutt.equilibrium.Equilibrium(model, network)
    -

    Bases: object

    +

    Bases: object

    Reaction thermodynamic equilibrium.

    @@ -199,8 +199,8 @@

    pmutt.equilibrium.Equilibrium
    Parameters:
      -
    • T (float) – Temperature in K

    • -
    • P (float) – Pressure in atm

    • +
    • T (float) – Temperature in K

    • +
    • P (float) – Pressure in atm

    Returns:
    diff --git a/api/equilibrium/equilibrium.html b/api/equilibrium/equilibrium.html index 6b7fc9eb..61834811 100644 --- a/api/equilibrium/equilibrium.html +++ b/api/equilibrium/equilibrium.html @@ -4,7 +4,7 @@ - Equilibrium Models — pmutt 1.4.7 documentation + Equilibrium Models — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    diff --git a/api/helper/helper.html b/api/helper/helper.html index c5184443..3bc8046f 100644 --- a/api/helper/helper.html +++ b/api/helper/helper.html @@ -4,7 +4,7 @@ - Helper Functions — pmutt 1.4.7 documentation + Helper Functions — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -119,7 +119,7 @@

    get_molecular_weighthttps://en.wikipedia.org/wiki/Standard_atomic_weight

    Parameters:
    -

    elements (dict or str) –

    Elemental composition of species.

    +

    elements (dict or str) –

    Elemental composition of species.

    If a dictionary is passed, the keys are the element symbol, atomic number, or element name and the value is the stoichiometric coefficient. @@ -131,7 +131,7 @@

    get_molecular_weight

    molecular_weight – Molecular weight as float in kg/mol

    Return type:
    -

    float

    +

    float

    @@ -148,7 +148,7 @@

    pmutt_list_to_dictParameters:
    @@ -156,10 +156,10 @@

    pmutt_list_to_dict

    pmutt_dict – Dictionary of pmutt objects

    Return type:
    -

    dict

    +

    dict

    Raises:
    -

    KeyError – Raised if key is not an attribute of the pmutt objects

    +

    KeyError – Raised if key is not an attribute of the pmutt objects

    @@ -175,14 +175,14 @@

    get_geometry_from_atomsParameters:
    Returns:

    geometry – Geometry

    Return type:
    -

    str

    +

    str

    diff --git a/api/io/chemkin/pmutt.io.chemkin.read_reactions.html b/api/io/chemkin/pmutt.io.chemkin.read_reactions.html index 297b8e8e..29d04021 100644 --- a/api/io/chemkin/pmutt.io.chemkin.read_reactions.html +++ b/api/io/chemkin/pmutt.io.chemkin.read_reactions.html @@ -4,7 +4,7 @@ - pmutt.io.chemkin.read_reactions — pmutt 1.4.7 documentation + pmutt.io.chemkin.read_reactions — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -130,7 +130,7 @@

    pmutt.io.chemkin.read_reactions
    Parameters:
      -
    • filename (str) – Input filename for Chemkin surf or gas .inp file

    • +
    • filename (str) – Input filename for Chemkin surf or gas .inp file

    • species (list of Nasa objects) – List of NASA objects containing thermodynamic properties for all Reactants and Products in Reactions default = None. Will not return React_obj and Prod_obj

    • @@ -150,9 +150,9 @@

      pmutt.io.chemkin.read_reactionsRaises:
      diff --git a/api/io/chemkin/pmutt.io.chemkin.write_EA.html b/api/io/chemkin/pmutt.io.chemkin.write_EA.html index 27cdc38f..27548c96 100644 --- a/api/io/chemkin/pmutt.io.chemkin.write_EA.html +++ b/api/io/chemkin/pmutt.io.chemkin.write_EA.html @@ -4,7 +4,7 @@ - pmutt.io.chemkin.write_EA — pmutt 1.4.7 documentation + pmutt.io.chemkin.write_EA — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
      - 1.4.7 + 1.4.9
      @@ -133,33 +133,33 @@

      pmutt.io.chemkin.write_EAChemkinReaction objects) – Reactions to write

    • conditions (list of dicts) – Conditions to evaluate each reaction. The key of the dictionaries should be a relevant quantity to evaluate the reaction (e.g. T, P)

    • -
    • write_gas_phase (bool, optional) – If True, only gas phase reactions are written (including +

    • write_gas_phase (bool, optional) – If True, only gas phase reactions are written (including adsorption). If False, only surface phase reactions are written. Default is False

    • -
    • filename (str, optional) – Filename for the EAs.inp file. If not specified, returns EAs file +

    • filename (str, optional) – Filename for the EAs.inp file. If not specified, returns EAs file as str

    • -
    • method_name (str, optional) –

      Method to use to calculate values. Typical values are:

      +
    • method_name (str, optional) –

      Method to use to calculate values. Typical values are:

      • ’get_EoRT_act’ (default)

      • ’get_HoRT_act’

      • ’get_GoRT_act’

    • -
    • ads_act_method (str, optional) – Name of method to use to calculate activation function of adsorption +

    • ads_act_method (str, optional) – Name of method to use to calculate activation function of adsorption reactions. Default is ‘get_HoRT_act’.

    • -
    • float_format (float, optional) – Format to write numbers. Default is ‘ .2E’ (scientific notation +

    • float_format (float, optional) – Format to write numbers. Default is ‘ .2E’ (scientific notation rounded to 2 decimal places with a preceding space if the value is positive)

    • -
    • stoich_format (float, optional) – Format to write stoichiometric numbers. Default is ‘.0f’ (integer)

    • -
    • newline (str, optional) – Newline character to use. Default is the Linux newline character

    • -
    • column_delimiter (str, optional) – Delimiter for columns. Default is ‘ ‘

    • +
    • stoich_format (float, optional) – Format to write stoichiometric numbers. Default is ‘.0f’ (integer)

    • +
    • newline (str, optional) – Newline character to use. Default is the Linux newline character

    • +
    • column_delimiter (str, optional) – Delimiter for columns. Default is ‘ ‘

    Returns:

    lines_out – EA.inp lines as a string if filename is None

    Return type:
    -

    str

    +

    str

    diff --git a/api/io/chemkin/pmutt.io.chemkin.write_T_flow.html b/api/io/chemkin/pmutt.io.chemkin.write_T_flow.html index 974058e5..c4e4097f 100644 --- a/api/io/chemkin/pmutt.io.chemkin.write_T_flow.html +++ b/api/io/chemkin/pmutt.io.chemkin.write_T_flow.html @@ -4,7 +4,7 @@ - pmutt.io.chemkin.write_T_flow — pmutt 1.4.7 documentation + pmutt.io.chemkin.write_T_flow — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -134,18 +134,18 @@

    pmutt.io.chemkin.write_T_flowstr, optional) – Name of the file. If not specified, returns file as str

    -
  • float_format (str, optional) – Format to write floating point numbers. Default is ‘.3E’ (i.e. +

  • filename (str, optional) – Name of the file. If not specified, returns file as str

  • +
  • float_format (str, optional) – Format to write floating point numbers. Default is ‘.3E’ (i.e. scientific notation rounded to 3 decimal places)

  • -
  • newline (str, optional) – Newline character. Default is the Linux newline character

  • -
  • column_delimiter (str, optional) – Delimiter for columns. Default is ‘ ‘

  • +
  • newline (str, optional) – Newline character. Default is the Linux newline character

  • +
  • column_delimiter (str, optional) – Delimiter for columns. Default is ‘ ‘

  • Returns:

    lines_out – T_flow lines as a string if filename is None

    Return type:
    -

    str

    +

    str

    diff --git a/api/io/chemkin/pmutt.io.chemkin.write_gas.html b/api/io/chemkin/pmutt.io.chemkin.write_gas.html index ef8a84f6..3d36913a 100644 --- a/api/io/chemkin/pmutt.io.chemkin.write_gas.html +++ b/api/io/chemkin/pmutt.io.chemkin.write_gas.html @@ -4,7 +4,7 @@ - pmutt.io.chemkin.write_gas — pmutt 1.4.7 documentation + pmutt.io.chemkin.write_gas — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -132,7 +132,7 @@

    pmutt.io.chemkin.write_gas
    • nasa_species (list of Nasa objects) – Surface and gas species used in Chemkin mechanism. Used to write elements section

    • -
    • filename (str, optional) – File name for gas.inp file. If not specified, returns gas.inp as +

    • filename (str, optional) – File name for gas.inp file. If not specified, returns gas.inp as string

    • reactions (Reactions object, optional) – Reactions in mechanism. Reactions with only gas-phase species will be written to this file

    • @@ -142,7 +142,7 @@

      pmutt.io.chemkin.write_gas

      lines_out – gas.inp lines as a string if filename is None

      Return type:
      -

      str

      +

      str

      diff --git a/api/io/chemkin/pmutt.io.chemkin.write_surf.html b/api/io/chemkin/pmutt.io.chemkin.write_surf.html index 740bad70..73a36f74 100644 --- a/api/io/chemkin/pmutt.io.chemkin.write_surf.html +++ b/api/io/chemkin/pmutt.io.chemkin.write_surf.html @@ -4,7 +4,7 @@ - pmutt.io.chemkin.write_surf — pmutt 1.4.7 documentation + pmutt.io.chemkin.write_surf — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
      - 1.4.7 + 1.4.9
      @@ -132,24 +132,24 @@

      pmutt.io.chemkin.write_surf
      • reactions (A Reaction object containing) – Chemkin reactions to write in surf.inp file. Purely gas-phase reactions will be ignored

      • -
      • filename (str, optional) – Filename for surf.inp file. If not specified, returns file as str

      • -
      • T (float, optional) – Temperature to calculate activation energy. Default is 298.15 K

      • -
      • species_delimiter (str, optional) – Delimiter to separate species when writing reactions. +

      • filename (str, optional) – Filename for surf.inp file. If not specified, returns file as str

      • +
      • T (float, optional) – Temperature to calculate activation energy. Default is 298.15 K

      • +
      • species_delimiter (str, optional) – Delimiter to separate species when writing reactions. Default is ‘+’

      • -
      • reaction_delimiter (str, optional) – Delimiter to separate reaction sides. Default is ‘=’

      • -
      • act_method_name (str, optional) – Name of method to use to calculate activation function of surface +

      • reaction_delimiter (str, optional) – Delimiter to separate reaction sides. Default is ‘=’

      • +
      • act_method_name (str, optional) – Name of method to use to calculate activation function of surface reactions. Default is ‘get_E_act’.

      • -
      • ads_act_method (str, optional) – Name of method to use to calculate activation function of adsorption +

      • ads_act_method (str, optional) – Name of method to use to calculate activation function of adsorption reactions. Default is ‘get_H_act’.

      • -
      • act_unit (str, optional) – Units to calculate activation energy. Default is ‘kcal/mol’

      • -
      • float_format (str, optional) – String format to print floating numbers. Default is ‘ .3E’ (i.e. +

      • act_unit (str, optional) – Units to calculate activation energy. Default is ‘kcal/mol’

      • +
      • float_format (str, optional) – String format to print floating numbers. Default is ‘ .3E’ (i.e. scientific notation rounded to 3 decimal places with a leading space for positive numbers)

      • -
      • stoich_format (str, optional) – String format to print stoichiometric coefficients. +

      • stoich_format (str, optional) – String format to print stoichiometric coefficients. Default is ‘.0f’ (i.e. integers)

      • -
      • newline (str, optional) – Newline character. Default is the Linux newline character

      • -
      • column_delimiter (str, optional) – Delimiter to separate columns. Default is ‘ ‘

      • -
      • use_mw_correction (bool, optional) – If True, uses the Motz-Wise corrections. Default is True

      • +
      • newline (str, optional) – Newline character. Default is the Linux newline character

      • +
      • column_delimiter (str, optional) – Delimiter to separate columns. Default is ‘ ‘

      • +
      • use_mw_correction (bool, optional) – If True, uses the Motz-Wise corrections. Default is True

      • kwargs (keyword arguments) – Parameters needed to calculate activation energy and preexponential factor

      @@ -158,7 +158,7 @@

      pmutt.io.chemkin.write_surf

      lines_out – surf.inp lines as a string if filename is None

      Return type:
      -

      str

      +

      str

      diff --git a/api/io/chemkin/pmutt.io.chemkin.write_tube_mole.html b/api/io/chemkin/pmutt.io.chemkin.write_tube_mole.html index 7d858cca..60a2f347 100644 --- a/api/io/chemkin/pmutt.io.chemkin.write_tube_mole.html +++ b/api/io/chemkin/pmutt.io.chemkin.write_tube_mole.html @@ -4,7 +4,7 @@ - pmutt.io.chemkin.write_tube_mole — pmutt 1.4.7 documentation + pmutt.io.chemkin.write_tube_mole — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
      - 1.4.7 + 1.4.9
      @@ -133,18 +133,18 @@

      pmutt.io.chemkin.write_tube_moleNasa objects) – Nasa species to find phase information

      -
    • filename (str, optional) – Name of the file. If not specified, returns file as str

    • -
    • float_format (str, optional) – Format to write floating point numbers. Default is ‘.3E’ (i.e. +

    • filename (str, optional) – Name of the file. If not specified, returns file as str

    • +
    • float_format (str, optional) – Format to write floating point numbers. Default is ‘.3E’ (i.e. scientific notation rounded to 3 decimal places)

    • -
    • newline (str, optional) – Newline character. Default is the Linux newline character

    • -
    • column_delimiter (str, optional) – Delimiter for columns. Default is ‘ ‘

    • +
    • newline (str, optional) – Newline character. Default is the Linux newline character

    • +
    • column_delimiter (str, optional) – Delimiter for columns. Default is ‘ ‘

    Returns:

    lines_out – tube_mole lines as a string if filename is None

    Return type:
    -

    str

    +

    str

    diff --git a/api/io/excel/pmutt.io.excel.read_excel.html b/api/io/excel/pmutt.io.excel.read_excel.html index eb1f1ee9..e9c83854 100644 --- a/api/io/excel/pmutt.io.excel.read_excel.html +++ b/api/io/excel/pmutt.io.excel.read_excel.html @@ -4,7 +4,7 @@ - pmutt.io.excel.read_excel — pmutt 1.4.7 documentation + pmutt.io.excel.read_excel — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -127,16 +127,16 @@

    pmutt.io.excel.read_excel
    Parameters:
      -
    • io (str) – Name of the Excel spreadsheet

    • -
    • skiprows (list, optional) – Rows to skip at the beginning (0-indexed). +

    • io (str) – Name of the Excel spreadsheet

    • +
    • skiprows (list, optional) – Rows to skip at the beginning (0-indexed). Default is [1] so comments can be put in that row

    • -
    • header (int, optional) – Location to find header names (0-index). Default is 0

    • -
    • min_frequency_cutoff (float, optional) – Applies for the vib_outcar header. Minimum frequency cutoff (cm-1). +

    • header (int, optional) – Location to find header names (0-index). Default is 0

    • +
    • min_frequency_cutoff (float, optional) – Applies for the vib_outcar header. Minimum frequency cutoff (cm-1). Only frequencies greater than min_frequency_cutoff are read from OUTCAR. Default is 0 cm-1

    • -
    • include_imaginary (bool, optional) – Applies for the vib_outcar header. Whether or not imaginary +

    • include_imaginary (bool, optional) – Applies for the vib_outcar header. Whether or not imaginary frequencies should be included. Default is False

    • -
    • delimiter (str, optional) – Delimiter to parse column names. Default is ‘.’

    • +
    • delimiter (str, optional) – Delimiter to parse column names. Default is ‘.’

    • **kwargs (keyword arguments) –

      Parameters used by pandas.read_excel. Not required but some potentially useful parameters include:

        diff --git a/api/io/excel/pmutt.io.excel.set_atoms.html b/api/io/excel/pmutt.io.excel.set_atoms.html index 914b2c9e..4c665315 100644 --- a/api/io/excel/pmutt.io.excel.set_atoms.html +++ b/api/io/excel/pmutt.io.excel.set_atoms.html @@ -4,7 +4,7 @@ - pmutt.io.excel.set_atoms — pmutt 1.4.7 documentation + pmutt.io.excel.set_atoms — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        @@ -143,11 +143,11 @@

        pmutt.io.excel.set_atoms
        Parameters:
          -
        • path (str) – Path to read the atoms object using ase.read or the string to +

        • path (str) – Path to read the atoms object using ase.read or the string to build the atoms object using ase.build.molecule. Path can be relative to the imported spreadsheet or absolute.

        • -
        • excel_path (str) – Location where excel path is located

        • -
        • output_structure (dict) – Structure to assign value. Will assign to output_structure[‘atoms’]

        • +
        • excel_path (str) – Location where excel path is located

        • +
        • output_structure (dict) – Structure to assign value. Will assign to output_structure[‘atoms’]

        Raises:
        diff --git a/api/io/excel/pmutt.io.excel.set_dict_value.html b/api/io/excel/pmutt.io.excel.set_dict_value.html index 9f2c82fc..b724413b 100644 --- a/api/io/excel/pmutt.io.excel.set_dict_value.html +++ b/api/io/excel/pmutt.io.excel.set_dict_value.html @@ -4,7 +4,7 @@ - pmutt.io.excel.set_dict_value — pmutt 1.4.7 documentation + pmutt.io.excel.set_dict_value — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        @@ -143,10 +143,10 @@

        pmutt.io.excel.set_dict_value
        Parameters:
          -
        • dict_name (str) – Name of the dictionary. ‘dict’ should already be removed.

        • -
        • key (str) – Key corresponding to value

        • -
        • value (float) – Value to assign to key

        • -
        • output_structure (dict) – Structure to assign value. Will assign to +

        • dict_name (str) – Name of the dictionary. ‘dict’ should already be removed.

        • +
        • key (str) – Key corresponding to value

        • +
        • value (float) – Value to assign to key

        • +
        • output_structure (dict) – Structure to assign value. Will assign to output_structure[dict_name]

        diff --git a/api/io/excel/pmutt.io.excel.set_elec_model.html b/api/io/excel/pmutt.io.excel.set_elec_model.html index fc8d2374..c82e049f 100644 --- a/api/io/excel/pmutt.io.excel.set_elec_model.html +++ b/api/io/excel/pmutt.io.excel.set_elec_model.html @@ -4,7 +4,7 @@ - pmutt.io.excel.set_elec_model — pmutt 1.4.7 documentation + pmutt.io.excel.set_elec_model — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        @@ -143,8 +143,8 @@

        pmutt.io.excel.set_elec_model
        Parameters:
          -
        • model (str) – Electronic model to import

        • -
        • output_structure (dict) – Structure to assign value. Will assign to +

        • model (str) – Electronic model to import

        • +
        • output_structure (dict) – Structure to assign value. Will assign to output_structure[‘elec_model’]

        diff --git a/api/io/excel/pmutt.io.excel.set_element.html b/api/io/excel/pmutt.io.excel.set_element.html index 207faf08..742e849d 100644 --- a/api/io/excel/pmutt.io.excel.set_element.html +++ b/api/io/excel/pmutt.io.excel.set_element.html @@ -4,7 +4,7 @@ - pmutt.io.excel.set_element — pmutt 1.4.7 documentation + pmutt.io.excel.set_element — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        @@ -143,12 +143,12 @@

        pmutt.io.excel.set_element
        Parameters:
          -
        • header (str) – String containing the element name. Element symbol should be at +

        • header (str) – String containing the element name. Element symbol should be at the end. e.g. ‘element.O’

        • -
        • value (int) – Amount found in formula

        • -
        • output_structure (dict) – Structure to assign value. Will assign to +

        • value (int) – Amount found in formula

        • +
        • output_structure (dict) – Structure to assign value. Will assign to output_structure[‘elements’][element]

        • -
        • delimiter (str) – Delimiter for element. Element symbol should be at the end

        • +
        • delimiter (str) – Delimiter for element. Element symbol should be at the end

        diff --git a/api/io/excel/pmutt.io.excel.set_formula.html b/api/io/excel/pmutt.io.excel.set_formula.html index 55360275..fe265197 100644 --- a/api/io/excel/pmutt.io.excel.set_formula.html +++ b/api/io/excel/pmutt.io.excel.set_formula.html @@ -4,7 +4,7 @@ - pmutt.io.excel.set_formula — pmutt 1.4.7 documentation + pmutt.io.excel.set_formula — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        @@ -143,10 +143,10 @@

        pmutt.io.excel.set_formula
        Parameters:
          -
        • formula (str) – Stoichiometric formula unit. e.g. H2O +

        • formula (str) – Stoichiometric formula unit. e.g. H2O Note that an element cannot be specified multiple times. e.g. CH3OH is not supported

        • -
        • output_structure (dict) – Structure to assign value. Will assign to +

        • output_structure (dict) – Structure to assign value. Will assign to output_structure[‘elements’]

        diff --git a/api/io/excel/pmutt.io.excel.set_list_value.html b/api/io/excel/pmutt.io.excel.set_list_value.html index 815c8a67..1b4a3aef 100644 --- a/api/io/excel/pmutt.io.excel.set_list_value.html +++ b/api/io/excel/pmutt.io.excel.set_list_value.html @@ -4,7 +4,7 @@ - pmutt.io.excel.set_list_value — pmutt 1.4.7 documentation + pmutt.io.excel.set_list_value — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        @@ -143,9 +143,9 @@

        pmutt.io.excel.set_list_value
        Parameters:
          -
        • header (str) – Name of the header. ‘list’ should already be removed.

        • -
        • value (float) – Value to assign

        • -
        • output_structure (dict) – Structure to assign value. Will assign to +

        • header (str) – Name of the header. ‘list’ should already be removed.

        • +
        • value (float) – Value to assign

        • +
        • output_structure (dict) – Structure to assign value. Will assign to output_structure[header]

        diff --git a/api/io/excel/pmutt.io.excel.set_nasa_a_high.html b/api/io/excel/pmutt.io.excel.set_nasa_a_high.html index 2bc8f522..8b807851 100644 --- a/api/io/excel/pmutt.io.excel.set_nasa_a_high.html +++ b/api/io/excel/pmutt.io.excel.set_nasa_a_high.html @@ -4,7 +4,7 @@ - pmutt.io.excel.set_nasa_a_high — pmutt 1.4.7 documentation + pmutt.io.excel.set_nasa_a_high — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        @@ -143,15 +143,15 @@

        pmutt.io.excel.set_nasa_a_high
        Parameters:
          -
        • header (str) –

          Name of the header. Used to determine coefficient. +

        • header (str) –

          Name of the header. Used to determine coefficient. Assumes zero index and header takes the format:

          nasa[delimiter]a_high[delimiter][index] e.g. nasa.a_high.0

        • -
        • value (float) – a_high value

        • -
        • output_structure (dict) – Structure to assign value. Will assign to +

        • value (float) – a_high value

        • +
        • output_structure (dict) – Structure to assign value. Will assign to output_structure[‘a_high’]

        • -
        • delimiter (str) – How to parse header to find the coefficient

        • +
        • delimiter (str) – How to parse header to find the coefficient

        diff --git a/api/io/excel/pmutt.io.excel.set_nasa_a_low.html b/api/io/excel/pmutt.io.excel.set_nasa_a_low.html index 091f129e..15279157 100644 --- a/api/io/excel/pmutt.io.excel.set_nasa_a_low.html +++ b/api/io/excel/pmutt.io.excel.set_nasa_a_low.html @@ -4,7 +4,7 @@ - pmutt.io.excel.set_nasa_a_low — pmutt 1.4.7 documentation + pmutt.io.excel.set_nasa_a_low — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        @@ -143,14 +143,14 @@

        pmutt.io.excel.set_nasa_a_low
        Parameters:
          -
        • header (str) –

          Name of the header. Used to determine coefficient. +

        • header (str) –

          Name of the header. Used to determine coefficient. Assumes zero index and header takes the format:

          nasa[delimiter]a_low[delimiter][index] e.g. nasa.a_low.0

        • -
        • value (float) – a_low value

        • -
        • output_structure (dict) – Structure to assign value. Will assign to output_structure[‘a_low’]

        • -
        • delimiter (str) – How to parse header to find the coefficient

        • +
        • value (float) – a_low value

        • +
        • output_structure (dict) – Structure to assign value. Will assign to output_structure[‘a_low’]

        • +
        • delimiter (str) – How to parse header to find the coefficient

        diff --git a/api/io/excel/pmutt.io.excel.set_nucl_model.html b/api/io/excel/pmutt.io.excel.set_nucl_model.html index 8f286576..1ca3d635 100644 --- a/api/io/excel/pmutt.io.excel.set_nucl_model.html +++ b/api/io/excel/pmutt.io.excel.set_nucl_model.html @@ -4,7 +4,7 @@ - pmutt.io.excel.set_nucl_model — pmutt 1.4.7 documentation + pmutt.io.excel.set_nucl_model — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        @@ -143,8 +143,8 @@

        pmutt.io.excel.set_nucl_model
        Parameters:
          -
        • model (str) – Nuclear model to import

        • -
        • output_structure (dict) – Structure to assign value. Will assign to +

        • model (str) – Nuclear model to import

        • +
        • output_structure (dict) – Structure to assign value. Will assign to output_structure[‘nucl_model’]

        diff --git a/api/io/excel/pmutt.io.excel.set_rot_model.html b/api/io/excel/pmutt.io.excel.set_rot_model.html index d71f773c..1fbb1729 100644 --- a/api/io/excel/pmutt.io.excel.set_rot_model.html +++ b/api/io/excel/pmutt.io.excel.set_rot_model.html @@ -4,7 +4,7 @@ - pmutt.io.excel.set_rot_model — pmutt 1.4.7 documentation + pmutt.io.excel.set_rot_model — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        @@ -143,8 +143,8 @@

        pmutt.io.excel.set_rot_model
        Parameters:
          -
        • model (str) – Rotational model to import

        • -
        • output_structure (dict) – Structure to assign value. Will assign to +

        • model (str) – Rotational model to import

        • +
        • output_structure (dict) – Structure to assign value. Will assign to output_structure[‘rot_model’]

        diff --git a/api/io/excel/pmutt.io.excel.set_rot_temperatures.html b/api/io/excel/pmutt.io.excel.set_rot_temperatures.html index b18dea0a..a353e767 100644 --- a/api/io/excel/pmutt.io.excel.set_rot_temperatures.html +++ b/api/io/excel/pmutt.io.excel.set_rot_temperatures.html @@ -4,7 +4,7 @@ - pmutt.io.excel.set_rot_temperatures — pmutt 1.4.7 documentation + pmutt.io.excel.set_rot_temperatures — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        @@ -144,8 +144,8 @@

        pmutt.io.excel.set_rot_temperatures
        Parameters:
          -
        • value (float) – Vibrational frequency in 1/cm

        • -
        • output_structure (dict) – Structure to assign value. Will assign to +

        • value (float) – Vibrational frequency in 1/cm

        • +
        • output_structure (dict) – Structure to assign value. Will assign to output_structure[‘elements’][element]

        diff --git a/api/io/excel/pmutt.io.excel.set_statmech_model.html b/api/io/excel/pmutt.io.excel.set_statmech_model.html index f28b7ad1..7dedfffb 100644 --- a/api/io/excel/pmutt.io.excel.set_statmech_model.html +++ b/api/io/excel/pmutt.io.excel.set_statmech_model.html @@ -4,7 +4,7 @@ - pmutt.io.excel.set_statmech_model — pmutt 1.4.7 documentation + pmutt.io.excel.set_statmech_model — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        @@ -143,9 +143,9 @@

        pmutt.io.excel.set_statmech_model
        Parameters:
          -
        • model (str) – Thermodynamic model to import. See pmutt.statmech.presets for +

        • model (str) – Thermodynamic model to import. See pmutt.statmech.presets for supported models.

        • -
        • output_structure (dict) – Structure to assign value. Will assign to +

        • output_structure (dict) – Structure to assign value. Will assign to output_structure[‘model’]

        diff --git a/api/io/excel/pmutt.io.excel.set_trans_model.html b/api/io/excel/pmutt.io.excel.set_trans_model.html index 2cd50579..deceb19c 100644 --- a/api/io/excel/pmutt.io.excel.set_trans_model.html +++ b/api/io/excel/pmutt.io.excel.set_trans_model.html @@ -4,7 +4,7 @@ - pmutt.io.excel.set_trans_model — pmutt 1.4.7 documentation + pmutt.io.excel.set_trans_model — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        @@ -143,8 +143,8 @@

        pmutt.io.excel.set_trans_model
        Parameters:
          -
        • model (str) – Translational model to import

        • -
        • output_structure (dict) – Structure to assign value. Will assign to +

        • model (str) – Translational model to import

        • +
        • output_structure (dict) – Structure to assign value. Will assign to output_structure[‘trans_model’]

        diff --git a/api/io/excel/pmutt.io.excel.set_vib_model.html b/api/io/excel/pmutt.io.excel.set_vib_model.html index e08fcc69..7ad6e4c7 100644 --- a/api/io/excel/pmutt.io.excel.set_vib_model.html +++ b/api/io/excel/pmutt.io.excel.set_vib_model.html @@ -4,7 +4,7 @@ - pmutt.io.excel.set_vib_model — pmutt 1.4.7 documentation + pmutt.io.excel.set_vib_model — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        @@ -143,8 +143,8 @@

        pmutt.io.excel.set_vib_model
        Parameters:
          -
        • model (str) – Vibrational model to import

        • -
        • output_structure (dict) – Structure to assign value. Will assign to +

        • model (str) – Vibrational model to import

        • +
        • output_structure (dict) – Structure to assign value. Will assign to output_structure[‘vib_model’]

        diff --git a/api/io/excel/pmutt.io.excel.set_vib_wavenumbers.html b/api/io/excel/pmutt.io.excel.set_vib_wavenumbers.html index 3ee75145..8562d13d 100644 --- a/api/io/excel/pmutt.io.excel.set_vib_wavenumbers.html +++ b/api/io/excel/pmutt.io.excel.set_vib_wavenumbers.html @@ -4,7 +4,7 @@ - pmutt.io.excel.set_vib_wavenumbers — pmutt 1.4.7 documentation + pmutt.io.excel.set_vib_wavenumbers — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        @@ -143,8 +143,8 @@

        pmutt.io.excel.set_vib_wavenumbers
        Parameters:
          -
        • value (float) – Vibrational frequency in 1/cm

        • -
        • output_structure (dict) – Structure to assign value. Will assign to +

        • value (float) – Vibrational frequency in 1/cm

        • +
        • output_structure (dict) – Structure to assign value. Will assign to output_structure[‘elements’][element]

        diff --git a/api/io/gaussian/pmutt.io.gaussian.read_electronic_and_zpe.html b/api/io/gaussian/pmutt.io.gaussian.read_electronic_and_zpe.html index cbb5f874..cc69c95b 100644 --- a/api/io/gaussian/pmutt.io.gaussian.read_electronic_and_zpe.html +++ b/api/io/gaussian/pmutt.io.gaussian.read_electronic_and_zpe.html @@ -4,7 +4,7 @@ - pmutt.io.gaussian.read_electronic_and_zpe — pmutt 1.4.7 documentation + pmutt.io.gaussian.read_electronic_and_zpe — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        @@ -132,8 +132,8 @@

        pmutt.io.gaussian.read_electronic_and_zpe
        Parameters:
          -
        • filename (str) – Log file

        • -
        • units (str, optional) – Units to return energy. Default is ‘eV/molecule’

        • +
        • filename (str) – Log file

        • +
        • units (str, optional) – Units to return energy. Default is ‘eV/molecule’

        Returns:
        @@ -141,7 +141,7 @@

        pmutt.io.gaussian.read_electronic_and_zpeReturn type: -

        float

        +

        float

    diff --git a/api/io/gaussian/pmutt.io.gaussian.read_frequencies.html b/api/io/gaussian/pmutt.io.gaussian.read_frequencies.html index a0f3b102..70980a10 100644 --- a/api/io/gaussian/pmutt.io.gaussian.read_frequencies.html +++ b/api/io/gaussian/pmutt.io.gaussian.read_frequencies.html @@ -4,7 +4,7 @@ - pmutt.io.gaussian.read_frequencies — pmutt 1.4.7 documentation + pmutt.io.gaussian.read_frequencies — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -131,8 +131,8 @@

    pmutt.io.gaussian.read_frequencies
    Parameters:
      -
    • filename (str) – Log file

    • -
    • units (str, optional) – Units to return frequencies. Default is ‘1/cm’

    • +
    • filename (str) – Log file

    • +
    • units (str, optional) – Units to return frequencies. Default is ‘1/cm’

    Returns:
    diff --git a/api/io/gaussian/pmutt.io.gaussian.read_molecular_mass.html b/api/io/gaussian/pmutt.io.gaussian.read_molecular_mass.html index 1eac0d68..703d46d4 100644 --- a/api/io/gaussian/pmutt.io.gaussian.read_molecular_mass.html +++ b/api/io/gaussian/pmutt.io.gaussian.read_molecular_mass.html @@ -4,7 +4,7 @@ - pmutt.io.gaussian.read_molecular_mass — pmutt 1.4.7 documentation + pmutt.io.gaussian.read_molecular_mass — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -131,15 +131,15 @@

    pmutt.io.gaussian.read_molecular_mass
    Parameters:
      -
    • filename (str) – Log file

    • -
    • units (str, optional) – Units for molecular mass. Default is ‘g/mol’

    • +
    • filename (str) – Log file

    • +
    • units (str, optional) – Units for molecular mass. Default is ‘g/mol’

    Returns:

    molecular_mass – Molecular mass in units. Default is ‘g/mol’

    Return type:
    -

    float

    +

    float

    diff --git a/api/io/gaussian/pmutt.io.gaussian.read_pattern.html b/api/io/gaussian/pmutt.io.gaussian.read_pattern.html index 14de3557..e1b1f59d 100644 --- a/api/io/gaussian/pmutt.io.gaussian.read_pattern.html +++ b/api/io/gaussian/pmutt.io.gaussian.read_pattern.html @@ -4,7 +4,7 @@ - pmutt.io.gaussian.read_pattern — pmutt 1.4.7 documentation + pmutt.io.gaussian.read_pattern — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -131,10 +131,10 @@

    pmutt.io.gaussian.read_pattern
    Parameters:
      -
    • filename (str) – Log file

    • -
    • pattern (str) – Regular expression pattern

    • -
    • group (int, optional) – Group to return. Default is 0

    • -
    • return_immediately (bool, optional) – If True, returns after the first instance. If False, reads the +

    • filename (str) – Log file

    • +
    • pattern (str) – Regular expression pattern

    • +
    • group (int, optional) – Group to return. Default is 0

    • +
    • return_immediately (bool, optional) – If True, returns after the first instance. If False, reads the whole file. Default is True

    @@ -148,7 +148,7 @@

    pmutt.io.gaussian.read_patternReturn type: -

    str or list of str

    +

    str or list of str

    diff --git a/api/io/gaussian/pmutt.io.gaussian.read_rot_symmetry_num.html b/api/io/gaussian/pmutt.io.gaussian.read_rot_symmetry_num.html index e6b5732a..0bc2dc2d 100644 --- a/api/io/gaussian/pmutt.io.gaussian.read_rot_symmetry_num.html +++ b/api/io/gaussian/pmutt.io.gaussian.read_rot_symmetry_num.html @@ -4,7 +4,7 @@ - pmutt.io.gaussian.read_rot_symmetry_num — pmutt 1.4.7 documentation + pmutt.io.gaussian.read_rot_symmetry_num — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -130,13 +130,13 @@

    pmutt.io.gaussian.read_rot_symmetry_num
    Parameters:
    -

    filename (str) – Log file

    +

    filename (str) – Log file

    Returns:

    rot_symmetry_num – Rotational symmetry number

    Return type:
    -

    int

    +

    int

    diff --git a/api/io/gaussian/pmutt.io.gaussian.read_rotational_temperatures.html b/api/io/gaussian/pmutt.io.gaussian.read_rotational_temperatures.html index ce47fbdf..80f27ae2 100644 --- a/api/io/gaussian/pmutt.io.gaussian.read_rotational_temperatures.html +++ b/api/io/gaussian/pmutt.io.gaussian.read_rotational_temperatures.html @@ -4,7 +4,7 @@ - pmutt.io.gaussian.read_rotational_temperatures — pmutt 1.4.7 documentation + pmutt.io.gaussian.read_rotational_temperatures — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -130,7 +130,7 @@

    pmutt.io.gaussian.read_rotational_temperatures
    Parameters:
    -

    filename (str) – Log file

    +

    filename (str) – Log file

    Returns:

    rotational_temperatures – Rotational temperatures in K

    diff --git a/api/io/gaussian/pmutt.io.gaussian.read_zpe.html b/api/io/gaussian/pmutt.io.gaussian.read_zpe.html index 6b83d210..3c3305d2 100644 --- a/api/io/gaussian/pmutt.io.gaussian.read_zpe.html +++ b/api/io/gaussian/pmutt.io.gaussian.read_zpe.html @@ -4,7 +4,7 @@ - pmutt.io.gaussian.read_zpe — pmutt 1.4.7 documentation + pmutt.io.gaussian.read_zpe — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -131,15 +131,15 @@

    pmutt.io.gaussian.read_zpe
    Parameters:
      -
    • filename (str) – Log file

    • -
    • units (str, optional) – Units to return energy. Default is ‘eV/molecule’

    • +
    • filename (str) – Log file

    • +
    • units (str, optional) – Units to return energy. Default is ‘eV/molecule’

    Returns:

    zero_point_energy – Zero point energy in units. Default units are ‘eV/molecule’

    Return type:
    -

    float

    +

    float

    diff --git a/api/io/io.html b/api/io/io.html index e9eb9d73..90a941d3 100644 --- a/api/io/io.html +++ b/api/io/io.html @@ -4,7 +4,7 @@ - Input and Output — pmutt 1.4.7 documentation + Input and Output — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    diff --git a/api/io/json/pmutt.io.json.json_to_pmutt.html b/api/io/json/pmutt.io.json.json_to_pmutt.html index e9160c10..875360c6 100644 --- a/api/io/json/pmutt.io.json.json_to_pmutt.html +++ b/api/io/json/pmutt.io.json.json_to_pmutt.html @@ -4,7 +4,7 @@ - pmutt.io.json.json_to_pmutt — pmutt 1.4.7 documentation + pmutt.io.json.json_to_pmutt — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    diff --git a/api/io/json/pmutt.io.json.pmuttEncoder.html b/api/io/json/pmutt.io.json.pmuttEncoder.html index a00d3233..abaf339c 100644 --- a/api/io/json/pmutt.io.json.pmuttEncoder.html +++ b/api/io/json/pmutt.io.json.pmuttEncoder.html @@ -4,7 +4,7 @@ - pmutt.io.json.pmuttEncoder — pmutt 1.4.7 documentation + pmutt.io.json.pmuttEncoder — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    diff --git a/api/io/omkm/pmutt.io.omkm.get_interactions_phases.html b/api/io/omkm/pmutt.io.omkm.get_interactions_phases.html index b74ada41..9f71b32a 100644 --- a/api/io/omkm/pmutt.io.omkm.get_interactions_phases.html +++ b/api/io/omkm/pmutt.io.omkm.get_interactions_phases.html @@ -4,7 +4,7 @@ - pmutt.io.omkm.get_interactions_phases — pmutt 1.4.7 documentation + pmutt.io.omkm.get_interactions_phases — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -139,7 +139,7 @@

    pmutt.io.omkm.get_interactions_phasesReturn type: -

    dict

    +

    dict

    diff --git a/api/io/omkm/pmutt.io.omkm.get_reactions_phases.html b/api/io/omkm/pmutt.io.omkm.get_reactions_phases.html index a60f7b87..4cfa4a74 100644 --- a/api/io/omkm/pmutt.io.omkm.get_reactions_phases.html +++ b/api/io/omkm/pmutt.io.omkm.get_reactions_phases.html @@ -4,7 +4,7 @@ - pmutt.io.omkm.get_reactions_phases — pmutt 1.4.7 documentation + pmutt.io.omkm.get_reactions_phases — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -136,7 +136,7 @@

    pmutt.io.omkm.get_reactions_phasesReturn type: -

    dict

    +

    dict

    diff --git a/api/io/omkm/pmutt.io.omkm.get_species_phases.html b/api/io/omkm/pmutt.io.omkm.get_species_phases.html index 0888ecad..1384dbdd 100644 --- a/api/io/omkm/pmutt.io.omkm.get_species_phases.html +++ b/api/io/omkm/pmutt.io.omkm.get_species_phases.html @@ -4,7 +4,7 @@ - pmutt.io.omkm.get_species_phases — pmutt 1.4.7 documentation + pmutt.io.omkm.get_species_phases — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -136,7 +136,7 @@

    pmutt.io.omkm.get_species_phasesReturn type: -

    dict

    +

    dict

    diff --git a/api/io/omkm/pmutt.io.omkm.organize_phases.html b/api/io/omkm/pmutt.io.omkm.organize_phases.html index ea8e6a66..50af3f79 100644 --- a/api/io/omkm/pmutt.io.omkm.organize_phases.html +++ b/api/io/omkm/pmutt.io.omkm.organize_phases.html @@ -4,7 +4,7 @@ - pmutt.io.omkm.organize_phases — pmutt 1.4.7 documentation + pmutt.io.omkm.organize_phases — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    diff --git a/api/io/omkm/pmutt.io.omkm.write_cti.html b/api/io/omkm/pmutt.io.omkm.write_cti.html index a04fc85c..8f5fb482 100644 --- a/api/io/omkm/pmutt.io.omkm.write_cti.html +++ b/api/io/omkm/pmutt.io.omkm.write_cti.html @@ -4,7 +4,7 @@ - pmutt.io.omkm.write_cti — pmutt 1.4.7 documentation + pmutt.io.omkm.write_cti — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -138,17 +138,17 @@

    pmutt.io.omkm.write_cti

    units (dict or Unit object, optional) – Units to write file. If a dict is inputted, the key is the quantity and the value is the unit. If not specified, uses the default units of Unit.

    -
  • filename (str, optional) – Filename for the input.cti file. If not specified, returns file +

  • filename (str, optional) – Filename for the input.cti file. If not specified, returns file as str.

  • -
  • T (float, optional) – Temperature in K. Default is 300 K.

  • -
  • P (float, optional) – Pressure in atm. Default is 1 atm.

  • -
  • newline (str, optional) – Type of newline to use. Default is Linux newline (’n’)

  • -
  • use_motz_wise (bool, optional) – Whether to use Motz-wise sticking coefficients or not. Default is +

  • T (float, optional) – Temperature in K. Default is 300 K.

  • +
  • P (float, optional) – Pressure in atm. Default is 1 atm.

  • +
  • newline (str, optional) – Type of newline to use. Default is Linux newline (’n’)

  • +
  • use_motz_wise (bool, optional) – Whether to use Motz-wise sticking coefficients or not. Default is False

  • -
  • ads_act_method (str, optional) – Activation method to use for adsorption reactions. Accepted +

  • ads_act_method (str, optional) – Activation method to use for adsorption reactions. Accepted options include ‘get_H_act’ and ‘get_G_act’. Default is ‘get_H_act’.

  • -
  • write_xml (bool, optional) – If True and filename is not None, automatically generates +

  • write_xml (bool, optional) – If True and filename is not None, automatically generates an XML file with the CTI file.

  • @@ -156,7 +156,7 @@

    pmutt.io.omkm.write_cti

    lines_out – If filename is None, CTI file is returned.

    Return type:
    -

    str

    +

    str

    diff --git a/api/io/omkm/pmutt.io.omkm.write_yaml.html b/api/io/omkm/pmutt.io.omkm.write_yaml.html index 9841b663..efbb294e 100644 --- a/api/io/omkm/pmutt.io.omkm.write_yaml.html +++ b/api/io/omkm/pmutt.io.omkm.write_yaml.html @@ -4,7 +4,7 @@ - pmutt.io.omkm.write_yaml — pmutt 1.4.7 documentation + pmutt.io.omkm.write_yaml — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -130,7 +130,7 @@

    pmutt.io.omkm.write_yaml
    Parameters:
      -
    • reactor_type (str) –

      Type of reactor. Supported options include:

      +
    • reactor_type (str) –

      Type of reactor. Supported options include:

      • pfr

      • pfr_0d

      • @@ -139,70 +139,70 @@

        pmutt.io.omkm.write_yamlreactor.type.

        -
      • temperature_mode (str) –

        Operation of reactor. Supported options include:

        +
      • temperature_mode (str) –

        Operation of reactor. Supported options include:

        • Isothermal

        • Adiabatic

        Value written to reactor.temperature_mode.

      • -
      • pressure_mode (str) –

        Operation of reactor. Supported options include:

        +
      • pressure_mode (str) –

        Operation of reactor. Supported options include:

        • Isobaric

        • Isochoric

        Value written to reactor.pressure_mode.

      • -
      • nodes (int) – Number of nodes to use if reactor_type is ‘pfr_0d’. Value +

      • nodes (int) – Number of nodes to use if reactor_type is ‘pfr_0d’. Value written to reactor.nodes

      • -
      • V (float or str) – Volume of reactor. Value written to reactor.volume. Units of +

      • V (float or str) – Volume of reactor. Value written to reactor.volume. Units of length^3. See Notes section regarding unit specification.

      • -
      • T (float) – Temperature (in K) of reactor. Value written to +

      • T (float) – Temperature (in K) of reactor. Value written to reactor.temperature.

      • -
      • P (float or str) – Pressure of reactor. Value written to reactor.pressure. Units +

      • P (float or str) – Pressure of reactor. Value written to reactor.pressure. Units of pressure. See Notes section regarding unit specification.

      • -
      • A (float or str) – Surface area of reactor. Value written to reactor.area. +

      • A (float or str) – Surface area of reactor. Value written to reactor.area. Units of length^2. See Notes section regarding unit specification.

      • -
      • L (float or str) – Length of reactor. Value written to reactor.length. +

      • L (float or str) – Length of reactor. Value written to reactor.length. Units of length. See Notes section regarding unit specification.

      • -
      • cat_abyv (float or str) – Catalyst surface area to volume ratio. Value written to +

      • cat_abyv (float or str) – Catalyst surface area to volume ratio. Value written to reactor.cat_abyv. Units of 1/length. See Notes section regarding unit specification.

      • -
      • flow_rate (float or str) – Volumetric flow rate of inlet. Value written to +

      • flow_rate (float or str) – Volumetric flow rate of inlet. Value written to inlet_gas.flow_rate. Units of length^3/time. See Notes section regarding unit specification.

      • -
      • residence_time (float or str) – Residence time of reactor. Value written to +

      • residence_time (float or str) – Residence time of reactor. Value written to inlet_gas.residence_time. Not required if flow_rate or mass_flow_rate already specified. Units of time. See Notes section regarding unit specification.

      • -
      • mass_flow_rate (float or str) – Mass flow rate of inlet. Value written to +

      • mass_flow_rate (float or str) – Mass flow rate of inlet. Value written to inlet_gas.mass_flow_rate. Units of mass^3/time. See Notes section regarding unit specification.

      • -
      • end_time (float or str) – Reactor simulation time. For continuous reactors, the system is +

      • end_time (float or str) – Reactor simulation time. For continuous reactors, the system is assumed to reach steady state by this time. Value written to simulation.end_time. Units of time. See Notes section regarding unit specification.

      • -
      • transient (bool) – If True, transient operation results are saved. Otherwise, +

      • transient (bool) – If True, transient operation results are saved. Otherwise, transient files are left blank. Value written to simulation.transient.

      • -
      • stepping (str) –

        Time steps taken to simulate reactor. Supported options include:

        +
      • stepping (str) –

        Time steps taken to simulate reactor. Supported options include:

        • logarithmic

        • regular

        Value written to simulation.stepping.

      • -
      • init_step (float or str) – Initial step to take. Value written to simulation.init_step.

      • -
      • step_size (float or str) – If stepping is logarithmic, represents the ratio between the +

      • init_step (float or str) – Initial step to take. Value written to simulation.init_step.

      • +
      • step_size (float or str) – If stepping is logarithmic, represents the ratio between the next step and the current step. If stepping is regular, represents the time between the next step and the current step in units of time. Value written to simulation.step_size. See Notes section regarding unit specification.

      • -
      • atol (float) – Absolute tolerance for solver. Value written to +

      • atol (float) – Absolute tolerance for solver. Value written to simulation.solver.atol.

      • -
      • rtol (float) – Relative tolerance for solver. Value written to +

      • rtol (float) – Relative tolerance for solver. Value written to simulation.solver.rtol.

      • -
      • full_SA (bool) – If True, OpenMKM will do a full sensitivity analysis using the +

      • full_SA (bool) – If True, OpenMKM will do a full sensitivity analysis using the Fisher Information Matrix (FIM). Value written to simulation.sensitivity.full.

      • reactions_SA (list of str or list of SurfaceReaction obj) – List of reactions to perturb using local sensitivity analysis (LSA). @@ -213,9 +213,9 @@

        pmutt.io.omkm.write_yamlname attribute will be used.

      • phases (list of Phase objects) – Phases present in reactor. Each phase should have the name and initial_state attribute.

      • -
      • reactor (dict) – Generic dictionary for reactor to specify values not supported by +

      • reactor (dict) – Generic dictionary for reactor to specify values not supported by write_yaml.

      • -
      • inlet_gas (dict) – Generic dictionary for inlet_gas to specify values not supported by +

      • inlet_gas (dict) – Generic dictionary for inlet_gas to specify values not supported by write_yaml.

      • multi_T (list of float) – Multiple temperatures (in K) of reactor. Value written to simulation.multi_input.temperature.

      • @@ -225,26 +225,26 @@

        pmutt.io.omkm.write_yamlsimulation.multi_input.flow_rate. Units of length3/time. See Notes section regarding unit specification.

        -
      • output_format (str) –

        Format for output files. Supported options include:

        +
      • output_format (str) –

        Format for output files. Supported options include:

        • CSV

        • DAT

        Value written to simulation.output_format.

      • -
      • misc (dict) – Generic dictionary for any parameter specified at the top level.

      • -
      • solver (dict) – Generic dictionary for solver to specify values not supported by +

      • misc (dict) – Generic dictionary for any parameter specified at the top level.

      • +
      • solver (dict) – Generic dictionary for solver to specify values not supported by write_yaml.

      • -
      • simulation (dict) – Generic dictionary for simultaion to specify values not supported by +

      • simulation (dict) – Generic dictionary for simultaion to specify values not supported by write_yaml.

      • -
      • multi_input (dict) – Generic dictionary for multi_input to specify values not supported +

      • multi_input (dict) – Generic dictionary for multi_input to specify values not supported by write_yaml.

      • units (dict or Unit object, optional) – Units used for file. If a dict is inputted, the key is the quantity and the value is the unit. If not specified, uses the default units of Unit.

      • -
      • filename (str, optional) – Filename for the input.cti file. If not specified, returns file +

      • filename (str, optional) – Filename for the input.cti file. If not specified, returns file as str.

      • -
      • yaml_options (dict) – Options to pass when converting the parameters to YAML format. See +

      • yaml_options (dict) – Options to pass when converting the parameters to YAML format. See PyYAML documentation for dump for available options.

    @@ -252,7 +252,7 @@

    pmutt.io.omkm.write_yaml

    lines_out – If filename is None, CTI file is returned

    Return type:
    -

    str

    +

    str

    Notes

    diff --git a/api/io/thermdat/pmutt.io.thermdat.read_thermdat.html b/api/io/thermdat/pmutt.io.thermdat.read_thermdat.html index 29c16bcf..4c4e459a 100644 --- a/api/io/thermdat/pmutt.io.thermdat.read_thermdat.html +++ b/api/io/thermdat/pmutt.io.thermdat.read_thermdat.html @@ -4,7 +4,7 @@ - pmutt.io.thermdat.read_thermdat — pmutt 1.4.7 documentation + pmutt.io.thermdat.read_thermdat — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -126,10 +126,10 @@

    pmutt.io.thermdat.read_thermdat
    Parameters:
      -
    • filename (str) – Input filename

    • -
    • format (str, optional) – Format to output NASA polynomials. Supported options are: +

    • filename (str) – Input filename

    • +
    • format (str, optional) – Format to output NASA polynomials. Supported options are: ‘list’, ‘tuple’, ‘dict’. Default is ‘list’

    • -
    • key (str, optional) – If format is ‘dict’, uses this attribute as the key for the +

    • key (str, optional) – If format is ‘dict’, uses this attribute as the key for the output dictionary. Default is ‘name’

    @@ -141,8 +141,8 @@

    pmutt.io.thermdat.read_thermdatRaises:
    diff --git a/api/io/thermdat/pmutt.io.thermdat.write_thermdat.html b/api/io/thermdat/pmutt.io.thermdat.write_thermdat.html index ab0906d7..fd8e5979 100644 --- a/api/io/thermdat/pmutt.io.thermdat.write_thermdat.html +++ b/api/io/thermdat/pmutt.io.thermdat.write_thermdat.html @@ -4,7 +4,7 @@ - pmutt.io.thermdat.write_thermdat — pmutt 1.4.7 documentation + pmutt.io.thermdat.write_thermdat — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -127,20 +127,20 @@

    pmutt.io.thermdat.write_thermdatParameters:
    • nasa_species (list or dict of Nasa) – List of species to populate thermdat

    • -
    • filename (str, optional) – Output file name. If not specified, returns thermdat as str

    • -
    • supp_data (str, optional) – Additional thermdat entries to include. Must be in therndat format.

    • -
    • supp_txt (str, optional) – Comment field to preceed nasa_species entries. Each line needs to +

    • filename (str, optional) – Output file name. If not specified, returns thermdat as str

    • +
    • supp_data (str, optional) – Additional thermdat entries to include. Must be in therndat format.

    • +
    • supp_txt (str, optional) – Comment field to preceed nasa_species entries. Each line needs to begin with a ! so it is recognized as a comment.

    • -
    • write_date (bool, optional) – Whether or not the date should be written. If False, writes the +

    • write_date (bool, optional) – Whether or not the date should be written. If False, writes the first 8 characters of notes attribute. Defaults to True

    • -
    • newline (str, optional) – Newline character to use. Default is the Unix convention (n)

    • +
    • newline (str, optional) – Newline character to use. Default is the Unix convention (n)

    Returns:

    lines_out – Thermdat lines as a string if filename is None

    Return type:
    -

    str

    +

    str

    diff --git a/api/io/vasp/pmutt.io.vasp.set_vib_wavenumbers_from_outcar.html b/api/io/vasp/pmutt.io.vasp.set_vib_wavenumbers_from_outcar.html index ed3f5dd4..d231c4df 100644 --- a/api/io/vasp/pmutt.io.vasp.set_vib_wavenumbers_from_outcar.html +++ b/api/io/vasp/pmutt.io.vasp.set_vib_wavenumbers_from_outcar.html @@ -4,7 +4,7 @@ - pmutt.io.vasp.set_vib_wavenumbers_from_outcar — pmutt 1.4.7 documentation + pmutt.io.vasp.set_vib_wavenumbers_from_outcar — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -127,16 +127,16 @@

    pmutt.io.vasp.set_vib_wavenumbers_from_outcar
    Parameters:
      -
    • in_file (str) – OUTCAR file of frequency jobs

    • -
    • output_structure (dict) – Structure to assign value. Will assign to +

    • in_file (str) – OUTCAR file of frequency jobs

    • +
    • output_structure (dict) – Structure to assign value. Will assign to output_structure[‘elements’][element]

    • -
    • min_frequency_cutoff (float, optional) – Only frequencies less than min_frequency_cutoff (in cm-1) +

    • min_frequency_cutoff (float, optional) – Only frequencies less than min_frequency_cutoff (in cm-1) are read from OUTCAR. Default is 0 cm-1

    • -
    • include_imaginary (bool, optional) – Whether imaginary frequencies should be included. Default is False.

    • +
    • include_imaginary (bool, optional) – Whether imaginary frequencies should be included. Default is False.

    Raises:
    -

    FileNotFoundError – Raised if in_file does not exist

    +

    FileNotFoundError – Raised if in_file does not exist

    diff --git a/api/kinetic_models/cantera_io/pmutt.io.cantera.obj_to_CTI.html b/api/kinetic_models/cantera_io/pmutt.io.cantera.obj_to_CTI.html index 24d9abe9..d65e1c14 100644 --- a/api/kinetic_models/cantera_io/pmutt.io.cantera.obj_to_CTI.html +++ b/api/kinetic_models/cantera_io/pmutt.io.cantera.obj_to_CTI.html @@ -4,7 +4,7 @@ - pmutt.io.cantera.obj_to_cti — pmutt 1.4.7 documentation + pmutt.io.cantera.obj_to_cti — pmutt 1.4.9 documentation @@ -36,7 +36,7 @@
    - 1.4.7 + 1.4.9
    @@ -110,9 +110,9 @@

    pmutt.io.cantera.obj_to_ctiParameters:
    • obj – Object to convert to CTI format

    • -
    • line_len (int, optional) – Number of characters available in line. Used to determine +

    • line_len (int, optional) – Number of characters available in line. Used to determine indentation. Default is 80

    • -
    • max_line_len (int, optional) – Maximum number of characters available in line. Used to determine +

    • max_line_len (int, optional) – Maximum number of characters available in line. Used to determine indentation. Default is 80

    • kwargs (keyword arguments) – Arguments to pass to obj.to_cti function

    @@ -121,7 +121,7 @@

    pmutt.io.cantera.obj_to_cti

    CTI_str – Object expressed in CTI format

    Return type:
    -

    str

    +

    str

    diff --git a/api/kinetic_models/cantera_phase/pmutt.cantera.phase.IdealGas.html b/api/kinetic_models/cantera_phase/pmutt.cantera.phase.IdealGas.html index ee4fafd8..b00cd106 100644 --- a/api/kinetic_models/cantera_phase/pmutt.cantera.phase.IdealGas.html +++ b/api/kinetic_models/cantera_phase/pmutt.cantera.phase.IdealGas.html @@ -4,7 +4,7 @@ - pmutt.cantera.phase.IdealGas — pmutt 1.4.7 documentation + pmutt.cantera.phase.IdealGas — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -133,7 +133,7 @@

    pmutt.cantera.phase.IdealGas
    Type:
    -

    str

    +

    str

    @@ -156,7 +156,7 @@

    pmutt.cantera.phase.IdealGas
    Type:
    -

    str, optional

    +

    str, optional

    @@ -167,7 +167,7 @@

    pmutt.cantera.phase.IdealGas
    Type:
    -

    str, optional

    +

    str, optional

    @@ -331,8 +331,8 @@

    pmutt.cantera.phase.IdealGas
    Parameters:
      -
    • max_line_len (int, optional) – Maximum number of characters in the line. Default is 80.

    • -
    • delimiter (str, optional) – Delimiter to use when specifying ranges for reactions. Default +

    • max_line_len (int, optional) – Maximum number of characters in the line. Default is 80.

    • +
    • delimiter (str, optional) – Delimiter to use when specifying ranges for reactions. Default is ‘_’.

    @@ -340,7 +340,7 @@

    pmutt.cantera.phase.IdealGas

    CTI_str – Object represented as a CTI string.

    Return type:
    -

    str

    +

    str

    diff --git a/api/kinetic_models/cantera_phase/pmutt.cantera.phase.Phase.html b/api/kinetic_models/cantera_phase/pmutt.cantera.phase.Phase.html index 418e89e3..4e77726b 100644 --- a/api/kinetic_models/cantera_phase/pmutt.cantera.phase.Phase.html +++ b/api/kinetic_models/cantera_phase/pmutt.cantera.phase.Phase.html @@ -4,7 +4,7 @@ - pmutt.cantera.phase.Phase — pmutt 1.4.7 documentation + pmutt.cantera.phase.Phase — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -124,7 +124,7 @@

    pmutt.cantera.phase.Phase
    class pmutt.cantera.phase.Phase(name, species=None, initial_state=None, kinetics=None, transport=None, reactions=None, options=None, note=None)
    -

    Bases: object

    +

    Bases: object

    Parent class for Cantera phases

    @@ -132,7 +132,7 @@

    pmutt.cantera.phase.Phase
    Type:
    -

    str

    +

    str

    @@ -154,7 +154,7 @@

    pmutt.cantera.phase.Phase
    Type:
    -

    dict, optional

    +

    dict, optional

    @@ -198,7 +198,7 @@

    pmutt.cantera.phase.Phase
    Type:
    -

    dict, optional

    +

    dict, optional

    @@ -209,7 +209,7 @@

    pmutt.cantera.phase.Phase
    Type:
    -

    str, optional

    +

    str, optional

    @@ -221,7 +221,7 @@

    pmutt.cantera.phase.Phasespecies attribute.

    Type:
    -

    set

    +

    set

    diff --git a/api/kinetic_models/cantera_phase/pmutt.cantera.phase.StoichSolid.html b/api/kinetic_models/cantera_phase/pmutt.cantera.phase.StoichSolid.html index a34dc2a9..c7446031 100644 --- a/api/kinetic_models/cantera_phase/pmutt.cantera.phase.StoichSolid.html +++ b/api/kinetic_models/cantera_phase/pmutt.cantera.phase.StoichSolid.html @@ -4,7 +4,7 @@ - pmutt.cantera.phase.StoichSolid — pmutt 1.4.7 documentation + pmutt.cantera.phase.StoichSolid — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -133,7 +133,7 @@

    pmutt.cantera.phase.StoichSolid
    Type:
    -

    str

    +

    str

    @@ -155,7 +155,7 @@

    pmutt.cantera.phase.StoichSolid
    Type:
    -

    float, optional

    +

    float, optional

    @@ -202,7 +202,7 @@

    pmutt.cantera.phase.StoichSolid
    Type:
    -

    str, optional

    +

    str, optional

    @@ -315,9 +315,9 @@

    pmutt.cantera.phase.StoichSolid
    Parameters:
      -
    • max_line_len (int, optional) – Maximum number of characters in the line. Default is 80.

    • -
    • mass_unit (str, optional) – Mass unit for density. Default is ‘g’

    • -
    • length_unit (str, optional) – Length unit for density. Default is ‘cm’

    • +
    • max_line_len (int, optional) – Maximum number of characters in the line. Default is 80.

    • +
    • mass_unit (str, optional) – Mass unit for density. Default is ‘g’

    • +
    • length_unit (str, optional) – Length unit for density. Default is ‘cm’

    • units (Units object, optional) – If specified, mass_unit and length_unit are overwritten. Default is None.

    @@ -326,7 +326,7 @@

    pmutt.cantera.phase.StoichSolid

    CTI_str – Object represented as a CTI string.

    Return type:
    -

    str

    +

    str

    diff --git a/api/kinetic_models/cantera_units/pmutt.cantera.units.Units.html b/api/kinetic_models/cantera_units/pmutt.cantera.units.Units.html index 853d46e2..ead83fad 100644 --- a/api/kinetic_models/cantera_units/pmutt.cantera.units.Units.html +++ b/api/kinetic_models/cantera_units/pmutt.cantera.units.Units.html @@ -4,7 +4,7 @@ - pmutt.cantera.units.Units — pmutt 1.4.7 documentation + pmutt.cantera.units.Units — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -122,7 +122,7 @@

    pmutt.cantera.units.Units
    class pmutt.cantera.units.Units(length='cm', time='s', quantity='molec', energy='cal', act_energy='cal/mol', pressure='bar', mass='kg')
    -

    Bases: object

    +

    Bases: object

    Expresses units as Cantera CTI file.

    @@ -130,7 +130,7 @@

    pmutt.cantera.units.Units
    Type:
    -

    str, optional

    +

    str, optional

    @@ -141,7 +141,7 @@

    pmutt.cantera.units.Units
    Type:
    -

    str, optional

    +

    str, optional

    @@ -152,7 +152,7 @@

    pmutt.cantera.units.Units
    Type:
    -

    str, optional

    +

    str, optional

    @@ -163,7 +163,7 @@

    pmutt.cantera.units.Units
    Type:
    -

    str, optional

    +

    str, optional

    @@ -174,7 +174,7 @@

    pmutt.cantera.units.Units
    Type:
    -

    str, optional

    +

    str, optional

    @@ -185,7 +185,7 @@

    pmutt.cantera.units.Units
    Type:
    -

    str, optional

    +

    str, optional

    @@ -196,7 +196,7 @@

    pmutt.cantera.units.Units
    Type:
    -

    str, optional

    +

    str, optional

    @@ -229,13 +229,13 @@

    pmutt.cantera.units.Units
    Parameters:
    -

    max_line_len (int, optional) – Maximum number of characters in the line. Default is 80.

    +

    max_line_len (int, optional) – Maximum number of characters in the line. Default is 80.

    Returns:

    CTI_str – Object represented as a CTI string.

    Return type:
    -

    str

    +

    str

    @@ -250,7 +250,7 @@

    pmutt.cantera.units.UnitsReturn type: -

    dict

    +

    dict

    @@ -264,7 +264,7 @@

    pmutt.cantera.units.Units

    yaml_dict – Dictionary compatible with Cantera’s YAML format

    Return type:
    -

    dict

    +

    dict

    diff --git a/api/kinetic_models/chemkin/pmutt.chemkin.CatSite.html b/api/kinetic_models/chemkin/pmutt.chemkin.CatSite.html index 73548de6..5cf7fe2d 100644 --- a/api/kinetic_models/chemkin/pmutt.chemkin.CatSite.html +++ b/api/kinetic_models/chemkin/pmutt.chemkin.CatSite.html @@ -4,7 +4,7 @@ - pmutt.chemkin.CatSite — pmutt 1.4.7 documentation + pmutt.chemkin.CatSite — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -131,7 +131,7 @@

    pmutt.chemkin.CatSite

    Name of the catalyst site

    Type:
    -

    str

    +

    str

    @@ -142,7 +142,7 @@

    pmutt.chemkin.CatSite

    Catalyst site density in mol/cm2

    Type:
    -

    float

    +

    float

    @@ -153,7 +153,7 @@

    pmutt.chemkin.CatSite

    Catalyst density in g/cm3

    Type:
    -

    float

    +

    float

    @@ -164,7 +164,7 @@

    pmutt.chemkin.CatSite

    Name of the bulk specie

    Type:
    -

    str

    +

    str

    @@ -194,7 +194,7 @@

    pmutt.chemkin.CatSite

    Recreate an object from the JSON representation.

    Parameters:
    -

    json_obj (dict) – JSON representation

    +

    json_obj (dict) – JSON representation

    Returns:

    Obj

    @@ -214,7 +214,7 @@

    pmutt.chemkin.CatSite

    obj_dict

    Return type:
    -

    dict

    +

    dict

    diff --git a/api/kinetic_models/chemkin/pmutt.reaction.ChemkinReaction.html b/api/kinetic_models/chemkin/pmutt.reaction.ChemkinReaction.html index 2f06a3c2..6d8b6e78 100644 --- a/api/kinetic_models/chemkin/pmutt.reaction.ChemkinReaction.html +++ b/api/kinetic_models/chemkin/pmutt.reaction.ChemkinReaction.html @@ -4,7 +4,7 @@ - pmutt.reaction.ChemkinReaction — pmutt 1.4.7 documentation + pmutt.reaction.ChemkinReaction — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
    - 1.4.7 + 1.4.9
    @@ -132,7 +132,7 @@

    pmutt.reaction.ChemkinReaction
    Type:
    -

    float, optional

    +

    float, optional

    @@ -143,7 +143,7 @@

    pmutt.reaction.ChemkinReaction
    Type:
    -

    bool, optional

    +

    bool, optional

    @@ -155,7 +155,7 @@

    pmutt.reaction.ChemkinReaction
    Type:
    -

    float, optional

    +

    float, optional

    @@ -167,7 +167,7 @@

    pmutt.reaction.ChemkinReaction
    Type:
    -

    bool

    +

    bool

    @@ -410,7 +410,7 @@

    pmutt.reaction.ChemkinReaction
    Raises:
    -

    ValueError – Raised if the reactants, products and/or transition state +

    ValueError – Raised if the reactants, products and/or transition state element composition does not agree.

    @@ -422,7 +422,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
    -

    json_obj (dict) – JSON representation

    +

    json_obj (dict) – JSON representation

    Returns:

    Reaction

    @@ -440,20 +440,20 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • reaction_str (str) – Reaction string.

    • -
    • species (dict) – Dictionary using the names as keys. If you have a list of +

    • reaction_str (str) – Reaction string.

    • +
    • species (dict) – Dictionary using the names as keys. If you have a list of species, use pmutt.pmutt_list_to_dict to make a dict.

    • -
    • species_delimiter (str, optional) – Delimiter that separate species. Leading and trailing spaces +

    • species_delimiter (str, optional) – Delimiter that separate species. Leading and trailing spaces will be trimmed. Default is ‘+’

    • -
    • reaction_delimiter (str, optional) – Delimiter that separate states of the reaction. Leading and +

    • reaction_delimiter (str, optional) – Delimiter that separate states of the reaction. Leading and trailing spaces will be trimmed. Default is ‘=’

    • -
    • notes (str or dict, optional) – Other notes such as the source of the reaction. Default is None

    • -
    • beta (float, optional) – Power to raise the temperature in the rate expression. +

    • notes (str or dict, optional) – Other notes such as the source of the reaction. Default is None

    • +
    • beta (float, optional) – Power to raise the temperature in the rate expression. Default is 1

    • -
    • is_adsorption (bool, optional) – If True, the reaction represents an adsorption. Default is False

    • -
    • sticking_coeff (float, optional) – Sticking coefficient. Only relevant if is_adsorption is +

    • is_adsorption (bool, optional) – If True, the reaction represents an adsorption. Default is False

    • +
    • sticking_coeff (float, optional) – Sticking coefficient. Only relevant if is_adsorption is True. Default is 0.5

    • -
    • gas_phase (bool) – True if the reaction has only gas-phase species. This attribute +

    • gas_phase (bool) – True if the reaction has only gas-phase species. This attribute is determined based on the reactants and products

    @@ -473,9 +473,9 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • sden_operation (str, optional) – Site density operation to use. Default is ‘sum’

    • -
    • include_entropy (bool, optional) – If True, includes the act entropy. Default is True

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • sden_operation (str, optional) – Site density operation to use. Default is ‘sum’

    • +
    • include_entropy (bool, optional) – If True, includes the act entropy. Default is True

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters required to calculate pre-exponential factor

    @@ -490,9 +490,9 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -504,7 +504,7 @@

      pmutt.reaction.ChemkinReactionReturn type: -

      float

      +

      float

    @@ -516,7 +516,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • state (str) –

      State to calculate quantity. Supported options:

      +
    • state (str) –

      State to calculate quantity. Supported options:

      • ’reactants’

      • ’products’

      • @@ -525,7 +525,7 @@

        pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
      • units (str) – Units as string. See R() for accepted units.

      • kwargs (keyword arguments) – Parameters required to calculate heat capacity at constant pressure. See class docstring to see how to pass specific @@ -536,7 +536,7 @@

        pmutt.reaction.ChemkinReaction

        Cp – Heat capacity at constant pressure of the reaction state

    Return type:
    -

    float

    +

    float

    @@ -549,7 +549,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -561,7 +561,7 @@

      pmutt.reaction.ChemkinReactionReturn type: -

      float

      +

      float

    @@ -573,7 +573,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • state (str) –

      state to calculate quantity. Supported options:

      +
    • state (str) –

      state to calculate quantity. Supported options:

    @@ -605,9 +605,9 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -618,7 +618,7 @@

      pmutt.reaction.ChemkinReaction

      Cv_act – Change in heat capacity between reactants and products

    Return type:
    -

    float

    +

    float

    @@ -630,7 +630,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • state (str) –

      State to calculate quantity. Supported options:

      +
    • state (str) –

      State to calculate quantity. Supported options:

      • ’reactants’

      • ’products’

      • @@ -639,7 +639,7 @@

        pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
      • units (str) – Units as string. See R() for accepted units.

      • kwargs (keyword arguments) – Parameters required to calculate heat capacity at constant volume. See class docstring to see how to pass specific @@ -650,7 +650,7 @@

        pmutt.reaction.ChemkinReaction

        Cv – Heat capacity at constant volume of the reaction state

    Return type:
    -

    float

    +

    float

    @@ -663,7 +663,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -675,7 +675,7 @@

      pmutt.reaction.ChemkinReactionReturn type: -

      float

      +

      float

    @@ -687,7 +687,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • state (str) –

      state to calculate quantity. Supported options:

      +
    • state (str) –

      state to calculate quantity. Supported options:

    @@ -719,12 +719,12 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float) – Temperature in K

    • -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • T (float) – Temperature in K

    • +
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. +

    • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. Condensed-phase and unimolecular gas-phase reactions should have a value of 0. Bimolecular gas-phase reactions should have a value of -1. If None specified, m will be calculated @@ -741,7 +741,7 @@

      pmutt.reaction.ChemkinReactionReturn type: -

      float

      +

      float

    @@ -753,7 +753,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • state (str) –

      State to calculate quantity. Supported options:

      +
    • state (str) –

      State to calculate quantity. Supported options:

      • ’reactants’

      • ’products’

      • @@ -762,10 +762,10 @@

        pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
      • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

      • -
      • T (float) – Temperature in K

      • -
      • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

      • +
      • T (float) – Temperature in K

      • +
      • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

      • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different species.

      • @@ -775,7 +775,7 @@

        pmutt.reaction.ChemkinReaction

        E – Electronic energy of the reaction state

    Return type:
    -

    float

    +

    float

    @@ -794,9 +794,9 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. +

    • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. Condensed-phase and unimolecular gas-phase reactions should have a value of 0. Bimolecular gas-phase reactions should have a value of -1. If None specified, m will be calculated @@ -812,7 +812,7 @@

      pmutt.reaction.ChemkinReactionReturn type: -

      float

      +

      float

    @@ -824,7 +824,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • state (str) –

      state to calculate quantity. Supported options:

      +
    • state (str) –

      state to calculate quantity. Supported options:

      • ’reactants’

      • ’products’

      • @@ -833,7 +833,7 @@

        pmutt.reaction.ChemkinReactionbool, optional) – If True, includes the zero point energy. Default is False

        +
      • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

      • kwargs (keyword arguments) – Parameters required to calculate dimensionless electronic energy. See class docstring to see how to pass specific parameters to different species.

      • @@ -843,7 +843,7 @@

        pmutt.reaction.ChemkinReaction

        EoRT – Dimensionless electronic energy of the reaction state.

    Return type:
    -

    float

    +

    float

    @@ -856,10 +856,10 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float) – Temperature in K

    • -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • T (float) – Temperature in K

    • +
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -871,7 +871,7 @@

      pmutt.reaction.ChemkinReactionReturn type: -

      float

      +

      float

    @@ -883,7 +883,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • state (str) –

      State to calculate quantity. Supported options:

      +
    • state (str) –

      State to calculate quantity. Supported options:

      • ’reactants’

      • ’products’

      • @@ -892,9 +892,9 @@

        pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
      • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

      • -
      • T (float) – Temperature in K

      • +
      • T (float) – Temperature in K

      • kwargs (keyword arguments) – Parameters required to calculate Helholtz energy. See class docstring to see how to pass specific parameters to different species.

      • @@ -904,7 +904,7 @@

        pmutt.reaction.ChemkinReaction

        F – Helmholtz energy of the reaction state

    Return type:
    -

    float

    +

    float

    @@ -917,7 +917,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -929,7 +929,7 @@

      pmutt.reaction.ChemkinReactionReturn type: -

      float

      +

      float

    @@ -941,7 +941,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
    Return type:
    -

    float

    +

    float

    @@ -973,10 +973,10 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float) – Temperature in K

    • -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • T (float) – Temperature in K

    • +
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -988,7 +988,7 @@

      pmutt.reaction.ChemkinReactionReturn type: -

      float

      +

      float

    @@ -1000,7 +1000,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • state (str) –

      State to calculate quantity. Supported options:

      +
    • state (str) –

      State to calculate quantity. Supported options:

      • ’reactants’

      • ’products’

      • @@ -1009,9 +1009,9 @@

        pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
      • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

      • -
      • T (float) – Temperature in K

      • +
      • T (float) – Temperature in K

      • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different species.

      • @@ -1021,7 +1021,7 @@

        pmutt.reaction.ChemkinReaction

        G – Gibbs energy of the reaction state

    Return type:
    -

    float

    +

    float

    @@ -1034,9 +1034,9 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • act (bool, optional) – If True, uses the transition state as the final state. Default +

    • act (bool, optional) – If True, uses the transition state as the final state. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1048,7 +1048,7 @@

      pmutt.reaction.ChemkinReactionReturn type: -

      float

      +

      float

    @@ -1060,7 +1060,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
    Return type:
    -

    float

    +

    float

    @@ -1091,10 +1091,10 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float) – Temperature in K

    • -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • T (float) – Temperature in K

    • +
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different @@ -1106,7 +1106,7 @@

      pmutt.reaction.ChemkinReactionReturn type: -

      float

      +

      float

    @@ -1118,7 +1118,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • state (str) –

      State to calculate quantity. Supported options:

      +
    • state (str) –

      State to calculate quantity. Supported options:

      • ’reactants’

      • ’products’

      • @@ -1127,9 +1127,9 @@

        pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
      • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

      • -
      • T (float) – Temperature in K

      • +
      • T (float) – Temperature in K

      • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different species.

      • @@ -1139,7 +1139,7 @@

        pmutt.reaction.ChemkinReaction

        H – Enthalpy of the reaction state

    Return type:
    -

    float

    +

    float

    @@ -1152,7 +1152,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1164,7 +1164,7 @@

      pmutt.reaction.ChemkinReactionReturn type: -

      float

      +

      float

    @@ -1176,7 +1176,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • state (str) –

      state to calculate quantity. Supported options:

      +
    • state (str) –

      state to calculate quantity. Supported options:

    @@ -1207,9 +1207,9 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • act (bool, optional) – If True, uses the transition state as the final state. Default +

    • act (bool, optional) – If True, uses the transition state as the final state. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate equilibrium constant. See class docstring to see how to pass specific parameters to @@ -1220,7 +1220,7 @@

      pmutt.reaction.ChemkinReaction

      Keq – Equilibrium constant between reactants and products

    Return type:
    -

    float

    +

    float

    @@ -1233,9 +1233,9 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1247,7 +1247,7 @@

      pmutt.reaction.ChemkinReactionReturn type: -

      float

      +

      float

    @@ -1259,7 +1259,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • state (str) –

      State to calculate quantity. Supported options:

      +
    • state (str) –

      State to calculate quantity. Supported options:

      • ’reactants’

      • ’products’

      • @@ -1268,7 +1268,7 @@

        pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
      • units (str) – Units as string. See R() for accepted units.

      • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to @@ -1279,7 +1279,7 @@

        pmutt.reaction.ChemkinReaction

        S – Entropy of the reaction state

    Return type:
    -

    float

    +

    float

    @@ -1292,7 +1292,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1304,7 +1304,7 @@

      pmutt.reaction.ChemkinReactionReturn type: -

      float

      +

      float

    @@ -1316,7 +1316,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
    Return type:
    -

    float

    +

    float

    @@ -1347,10 +1347,10 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float) – Temperature in K

    • -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • T (float) – Temperature in K

    • +
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1362,7 +1362,7 @@

      pmutt.reaction.ChemkinReactionReturn type: -

      float

      +

      float

    @@ -1374,7 +1374,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • state (str) –

      State to calculate quantity. Supported options:

      +
    • state (str) –

      State to calculate quantity. Supported options:

      • ’reactants’

      • ’products’

      • @@ -1383,9 +1383,9 @@

        pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
      • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

      • -
      • T (float) – Temperature in K

      • +
      • T (float) – Temperature in K

      • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different species.

      • @@ -1395,7 +1395,7 @@

        pmutt.reaction.ChemkinReaction

        U – Internal energy of the reaction state

    Return type:
    -

    float

    +

    float

    @@ -1408,7 +1408,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1420,7 +1420,7 @@

      pmutt.reaction.ChemkinReactionReturn type: -

      float

      +

      float

    @@ -1432,7 +1432,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
    Return type:
    -

    float

    +

    float

    @@ -1463,11 +1463,11 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • act (bool, optional) – If True, uses the transition state as the final state. Default +

    • act (bool, optional) – If True, uses the transition state as the final state. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1478,7 +1478,7 @@

      pmutt.reaction.ChemkinReaction

      delta_Cp – Change in heat capacity between reactants and products

    Return type:
    -

    float

    +

    float

    @@ -1491,9 +1491,9 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • act (bool, optional) – If True, uses the transition state as the final state. Default +

    • act (bool, optional) – If True, uses the transition state as the final state. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1504,7 +1504,7 @@

      pmutt.reaction.ChemkinReaction

      delta_CvoR – Change in heat capacity between reactants and products

    Return type:
    -

    float

    +

    float

    @@ -1517,11 +1517,11 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • act (bool, optional) – If True, uses the transition state as the final state. Default +

    • act (bool, optional) – If True, uses the transition state as the final state. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1532,7 +1532,7 @@

      pmutt.reaction.ChemkinReaction

      delta_Cv – Change in heat capacity between reactants and products

    Return type:
    -

    float

    +

    float

    @@ -1545,9 +1545,9 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • act (bool, optional) – If True, uses the transition state as the final state. Default +

    • act (bool, optional) – If True, uses the transition state as the final state. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1558,7 +1558,7 @@

      pmutt.reaction.ChemkinReaction

      delta_CvoR – Change in heat capacity between reactants and products

    Return type:
    -

    float

    +

    float

    @@ -1570,12 +1570,12 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float) – Temperature in K

    • -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • T (float) – Temperature in K

    • +
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • act (bool, optional) – If True, uses the transition state as the final state. Default +

    • act (bool, optional) – If True, uses the transition state as the final state. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different @@ -1586,7 +1586,7 @@

      pmutt.reaction.ChemkinReaction

      delta_E – Change in electronic energy between reactants and products

    Return type:
    -

    float

    +

    float

    @@ -1599,9 +1599,9 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • act (bool, optional) – If True, uses the transition state as the final state. Default +

    • act (bool, optional) – If True, uses the transition state as the final state. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different @@ -1612,7 +1612,7 @@

      pmutt.reaction.ChemkinReaction

      delta_EoRT – Change in electronic energy between reactants and products

    Return type:
    -

    float

    +

    float

    @@ -1624,12 +1624,12 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float) – Temperature in K

    • -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • T (float) – Temperature in K

    • +
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • act (bool, optional) – If True, uses the transition state as the final state. Default +

    • act (bool, optional) – If True, uses the transition state as the final state. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -1640,7 +1640,7 @@

      pmutt.reaction.ChemkinReaction

      delta_F – Change in Helmholtz energy between reactants and products

    Return type:
    -

    float

    +

    float

    @@ -1653,9 +1653,9 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • act (bool, optional) – If True, uses the transition state as the final state. Default +

    • act (bool, optional) – If True, uses the transition state as the final state. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -1666,7 +1666,7 @@

      pmutt.reaction.ChemkinReaction

      delta_FoRT – Change in Helmholtz energy between reactants and products

    Return type:
    -

    float

    +

    float

    @@ -1678,12 +1678,12 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float) – Temperature in K

    • -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • T (float) – Temperature in K

    • +
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • act (bool, optional) – If True, uses the transition state as the final state. Default +

    • act (bool, optional) – If True, uses the transition state as the final state. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1694,7 +1694,7 @@

      pmutt.reaction.ChemkinReaction

      delta_G – Change in Gibbs energy between reactants and products

    Return type:
    -

    float

    +

    float

    @@ -1707,9 +1707,9 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • act (bool, optional) – If True, uses the transition state as the final state. Default +

    • act (bool, optional) – If True, uses the transition state as the final state. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1720,7 +1720,7 @@

      pmutt.reaction.ChemkinReaction

      delta_GoRT – Change in Gibbs energy between reactants and products

    Return type:
    -

    float

    +

    float

    @@ -1732,12 +1732,12 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float) – Temperature in K

    • -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • T (float) – Temperature in K

    • +
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • act (bool, optional) – If True, uses the transition state as the final state. Default +

    • act (bool, optional) – If True, uses the transition state as the final state. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different @@ -1748,7 +1748,7 @@

      pmutt.reaction.ChemkinReaction

      delta_H – Change in enthalpy between reactants and products

    Return type:
    -

    float

    +

    float

    @@ -1760,9 +1760,9 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • act (bool, optional) – If True, uses the transition state as the final state. Default +

    • act (bool, optional) – If True, uses the transition state as the final state. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different @@ -1773,7 +1773,7 @@

      pmutt.reaction.ChemkinReaction

      delta_HoRT – Change in enthalpy between reactants and products

    Return type:
    -

    float

    +

    float

    @@ -1785,11 +1785,11 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • act (bool, optional) – If True, uses the transition state as the final state. Default +

    • act (bool, optional) – If True, uses the transition state as the final state. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1800,7 +1800,7 @@

      pmutt.reaction.ChemkinReaction

      delta_S – Change in entropy between reactants and products

    Return type:
    -

    float

    +

    float

    @@ -1812,9 +1812,9 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • act (bool, optional) – If True, uses the transition state as the final state. Default +

    • act (bool, optional) – If True, uses the transition state as the final state. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1825,7 +1825,7 @@

      pmutt.reaction.ChemkinReaction

      delta_SoR – Change in entropy between reactants and products

    Return type:
    -

    float

    +

    float

    @@ -1837,12 +1837,12 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float) – Temperature in K

    • -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • T (float) – Temperature in K

    • +
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • act (bool, optional) – If True, uses the transition state as the final state. Default +

    • act (bool, optional) – If True, uses the transition state as the final state. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1853,7 +1853,7 @@

      pmutt.reaction.ChemkinReaction

      delta_U – Change in internal energy between reactants and products

    Return type:
    -

    float

    +

    float

    @@ -1866,9 +1866,9 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • act (bool, optional) – If True, uses the transition state as the final state. Default +

    • act (bool, optional) – If True, uses the transition state as the final state. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1879,7 +1879,7 @@

      pmutt.reaction.ChemkinReaction

      delta_UoRT – Change in internal energy between reactants and products

    Return type:
    -

    float

    +

    float

    @@ -1891,9 +1891,9 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • act (bool, optional) – If True, uses the transition state as the final state. Default +

    • act (bool, optional) – If True, uses the transition state as the final state. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate partition function. See class docstring to see how to pass specific parameters to different @@ -1904,7 +1904,7 @@

      pmutt.reaction.ChemkinReaction

      delta_q – Change in partition function between reactants and products

    Return type:
    -

    float

    +

    float

    @@ -1917,21 +1917,21 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • initial_state (str) –

      Thermodynamic state. Supported options:

      +
    • initial_state (str) –

      Thermodynamic state. Supported options:

      • ’reactants’

      • ’products’

      • ’transition state’

    • -
    • final_state (str) –

      Thermodynamic state. Supported options:

      +
    • final_state (str) –

      Thermodynamic state. Supported options:

      • ’reactants’

      • ’products’

      • ’transition state’

    • -
    • method_name (str) – Name of method to use to calculate quantity. Calculates any +

    • method_name (str) – Name of method to use to calculate quantity. Calculates any quantity as long as the relevant objects have the same method name

    • kwargs (keyword arguments) – Arguments passed to evaluate the quantity of the reactants and @@ -1942,7 +1942,7 @@

      pmutt.reaction.ChemkinReaction

      delta_quantity – Change in thermodynamic quantity between particular states

    Return type:
    -

    float

    +

    float

    @@ -1955,9 +1955,9 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • include_ZPE (bool, optional) – If True, includes zero-point energy when calculating the +

    • include_ZPE (bool, optional) – If True, includes zero-point energy when calculating the value of the partition functions. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate partition function. See class docstring to see how to pass specific parameters to different @@ -1969,7 +1969,7 @@

      pmutt.reaction.ChemkinReactionReturn type: -

      float

      +

      float

    @@ -1981,7 +1981,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
    Return type:
    -

    float

    +

    float

    @@ -2011,8 +2011,8 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • include_TS (bool, optional) – Whether transition states should be included. Default is True

    • -
    • key (str, optional) – Attribute to use as the key in the output dictionary. Default +

    • include_TS (bool, optional) – Whether transition states should be included. Default is True

    • +
    • key (str, optional) – Attribute to use as the key in the output dictionary. Default is name

    @@ -2020,7 +2020,7 @@

    pmutt.reaction.ChemkinReaction

    species – Unique species in the reaction

    Return type:
    -

    dict

    +

    dict

    @@ -2032,7 +2032,7 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • state (str) –

      Thermodynamic state. Supported options:

      +
    • state (str) –

      Thermodynamic state. Supported options:

      • ’reactants’

      • ’products’

      • @@ -2041,7 +2041,7 @@

        pmutt.reaction.ChemkinReactionstr) – Name of method to use to calculate quantity. Calculates any +
      • method_name (str) – Name of method to use to calculate quantity. Calculates any quantity as long as the relevant objects have the same method name

      • kwargs (keyword arguments) – Arguments required to calculate the thermodynamic quantity of @@ -2052,7 +2052,7 @@

        pmutt.reaction.ChemkinReaction

        state_quantity – Thermodynamic quantity of particular state

    Return type:
    -

    float

    +

    float

    @@ -2086,7 +2086,7 @@

    pmutt.reaction.ChemkinReaction

    obj_dict

    Return type:
    -

    dict

    +

    dict

    @@ -2098,21 +2098,21 @@

    pmutt.reaction.ChemkinReaction
    Parameters:
      -
    • species_delimiter (str, optional) – Separates species. Default is ‘+’

    • -
    • reaction_delimiter (str, optional) – Separates reaction states. Default is ‘=’

    • -
    • stoich_format (float, optional) – Format to write stoichiometric numbers. Default is ‘.2f’ (float +

    • species_delimiter (str, optional) – Separates species. Default is ‘+’

    • +
    • reaction_delimiter (str, optional) – Separates reaction states. Default is ‘=’

    • +
    • stoich_format (float, optional) – Format to write stoichiometric numbers. Default is ‘.2f’ (float rounded to 2 decimal places)

    • -
    • include_TS (bool, optional) – If True, includes transition states in output. Default is True

    • -
    • stoich_space (bool, optional) – If True, inserts a space between stoichiometric coefficients +

    • include_TS (bool, optional) – If True, includes transition states in output. Default is True

    • +
    • stoich_space (bool, optional) – If True, inserts a space between stoichiometric coefficients and the species name. Default is False

    • -
    • key (str, optional) – Attribute to use to print out species. Default is name

    • +
    • key (str, optional) – Attribute to use to print out species. Default is name

    Returns:

    reaction_str – Reaction string

    Return type:
    -

    str

    +

    str

    diff --git a/api/kinetic_models/kinetic_models.html b/api/kinetic_models/kinetic_models.html index f7258950..a729bbb0 100644 --- a/api/kinetic_models/kinetic_models.html +++ b/api/kinetic_models/kinetic_models.html @@ -4,7 +4,7 @@ - Kinetic Models — pmutt 1.4.7 documentation + Kinetic Models — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    diff --git a/api/kinetic_models/omkm/pmutt.io.omkm.get_interactions_phases.html b/api/kinetic_models/omkm/pmutt.io.omkm.get_interactions_phases.html index 71bb7356..6baab5cf 100644 --- a/api/kinetic_models/omkm/pmutt.io.omkm.get_interactions_phases.html +++ b/api/kinetic_models/omkm/pmutt.io.omkm.get_interactions_phases.html @@ -4,7 +4,7 @@ - pmutt.io.omkm.get_interactions_phases — pmutt 1.4.7 documentation + pmutt.io.omkm.get_interactions_phases — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -142,7 +142,7 @@

    pmutt.io.omkm.get_interactions_phasesReturn type: -

    dict

    +

    dict

    diff --git a/api/kinetic_models/omkm/pmutt.io.omkm.get_reactions_phases.html b/api/kinetic_models/omkm/pmutt.io.omkm.get_reactions_phases.html index 3a9aef97..5084fcb4 100644 --- a/api/kinetic_models/omkm/pmutt.io.omkm.get_reactions_phases.html +++ b/api/kinetic_models/omkm/pmutt.io.omkm.get_reactions_phases.html @@ -4,7 +4,7 @@ - pmutt.io.omkm.get_reactions_phases — pmutt 1.4.7 documentation + pmutt.io.omkm.get_reactions_phases — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -139,7 +139,7 @@

    pmutt.io.omkm.get_reactions_phasesReturn type: -

    dict

    +

    dict

    diff --git a/api/kinetic_models/omkm/pmutt.io.omkm.get_species_phases.html b/api/kinetic_models/omkm/pmutt.io.omkm.get_species_phases.html index 7d0b5f76..a72ab384 100644 --- a/api/kinetic_models/omkm/pmutt.io.omkm.get_species_phases.html +++ b/api/kinetic_models/omkm/pmutt.io.omkm.get_species_phases.html @@ -4,7 +4,7 @@ - pmutt.io.omkm.get_species_phases — pmutt 1.4.7 documentation + pmutt.io.omkm.get_species_phases — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -139,7 +139,7 @@

    pmutt.io.omkm.get_species_phasesReturn type: -

    dict

    +

    dict

    diff --git a/api/kinetic_models/omkm/pmutt.io.omkm.organize_phases.html b/api/kinetic_models/omkm/pmutt.io.omkm.organize_phases.html index 37361661..c60d3817 100644 --- a/api/kinetic_models/omkm/pmutt.io.omkm.organize_phases.html +++ b/api/kinetic_models/omkm/pmutt.io.omkm.organize_phases.html @@ -4,7 +4,7 @@ - pmutt.io.omkm.organize_phases — pmutt 1.4.7 documentation + pmutt.io.omkm.organize_phases — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    diff --git a/api/kinetic_models/omkm/pmutt.io.omkm.write_cti.html b/api/kinetic_models/omkm/pmutt.io.omkm.write_cti.html index bf128944..f8b506fe 100644 --- a/api/kinetic_models/omkm/pmutt.io.omkm.write_cti.html +++ b/api/kinetic_models/omkm/pmutt.io.omkm.write_cti.html @@ -4,7 +4,7 @@ - pmutt.io.omkm.write_cti — pmutt 1.4.7 documentation + pmutt.io.omkm.write_cti — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -141,17 +141,17 @@

    pmutt.io.omkm.write_cti

    units (dict or Unit object, optional) – Units to write file. If a dict is inputted, the key is the quantity and the value is the unit. If not specified, uses the default units of Unit.

    -
  • filename (str, optional) – Filename for the input.cti file. If not specified, returns file +

  • filename (str, optional) – Filename for the input.cti file. If not specified, returns file as str.

  • -
  • T (float, optional) – Temperature in K. Default is 300 K.

  • -
  • P (float, optional) – Pressure in atm. Default is 1 atm.

  • -
  • newline (str, optional) – Type of newline to use. Default is Linux newline (’n’)

  • -
  • use_motz_wise (bool, optional) – Whether to use Motz-wise sticking coefficients or not. Default is +

  • T (float, optional) – Temperature in K. Default is 300 K.

  • +
  • P (float, optional) – Pressure in atm. Default is 1 atm.

  • +
  • newline (str, optional) – Type of newline to use. Default is Linux newline (’n’)

  • +
  • use_motz_wise (bool, optional) – Whether to use Motz-wise sticking coefficients or not. Default is False

  • -
  • ads_act_method (str, optional) – Activation method to use for adsorption reactions. Accepted +

  • ads_act_method (str, optional) – Activation method to use for adsorption reactions. Accepted options include ‘get_H_act’ and ‘get_G_act’. Default is ‘get_H_act’.

  • -
  • write_xml (bool, optional) – If True and filename is not None, automatically generates +

  • write_xml (bool, optional) – If True and filename is not None, automatically generates an XML file with the CTI file.

  • @@ -159,7 +159,7 @@

    pmutt.io.omkm.write_cti

    lines_out – If filename is None, CTI file is returned.

    Return type:
    -

    str

    +

    str

    diff --git a/api/kinetic_models/omkm/pmutt.io.omkm.write_yaml.html b/api/kinetic_models/omkm/pmutt.io.omkm.write_yaml.html index bc362d65..de1142de 100644 --- a/api/kinetic_models/omkm/pmutt.io.omkm.write_yaml.html +++ b/api/kinetic_models/omkm/pmutt.io.omkm.write_yaml.html @@ -4,7 +4,7 @@ - pmutt.io.omkm.write_yaml — pmutt 1.4.7 documentation + pmutt.io.omkm.write_yaml — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -133,7 +133,7 @@

    pmutt.io.omkm.write_yaml
    Parameters:
      -
    • reactor_type (str) –

      Type of reactor. Supported options include:

      +
    • reactor_type (str) –

      Type of reactor. Supported options include:

      • pfr

      • pfr_0d

      • @@ -142,70 +142,70 @@

        pmutt.io.omkm.write_yamlreactor.type.

        -
      • temperature_mode (str) –

        Operation of reactor. Supported options include:

        +
      • temperature_mode (str) –

        Operation of reactor. Supported options include:

        • Isothermal

        • Adiabatic

        Value written to reactor.temperature_mode.

      • -
      • pressure_mode (str) –

        Operation of reactor. Supported options include:

        +
      • pressure_mode (str) –

        Operation of reactor. Supported options include:

        • Isobaric

        • Isochoric

        Value written to reactor.pressure_mode.

      • -
      • nodes (int) – Number of nodes to use if reactor_type is ‘pfr_0d’. Value +

      • nodes (int) – Number of nodes to use if reactor_type is ‘pfr_0d’. Value written to reactor.nodes

      • -
      • V (float or str) – Volume of reactor. Value written to reactor.volume. Units of +

      • V (float or str) – Volume of reactor. Value written to reactor.volume. Units of length^3. See Notes section regarding unit specification.

      • -
      • T (float) – Temperature (in K) of reactor. Value written to +

      • T (float) – Temperature (in K) of reactor. Value written to reactor.temperature.

      • -
      • P (float or str) – Pressure of reactor. Value written to reactor.pressure. Units +

      • P (float or str) – Pressure of reactor. Value written to reactor.pressure. Units of pressure. See Notes section regarding unit specification.

      • -
      • A (float or str) – Surface area of reactor. Value written to reactor.area. +

      • A (float or str) – Surface area of reactor. Value written to reactor.area. Units of length^2. See Notes section regarding unit specification.

      • -
      • L (float or str) – Length of reactor. Value written to reactor.length. +

      • L (float or str) – Length of reactor. Value written to reactor.length. Units of length. See Notes section regarding unit specification.

      • -
      • cat_abyv (float or str) – Catalyst surface area to volume ratio. Value written to +

      • cat_abyv (float or str) – Catalyst surface area to volume ratio. Value written to reactor.cat_abyv. Units of 1/length. See Notes section regarding unit specification.

      • -
      • flow_rate (float or str) – Volumetric flow rate of inlet. Value written to +

      • flow_rate (float or str) – Volumetric flow rate of inlet. Value written to inlet_gas.flow_rate. Units of length^3/time. See Notes section regarding unit specification.

      • -
      • residence_time (float or str) – Residence time of reactor. Value written to +

      • residence_time (float or str) – Residence time of reactor. Value written to inlet_gas.residence_time. Not required if flow_rate or mass_flow_rate already specified. Units of time. See Notes section regarding unit specification.

      • -
      • mass_flow_rate (float or str) – Mass flow rate of inlet. Value written to +

      • mass_flow_rate (float or str) – Mass flow rate of inlet. Value written to inlet_gas.mass_flow_rate. Units of mass^3/time. See Notes section regarding unit specification.

      • -
      • end_time (float or str) – Reactor simulation time. For continuous reactors, the system is +

      • end_time (float or str) – Reactor simulation time. For continuous reactors, the system is assumed to reach steady state by this time. Value written to simulation.end_time. Units of time. See Notes section regarding unit specification.

      • -
      • transient (bool) – If True, transient operation results are saved. Otherwise, +

      • transient (bool) – If True, transient operation results are saved. Otherwise, transient files are left blank. Value written to simulation.transient.

      • -
      • stepping (str) –

        Time steps taken to simulate reactor. Supported options include:

        +
      • stepping (str) –

        Time steps taken to simulate reactor. Supported options include:

        • logarithmic

        • regular

        Value written to simulation.stepping.

      • -
      • init_step (float or str) – Initial step to take. Value written to simulation.init_step.

      • -
      • step_size (float or str) – If stepping is logarithmic, represents the ratio between the +

      • init_step (float or str) – Initial step to take. Value written to simulation.init_step.

      • +
      • step_size (float or str) – If stepping is logarithmic, represents the ratio between the next step and the current step. If stepping is regular, represents the time between the next step and the current step in units of time. Value written to simulation.step_size. See Notes section regarding unit specification.

      • -
      • atol (float) – Absolute tolerance for solver. Value written to +

      • atol (float) – Absolute tolerance for solver. Value written to simulation.solver.atol.

      • -
      • rtol (float) – Relative tolerance for solver. Value written to +

      • rtol (float) – Relative tolerance for solver. Value written to simulation.solver.rtol.

      • -
      • full_SA (bool) – If True, OpenMKM will do a full sensitivity analysis using the +

      • full_SA (bool) – If True, OpenMKM will do a full sensitivity analysis using the Fisher Information Matrix (FIM). Value written to simulation.sensitivity.full.

      • reactions_SA (list of str or list of SurfaceReaction obj) – List of reactions to perturb using local sensitivity analysis (LSA). @@ -216,9 +216,9 @@

        pmutt.io.omkm.write_yamlname attribute will be used.

      • phases (list of Phase objects) – Phases present in reactor. Each phase should have the name and initial_state attribute.

      • -
      • reactor (dict) – Generic dictionary for reactor to specify values not supported by +

      • reactor (dict) – Generic dictionary for reactor to specify values not supported by write_yaml.

      • -
      • inlet_gas (dict) – Generic dictionary for inlet_gas to specify values not supported by +

      • inlet_gas (dict) – Generic dictionary for inlet_gas to specify values not supported by write_yaml.

      • multi_T (list of float) – Multiple temperatures (in K) of reactor. Value written to simulation.multi_input.temperature.

      • @@ -228,26 +228,26 @@

        pmutt.io.omkm.write_yamlsimulation.multi_input.flow_rate. Units of length3/time. See Notes section regarding unit specification.

        -
      • output_format (str) –

        Format for output files. Supported options include:

        +
      • output_format (str) –

        Format for output files. Supported options include:

        • CSV

        • DAT

        Value written to simulation.output_format.

      • -
      • misc (dict) – Generic dictionary for any parameter specified at the top level.

      • -
      • solver (dict) – Generic dictionary for solver to specify values not supported by +

      • misc (dict) – Generic dictionary for any parameter specified at the top level.

      • +
      • solver (dict) – Generic dictionary for solver to specify values not supported by write_yaml.

      • -
      • simulation (dict) – Generic dictionary for simultaion to specify values not supported by +

      • simulation (dict) – Generic dictionary for simultaion to specify values not supported by write_yaml.

      • -
      • multi_input (dict) – Generic dictionary for multi_input to specify values not supported +

      • multi_input (dict) – Generic dictionary for multi_input to specify values not supported by write_yaml.

      • units (dict or Unit object, optional) – Units used for file. If a dict is inputted, the key is the quantity and the value is the unit. If not specified, uses the default units of Unit.

      • -
      • filename (str, optional) – Filename for the input.cti file. If not specified, returns file +

      • filename (str, optional) – Filename for the input.cti file. If not specified, returns file as str.

      • -
      • yaml_options (dict) – Options to pass when converting the parameters to YAML format. See +

      • yaml_options (dict) – Options to pass when converting the parameters to YAML format. See PyYAML documentation for dump for available options.

    @@ -255,7 +255,7 @@

    pmutt.io.omkm.write_yaml

    lines_out – If filename is None, CTI file is returned

    Return type:
    -

    str

    +

    str

    Notes

    diff --git a/api/kinetic_models/omkm_phases/pmutt.omkm.phase.IdealGas.html b/api/kinetic_models/omkm_phases/pmutt.omkm.phase.IdealGas.html index 73724d50..66a3bfd8 100644 --- a/api/kinetic_models/omkm_phases/pmutt.omkm.phase.IdealGas.html +++ b/api/kinetic_models/omkm_phases/pmutt.omkm.phase.IdealGas.html @@ -4,7 +4,7 @@ - pmutt.omkm.phase.IdealGas — pmutt 1.4.7 documentation + pmutt.omkm.phase.IdealGas — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -241,8 +241,8 @@

    pmutt.omkm.phase.IdealGas
    Parameters:
      -
    • max_line_len (int, optional) – Maximum number of characters in the line. Default is 80.

    • -
    • delimiter (str, optional) – Delimiter to use when specifying ranges for reactions. Default +

    • max_line_len (int, optional) – Maximum number of characters in the line. Default is 80.

    • +
    • delimiter (str, optional) – Delimiter to use when specifying ranges for reactions. Default is ‘_’.

    @@ -250,7 +250,7 @@

    pmutt.omkm.phase.IdealGas

    CTI_str – Object represented as a CTI string.

    Return type:
    -

    str

    +

    str

    @@ -262,13 +262,13 @@

    pmutt.omkm.phase.IdealGas
    Parameters:
      -
    • T (float, optional) – Temperature in K. Default is 300 K

    • -
    • P (float, optional) – Pressure in atm. Default is 1 atm

    • -
    • quantity_unit (str, optional) – Quantity unit to use to calculate A. Default is ‘molec’

    • -
    • length_unit (str, optional) – Length unit to use to calculate A. Default is ‘cm’

    • +
    • T (float, optional) – Temperature in K. Default is 300 K

    • +
    • P (float, optional) – Pressure in atm. Default is 1 atm

    • +
    • quantity_unit (str, optional) – Quantity unit to use to calculate A. Default is ‘molec’

    • +
    • length_unit (str, optional) – Length unit to use to calculate A. Default is ‘cm’

    • units (Units object) – If specified, quantity_unit and length_unit are overwritten. Default is None.

    • -
    • delimiter (str, optional) – Delimiter used to separate header from footer of reaction and +

    • delimiter (str, optional) – Delimiter used to separate header from footer of reaction and lateral interaction IDs. Default is ‘_’.

    diff --git a/api/kinetic_models/omkm_phases/pmutt.omkm.phase.InteractingInterface.html b/api/kinetic_models/omkm_phases/pmutt.omkm.phase.InteractingInterface.html index 763ecd21..63549285 100644 --- a/api/kinetic_models/omkm_phases/pmutt.omkm.phase.InteractingInterface.html +++ b/api/kinetic_models/omkm_phases/pmutt.omkm.phase.InteractingInterface.html @@ -4,7 +4,7 @@ - pmutt.omkm.phase.InteractingInterface — pmutt 1.4.7 documentation + pmutt.omkm.phase.InteractingInterface — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -135,7 +135,7 @@

    pmutt.omkm.phase.InteractingInterface
    Type:
    -

    str

    +

    str

    @@ -157,7 +157,7 @@

    pmutt.omkm.phase.InteractingInterface
    Type:
    -

    float, optional

    +

    float, optional

    @@ -180,7 +180,7 @@

    pmutt.omkm.phase.InteractingInterface
    Type:
    -

    str, optional

    +

    str, optional

    @@ -191,7 +191,7 @@

    pmutt.omkm.phase.InteractingInterface
    Type:
    -

    str, optional

    +

    str, optional

    @@ -351,12 +351,12 @@

    pmutt.omkm.phase.InteractingInterface
    Parameters:
      -
    • max_line_len (int, optional) – Maximum number of characters in the line. Default is 80.

    • -
    • quantity_unit (str, optional) – Quantity unit to use to calculate A. Default is ‘molec’

    • -
    • length_unit (str, optional) – Length unit to use to calculate A. Default is ‘cm’

    • +
    • max_line_len (int, optional) – Maximum number of characters in the line. Default is 80.

    • +
    • quantity_unit (str, optional) – Quantity unit to use to calculate A. Default is ‘molec’

    • +
    • length_unit (str, optional) – Length unit to use to calculate A. Default is ‘cm’

    • units (Units object) – If specified, quantity_unit and length_unit are overwritten. Default is None.

    • -
    • delimiter (str, optional) – Delimiter used to separate header from footer of reaction and +

    • delimiter (str, optional) – Delimiter used to separate header from footer of reaction and lateral interaction IDs. Default is ‘_’.

    @@ -364,7 +364,7 @@

    pmutt.omkm.phase.InteractingInterface

    CTI_str – Object represented as a CTI string.

    Return type:
    -

    str

    +

    str

    @@ -376,10 +376,10 @@

    pmutt.omkm.phase.InteractingInterface
    Parameters:
      -
    • T (float, optional) – Temperature in K. Default is 300 K

    • -
    • P (float, optional) – Pressure in atm. Default is 1 atm

    • -
    • quantity_unit (str, optional) – Quantity unit to use to calculate A. Default is ‘molec’

    • -
    • length_unit (str, optional) – Length unit to use to calculate A. Default is ‘cm’

    • +
    • T (float, optional) – Temperature in K. Default is 300 K

    • +
    • P (float, optional) – Pressure in atm. Default is 1 atm

    • +
    • quantity_unit (str, optional) – Quantity unit to use to calculate A. Default is ‘molec’

    • +
    • length_unit (str, optional) – Length unit to use to calculate A. Default is ‘cm’

    • units (Units object) – If specified, quantity_unit and length_unit are overwritten. Default is None.

    diff --git a/api/kinetic_models/omkm_phases/pmutt.omkm.phase.StoichSolid.html b/api/kinetic_models/omkm_phases/pmutt.omkm.phase.StoichSolid.html index aeaf0467..1227b80d 100644 --- a/api/kinetic_models/omkm_phases/pmutt.omkm.phase.StoichSolid.html +++ b/api/kinetic_models/omkm_phases/pmutt.omkm.phase.StoichSolid.html @@ -4,7 +4,7 @@ - pmutt.omkm.phase.StoichSolid — pmutt 1.4.7 documentation + pmutt.omkm.phase.StoichSolid — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -242,9 +242,9 @@

    pmutt.omkm.phase.StoichSolid
    Parameters:
      -
    • max_line_len (int, optional) – Maximum number of characters in the line. Default is 80.

    • -
    • mass_unit (str, optional) – Mass unit for density. Default is ‘g’

    • -
    • length_unit (str, optional) – Length unit for density. Default is ‘cm’

    • +
    • max_line_len (int, optional) – Maximum number of characters in the line. Default is 80.

    • +
    • mass_unit (str, optional) – Mass unit for density. Default is ‘g’

    • +
    • length_unit (str, optional) – Length unit for density. Default is ‘cm’

    • units (Units object, optional) – If specified, mass_unit and length_unit are overwritten. Default is None.

    @@ -253,7 +253,7 @@

    pmutt.omkm.phase.StoichSolid

    CTI_str – Object represented as a CTI string.

    Return type:
    -

    str

    +

    str

    @@ -265,10 +265,10 @@

    pmutt.omkm.phase.StoichSolid
    Parameters:
      -
    • T (float, optional) – Temperature in K. Default is 300 K

    • -
    • P (float, optional) – Pressure in atm. Default is 1 atm

    • -
    • quantity_unit (str, optional) – Quantity unit to use to calculate A. Default is ‘molec’

    • -
    • length_unit (str, optional) – Length unit to use to calculate A. Default is ‘cm’

    • +
    • T (float, optional) – Temperature in K. Default is 300 K

    • +
    • P (float, optional) – Pressure in atm. Default is 1 atm

    • +
    • quantity_unit (str, optional) – Quantity unit to use to calculate A. Default is ‘molec’

    • +
    • length_unit (str, optional) – Length unit to use to calculate A. Default is ‘cm’

    • units (Units object) – If specified, quantity_unit and length_unit are overwritten. Default is None.

    diff --git a/api/kinetic_models/omkm_reactions/pmutt.omkm.reaction.BEP.html b/api/kinetic_models/omkm_reactions/pmutt.omkm.reaction.BEP.html index 45ec9d13..565558d0 100644 --- a/api/kinetic_models/omkm_reactions/pmutt.omkm.reaction.BEP.html +++ b/api/kinetic_models/omkm_reactions/pmutt.omkm.reaction.BEP.html @@ -4,7 +4,7 @@ - pmutt.omkm.reaction.BEP — pmutt 1.4.7 documentation + pmutt.omkm.reaction.BEP — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
    - 1.4.7 + 1.4.9
    @@ -135,7 +135,7 @@

    pmutt.omkm.reaction.BEP
    Type:
    -

    str, optional

    +

    str, optional

    @@ -234,7 +234,7 @@

    pmutt.omkm.reaction.BEP

    Recreate an object from the JSON representation.

    Parameters:
    -

    json_obj (dict) – JSON representation

    +

    json_obj (dict) – JSON representation

    Returns:

    Obj

    @@ -252,7 +252,7 @@

    pmutt.omkm.reaction.BEP
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • kwargs (keyword arguments) – Parameters needed by get_CpoR

    @@ -261,7 +261,7 @@

    pmutt.omkm.reaction.BEP

    Cp – Heat capacity (constant P) in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -276,7 +276,7 @@

    pmutt.omkm.reaction.BEP

    CpoR – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -288,7 +288,7 @@

    pmutt.omkm.reaction.BEP
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • kwargs (keyword arguments) – Parameters needed by get_CvoR

    @@ -297,7 +297,7 @@

    pmutt.omkm.reaction.BEP

    Cv – Heat capacity (constant V) in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -312,7 +312,7 @@

    pmutt.omkm.reaction.BEP

    CvoR – Returns 0

    Return type:
    -

    float

    +

    float

    @@ -324,10 +324,10 @@

    pmutt.omkm.reaction.BEP
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • reaction (Reaction object) – Reaction related to BEP.

    • -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • kwargs (keyword arguments) – Parameters required to calculate the descriptor

    @@ -336,7 +336,7 @@

    pmutt.omkm.reaction.BEP

    E_act – Dimensionless activation energy

    Return type:
    -

    float

    +

    float

    @@ -350,9 +350,9 @@

    pmutt.omkm.reaction.BEPParameters:
    • reaction (Reaction object) – Reaction related to BEP.

    • -
    • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

    • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

    • -
    • T (float, optional) – Temperature in K. Default is 298.15

    • +
    • T (float, optional) – Temperature in K. Default is 298.15

    • kwargs (keyword arguments) – Parameters required to calculate the descriptor

    @@ -360,7 +360,7 @@

    pmutt.omkm.reaction.BEP

    EoRT_act – Dimensionless activation energy

    Return type:
    -

    float

    +

    float

    @@ -372,9 +372,9 @@

    pmutt.omkm.reaction.BEP
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_FoRT

    @@ -382,7 +382,7 @@

    pmutt.omkm.reaction.BEP

    F – Hemholtz energy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -399,7 +399,7 @@

    pmutt.omkm.reaction.BEP

    FoRT – Dimensionless Helmholtz energy

    Return type:
    -

    float

    +

    float

    @@ -411,9 +411,9 @@

    pmutt.omkm.reaction.BEP
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_GoRT

    @@ -421,7 +421,7 @@

    pmutt.omkm.reaction.BEP

    G – Gibbs energy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -436,8 +436,8 @@

    pmutt.omkm.reaction.BEPParameters:
    • reaction (Reaction object) – Reaction related to BEP.

    • -
    • T (float, optional) – Temperature in K. Default is 298.15

    • -
    • entropy_state (str or None, optional) –

      State to use to estimate entropy. Supported arguments:

      +
    • T (float, optional) – Temperature in K. Default is 298.15

    • +
    • entropy_state (str or None, optional) –

      State to use to estimate entropy. Supported arguments:

    Return type:
    -

    float

    +

    float

    @@ -464,9 +464,9 @@

    pmutt.omkm.reaction.BEP
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

    • -
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • +
    • T (float, optional) – Temperature in K. Default is 298.15 K

    • kwargs (keyword arguments) – Parameters needed by get_HoRT

    @@ -474,7 +474,7 @@

    pmutt.omkm.reaction.BEP

    H – Enthalpy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -488,7 +488,7 @@

    pmutt.omkm.reaction.BEPParameters:
    • reaction (Reaction object) – Reaction related to BEP.

    • -
    • T (float, optional) – Temperature in K. Default is 298.15

    • +
    • T (float, optional) – Temperature in K. Default is 298.15

    • kwargs (keyword arguments) – Parameters required to calculate the descriptor

    @@ -496,7 +496,7 @@

    pmutt.omkm.reaction.BEP

    HoRT – Dimensionless enthalpy

    Return type:
    -

    float

    +

    float

    @@ -508,7 +508,7 @@

    pmutt.omkm.reaction.BEP
    Parameters:
      -
    • units (str) – Units as string. See R() for accepted +

    • units (str) – Units as string. See R() for accepted units.

    • kwargs (keyword arguments) – Parameters needed by get_SoR

    @@ -517,7 +517,7 @@

    pmutt.omkm.reaction.BEP

    S – Entropy in appropriate units

    Return type:
    -

    float

    +

    float

    @@ -532,8 +532,8 @@

    pmutt.omkm.reaction.BEP
    • reaction (Reaction object, optional) – Reaction related to BEP. If entropy_state is None, reaction is not required.

    • -
    • T (float, optional) – Temperature in K. Default is 298.15

    • -
    • entropy_state (str or None, optional) –

      State to use to estimate entropy. Supported arguments:

      +
    • T (float, optional) – Temperature in K. Default is 298.15

    • +
    • entropy_state (str or None, optional) –

      State to use to estimate entropy. Supported arguments:

      • ’reactants’ (default)

      • ’products’

      • @@ -548,7 +548,7 @@

        pmutt.omkm.reaction.BEP

        SoR – Dimensionless entropy

        Return type:
        -

        float

        +

        float

        @@ -560,9 +560,9 @@

        pmutt.omkm.reaction.BEP
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • -
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • +
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • kwargs (keyword arguments) – Parameters needed by get_UoRT

        @@ -570,7 +570,7 @@

        pmutt.omkm.reaction.BEP

        U – Internal energy in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -584,7 +584,7 @@

        pmutt.omkm.reaction.BEPParameters:
        • reaction (Reaction object) – Reaction related to BEP.

        • -
        • T (float, optional) – Temperature in K. Default is 298.15

        • +
        • T (float, optional) – Temperature in K. Default is 298.15

        • kwargs (keyword arguments) – Parameters required to calculate the descriptor

        @@ -592,7 +592,7 @@

        pmutt.omkm.reaction.BEP

        UoRT – Dimensionless internal energy

        Return type:
        -

        float

        +

        float

        @@ -606,7 +606,7 @@

        pmutt.omkm.reaction.BEP

        q – Returns 1

        Return type:
        -

        float

        +

        float

        @@ -618,7 +618,7 @@

        pmutt.omkm.reaction.BEP
        Parameters:
          -
        • act_energy_unit (str, optional) – Unit to use for energy. Default is ‘cal/mol’

        • +
        • act_energy_unit (str, optional) – Unit to use for energy. Default is ‘cal/mol’

        • units (Units object) – If specified, energy_unit is overwritten. Default is None.

        @@ -626,7 +626,7 @@

        pmutt.omkm.reaction.BEP

        cti_str – Surface reaction string in CTI format

        Return type:
        -

        str

        +

        str

        @@ -640,7 +640,7 @@

        pmutt.omkm.reaction.BEP

        obj_dict

        Return type:
        -

        dict

        +

        dict

        @@ -652,7 +652,7 @@

        pmutt.omkm.reaction.BEP
        Parameters:
          -
        • act_energy_unit (str, optional) – Unit to use for activation energy. Default is ‘cal/mol’

        • +
        • act_energy_unit (str, optional) – Unit to use for activation energy. Default is ‘cal/mol’

        • units (Units object) – If specified, act_energy_unit is overwritten. Default is None.

        @@ -661,7 +661,7 @@

        pmutt.omkm.reaction.BEP

        yaml_dict – Dictionary compatible with Cantera’s YAML format

        Return type:
        -

        dict

        +

        dict

        diff --git a/api/kinetic_models/omkm_reactions/pmutt.omkm.reaction.SurfaceReaction.html b/api/kinetic_models/omkm_reactions/pmutt.omkm.reaction.SurfaceReaction.html index 874e77ee..f7ec9ad5 100644 --- a/api/kinetic_models/omkm_reactions/pmutt.omkm.reaction.SurfaceReaction.html +++ b/api/kinetic_models/omkm_reactions/pmutt.omkm.reaction.SurfaceReaction.html @@ -4,7 +4,7 @@ - pmutt.omkm.reaction.SurfaceReaction — pmutt 1.4.7 documentation + pmutt.omkm.reaction.SurfaceReaction — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
        - 1.4.7 + 1.4.9
        @@ -135,7 +135,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Type:
        -

        str, optional

        +

        str, optional

        @@ -146,7 +146,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Type:
        -

        bool, optional

        +

        bool, optional

        @@ -158,7 +158,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Type:
        -

        float, optional

        +

        float, optional

        @@ -170,7 +170,7 @@

        pmutt.omkm.reaction.SurfaceReactionis_adsorption is False, 0 if is_adsorption is True.

        Type:
        -

        float, optional

        +

        float, optional

        @@ -182,7 +182,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Type:
        -

        float, optional

        +

        float, optional

        @@ -195,7 +195,7 @@

        pmutt.omkm.reaction.SurfaceReactionis_adsorption is False.

        Type:
        -

        float, optional

        +

        float, optional

        @@ -207,7 +207,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Type:
        -

        str, optional

        +

        str, optional

        @@ -220,7 +220,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Type:
        -

        bool, optional

        +

        bool, optional

        @@ -483,7 +483,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Raises:
        -

        ValueError – Raised if the reactants, products and/or transition state +

        ValueError – Raised if the reactants, products and/or transition state element composition does not agree.

        @@ -495,7 +495,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
        -

        json_obj (dict) – JSON representation

        +

        json_obj (dict) – JSON representation

        Returns:

        Reaction

        @@ -513,27 +513,27 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • reaction_str (str) – Reaction string.

        • -
        • species (dict) – Dictionary using the names as keys. If you have a list of +

        • reaction_str (str) – Reaction string.

        • +
        • species (dict) – Dictionary using the names as keys. If you have a list of species, use pmutt.pmutt_list_to_dict to make a dict.

        • -
        • species_delimiter (str, optional) – Delimiter that separate species. Leading and trailing spaces +

        • species_delimiter (str, optional) – Delimiter that separate species. Leading and trailing spaces will be trimmed. Default is ‘+’

        • -
        • reaction_delimiter (str, optional) – Delimiter that separate states of the reaction. Leading and +

        • reaction_delimiter (str, optional) – Delimiter that separate states of the reaction. Leading and trailing spaces will be trimmed. Default is ‘=’

        • -
        • notes (str or dict, optional) – Other notes such as the source of the reaction. Default is None

        • -
        • A (float, optional) – Pre-exponential constant. If not specified, uses reaction to +

        • notes (str or dict, optional) – Other notes such as the source of the reaction. Default is None

        • +
        • A (float, optional) – Pre-exponential constant. If not specified, uses reaction to determine value.

        • -
        • beta (float, optional) – Power to raise the temperature in the rate expression. Default +

        • beta (float, optional) – Power to raise the temperature in the rate expression. Default is 1 if is_adsorption is False, 0 if is_adsorption is True.

        • -
        • Ea (float, optional) – Activation energy. If not specified, uses reaction to determine +

        • Ea (float, optional) – Activation energy. If not specified, uses reaction to determine value.

        • -
        • is_adsorption (bool, optional) – If True, the reaction represents an adsorption. Default is False

        • -
        • sticking_coeff (float, optional) – Sticking coefficient. Only relevant if is_adsorption is +

        • is_adsorption (bool, optional) – If True, the reaction represents an adsorption. Default is False

        • +
        • sticking_coeff (float, optional) – Sticking coefficient. Only relevant if is_adsorption is True. Default is 0.5

        • -
        • gas_phase (bool) – True if the reaction has only gas-phase species. This attribute +

        • gas_phase (bool) – True if the reaction has only gas-phase species. This attribute is determined based on the reactants and products

        • -
        • use_motz_wise (bool, optional) – Used when generating OpenMKM YAML file. If True, uses Motz-Wise +

        • use_motz_wise (bool, optional) – Used when generating OpenMKM YAML file. If True, uses Motz-Wise correction to sticking coefficient. Only applicable to adsorption reactions. Default is False.

        @@ -554,9 +554,9 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • sden_operation (str, optional) – Site density operation to use. Default is ‘min’

        • -
        • include_entropy (bool, optional) – If True, includes the entropy of activation. Default is True

        • -
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • +
        • sden_operation (str, optional) – Site density operation to use. Default is ‘min’

        • +
        • include_entropy (bool, optional) – If True, includes the entropy of activation. Default is True

        • +
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • units (str or Units, optional) – Units for A. If Units class specified, determines the units for A. Default is ‘molec/cm2’

        • kwargs (keyword arguments) – Parameters required to calculate pre-exponential factor

        • @@ -573,9 +573,9 @@

          pmutt.omkm.reaction.SurfaceReaction
          Parameters:
            -
          • units (str) – Units as string. See R() for accepted +

          • units (str) – Units as string. See R() for accepted units.

          • -
          • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

          • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

          • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -587,7 +587,7 @@

            pmutt.omkm.reaction.SurfaceReactionReturn type: -

            float

            +

            float

          @@ -599,7 +599,7 @@

          pmutt.omkm.reaction.SurfaceReaction
          Parameters:
            -
          • state (str) –

            State to calculate quantity. Supported options:

            +
          • state (str) –

            State to calculate quantity. Supported options:

            • ’reactants’

            • ’products’

            • @@ -608,7 +608,7 @@

              pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
            • units (str) – Units as string. See R() for accepted units.

            • kwargs (keyword arguments) – Parameters required to calculate heat capacity at constant pressure. See class docstring to see how to pass specific @@ -619,7 +619,7 @@

              pmutt.omkm.reaction.SurfaceReaction

              Cp – Heat capacity at constant pressure of the reaction state

          Return type:
          -

          float

          +

          float

        @@ -632,7 +632,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -644,7 +644,7 @@

          pmutt.omkm.reaction.SurfaceReactionReturn type: -

          float

          +

          float

        @@ -656,7 +656,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • state (str) –

          state to calculate quantity. Supported options:

          +
        • state (str) –

          state to calculate quantity. Supported options:

        @@ -688,9 +688,9 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units.

        • -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -701,7 +701,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          Cv_act – Change in heat capacity between reactants and products

        Return type:
        -

        float

        +

        float

        @@ -713,7 +713,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • state (str) –

          State to calculate quantity. Supported options:

          +
        • state (str) –

          State to calculate quantity. Supported options:

          • ’reactants’

          • ’products’

          • @@ -722,7 +722,7 @@

            pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
          • units (str) – Units as string. See R() for accepted units.

          • kwargs (keyword arguments) – Parameters required to calculate heat capacity at constant volume. See class docstring to see how to pass specific @@ -733,7 +733,7 @@

            pmutt.omkm.reaction.SurfaceReaction

            Cv – Heat capacity at constant volume of the reaction state

        Return type:
        -

        float

        +

        float

        @@ -746,7 +746,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -758,7 +758,7 @@

          pmutt.omkm.reaction.SurfaceReactionReturn type: -

          float

          +

          float

        @@ -770,7 +770,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • state (str) –

          state to calculate quantity. Supported options:

          +
        • state (str) –

          state to calculate quantity. Supported options:

        @@ -802,12 +802,12 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • -
        • T (float) – Temperature in K

        • -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • T (float) – Temperature in K

        • +
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. +

        • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. Condensed-phase and unimolecular gas-phase reactions should have a value of 0. Bimolecular gas-phase reactions should have a value of -1. If None specified, m will be calculated @@ -824,7 +824,7 @@

          pmutt.omkm.reaction.SurfaceReactionReturn type: -

          float

          +

          float

        @@ -836,7 +836,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • state (str) –

          State to calculate quantity. Supported options:

          +
        • state (str) –

          State to calculate quantity. Supported options:

          • ’reactants’

          • ’products’

          • @@ -845,10 +845,10 @@

            pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
          • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

          • -
          • T (float) – Temperature in K

          • -
          • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

          • +
          • T (float) – Temperature in K

          • +
          • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

          • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different species.

          • @@ -858,7 +858,7 @@

            pmutt.omkm.reaction.SurfaceReaction

            E – Electronic energy of the reaction state

        Return type:
        -

        float

        +

        float

        @@ -877,9 +877,9 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. +

        • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. Condensed-phase and unimolecular gas-phase reactions should have a value of 0. Bimolecular gas-phase reactions should have a value of -1. If None specified, m will be calculated @@ -895,7 +895,7 @@

          pmutt.omkm.reaction.SurfaceReactionReturn type: -

          float

          +

          float

        @@ -907,7 +907,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • state (str) –

          state to calculate quantity. Supported options:

          +
        • state (str) –

          state to calculate quantity. Supported options:

          • ’reactants’

          • ’products’

          • @@ -916,7 +916,7 @@

            pmutt.omkm.reaction.SurfaceReactionbool, optional) – If True, includes the zero point energy. Default is False

            +
          • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

          • kwargs (keyword arguments) – Parameters required to calculate dimensionless electronic energy. See class docstring to see how to pass specific parameters to different species.

          • @@ -926,7 +926,7 @@

            pmutt.omkm.reaction.SurfaceReaction

            EoRT – Dimensionless electronic energy of the reaction state.

        Return type:
        -

        float

        +

        float

        @@ -939,10 +939,10 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • -
        • T (float) – Temperature in K

        • -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • T (float) – Temperature in K

        • +
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -954,7 +954,7 @@

          pmutt.omkm.reaction.SurfaceReactionReturn type: -

          float

          +

          float

        @@ -966,7 +966,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • state (str) –

          State to calculate quantity. Supported options:

          +
        • state (str) –

          State to calculate quantity. Supported options:

          • ’reactants’

          • ’products’

          • @@ -975,9 +975,9 @@

            pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
          • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

          • -
          • T (float) – Temperature in K

          • +
          • T (float) – Temperature in K

          • kwargs (keyword arguments) – Parameters required to calculate Helholtz energy. See class docstring to see how to pass specific parameters to different species.

          • @@ -987,7 +987,7 @@

            pmutt.omkm.reaction.SurfaceReaction

            F – Helmholtz energy of the reaction state

        Return type:
        -

        float

        +

        float

        @@ -1000,7 +1000,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -1012,7 +1012,7 @@

          pmutt.omkm.reaction.SurfaceReactionReturn type: -

          float

          +

          float

        @@ -1024,7 +1024,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
        Return type:
        -

        float

        +

        float

        @@ -1056,10 +1056,10 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • T (float) – Temperature in K

        • -
        • P (float, optional) – Pressure in bar. Default is 1 bar

        • +
        • T (float) – Temperature in K

        • +
        • P (float, optional) – Pressure in bar. Default is 1 bar

        • kwargs (keyword arguments) – Parameters required to calculate enthalpy of activation.

        @@ -1071,7 +1071,7 @@

        pmutt.omkm.reaction.SurfaceReactionReturn type: -

        float

        +

        float

        @@ -1083,7 +1083,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • state (str) –

          State to calculate quantity. Supported options:

          +
        • state (str) –

          State to calculate quantity. Supported options:

          • ’reactants’

          • ’products’

          • @@ -1092,9 +1092,9 @@

            pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
          • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

          • -
          • T (float) – Temperature in K

          • +
          • T (float) – Temperature in K

          • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different species.

          • @@ -1104,7 +1104,7 @@

            pmutt.omkm.reaction.SurfaceReaction

            G – Gibbs energy of the reaction state

        Return type:
        -

        float

        +

        float

        @@ -1118,9 +1118,9 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • act (bool, optional) – If True, uses the transition state as the final state. Default +

        • act (bool, optional) – If True, uses the transition state as the final state. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy.

        @@ -1133,7 +1133,7 @@

        pmutt.omkm.reaction.SurfaceReactionReturn type: -

        float

        +

        float

        @@ -1145,7 +1145,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
        Return type:
        -

        float

        +

        float

        @@ -1176,9 +1176,9 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • T (float) – Temperature in K

        • +
        • T (float) – Temperature in K

        • kwargs (keyword arguments) – Parameters required to calculate enthalpy of activation.

        @@ -1190,7 +1190,7 @@

        pmutt.omkm.reaction.SurfaceReactionReturn type: -

        float

        +

        float

        @@ -1202,7 +1202,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • state (str) –

          State to calculate quantity. Supported options:

          +
        • state (str) –

          State to calculate quantity. Supported options:

          • ’reactants’

          • ’products’

          • @@ -1211,9 +1211,9 @@

            pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
          • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

          • -
          • T (float) – Temperature in K

          • +
          • T (float) – Temperature in K

          • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different species.

          • @@ -1223,7 +1223,7 @@

            pmutt.omkm.reaction.SurfaceReaction

            H – Enthalpy of the reaction state

        Return type:
        -

        float

        +

        float

        @@ -1236,7 +1236,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate enthalpy of activation.

        @@ -1249,7 +1249,7 @@

        pmutt.omkm.reaction.SurfaceReactionReturn type: -

        float

        +

        float

        @@ -1261,7 +1261,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • state (str) –

          state to calculate quantity. Supported options:

          +
        • state (str) –

          state to calculate quantity. Supported options:

        @@ -1292,9 +1292,9 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • act (bool, optional) – If True, uses the transition state as the final state. Default +

        • act (bool, optional) – If True, uses the transition state as the final state. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate equilibrium constant. See class docstring to see how to pass specific parameters to @@ -1305,7 +1305,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          Keq – Equilibrium constant between reactants and products

        Return type:
        -

        float

        +

        float

        @@ -1318,9 +1318,9 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units.

        • -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1332,7 +1332,7 @@

          pmutt.omkm.reaction.SurfaceReactionReturn type: -

          float

          +

          float

        @@ -1344,7 +1344,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • state (str) –

          State to calculate quantity. Supported options:

          +
        • state (str) –

          State to calculate quantity. Supported options:

          • ’reactants’

          • ’products’

          • @@ -1353,7 +1353,7 @@

            pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
          • units (str) – Units as string. See R() for accepted units.

          • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to @@ -1364,7 +1364,7 @@

            pmutt.omkm.reaction.SurfaceReaction

            S – Entropy of the reaction state

        Return type:
        -

        float

        +

        float

        @@ -1377,7 +1377,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1389,7 +1389,7 @@

          pmutt.omkm.reaction.SurfaceReactionReturn type: -

          float

          +

          float

        @@ -1401,7 +1401,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
        Return type:
        -

        float

        +

        float

        @@ -1432,10 +1432,10 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • -
        • T (float) – Temperature in K

        • -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • T (float) – Temperature in K

        • +
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1447,7 +1447,7 @@

          pmutt.omkm.reaction.SurfaceReactionReturn type: -

          float

          +

          float

        @@ -1459,7 +1459,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • state (str) –

          State to calculate quantity. Supported options:

          +
        • state (str) –

          State to calculate quantity. Supported options:

          • ’reactants’

          • ’products’

          • @@ -1468,9 +1468,9 @@

            pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
          • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

          • -
          • T (float) – Temperature in K

          • +
          • T (float) – Temperature in K

          • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different species.

          • @@ -1480,7 +1480,7 @@

            pmutt.omkm.reaction.SurfaceReaction

            U – Internal energy of the reaction state

        Return type:
        -

        float

        +

        float

        @@ -1493,7 +1493,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1505,7 +1505,7 @@

          pmutt.omkm.reaction.SurfaceReactionReturn type: -

          float

          +

          float

        @@ -1517,7 +1517,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
        Return type:
        -

        float

        +

        float

        @@ -1548,11 +1548,11 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units.

        • -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • act (bool, optional) – If True, uses the transition state as the final state. Default +

        • act (bool, optional) – If True, uses the transition state as the final state. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1563,7 +1563,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          delta_Cp – Change in heat capacity between reactants and products

        Return type:
        -

        float

        +

        float

        @@ -1576,9 +1576,9 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • act (bool, optional) – If True, uses the transition state as the final state. Default +

        • act (bool, optional) – If True, uses the transition state as the final state. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1589,7 +1589,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          delta_CvoR – Change in heat capacity between reactants and products

        Return type:
        -

        float

        +

        float

        @@ -1602,11 +1602,11 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units.

        • -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • act (bool, optional) – If True, uses the transition state as the final state. Default +

        • act (bool, optional) – If True, uses the transition state as the final state. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1617,7 +1617,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          delta_Cv – Change in heat capacity between reactants and products

        Return type:
        -

        float

        +

        float

        @@ -1630,9 +1630,9 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • act (bool, optional) – If True, uses the transition state as the final state. Default +

        • act (bool, optional) – If True, uses the transition state as the final state. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1643,7 +1643,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          delta_CvoR – Change in heat capacity between reactants and products

        Return type:
        -

        float

        +

        float

        @@ -1655,12 +1655,12 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • -
        • T (float) – Temperature in K

        • -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • T (float) – Temperature in K

        • +
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • act (bool, optional) – If True, uses the transition state as the final state. Default +

        • act (bool, optional) – If True, uses the transition state as the final state. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different @@ -1671,7 +1671,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          delta_E – Change in electronic energy between reactants and products

        Return type:
        -

        float

        +

        float

        @@ -1684,9 +1684,9 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • act (bool, optional) – If True, uses the transition state as the final state. Default +

        • act (bool, optional) – If True, uses the transition state as the final state. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different @@ -1697,7 +1697,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          delta_EoRT – Change in electronic energy between reactants and products

        Return type:
        -

        float

        +

        float

        @@ -1709,12 +1709,12 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • -
        • T (float) – Temperature in K

        • -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • T (float) – Temperature in K

        • +
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • act (bool, optional) – If True, uses the transition state as the final state. Default +

        • act (bool, optional) – If True, uses the transition state as the final state. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -1725,7 +1725,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          delta_F – Change in Helmholtz energy between reactants and products

        Return type:
        -

        float

        +

        float

        @@ -1738,9 +1738,9 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • act (bool, optional) – If True, uses the transition state as the final state. Default +

        • act (bool, optional) – If True, uses the transition state as the final state. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -1751,7 +1751,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          delta_FoRT – Change in Helmholtz energy between reactants and products

        Return type:
        -

        float

        +

        float

        @@ -1763,12 +1763,12 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • -
        • T (float) – Temperature in K

        • -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • T (float) – Temperature in K

        • +
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • act (bool, optional) – If True, uses the transition state as the final state. Default +

        • act (bool, optional) – If True, uses the transition state as the final state. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1779,7 +1779,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          delta_G – Change in Gibbs energy between reactants and products

        Return type:
        -

        float

        +

        float

        @@ -1792,9 +1792,9 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • act (bool, optional) – If True, uses the transition state as the final state. Default +

        • act (bool, optional) – If True, uses the transition state as the final state. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1805,7 +1805,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          delta_GoRT – Change in Gibbs energy between reactants and products

        Return type:
        -

        float

        +

        float

        @@ -1817,12 +1817,12 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • -
        • T (float) – Temperature in K

        • -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • T (float) – Temperature in K

        • +
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • act (bool, optional) – If True, uses the transition state as the final state. Default +

        • act (bool, optional) – If True, uses the transition state as the final state. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different @@ -1833,7 +1833,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          delta_H – Change in enthalpy between reactants and products

        Return type:
        -

        float

        +

        float

        @@ -1845,9 +1845,9 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • act (bool, optional) – If True, uses the transition state as the final state. Default +

        • act (bool, optional) – If True, uses the transition state as the final state. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different @@ -1858,7 +1858,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          delta_HoRT – Change in enthalpy between reactants and products

        Return type:
        -

        float

        +

        float

        @@ -1870,11 +1870,11 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units.

        • -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • act (bool, optional) – If True, uses the transition state as the final state. Default +

        • act (bool, optional) – If True, uses the transition state as the final state. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1885,7 +1885,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          delta_S – Change in entropy between reactants and products

        Return type:
        -

        float

        +

        float

        @@ -1897,9 +1897,9 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • act (bool, optional) – If True, uses the transition state as the final state. Default +

        • act (bool, optional) – If True, uses the transition state as the final state. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1910,7 +1910,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          delta_SoR – Change in entropy between reactants and products

        Return type:
        -

        float

        +

        float

        @@ -1922,12 +1922,12 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • -
        • T (float) – Temperature in K

        • -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • T (float) – Temperature in K

        • +
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • act (bool, optional) – If True, uses the transition state as the final state. Default +

        • act (bool, optional) – If True, uses the transition state as the final state. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1938,7 +1938,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          delta_U – Change in internal energy between reactants and products

        Return type:
        -

        float

        +

        float

        @@ -1951,9 +1951,9 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • act (bool, optional) – If True, uses the transition state as the final state. Default +

        • act (bool, optional) – If True, uses the transition state as the final state. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1964,7 +1964,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          delta_UoRT – Change in internal energy between reactants and products

        Return type:
        -

        float

        +

        float

        @@ -1976,9 +1976,9 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • act (bool, optional) – If True, uses the transition state as the final state. Default +

        • act (bool, optional) – If True, uses the transition state as the final state. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate partition function. See class docstring to see how to pass specific parameters to different @@ -1989,7 +1989,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          delta_q – Change in partition function between reactants and products

        Return type:
        -

        float

        +

        float

        @@ -2002,21 +2002,21 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • initial_state (str) –

          Thermodynamic state. Supported options:

          +
        • initial_state (str) –

          Thermodynamic state. Supported options:

          • ’reactants’

          • ’products’

          • ’transition state’

        • -
        • final_state (str) –

          Thermodynamic state. Supported options:

          +
        • final_state (str) –

          Thermodynamic state. Supported options:

          • ’reactants’

          • ’products’

          • ’transition state’

        • -
        • method_name (str) – Name of method to use to calculate quantity. Calculates any +

        • method_name (str) – Name of method to use to calculate quantity. Calculates any quantity as long as the relevant objects have the same method name

        • kwargs (keyword arguments) – Arguments passed to evaluate the quantity of the reactants and @@ -2027,7 +2027,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          delta_quantity – Change in thermodynamic quantity between particular states

        Return type:
        -

        float

        +

        float

        @@ -2040,9 +2040,9 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • include_ZPE (bool, optional) – If True, includes zero-point energy when calculating the +

        • include_ZPE (bool, optional) – If True, includes zero-point energy when calculating the value of the partition functions. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate partition function. See class docstring to see how to pass specific parameters to different @@ -2054,7 +2054,7 @@

          pmutt.omkm.reaction.SurfaceReactionReturn type: -

          float

          +

          float

        @@ -2066,7 +2066,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
        Return type:
        -

        float

        +

        float

        @@ -2096,8 +2096,8 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • include_TS (bool, optional) – Whether transition states should be included. Default is True

        • -
        • key (str, optional) – Attribute to use as the key in the output dictionary. Default +

        • include_TS (bool, optional) – Whether transition states should be included. Default is True

        • +
        • key (str, optional) – Attribute to use as the key in the output dictionary. Default is name

        @@ -2105,7 +2105,7 @@

        pmutt.omkm.reaction.SurfaceReaction

        species – Unique species in the reaction

        Return type:
        -

        dict

        +

        dict

        @@ -2117,7 +2117,7 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • state (str) –

          Thermodynamic state. Supported options:

          +
        • state (str) –

          Thermodynamic state. Supported options:

          • ’reactants’

          • ’products’

          • @@ -2126,7 +2126,7 @@

            pmutt.omkm.reaction.SurfaceReactionstr) – Name of method to use to calculate quantity. Calculates any +
          • method_name (str) – Name of method to use to calculate quantity. Calculates any quantity as long as the relevant objects have the same method name

          • kwargs (keyword arguments) – Arguments required to calculate the thermodynamic quantity of @@ -2137,7 +2137,7 @@

            pmutt.omkm.reaction.SurfaceReaction

            state_quantity – Thermodynamic quantity of particular state

        Return type:
        -

        float

        +

        float

        @@ -2179,12 +2179,12 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • -
        • P (float, optional) – Pressure in bar. Default is 1 bar

        • -
        • quantity_unit (str, optional) – Quantity unit to calculate A. Default is ‘molec’

        • -
        • length_unit (str, optional) – Length unit to calculate A. Default is ‘cm’

        • -
        • act_energy_unit (str, optional) – Unit to use for activation energy. Default is ‘cal/mol’

        • -
        • ads_act_method (str, optional) – Activation method to use for adsorption reactions. Accepted +

        • T (float, optional) – Temperature in K. Default is 298.15 K

        • +
        • P (float, optional) – Pressure in bar. Default is 1 bar

        • +
        • quantity_unit (str, optional) – Quantity unit to calculate A. Default is ‘molec’

        • +
        • length_unit (str, optional) – Length unit to calculate A. Default is ‘cm’

        • +
        • act_energy_unit (str, optional) – Unit to use for activation energy. Default is ‘cal/mol’

        • +
        • ads_act_method (str, optional) – Activation method to use for adsorption reactions. Accepted options include ‘get_H_act’ and ‘get_G_act’. Default is ‘get_H_act’.

        • units (Units object) – If specified, quantity_unit, length_unit, and @@ -2195,7 +2195,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          cti_str – Surface reaction string in CTI format

        Return type:
        -

        str

        +

        str

        @@ -2209,7 +2209,7 @@

        pmutt.omkm.reaction.SurfaceReaction

        obj_dict

        Return type:
        -

        dict

        +

        dict

        @@ -2221,12 +2221,12 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • -
        • P (float, optional) – Pressure in bar. Default is 1 bar

        • -
        • quantity_unit (str, optional) – Quantity unit to calculate A. Default is ‘molec’

        • -
        • length_unit (str, optional) – Length unit to calculate A. Default is ‘cm’

        • -
        • act_energy_unit (str, optional) – Unit to use for activation energy. Default is ‘cal/mol’

        • -
        • ads_act_method (str, optional) – Activation method to use for adsorption reactions. Accepted +

        • T (float, optional) – Temperature in K. Default is 298.15 K

        • +
        • P (float, optional) – Pressure in bar. Default is 1 bar

        • +
        • quantity_unit (str, optional) – Quantity unit to calculate A. Default is ‘molec’

        • +
        • length_unit (str, optional) – Length unit to calculate A. Default is ‘cm’

        • +
        • act_energy_unit (str, optional) – Unit to use for activation energy. Default is ‘cal/mol’

        • +
        • ads_act_method (str, optional) – Activation method to use for adsorption reactions. Accepted options include ‘get_H_act’ and ‘get_G_act’. Default is ‘get_H_act’.

        • units (Units object) – If specified, quantity_unit, length_unit, and @@ -2237,7 +2237,7 @@

          pmutt.omkm.reaction.SurfaceReaction

          yaml_dict – Dictionary compatible with Cantera’s YAML format

        Return type:
        -

        dict

        +

        dict

        @@ -2249,21 +2249,21 @@

        pmutt.omkm.reaction.SurfaceReaction
        Parameters:
          -
        • species_delimiter (str, optional) – Separates species. Default is ‘+’

        • -
        • reaction_delimiter (str, optional) – Separates reaction states. Default is ‘=’

        • -
        • stoich_format (float, optional) – Format to write stoichiometric numbers. Default is ‘.2f’ (float +

        • species_delimiter (str, optional) – Separates species. Default is ‘+’

        • +
        • reaction_delimiter (str, optional) – Separates reaction states. Default is ‘=’

        • +
        • stoich_format (float, optional) – Format to write stoichiometric numbers. Default is ‘.2f’ (float rounded to 2 decimal places)

        • -
        • include_TS (bool, optional) – If True, includes transition states in output. Default is True

        • -
        • stoich_space (bool, optional) – If True, inserts a space between stoichiometric coefficients +

        • include_TS (bool, optional) – If True, includes transition states in output. Default is True

        • +
        • stoich_space (bool, optional) – If True, inserts a space between stoichiometric coefficients and the species name. Default is False

        • -
        • key (str, optional) – Attribute to use to print out species. Default is name

        • +
        • key (str, optional) – Attribute to use to print out species. Default is name

        Returns:

        reaction_str – Reaction string

        Return type:
        -

        str

        +

        str

        diff --git a/api/kinetic_models/omkm_units/pmutt.omkm.units.Units.html b/api/kinetic_models/omkm_units/pmutt.omkm.units.Units.html index 99ad968f..6582555c 100644 --- a/api/kinetic_models/omkm_units/pmutt.omkm.units.Units.html +++ b/api/kinetic_models/omkm_units/pmutt.omkm.units.Units.html @@ -4,7 +4,7 @@ - pmutt.omkm.units.Units — pmutt 1.4.7 documentation + pmutt.omkm.units.Units — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        @@ -156,13 +156,13 @@

        pmutt.omkm.units.Units

        Writes the object in Cantera’s CTI format.

        Parameters:
        -

        max_line_len (int, optional) – Maximum number of characters in the line. Default is 80.

        +

        max_line_len (int, optional) – Maximum number of characters in the line. Default is 80.

        Returns:

        CTI_str – Object represented as a CTI string.

        Return type:
        -

        str

        +

        str

        @@ -177,7 +177,7 @@

        pmutt.omkm.units.Units
        Return type:
        -

        dict

        +

        dict

        @@ -191,7 +191,7 @@

        pmutt.omkm.units.Units

        yaml_dict – Dictionary compatible with Cantera’s YAML format

        Return type:
        -

        dict

        +

        dict

        diff --git a/api/kinetic_models/zacros/pmutt.empirical.zacros.Zacros.html b/api/kinetic_models/zacros/pmutt.empirical.zacros.Zacros.html index b5575040..29c5810f 100644 --- a/api/kinetic_models/zacros/pmutt.empirical.zacros.Zacros.html +++ b/api/kinetic_models/zacros/pmutt.empirical.zacros.Zacros.html @@ -4,7 +4,7 @@ - pmutt.empirical.zacros.Zacros — pmutt 1.4.7 documentation + pmutt.empirical.zacros.Zacros — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        @@ -298,7 +298,7 @@

        pmutt.empirical.zacros.Zacros
        Parameters:
        -

        json_obj (dict) – JSON representation

        +

        json_obj (dict) – JSON representation

        Returns:

        Zacros

        @@ -316,7 +316,7 @@

        pmutt.empirical.zacros.Zacros
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units.

        • kwargs (keyword arguments) – Parameters needed by get_CpoR

        @@ -325,7 +325,7 @@

        pmutt.empirical.zacros.Zacros

        Cp – Heat capacity (constant P) in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -340,7 +340,7 @@

        pmutt.empirical.zacros.Zacros

        CpoR – Returns 0

        Return type:
        -

        float

        +

        float

        @@ -352,7 +352,7 @@

        pmutt.empirical.zacros.Zacros
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units.

        • kwargs (keyword arguments) – Parameters needed by get_CvoR

        @@ -361,7 +361,7 @@

        pmutt.empirical.zacros.Zacros

        Cv – Heat capacity (constant V) in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -376,7 +376,7 @@

        pmutt.empirical.zacros.Zacros

        CvoR – Returns 0

        Return type:
        -

        float

        +

        float

        @@ -388,9 +388,9 @@

        pmutt.empirical.zacros.Zacros
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • -
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • +
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • kwargs (keyword arguments) – Parameters needed by get_FoRT

        @@ -398,7 +398,7 @@

        pmutt.empirical.zacros.Zacros

        F – Hemholtz energy in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -415,7 +415,7 @@

        pmutt.empirical.zacros.Zacros

        FoRT – Dimensionless Helmholtz energy

        Return type:
        -

        float

        +

        float

        @@ -427,9 +427,9 @@

        pmutt.empirical.zacros.Zacros
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • -
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • +
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • kwargs (keyword arguments) – Parameters needed by get_GoRT

        @@ -437,7 +437,7 @@

        pmutt.empirical.zacros.Zacros

        G – Gibbs energy in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -454,7 +454,7 @@

        pmutt.empirical.zacros.Zacros

        GoRT – Dimensionless Gibbs free energy

        Return type:
        -

        float

        +

        float

        @@ -466,9 +466,9 @@

        pmutt.empirical.zacros.Zacros
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • -
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • +
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • kwargs (keyword arguments) – Parameters needed by get_HoRT

        @@ -476,7 +476,7 @@

        pmutt.empirical.zacros.Zacros

        H – Enthalpy in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -490,7 +490,7 @@

        pmutt.empirical.zacros.Zacros

        HoRT – Returns 0

        Return type:
        -

        float

        +

        float

        @@ -502,7 +502,7 @@

        pmutt.empirical.zacros.Zacros
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units.

        • kwargs (keyword arguments) – Parameters needed by get_SoR

        @@ -511,7 +511,7 @@

        pmutt.empirical.zacros.Zacros

        S – Entropy in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -525,7 +525,7 @@

        pmutt.empirical.zacros.Zacros

        SoR – Returns 0

        Return type:
        -

        float

        +

        float

        @@ -537,9 +537,9 @@

        pmutt.empirical.zacros.Zacros
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • -
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • +
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • kwargs (keyword arguments) – Parameters needed by get_UoRT

        @@ -547,7 +547,7 @@

        pmutt.empirical.zacros.Zacros

        U – Internal energy in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -561,7 +561,7 @@

        pmutt.empirical.zacros.Zacros

        UoRT – Returns 0

        Return type:
        -

        float

        +

        float

        @@ -575,7 +575,7 @@

        pmutt.empirical.zacros.Zacros

        q – Returns 1

        Return type:
        -

        float

        +

        float

        @@ -588,18 +588,18 @@

        pmutt.empirical.zacros.Zacros
        Parameters:
          -
        • T_low (float) – Lower temperature in K. If not specified, +

        • T_low (float) – Lower temperature in K. If not specified, T_low attribute used.

        • -
        • T_high (float) – Upper temperature in K. If not specified, +

        • T_high (float) – Upper temperature in K. If not specified, T_high attribute used.

        • -
        • Cp_units (str) – Units to plot heat capacity. See R() +

        • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

        • -
        • H_units (str) – Units to plot enthalpy. See R() for +

        • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

        • -
        • S_units (str) – Units to plot entropy. See R() for +

        • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

        • -
        • G_units (str) – Units to plot Gibbs free energy. See R() +

        • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

        @@ -626,18 +626,18 @@

        pmutt.empirical.zacros.Zacros
        Parameters:
          -
        • T_low (float) – Lower temperature in K. If not specified, +

        • T_low (float) – Lower temperature in K. If not specified, T_low attribute used

        • -
        • T_high (float) – Upper temperature in K. If not specified, +

        • T_high (float) – Upper temperature in K. If not specified, T_high attribute used

        • -
        • Cp_units (str) – Units to plot heat capacity. See R() +

        • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

        • -
        • H_units (str) – Units to plot enthalpy. See R() for +

        • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

        • -
        • S_units (str) – Units to plot entropy. See R() for +

        • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

        • -
        • G_units (str) – Units to plot Gibbs free energy. See R() +

        • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

        @@ -664,18 +664,18 @@

        pmutt.empirical.zacros.Zacros
        Parameters:
          -
        • T_low (float) – Lower temperature in K. If not specified, T_low +

        • T_low (float) – Lower temperature in K. If not specified, T_low attribute used

        • -
        • T_high (float) – Upper temperature in K. If not specified, T_high +

        • T_high (float) – Upper temperature in K. If not specified, T_high attribute used

        • -
        • Cp_units (str) – Units to plot heat capacity. See R() for +

        • Cp_units (str) – Units to plot heat capacity. See R() for accepted units. If not specified, dimensionless units used.

        • -
        • H_units (str) – Units to plot enthalpy. See R() for +

        • H_units (str) – Units to plot enthalpy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

        • -
        • S_units (str) – Units to plot entropy. See R() for +

        • S_units (str) – Units to plot entropy. See R() for accepted units. If not specified, dimensionless units used.

        • -
        • G_units (str) – Units to plot Gibbs free energy. See R() +

        • G_units (str) – Units to plot Gibbs free energy. See R() for accepted units but omit the ‘/K’ (e.g. J/mol). If not specified, dimensionless units used.

        @@ -703,7 +703,7 @@

        pmutt.empirical.zacros.Zacros

        obj_dict

        Return type:
        -

        dict

        +

        dict

        diff --git a/api/mixture/cov/pmutt.mixture.cov.PiecewiseCovEffect.html b/api/mixture/cov/pmutt.mixture.cov.PiecewiseCovEffect.html index d8f36ab9..381f1c92 100644 --- a/api/mixture/cov/pmutt.mixture.cov.PiecewiseCovEffect.html +++ b/api/mixture/cov/pmutt.mixture.cov.PiecewiseCovEffect.html @@ -4,7 +4,7 @@ - pmutt.mixture.cov.PiecewiseCovEffect — pmutt 1.4.7 documentation + pmutt.mixture.cov.PiecewiseCovEffect — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        @@ -123,7 +123,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Type:
        -

        str

        +

        str

        @@ -134,7 +134,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Type:
        -

        str

        +

        str

        @@ -148,7 +148,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Type:
        -

        list (length N) of float

        +

        list (length N) of float

        @@ -159,7 +159,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Type:
        -

        list (length N) of float

        +

        list (length N) of float

        @@ -170,7 +170,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Type:
        -

        str, optional

        +

        str, optional

        @@ -257,7 +257,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Parameters:
        -

        json_obj (dict) – JSON representation

        +

        json_obj (dict) – JSON representation

        Returns:

        EmpiricalBase

        @@ -275,7 +275,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units.

        • kwargs (keyword arguments) – Parameters needed by get_CpoR

        @@ -284,7 +284,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect

        Cp – Heat capacity (constant P) in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -299,7 +299,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect

        CpoR – Returns 0

        Return type:
        -

        float

        +

        float

        @@ -311,7 +311,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units.

        • kwargs (keyword arguments) – Parameters needed by get_CvoR

        @@ -320,7 +320,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect

        Cv – Heat capacity (constant V) in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -335,7 +335,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect

        CvoR – Returns 0

        Return type:
        -

        float

        +

        float

        @@ -347,9 +347,9 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • -
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • +
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • kwargs (keyword arguments) – Parameters needed by get_FoRT

        @@ -357,7 +357,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect

        F – Hemholtz energy in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -369,15 +369,15 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Parameters:
          -
        • x (float, optional) – Coverage (in ML) of species j. Default is 0

        • -
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • +
        • x (float, optional) – Coverage (in ML) of species j. Default is 0

        • +
        • T (float, optional) – Temperature in K. Default is 298.15 K

        Returns:

        FoRT – Dimensionless excess Helmholtz energy

        Return type:
        -

        float

        +

        float

        @@ -389,9 +389,9 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • -
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • +
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • kwargs (keyword arguments) – Parameters needed by get_GoRT

        @@ -399,7 +399,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect

        G – Gibbs energy in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -411,15 +411,15 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Parameters:
          -
        • x (float, optional) – Coverage (in ML) of species j. Default is 0

        • -
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • +
        • x (float, optional) – Coverage (in ML) of species j. Default is 0

        • +
        • T (float, optional) – Temperature in K. Default is 298.15 K

        Returns:

        GoRT – Dimensionless excess Gibbs energy

        Return type:
        -

        float

        +

        float

        @@ -431,9 +431,9 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • -
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • +
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • kwargs (keyword arguments) – Parameters needed by get_HoRT

        @@ -441,7 +441,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect

        H – Enthalpy in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -453,15 +453,15 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Parameters:
          -
        • x (float, optional) – Coverage (in ML) of species j. Default is 0

        • -
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • +
        • x (float, optional) – Coverage (in ML) of species j. Default is 0

        • +
        • T (float, optional) – Temperature in K. Default is 298.15 K

        Returns:

        HoRT – Dimensionless excess enthalpy

        Return type:
        -

        float

        +

        float

        @@ -473,7 +473,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units.

        • kwargs (keyword arguments) – Parameters needed by get_SoR

        @@ -482,7 +482,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect

        S – Entropy in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -496,7 +496,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect

        SoR – Returns 0

        Return type:
        -

        float

        +

        float

        @@ -508,9 +508,9 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • -
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • +
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • kwargs (keyword arguments) – Parameters needed by get_UoRT

        @@ -518,7 +518,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect

        U – Internal energy in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -530,15 +530,15 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Parameters:
          -
        • x (float, optional) – Coverage (in ML) of species j. Default is 0

        • -
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • +
        • x (float, optional) – Coverage (in ML) of species j. Default is 0

        • +
        • T (float, optional) – Temperature in K. Default is 298.15 K

        Returns:

        UoRT – Dimensionless internal energy

        Return type:
        -

        float

        +

        float

        @@ -552,7 +552,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect

        q – Returns 1

        Return type:
        -

        float

        +

        float

        @@ -564,10 +564,10 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Parameters:
          -
        • interval (float) – Interval to insert. It will automatically be inserted in the +

        • interval (float) – Interval to insert. It will automatically be inserted in the intervals list in the position so that piecewise function remains continuous

        • -
        • slope (float) – Slope to insert. Inserted into the same position as interval

        • +
        • slope (float) – Slope to insert. Inserted into the same position as interval

        @@ -579,12 +579,12 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Parameters:
        -

        i (float) – Index to remove from self.intervals and self.slopes. +

        i (float) – Index to remove from self.intervals and self.slopes. Value cannot be 0 since removing this index would not allow mole fractions to span from 0 to 1

        Raises:
        -

        ValueError – Raised when i = 0

        +

        ValueError – Raised when i = 0

        @@ -596,8 +596,8 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Parameters:
          -
        • energy_unit (str, optional) – Energy unit for slopes. Default is ‘kcal’

        • -
        • quantity_unit (str, optional) – Quantity unit for slopes. Default is ‘mol’

        • +
        • energy_unit (str, optional) – Energy unit for slopes. Default is ‘kcal’

        • +
        • quantity_unit (str, optional) – Quantity unit for slopes. Default is ‘mol’

        • units (Units object) – If specified, energy_unit and quantity_unit are overwritten. Default is None.

        @@ -606,7 +606,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect

        lat_inter_str – Lateral interaction in CTI format

        Return type:
        -

        str

        +

        str

        @@ -620,7 +620,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect

        obj_dict

        Return type:
        -

        dict

        +

        dict

        @@ -632,8 +632,8 @@

        pmutt.mixture.cov.PiecewiseCovEffect
        Parameters:
          -
        • energy_unit (str, optional) – Energy unit for slopes. Default is ‘kcal’

        • -
        • quantity_unit (str, optional) – Quantity unit for slopes. Default is ‘mol’

        • +
        • energy_unit (str, optional) – Energy unit for slopes. Default is ‘kcal’

        • +
        • quantity_unit (str, optional) – Quantity unit for slopes. Default is ‘mol’

        • units (Units object) – If specified, energy_unit is overwritten. Default is None.

        @@ -641,7 +641,7 @@

        pmutt.mixture.cov.PiecewiseCovEffect

        yaml_dict – Dictionary compatible with Cantera’s YAML format

        Return type:
        -

        dict

        +

        dict

        diff --git a/api/mixture/mixture.html b/api/mixture/mixture.html index e79210c1..0719cefc 100644 --- a/api/mixture/mixture.html +++ b/api/mixture/mixture.html @@ -4,7 +4,7 @@ - Mixture Models — pmutt 1.4.7 documentation + Mixture Models — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        diff --git a/api/phase_diagram/phase_diagram.html b/api/phase_diagram/phase_diagram.html index 106101dc..1140e4c2 100644 --- a/api/phase_diagram/phase_diagram.html +++ b/api/phase_diagram/phase_diagram.html @@ -4,7 +4,7 @@ - Phase Diagrams — pmutt 1.4.7 documentation + Phase Diagrams — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        diff --git a/api/phase_diagram/phase_diagram/pmutt.reaction.phasediagram.PhaseDiagram.html b/api/phase_diagram/phase_diagram/pmutt.reaction.phasediagram.PhaseDiagram.html index f24b20a6..adeb2c61 100644 --- a/api/phase_diagram/phase_diagram/pmutt.reaction.phasediagram.PhaseDiagram.html +++ b/api/phase_diagram/phase_diagram/pmutt.reaction.phasediagram.PhaseDiagram.html @@ -4,7 +4,7 @@ - pmutt.reaction.phasediagram.PhaseDiagram — pmutt 1.4.7 documentation + pmutt.reaction.phasediagram.PhaseDiagram — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
        - 1.4.7 + 1.4.9
        @@ -188,7 +188,7 @@

        pmutt.reaction.phasediagram.PhaseDiagram
        Parameters:
        -

        json_obj (dict) – JSON representation

        +

        json_obj (dict) – JSON representation

        Returns:

        PhaseDiagram

        @@ -216,7 +216,7 @@

        pmutt.reaction.phasediagram.PhaseDiagram
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • kwargs (keyword arguments) – Parameters to evaluate Gibbs energy at each state.

        @@ -225,7 +225,7 @@

        pmutt.reaction.phasediagram.PhaseDiagram

        E_span – Energy span of the Reactions

        Return type:
        -

        float

        +

        float

        @@ -238,9 +238,9 @@

        pmutt.reaction.phasediagram.PhaseDiagram
        Parameters:
          -
        • x_name (str) – Name of variable to vary

        • +
        • x_name (str) – Name of variable to vary

        • x_values (iterable object) – x values to use

        • -
        • G_units (str, optional) – Units for G. If None, uses GoRT. Default is None

        • +
        • G_units (str, optional) – Units for G. If None, uses GoRT. Default is None

        • kwargs (keyword arguments) – Other variables to use in the calculation

        @@ -265,11 +265,11 @@

        pmutt.reaction.phasediagram.PhaseDiagram
        Parameters:
          -
        • x1_name (str) – Name of first variable to vary

        • +
        • x1_name (str) – Name of first variable to vary

        • x1_values (iterable object) – x1 values to use

        • -
        • x2_name (str) – Name of second variable to vary

        • +
        • x2_name (str) – Name of second variable to vary

        • x2_values (iterable object) – x2 values to use

        • -
        • G_units (str, optional) – Units for G. If None, uses GoRT. Default is None

        • +
        • G_units (str, optional) – Units for G. If None, uses GoRT. Default is None

        • kwargs (keyword arguments) – Other variables to use in the calculation

        @@ -293,8 +293,8 @@

        pmutt.reaction.phasediagram.PhaseDiagram
        Parameters:
          -
        • include_TS (bool, optional) – Whether transition states should be included. Default is True

        • -
        • key (str, optional) – Attribute to use as the key in the output dictionary. +

        • include_TS (bool, optional) – Whether transition states should be included. Default is True

        • +
        • key (str, optional) – Attribute to use as the key in the output dictionary. Default is name

        @@ -302,7 +302,7 @@

        pmutt.reaction.phasediagram.PhaseDiagram

        species – Unique species in the reactions

        Return type:
        -

        dict

        +

        dict

        @@ -314,9 +314,9 @@

        pmutt.reaction.phasediagram.PhaseDiagram
        Parameters:
          -
        • x_name (str) – Name of variable to vary

        • +
        • x_name (str) – Name of variable to vary

        • x_values (iterable object) – x values to use

        • -
        • G_units (str, optional) – Units for G. If None, uses GoRT. Default is None

        • +
        • G_units (str, optional) – Units for G. If None, uses GoRT. Default is None

        • kwargs (keyword arguments) – Other variables to use in the calculation

        @@ -337,11 +337,11 @@

        pmutt.reaction.phasediagram.PhaseDiagram
        Parameters:
          -
        • x1_name (str) – Name of first variable to vary

        • +
        • x1_name (str) – Name of first variable to vary

        • x1_values (iterable object) – x1 values to use

        • -
        • x2_name (str) – Name of first variable to vary

        • +
        • x2_name (str) – Name of first variable to vary

        • x2_values (iterable object) – x2 values to use

        • -
        • G_units (str, optional) – Units for G. If None, uses GoRT. Default is None

        • +
        • G_units (str, optional) – Units for G. If None, uses GoRT. Default is None

        • kwargs (keyword arguments) – Other variables to use in the calculation

        @@ -364,13 +364,13 @@

        pmutt.reaction.phasediagram.PhaseDiagram
        Parameters:
          -
        • method_name (str) – Name of method to use to calculate quantity. Calculates any +

        • method_name (str) – Name of method to use to calculate quantity. Calculates any quantity as long as the relevant objects have the same method name. Some examples include: get_HoRT, get_H, get_EoRT, get_E

        • -
        • ref_index (int, optional) – Reaction index to use to reference states. Default is the first +

        • ref_index (int, optional) – Reaction index to use to reference states. Default is the first reaction (i.e. ref_index = 0)

        • -
        • ref_state (str, optional) –

          State of the reference to use. Supported options include:

          +
        • ref_state (str, optional) –

          State of the reference to use. Supported options include:

          • reactants (default)

          • products

          • @@ -378,32 +378,32 @@

            pmutt.reaction.phasediagram.PhaseDiagramfloat, optional) – Spacing between reaction states. Shape of curve likely does not +
          • x_offset (float, optional) – Spacing between reaction states. Shape of curve likely does not change with this parameter since the x axis would rescale appropriately

          • -
          • include_TS (bool, optional) – Whether transition states should be included. Default is True

          • -
          • x_scale_TS (float, optional) – Value between 0 and 1 that controls curvature of transition +

          • include_TS (bool, optional) – Whether transition states should be included. Default is True

          • +
          • x_scale_TS (float, optional) – Value between 0 and 1 that controls curvature of transition state peaks. Higher values produce sharper peaks. Default is 0.5

          • -
          • y_scale_TS (float, optional) – Value between 0 and 1 that controls curvature of transition +

          • y_scale_TS (float, optional) – Value between 0 and 1 that controls curvature of transition state peaks. Higher values produce sharper peaks. Default is 0.5

          • -
          • include_TS_labels (bool, optional) – If True, adds a label to the peaks indicating the difference +

          • include_TS_labels (bool, optional) – If True, adds a label to the peaks indicating the difference between the reactants and the transition state. Default is True

          • -
          • y_TS_label_offset (float, optional) – Vertical value to offset TS_label from the TS position. This +

          • y_TS_label_offset (float, optional) – Vertical value to offset TS_label from the TS position. This value scales with the difference between major ticks. Negative values will shift the label downwards. Default is 0.10

          • -
          • x_TS_label_offset (float, optional) – Horizontal value to offset TS_label from the TS_position. This +

          • x_TS_label_offset (float, optional) – Horizontal value to offset TS_label from the TS_position. This value scales with the x_offset value. Negative values will shift the label rightward. Default is 0 (i.e. labels are directly above peaks by default)

          • -
          • TS_label_format (str, optional) – String format to print TS_labels. Uses the +

          • TS_label_format (str, optional) – String format to print TS_labels. Uses the str.format syntax. Default is ‘.2f’ (i.e. a floating point value rounded to the second decimal place)

          • figure (matplotlib.figure.Figure) – Add plot to this figure. If not specified, one will be generated

          • axes (matplotlib.axes.Axes.axis, optional) – Adds plot to this axis. If not specified, one will be generated

          • -
          • plt_kwargs (dict, optional) – Extra arguments that will be fed to +

          • plt_kwargs (dict, optional) – Extra arguments that will be fed to matplotlib.pyplot.subplots

          • reaction_kwargs (keyword arguments) – Extra arguments that will be fed to the reactions

          @@ -427,7 +427,7 @@

          pmutt.reaction.phasediagram.PhaseDiagram

          obj_dict

        Return type:
        -

        dict

        +

        dict

        diff --git a/api/reactions/bep/pmutt.omkm.reaction.BEP.html b/api/reactions/bep/pmutt.omkm.reaction.BEP.html index eec1fcde..fa583f42 100644 --- a/api/reactions/bep/pmutt.omkm.reaction.BEP.html +++ b/api/reactions/bep/pmutt.omkm.reaction.BEP.html @@ -4,7 +4,7 @@ - pmutt.omkm.reaction.BEP — pmutt 1.4.7 documentation + pmutt.omkm.reaction.BEP — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
        - 1.4.7 + 1.4.9
        @@ -127,7 +127,7 @@

        pmutt.omkm.reaction.BEP
        Type:
        -

        str, optional

        +

        str, optional

        @@ -226,7 +226,7 @@

        pmutt.omkm.reaction.BEP

        Recreate an object from the JSON representation.

        Parameters:
        -

        json_obj (dict) – JSON representation

        +

        json_obj (dict) – JSON representation

        Returns:

        Obj

        @@ -244,7 +244,7 @@

        pmutt.omkm.reaction.BEP
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units.

        • kwargs (keyword arguments) – Parameters needed by get_CpoR

        @@ -253,7 +253,7 @@

        pmutt.omkm.reaction.BEP

        Cp – Heat capacity (constant P) in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -268,7 +268,7 @@

        pmutt.omkm.reaction.BEP

        CpoR – Returns 0

        Return type:
        -

        float

        +

        float

        @@ -280,7 +280,7 @@

        pmutt.omkm.reaction.BEP
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units.

        • kwargs (keyword arguments) – Parameters needed by get_CvoR

        @@ -289,7 +289,7 @@

        pmutt.omkm.reaction.BEP

        Cv – Heat capacity (constant V) in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -304,7 +304,7 @@

        pmutt.omkm.reaction.BEP

        CvoR – Returns 0

        Return type:
        -

        float

        +

        float

        @@ -316,10 +316,10 @@

        pmutt.omkm.reaction.BEP
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • reaction (Reaction object) – Reaction related to BEP.

        • -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • kwargs (keyword arguments) – Parameters required to calculate the descriptor

        @@ -328,7 +328,7 @@

        pmutt.omkm.reaction.BEP

        E_act – Dimensionless activation energy

        Return type:
        -

        float

        +

        float

        @@ -342,9 +342,9 @@

        pmutt.omkm.reaction.BEPParameters:
        • reaction (Reaction object) – Reaction related to BEP.

        • -
        • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

        • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

        • -
        • T (float, optional) – Temperature in K. Default is 298.15

        • +
        • T (float, optional) – Temperature in K. Default is 298.15

        • kwargs (keyword arguments) – Parameters required to calculate the descriptor

        @@ -352,7 +352,7 @@

        pmutt.omkm.reaction.BEP

        EoRT_act – Dimensionless activation energy

        Return type:
        -

        float

        +

        float

        @@ -364,9 +364,9 @@

        pmutt.omkm.reaction.BEP
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • -
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • +
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • kwargs (keyword arguments) – Parameters needed by get_FoRT

        @@ -374,7 +374,7 @@

        pmutt.omkm.reaction.BEP

        F – Hemholtz energy in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -391,7 +391,7 @@

        pmutt.omkm.reaction.BEP

        FoRT – Dimensionless Helmholtz energy

        Return type:
        -

        float

        +

        float

        @@ -403,9 +403,9 @@

        pmutt.omkm.reaction.BEP
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • -
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • +
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • kwargs (keyword arguments) – Parameters needed by get_GoRT

        @@ -413,7 +413,7 @@

        pmutt.omkm.reaction.BEP

        G – Gibbs energy in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -428,8 +428,8 @@

        pmutt.omkm.reaction.BEPParameters:
        • reaction (Reaction object) – Reaction related to BEP.

        • -
        • T (float, optional) – Temperature in K. Default is 298.15

        • -
        • entropy_state (str or None, optional) –

          State to use to estimate entropy. Supported arguments:

          +
        • T (float, optional) – Temperature in K. Default is 298.15

        • +
        • entropy_state (str or None, optional) –

          State to use to estimate entropy. Supported arguments:

        Return type:
        -

        float

        +

        float

        @@ -456,9 +456,9 @@

        pmutt.omkm.reaction.BEP
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

        • -
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • +
        • T (float, optional) – Temperature in K. Default is 298.15 K

        • kwargs (keyword arguments) – Parameters needed by get_HoRT

        @@ -466,7 +466,7 @@

        pmutt.omkm.reaction.BEP

        H – Enthalpy in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -480,7 +480,7 @@

        pmutt.omkm.reaction.BEPParameters:
        • reaction (Reaction object) – Reaction related to BEP.

        • -
        • T (float, optional) – Temperature in K. Default is 298.15

        • +
        • T (float, optional) – Temperature in K. Default is 298.15

        • kwargs (keyword arguments) – Parameters required to calculate the descriptor

        @@ -488,7 +488,7 @@

        pmutt.omkm.reaction.BEP

        HoRT – Dimensionless enthalpy

        Return type:
        -

        float

        +

        float

        @@ -500,7 +500,7 @@

        pmutt.omkm.reaction.BEP
        Parameters:
          -
        • units (str) – Units as string. See R() for accepted +

        • units (str) – Units as string. See R() for accepted units.

        • kwargs (keyword arguments) – Parameters needed by get_SoR

        @@ -509,7 +509,7 @@

        pmutt.omkm.reaction.BEP

        S – Entropy in appropriate units

        Return type:
        -

        float

        +

        float

        @@ -524,8 +524,8 @@

        pmutt.omkm.reaction.BEP
        • reaction (Reaction object, optional) – Reaction related to BEP. If entropy_state is None, reaction is not required.

        • -
        • T (float, optional) – Temperature in K. Default is 298.15

        • -
        • entropy_state (str or None, optional) –

          State to use to estimate entropy. Supported arguments:

          +
        • T (float, optional) – Temperature in K. Default is 298.15

        • +
        • entropy_state (str or None, optional) –

          State to use to estimate entropy. Supported arguments:

          • ’reactants’ (default)

          • ’products’

          • @@ -540,7 +540,7 @@

            pmutt.omkm.reaction.BEP

            SoR – Dimensionless entropy

            Return type:
            -

            float

            +

            float

            @@ -552,9 +552,9 @@

            pmutt.omkm.reaction.BEP
            Parameters:
              -
            • units (str) – Units as string. See R() for accepted +

            • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

            • -
            • T (float, optional) – Temperature in K. Default is 298.15 K

            • +
            • T (float, optional) – Temperature in K. Default is 298.15 K

            • kwargs (keyword arguments) – Parameters needed by get_UoRT

            @@ -562,7 +562,7 @@

            pmutt.omkm.reaction.BEP

            U – Internal energy in appropriate units

            Return type:
            -

            float

            +

            float

            @@ -576,7 +576,7 @@

            pmutt.omkm.reaction.BEPParameters:
            • reaction (Reaction object) – Reaction related to BEP.

            • -
            • T (float, optional) – Temperature in K. Default is 298.15

            • +
            • T (float, optional) – Temperature in K. Default is 298.15

            • kwargs (keyword arguments) – Parameters required to calculate the descriptor

            @@ -584,7 +584,7 @@

            pmutt.omkm.reaction.BEP

            UoRT – Dimensionless internal energy

            Return type:
            -

            float

            +

            float

            @@ -598,7 +598,7 @@

            pmutt.omkm.reaction.BEP

            q – Returns 1

            Return type:
            -

            float

            +

            float

            @@ -610,7 +610,7 @@

            pmutt.omkm.reaction.BEP
            Parameters:
              -
            • act_energy_unit (str, optional) – Unit to use for energy. Default is ‘cal/mol’

            • +
            • act_energy_unit (str, optional) – Unit to use for energy. Default is ‘cal/mol’

            • units (Units object) – If specified, energy_unit is overwritten. Default is None.

            @@ -618,7 +618,7 @@

            pmutt.omkm.reaction.BEP

            cti_str – Surface reaction string in CTI format

            Return type:
            -

            str

            +

            str

            @@ -632,7 +632,7 @@

            pmutt.omkm.reaction.BEP

            obj_dict

            Return type:
            -

            dict

            +

            dict

            @@ -644,7 +644,7 @@

            pmutt.omkm.reaction.BEP
            Parameters:
              -
            • act_energy_unit (str, optional) – Unit to use for activation energy. Default is ‘cal/mol’

            • +
            • act_energy_unit (str, optional) – Unit to use for activation energy. Default is ‘cal/mol’

            • units (Units object) – If specified, act_energy_unit is overwritten. Default is None.

            @@ -653,7 +653,7 @@

            pmutt.omkm.reaction.BEP

            yaml_dict – Dictionary compatible with Cantera’s YAML format

            Return type:
            -

            dict

            +

            dict

            diff --git a/api/reactions/bep/pmutt.reaction.bep.BEP.html b/api/reactions/bep/pmutt.reaction.bep.BEP.html index d98bf5e4..b1fc3d67 100644 --- a/api/reactions/bep/pmutt.reaction.bep.BEP.html +++ b/api/reactions/bep/pmutt.reaction.bep.BEP.html @@ -4,7 +4,7 @@ - pmutt.reaction.bep.BEP — pmutt 1.4.7 documentation + pmutt.reaction.bep.BEP — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
            - 1.4.7 + 1.4.9
            @@ -128,7 +128,7 @@

            pmutt.reaction.bep.BEP

            Slope of BEP relationship.

            Type:
            -

            float

            +

            float

            @@ -139,7 +139,7 @@

            pmutt.reaction.bep.BEP

            Intercept of BEP relationship in kcal/mol.

            Type:
            -

            float

            +

            float

            @@ -150,7 +150,7 @@

            pmutt.reaction.bep.BEP

            Name of the BEP. Default is None

            Type:
            -

            str, optional

            +

            str, optional

            @@ -195,7 +195,7 @@

            pmutt.reaction.bep.BEPDefault is ‘delta_H’.

            Type:
            -

            str, optional

            +

            str, optional

            @@ -210,7 +210,7 @@

            pmutt.reaction.bep.BEP
            Type:
            -

            dict

            +

            dict

            @@ -223,7 +223,7 @@

            pmutt.reaction.bep.BEP
            Type:
            -

            str or dict

            +

            str or dict

            @@ -304,7 +304,7 @@

            pmutt.reaction.bep.BEP

            Recreate an object from the JSON representation.

            Parameters:
            -

            json_obj (dict) – JSON representation

            +

            json_obj (dict) – JSON representation

            Returns:

            Obj

            @@ -322,7 +322,7 @@

            pmutt.reaction.bep.BEP
            Parameters:
              -
            • units (str) – Units as string. See R() for accepted +

            • units (str) – Units as string. See R() for accepted units.

            • kwargs (keyword arguments) – Parameters needed by get_CpoR

            @@ -331,7 +331,7 @@

            pmutt.reaction.bep.BEP

            Cp – Heat capacity (constant P) in appropriate units

            Return type:
            -

            float

            +

            float

            @@ -346,7 +346,7 @@

            pmutt.reaction.bep.BEP

            CpoR – Returns 0

            Return type:
            -

            float

            +

            float

            @@ -358,7 +358,7 @@

            pmutt.reaction.bep.BEP
            Parameters:
              -
            • units (str) – Units as string. See R() for accepted +

            • units (str) – Units as string. See R() for accepted units.

            • kwargs (keyword arguments) – Parameters needed by get_CvoR

            @@ -367,7 +367,7 @@

            pmutt.reaction.bep.BEP

            Cv – Heat capacity (constant V) in appropriate units

            Return type:
            -

            float

            +

            float

            @@ -382,7 +382,7 @@

            pmutt.reaction.bep.BEP

            CvoR – Returns 0

            Return type:
            -

            float

            +

            float

            @@ -394,10 +394,10 @@

            pmutt.reaction.bep.BEP
            Parameters:
              -
            • units (str) – Units as string. See R() for accepted +

            • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

            • reaction (Reaction object) – Reaction related to BEP.

            • -
            • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

            • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

            • kwargs (keyword arguments) – Parameters required to calculate the descriptor

            @@ -406,7 +406,7 @@

            pmutt.reaction.bep.BEP

            E_act – Dimensionless activation energy

            Return type:
            -

            float

            +

            float

            @@ -420,9 +420,9 @@

            pmutt.reaction.bep.BEPParameters:
            • reaction (Reaction object) – Reaction related to BEP.

            • -
            • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

            • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

            • -
            • T (float, optional) – Temperature in K. Default is 298.15

            • +
            • T (float, optional) – Temperature in K. Default is 298.15

            • kwargs (keyword arguments) – Parameters required to calculate the descriptor

            @@ -430,7 +430,7 @@

            pmutt.reaction.bep.BEP

            EoRT_act – Dimensionless activation energy

            Return type:
            -

            float

            +

            float

            @@ -442,9 +442,9 @@

            pmutt.reaction.bep.BEP
            Parameters:
              -
            • units (str) – Units as string. See R() for accepted +

            • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

            • -
            • T (float, optional) – Temperature in K. Default is 298.15 K

            • +
            • T (float, optional) – Temperature in K. Default is 298.15 K

            • kwargs (keyword arguments) – Parameters needed by get_FoRT

            @@ -452,7 +452,7 @@

            pmutt.reaction.bep.BEP

            F – Hemholtz energy in appropriate units

            Return type:
            -

            float

            +

            float

            @@ -469,7 +469,7 @@

            pmutt.reaction.bep.BEP

            FoRT – Dimensionless Helmholtz energy

            Return type:
            -

            float

            +

            float

            @@ -481,9 +481,9 @@

            pmutt.reaction.bep.BEP
            Parameters:
              -
            • units (str) – Units as string. See R() for accepted +

            • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

            • -
            • T (float, optional) – Temperature in K. Default is 298.15 K

            • +
            • T (float, optional) – Temperature in K. Default is 298.15 K

            • kwargs (keyword arguments) – Parameters needed by get_GoRT

            @@ -491,7 +491,7 @@

            pmutt.reaction.bep.BEP

            G – Gibbs energy in appropriate units

            Return type:
            -

            float

            +

            float

            @@ -506,8 +506,8 @@

            pmutt.reaction.bep.BEPParameters:
            • reaction (Reaction object) – Reaction related to BEP.

            • -
            • T (float, optional) – Temperature in K. Default is 298.15

            • -
            • entropy_state (str or None, optional) –

              State to use to estimate entropy. Supported arguments:

              +
            • T (float, optional) – Temperature in K. Default is 298.15

            • +
            • entropy_state (str or None, optional) –

              State to use to estimate entropy. Supported arguments:

            Return type:
            -

            float

            +

            float

            @@ -534,9 +534,9 @@

            pmutt.reaction.bep.BEP
            Parameters:
              -
            • units (str) – Units as string. See R() for accepted +

            • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

            • -
            • T (float, optional) – Temperature in K. Default is 298.15 K

            • +
            • T (float, optional) – Temperature in K. Default is 298.15 K

            • kwargs (keyword arguments) – Parameters needed by get_HoRT

            @@ -544,7 +544,7 @@

            pmutt.reaction.bep.BEP

            H – Enthalpy in appropriate units

            Return type:
            -

            float

            +

            float

            @@ -558,7 +558,7 @@

            pmutt.reaction.bep.BEPParameters:
            • reaction (Reaction object) – Reaction related to BEP.

            • -
            • T (float, optional) – Temperature in K. Default is 298.15

            • +
            • T (float, optional) – Temperature in K. Default is 298.15

            • kwargs (keyword arguments) – Parameters required to calculate the descriptor

            @@ -566,7 +566,7 @@

            pmutt.reaction.bep.BEP

            HoRT – Dimensionless enthalpy

            Return type:
            -

            float

            +

            float

            @@ -578,7 +578,7 @@

            pmutt.reaction.bep.BEP
            Parameters:
              -
            • units (str) – Units as string. See R() for accepted +

            • units (str) – Units as string. See R() for accepted units.

            • kwargs (keyword arguments) – Parameters needed by get_SoR

            @@ -587,7 +587,7 @@

            pmutt.reaction.bep.BEP

            S – Entropy in appropriate units

            Return type:
            -

            float

            +

            float

            @@ -602,8 +602,8 @@

            pmutt.reaction.bep.BEP
            • reaction (Reaction object, optional) – Reaction related to BEP. If entropy_state is None, reaction is not required.

            • -
            • T (float, optional) – Temperature in K. Default is 298.15

            • -
            • entropy_state (str or None, optional) –

              State to use to estimate entropy. Supported arguments:

              +
            • T (float, optional) – Temperature in K. Default is 298.15

            • +
            • entropy_state (str or None, optional) –

              State to use to estimate entropy. Supported arguments:

              • ’reactants’ (default)

              • ’products’

              • @@ -618,7 +618,7 @@

                pmutt.reaction.bep.BEP

                SoR – Dimensionless entropy

                Return type:
                -

                float

                +

                float

                @@ -630,9 +630,9 @@

                pmutt.reaction.bep.BEP
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_UoRT

                @@ -640,7 +640,7 @@

                pmutt.reaction.bep.BEP

                U – Internal energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -654,7 +654,7 @@

                pmutt.reaction.bep.BEPParameters:
                • reaction (Reaction object) – Reaction related to BEP.

                • -
                • T (float, optional) – Temperature in K. Default is 298.15

                • +
                • T (float, optional) – Temperature in K. Default is 298.15

                • kwargs (keyword arguments) – Parameters required to calculate the descriptor

                @@ -662,7 +662,7 @@

                pmutt.reaction.bep.BEP

                UoRT – Dimensionless internal energy

                Return type:
                -

                float

                +

                float

                @@ -676,7 +676,7 @@

                pmutt.reaction.bep.BEP

                q – Returns 1

                Return type:
                -

                float

                +

                float

                @@ -690,7 +690,7 @@

                pmutt.reaction.bep.BEP

                obj_dict

                Return type:
                -

                dict

                +

                dict

                diff --git a/api/reactions/reaction/pmutt.omkm.reaction.SurfaceReaction.html b/api/reactions/reaction/pmutt.omkm.reaction.SurfaceReaction.html index e28a6c8e..1db0e502 100644 --- a/api/reactions/reaction/pmutt.omkm.reaction.SurfaceReaction.html +++ b/api/reactions/reaction/pmutt.omkm.reaction.SurfaceReaction.html @@ -4,7 +4,7 @@ - pmutt.omkm.reaction.SurfaceReaction — pmutt 1.4.7 documentation + pmutt.omkm.reaction.SurfaceReaction — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
                - 1.4.7 + 1.4.9
                @@ -128,7 +128,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Type:
                -

                str, optional

                +

                str, optional

                @@ -139,7 +139,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Type:
                -

                bool, optional

                +

                bool, optional

                @@ -151,7 +151,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Type:
                -

                float, optional

                +

                float, optional

                @@ -163,7 +163,7 @@

                pmutt.omkm.reaction.SurfaceReactionis_adsorption is False, 0 if is_adsorption is True.

                Type:
                -

                float, optional

                +

                float, optional

                @@ -175,7 +175,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Type:
                -

                float, optional

                +

                float, optional

                @@ -188,7 +188,7 @@

                pmutt.omkm.reaction.SurfaceReactionis_adsorption is False.

                Type:
                -

                float, optional

                +

                float, optional

                @@ -200,7 +200,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Type:
                -

                str, optional

                +

                str, optional

                @@ -213,7 +213,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Type:
                -

                bool, optional

                +

                bool, optional

                @@ -476,7 +476,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Raises:
                -

                ValueError – Raised if the reactants, products and/or transition state +

                ValueError – Raised if the reactants, products and/or transition state element composition does not agree.

                @@ -488,7 +488,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                -

                json_obj (dict) – JSON representation

                +

                json_obj (dict) – JSON representation

                Returns:

                Reaction

                @@ -506,27 +506,27 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • reaction_str (str) – Reaction string.

                • -
                • species (dict) – Dictionary using the names as keys. If you have a list of +

                • reaction_str (str) – Reaction string.

                • +
                • species (dict) – Dictionary using the names as keys. If you have a list of species, use pmutt.pmutt_list_to_dict to make a dict.

                • -
                • species_delimiter (str, optional) – Delimiter that separate species. Leading and trailing spaces +

                • species_delimiter (str, optional) – Delimiter that separate species. Leading and trailing spaces will be trimmed. Default is ‘+’

                • -
                • reaction_delimiter (str, optional) – Delimiter that separate states of the reaction. Leading and +

                • reaction_delimiter (str, optional) – Delimiter that separate states of the reaction. Leading and trailing spaces will be trimmed. Default is ‘=’

                • -
                • notes (str or dict, optional) – Other notes such as the source of the reaction. Default is None

                • -
                • A (float, optional) – Pre-exponential constant. If not specified, uses reaction to +

                • notes (str or dict, optional) – Other notes such as the source of the reaction. Default is None

                • +
                • A (float, optional) – Pre-exponential constant. If not specified, uses reaction to determine value.

                • -
                • beta (float, optional) – Power to raise the temperature in the rate expression. Default +

                • beta (float, optional) – Power to raise the temperature in the rate expression. Default is 1 if is_adsorption is False, 0 if is_adsorption is True.

                • -
                • Ea (float, optional) – Activation energy. If not specified, uses reaction to determine +

                • Ea (float, optional) – Activation energy. If not specified, uses reaction to determine value.

                • -
                • is_adsorption (bool, optional) – If True, the reaction represents an adsorption. Default is False

                • -
                • sticking_coeff (float, optional) – Sticking coefficient. Only relevant if is_adsorption is +

                • is_adsorption (bool, optional) – If True, the reaction represents an adsorption. Default is False

                • +
                • sticking_coeff (float, optional) – Sticking coefficient. Only relevant if is_adsorption is True. Default is 0.5

                • -
                • gas_phase (bool) – True if the reaction has only gas-phase species. This attribute +

                • gas_phase (bool) – True if the reaction has only gas-phase species. This attribute is determined based on the reactants and products

                • -
                • use_motz_wise (bool, optional) – Used when generating OpenMKM YAML file. If True, uses Motz-Wise +

                • use_motz_wise (bool, optional) – Used when generating OpenMKM YAML file. If True, uses Motz-Wise correction to sticking coefficient. Only applicable to adsorption reactions. Default is False.

                @@ -547,9 +547,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • sden_operation (str, optional) – Site density operation to use. Default is ‘min’

                • -
                • include_entropy (bool, optional) – If True, includes the entropy of activation. Default is True

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • sden_operation (str, optional) – Site density operation to use. Default is ‘min’

                • +
                • include_entropy (bool, optional) – If True, includes the entropy of activation. Default is True

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • units (str or Units, optional) – Units for A. If Units class specified, determines the units for A. Default is ‘molec/cm2’

                • kwargs (keyword arguments) – Parameters required to calculate pre-exponential factor

                • @@ -566,9 +566,9 @@

                  pmutt.omkm.reaction.SurfaceReaction
                  Parameters:
                    -
                  • units (str) – Units as string. See R() for accepted +

                  • units (str) – Units as string. See R() for accepted units.

                  • -
                  • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                  • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                  • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -580,7 +580,7 @@

                    pmutt.omkm.reaction.SurfaceReactionReturn type: -

                    float

                    +

                    float

                  @@ -592,7 +592,7 @@

                  pmutt.omkm.reaction.SurfaceReaction
                  Parameters:
                    -
                  • state (str) –

                    State to calculate quantity. Supported options:

                    +
                  • state (str) –

                    State to calculate quantity. Supported options:

                    • ’reactants’

                    • ’products’

                    • @@ -601,7 +601,7 @@

                      pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
                    • units (str) – Units as string. See R() for accepted units.

                    • kwargs (keyword arguments) – Parameters required to calculate heat capacity at constant pressure. See class docstring to see how to pass specific @@ -612,7 +612,7 @@

                      pmutt.omkm.reaction.SurfaceReaction

                      Cp – Heat capacity at constant pressure of the reaction state

                  Return type:
                  -

                  float

                  +

                  float

                @@ -625,7 +625,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -637,7 +637,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -649,7 +649,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  state to calculate quantity. Supported options:

                  +
                • state (str) –

                  state to calculate quantity. Supported options:

                @@ -681,9 +681,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -694,7 +694,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  Cv_act – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -706,7 +706,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -715,7 +715,7 @@

                    pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units.

                  • kwargs (keyword arguments) – Parameters required to calculate heat capacity at constant volume. See class docstring to see how to pass specific @@ -726,7 +726,7 @@

                    pmutt.omkm.reaction.SurfaceReaction

                    Cv – Heat capacity at constant volume of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -739,7 +739,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -751,7 +751,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -763,7 +763,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  state to calculate quantity. Supported options:

                  +
                • state (str) –

                  state to calculate quantity. Supported options:

                @@ -795,12 +795,12 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. +

                • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. Condensed-phase and unimolecular gas-phase reactions should have a value of 0. Bimolecular gas-phase reactions should have a value of -1. If None specified, m will be calculated @@ -817,7 +817,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -829,7 +829,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -838,10 +838,10 @@

                    pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                  • -
                  • T (float) – Temperature in K

                  • -
                  • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

                  • +
                  • T (float) – Temperature in K

                  • +
                  • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

                  • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -851,7 +851,7 @@

                    pmutt.omkm.reaction.SurfaceReaction

                    E – Electronic energy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -870,9 +870,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. +

                • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. Condensed-phase and unimolecular gas-phase reactions should have a value of 0. Bimolecular gas-phase reactions should have a value of -1. If None specified, m will be calculated @@ -888,7 +888,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -900,7 +900,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  state to calculate quantity. Supported options:

                  +
                • state (str) –

                  state to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -909,7 +909,7 @@

                    pmutt.omkm.reaction.SurfaceReactionbool, optional) – If True, includes the zero point energy. Default is False

                    +
                  • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

                  • kwargs (keyword arguments) – Parameters required to calculate dimensionless electronic energy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -919,7 +919,7 @@

                    pmutt.omkm.reaction.SurfaceReaction

                    EoRT – Dimensionless electronic energy of the reaction state.

                Return type:
                -

                float

                +

                float

                @@ -932,10 +932,10 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -947,7 +947,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -959,7 +959,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -968,9 +968,9 @@

                    pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                  • -
                  • T (float) – Temperature in K

                  • +
                  • T (float) – Temperature in K

                  • kwargs (keyword arguments) – Parameters required to calculate Helholtz energy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -980,7 +980,7 @@

                    pmutt.omkm.reaction.SurfaceReaction

                    F – Helmholtz energy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -993,7 +993,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -1005,7 +1005,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -1017,7 +1017,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -1049,10 +1049,10 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • T (float) – Temperature in K

                • -
                • P (float, optional) – Pressure in bar. Default is 1 bar

                • +
                • T (float) – Temperature in K

                • +
                • P (float, optional) – Pressure in bar. Default is 1 bar

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy of activation.

                @@ -1064,7 +1064,7 @@

                pmutt.omkm.reaction.SurfaceReactionReturn type: -

                float

                +

                float

                @@ -1076,7 +1076,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -1085,9 +1085,9 @@

                    pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                  • -
                  • T (float) – Temperature in K

                  • +
                  • T (float) – Temperature in K

                  • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -1097,7 +1097,7 @@

                    pmutt.omkm.reaction.SurfaceReaction

                    G – Gibbs energy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -1111,9 +1111,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy.

                @@ -1126,7 +1126,7 @@

                pmutt.omkm.reaction.SurfaceReactionReturn type: -

                float

                +

                float

                @@ -1138,7 +1138,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -1169,9 +1169,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • T (float) – Temperature in K

                • +
                • T (float) – Temperature in K

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy of activation.

                @@ -1183,7 +1183,7 @@

                pmutt.omkm.reaction.SurfaceReactionReturn type: -

                float

                +

                float

                @@ -1195,7 +1195,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -1204,9 +1204,9 @@

                    pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                  • -
                  • T (float) – Temperature in K

                  • +
                  • T (float) – Temperature in K

                  • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -1216,7 +1216,7 @@

                    pmutt.omkm.reaction.SurfaceReaction

                    H – Enthalpy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -1229,7 +1229,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy of activation.

                @@ -1242,7 +1242,7 @@

                pmutt.omkm.reaction.SurfaceReactionReturn type: -

                float

                +

                float

                @@ -1254,7 +1254,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  state to calculate quantity. Supported options:

                  +
                • state (str) –

                  state to calculate quantity. Supported options:

                @@ -1285,9 +1285,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate equilibrium constant. See class docstring to see how to pass specific parameters to @@ -1298,7 +1298,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  Keq – Equilibrium constant between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1311,9 +1311,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1325,7 +1325,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -1337,7 +1337,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -1346,7 +1346,7 @@

                    pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units.

                  • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to @@ -1357,7 +1357,7 @@

                    pmutt.omkm.reaction.SurfaceReaction

                    S – Entropy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -1370,7 +1370,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1382,7 +1382,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -1394,7 +1394,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -1425,10 +1425,10 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1440,7 +1440,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -1452,7 +1452,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -1461,9 +1461,9 @@

                    pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                  • -
                  • T (float) – Temperature in K

                  • +
                  • T (float) – Temperature in K

                  • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -1473,7 +1473,7 @@

                    pmutt.omkm.reaction.SurfaceReaction

                    U – Internal energy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -1486,7 +1486,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1498,7 +1498,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -1510,7 +1510,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -1541,11 +1541,11 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1556,7 +1556,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_Cp – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1569,9 +1569,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1582,7 +1582,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_CvoR – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1595,11 +1595,11 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1610,7 +1610,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_Cv – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1623,9 +1623,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1636,7 +1636,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_CvoR – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1648,12 +1648,12 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different @@ -1664,7 +1664,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_E – Change in electronic energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1677,9 +1677,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different @@ -1690,7 +1690,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_EoRT – Change in electronic energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1702,12 +1702,12 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -1718,7 +1718,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_F – Change in Helmholtz energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1731,9 +1731,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -1744,7 +1744,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_FoRT – Change in Helmholtz energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1756,12 +1756,12 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1772,7 +1772,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_G – Change in Gibbs energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1785,9 +1785,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1798,7 +1798,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_GoRT – Change in Gibbs energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1810,12 +1810,12 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different @@ -1826,7 +1826,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_H – Change in enthalpy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1838,9 +1838,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different @@ -1851,7 +1851,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_HoRT – Change in enthalpy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1863,11 +1863,11 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1878,7 +1878,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_S – Change in entropy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1890,9 +1890,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1903,7 +1903,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_SoR – Change in entropy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1915,12 +1915,12 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1931,7 +1931,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_U – Change in internal energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1944,9 +1944,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1957,7 +1957,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_UoRT – Change in internal energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1969,9 +1969,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate partition function. See class docstring to see how to pass specific parameters to different @@ -1982,7 +1982,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_q – Change in partition function between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1995,21 +1995,21 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • initial_state (str) –

                  Thermodynamic state. Supported options:

                  +
                • initial_state (str) –

                  Thermodynamic state. Supported options:

                  • ’reactants’

                  • ’products’

                  • ’transition state’

                • -
                • final_state (str) –

                  Thermodynamic state. Supported options:

                  +
                • final_state (str) –

                  Thermodynamic state. Supported options:

                  • ’reactants’

                  • ’products’

                  • ’transition state’

                • -
                • method_name (str) – Name of method to use to calculate quantity. Calculates any +

                • method_name (str) – Name of method to use to calculate quantity. Calculates any quantity as long as the relevant objects have the same method name

                • kwargs (keyword arguments) – Arguments passed to evaluate the quantity of the reactants and @@ -2020,7 +2020,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_quantity – Change in thermodynamic quantity between particular states

                Return type:
                -

                float

                +

                float

                @@ -2033,9 +2033,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • include_ZPE (bool, optional) – If True, includes zero-point energy when calculating the +

                • include_ZPE (bool, optional) – If True, includes zero-point energy when calculating the value of the partition functions. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate partition function. See class docstring to see how to pass specific parameters to different @@ -2047,7 +2047,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -2059,7 +2059,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -2089,8 +2089,8 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • include_TS (bool, optional) – Whether transition states should be included. Default is True

                • -
                • key (str, optional) – Attribute to use as the key in the output dictionary. Default +

                • include_TS (bool, optional) – Whether transition states should be included. Default is True

                • +
                • key (str, optional) – Attribute to use as the key in the output dictionary. Default is name

                @@ -2098,7 +2098,7 @@

                pmutt.omkm.reaction.SurfaceReaction

                species – Unique species in the reaction

                Return type:
                -

                dict

                +

                dict

                @@ -2110,7 +2110,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  Thermodynamic state. Supported options:

                  +
                • state (str) –

                  Thermodynamic state. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -2119,7 +2119,7 @@

                    pmutt.omkm.reaction.SurfaceReactionstr) – Name of method to use to calculate quantity. Calculates any +
                  • method_name (str) – Name of method to use to calculate quantity. Calculates any quantity as long as the relevant objects have the same method name

                  • kwargs (keyword arguments) – Arguments required to calculate the thermodynamic quantity of @@ -2130,7 +2130,7 @@

                    pmutt.omkm.reaction.SurfaceReaction

                    state_quantity – Thermodynamic quantity of particular state

                Return type:
                -

                float

                +

                float

                @@ -2172,12 +2172,12 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • -
                • P (float, optional) – Pressure in bar. Default is 1 bar

                • -
                • quantity_unit (str, optional) – Quantity unit to calculate A. Default is ‘molec’

                • -
                • length_unit (str, optional) – Length unit to calculate A. Default is ‘cm’

                • -
                • act_energy_unit (str, optional) – Unit to use for activation energy. Default is ‘cal/mol’

                • -
                • ads_act_method (str, optional) – Activation method to use for adsorption reactions. Accepted +

                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • P (float, optional) – Pressure in bar. Default is 1 bar

                • +
                • quantity_unit (str, optional) – Quantity unit to calculate A. Default is ‘molec’

                • +
                • length_unit (str, optional) – Length unit to calculate A. Default is ‘cm’

                • +
                • act_energy_unit (str, optional) – Unit to use for activation energy. Default is ‘cal/mol’

                • +
                • ads_act_method (str, optional) – Activation method to use for adsorption reactions. Accepted options include ‘get_H_act’ and ‘get_G_act’. Default is ‘get_H_act’.

                • units (Units object) – If specified, quantity_unit, length_unit, and @@ -2188,7 +2188,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  cti_str – Surface reaction string in CTI format

                Return type:
                -

                str

                +

                str

                @@ -2202,7 +2202,7 @@

                pmutt.omkm.reaction.SurfaceReaction

                obj_dict

                Return type:
                -

                dict

                +

                dict

                @@ -2214,12 +2214,12 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • -
                • P (float, optional) – Pressure in bar. Default is 1 bar

                • -
                • quantity_unit (str, optional) – Quantity unit to calculate A. Default is ‘molec’

                • -
                • length_unit (str, optional) – Length unit to calculate A. Default is ‘cm’

                • -
                • act_energy_unit (str, optional) – Unit to use for activation energy. Default is ‘cal/mol’

                • -
                • ads_act_method (str, optional) – Activation method to use for adsorption reactions. Accepted +

                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • P (float, optional) – Pressure in bar. Default is 1 bar

                • +
                • quantity_unit (str, optional) – Quantity unit to calculate A. Default is ‘molec’

                • +
                • length_unit (str, optional) – Length unit to calculate A. Default is ‘cm’

                • +
                • act_energy_unit (str, optional) – Unit to use for activation energy. Default is ‘cal/mol’

                • +
                • ads_act_method (str, optional) – Activation method to use for adsorption reactions. Accepted options include ‘get_H_act’ and ‘get_G_act’. Default is ‘get_H_act’.

                • units (Units object) – If specified, quantity_unit, length_unit, and @@ -2230,7 +2230,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  yaml_dict – Dictionary compatible with Cantera’s YAML format

                Return type:
                -

                dict

                +

                dict

                @@ -2242,21 +2242,21 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • species_delimiter (str, optional) – Separates species. Default is ‘+’

                • -
                • reaction_delimiter (str, optional) – Separates reaction states. Default is ‘=’

                • -
                • stoich_format (float, optional) – Format to write stoichiometric numbers. Default is ‘.2f’ (float +

                • species_delimiter (str, optional) – Separates species. Default is ‘+’

                • +
                • reaction_delimiter (str, optional) – Separates reaction states. Default is ‘=’

                • +
                • stoich_format (float, optional) – Format to write stoichiometric numbers. Default is ‘.2f’ (float rounded to 2 decimal places)

                • -
                • include_TS (bool, optional) – If True, includes transition states in output. Default is True

                • -
                • stoich_space (bool, optional) – If True, inserts a space between stoichiometric coefficients +

                • include_TS (bool, optional) – If True, includes transition states in output. Default is True

                • +
                • stoich_space (bool, optional) – If True, inserts a space between stoichiometric coefficients and the species name. Default is False

                • -
                • key (str, optional) – Attribute to use to print out species. Default is name

                • +
                • key (str, optional) – Attribute to use to print out species. Default is name

                Returns:

                reaction_str – Reaction string

                Return type:
                -

                str

                +

                str

                diff --git a/api/reactions/reaction/pmutt.reaction.ChemkinReaction.html b/api/reactions/reaction/pmutt.reaction.ChemkinReaction.html index af0456ca..1cbad28e 100644 --- a/api/reactions/reaction/pmutt.reaction.ChemkinReaction.html +++ b/api/reactions/reaction/pmutt.reaction.ChemkinReaction.html @@ -4,7 +4,7 @@ - pmutt.reaction.ChemkinReaction — pmutt 1.4.7 documentation + pmutt.reaction.ChemkinReaction — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
                - 1.4.7 + 1.4.9
                @@ -127,7 +127,7 @@

                pmutt.reaction.ChemkinReaction
                Type:
                -

                float, optional

                +

                float, optional

                @@ -138,7 +138,7 @@

                pmutt.reaction.ChemkinReaction
                Type:
                -

                bool, optional

                +

                bool, optional

                @@ -150,7 +150,7 @@

                pmutt.reaction.ChemkinReaction
                Type:
                -

                float, optional

                +

                float, optional

                @@ -162,7 +162,7 @@

                pmutt.reaction.ChemkinReaction
                Type:
                -

                bool

                +

                bool

                @@ -405,7 +405,7 @@

                pmutt.reaction.ChemkinReaction
                Raises:
                -

                ValueError – Raised if the reactants, products and/or transition state +

                ValueError – Raised if the reactants, products and/or transition state element composition does not agree.

                @@ -417,7 +417,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                -

                json_obj (dict) – JSON representation

                +

                json_obj (dict) – JSON representation

                Returns:

                Reaction

                @@ -435,20 +435,20 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • reaction_str (str) – Reaction string.

                • -
                • species (dict) – Dictionary using the names as keys. If you have a list of +

                • reaction_str (str) – Reaction string.

                • +
                • species (dict) – Dictionary using the names as keys. If you have a list of species, use pmutt.pmutt_list_to_dict to make a dict.

                • -
                • species_delimiter (str, optional) – Delimiter that separate species. Leading and trailing spaces +

                • species_delimiter (str, optional) – Delimiter that separate species. Leading and trailing spaces will be trimmed. Default is ‘+’

                • -
                • reaction_delimiter (str, optional) – Delimiter that separate states of the reaction. Leading and +

                • reaction_delimiter (str, optional) – Delimiter that separate states of the reaction. Leading and trailing spaces will be trimmed. Default is ‘=’

                • -
                • notes (str or dict, optional) – Other notes such as the source of the reaction. Default is None

                • -
                • beta (float, optional) – Power to raise the temperature in the rate expression. +

                • notes (str or dict, optional) – Other notes such as the source of the reaction. Default is None

                • +
                • beta (float, optional) – Power to raise the temperature in the rate expression. Default is 1

                • -
                • is_adsorption (bool, optional) – If True, the reaction represents an adsorption. Default is False

                • -
                • sticking_coeff (float, optional) – Sticking coefficient. Only relevant if is_adsorption is +

                • is_adsorption (bool, optional) – If True, the reaction represents an adsorption. Default is False

                • +
                • sticking_coeff (float, optional) – Sticking coefficient. Only relevant if is_adsorption is True. Default is 0.5

                • -
                • gas_phase (bool) – True if the reaction has only gas-phase species. This attribute +

                • gas_phase (bool) – True if the reaction has only gas-phase species. This attribute is determined based on the reactants and products

                @@ -468,9 +468,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • sden_operation (str, optional) – Site density operation to use. Default is ‘sum’

                • -
                • include_entropy (bool, optional) – If True, includes the act entropy. Default is True

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • sden_operation (str, optional) – Site density operation to use. Default is ‘sum’

                • +
                • include_entropy (bool, optional) – If True, includes the act entropy. Default is True

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters required to calculate pre-exponential factor

                @@ -485,9 +485,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -499,7 +499,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -511,7 +511,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -520,7 +520,7 @@

                    pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units.

                  • kwargs (keyword arguments) – Parameters required to calculate heat capacity at constant pressure. See class docstring to see how to pass specific @@ -531,7 +531,7 @@

                    pmutt.reaction.ChemkinReaction

                    Cp – Heat capacity at constant pressure of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -544,7 +544,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -556,7 +556,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -568,7 +568,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  state to calculate quantity. Supported options:

                  +
                • state (str) –

                  state to calculate quantity. Supported options:

                @@ -600,9 +600,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -613,7 +613,7 @@

                  pmutt.reaction.ChemkinReaction

                  Cv_act – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -625,7 +625,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -634,7 +634,7 @@

                    pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units.

                  • kwargs (keyword arguments) – Parameters required to calculate heat capacity at constant volume. See class docstring to see how to pass specific @@ -645,7 +645,7 @@

                    pmutt.reaction.ChemkinReaction

                    Cv – Heat capacity at constant volume of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -658,7 +658,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -670,7 +670,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -682,7 +682,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  state to calculate quantity. Supported options:

                  +
                • state (str) –

                  state to calculate quantity. Supported options:

                @@ -714,12 +714,12 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. +

                • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. Condensed-phase and unimolecular gas-phase reactions should have a value of 0. Bimolecular gas-phase reactions should have a value of -1. If None specified, m will be calculated @@ -736,7 +736,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -748,7 +748,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -757,10 +757,10 @@

                    pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                  • -
                  • T (float) – Temperature in K

                  • -
                  • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

                  • +
                  • T (float) – Temperature in K

                  • +
                  • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

                  • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -770,7 +770,7 @@

                    pmutt.reaction.ChemkinReaction

                    E – Electronic energy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -789,9 +789,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. +

                • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. Condensed-phase and unimolecular gas-phase reactions should have a value of 0. Bimolecular gas-phase reactions should have a value of -1. If None specified, m will be calculated @@ -807,7 +807,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -819,7 +819,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  state to calculate quantity. Supported options:

                  +
                • state (str) –

                  state to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -828,7 +828,7 @@

                    pmutt.reaction.ChemkinReactionbool, optional) – If True, includes the zero point energy. Default is False

                    +
                  • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

                  • kwargs (keyword arguments) – Parameters required to calculate dimensionless electronic energy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -838,7 +838,7 @@

                    pmutt.reaction.ChemkinReaction

                    EoRT – Dimensionless electronic energy of the reaction state.

                Return type:
                -

                float

                +

                float

                @@ -851,10 +851,10 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -866,7 +866,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -878,7 +878,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -887,9 +887,9 @@

                    pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                  • -
                  • T (float) – Temperature in K

                  • +
                  • T (float) – Temperature in K

                  • kwargs (keyword arguments) – Parameters required to calculate Helholtz energy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -899,7 +899,7 @@

                    pmutt.reaction.ChemkinReaction

                    F – Helmholtz energy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -912,7 +912,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -924,7 +924,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -936,7 +936,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -968,10 +968,10 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -983,7 +983,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -995,7 +995,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -1004,9 +1004,9 @@

                    pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                  • -
                  • T (float) – Temperature in K

                  • +
                  • T (float) – Temperature in K

                  • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -1016,7 +1016,7 @@

                    pmutt.reaction.ChemkinReaction

                    G – Gibbs energy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -1029,9 +1029,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1043,7 +1043,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -1055,7 +1055,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -1086,10 +1086,10 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different @@ -1101,7 +1101,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -1113,7 +1113,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -1122,9 +1122,9 @@

                    pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                  • -
                  • T (float) – Temperature in K

                  • +
                  • T (float) – Temperature in K

                  • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -1134,7 +1134,7 @@

                    pmutt.reaction.ChemkinReaction

                    H – Enthalpy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -1147,7 +1147,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1159,7 +1159,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -1171,7 +1171,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  state to calculate quantity. Supported options:

                  +
                • state (str) –

                  state to calculate quantity. Supported options:

                @@ -1202,9 +1202,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate equilibrium constant. See class docstring to see how to pass specific parameters to @@ -1215,7 +1215,7 @@

                  pmutt.reaction.ChemkinReaction

                  Keq – Equilibrium constant between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1228,9 +1228,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1242,7 +1242,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -1254,7 +1254,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -1263,7 +1263,7 @@

                    pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units.

                  • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to @@ -1274,7 +1274,7 @@

                    pmutt.reaction.ChemkinReaction

                    S – Entropy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -1287,7 +1287,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1299,7 +1299,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -1311,7 +1311,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -1342,10 +1342,10 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1357,7 +1357,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -1369,7 +1369,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -1378,9 +1378,9 @@

                    pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                  • -
                  • T (float) – Temperature in K

                  • +
                  • T (float) – Temperature in K

                  • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -1390,7 +1390,7 @@

                    pmutt.reaction.ChemkinReaction

                    U – Internal energy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -1403,7 +1403,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1415,7 +1415,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -1427,7 +1427,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -1458,11 +1458,11 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1473,7 +1473,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_Cp – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1486,9 +1486,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1499,7 +1499,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_CvoR – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1512,11 +1512,11 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1527,7 +1527,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_Cv – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1540,9 +1540,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1553,7 +1553,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_CvoR – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1565,12 +1565,12 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different @@ -1581,7 +1581,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_E – Change in electronic energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1594,9 +1594,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different @@ -1607,7 +1607,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_EoRT – Change in electronic energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1619,12 +1619,12 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -1635,7 +1635,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_F – Change in Helmholtz energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1648,9 +1648,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -1661,7 +1661,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_FoRT – Change in Helmholtz energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1673,12 +1673,12 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1689,7 +1689,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_G – Change in Gibbs energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1702,9 +1702,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1715,7 +1715,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_GoRT – Change in Gibbs energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1727,12 +1727,12 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different @@ -1743,7 +1743,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_H – Change in enthalpy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1755,9 +1755,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different @@ -1768,7 +1768,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_HoRT – Change in enthalpy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1780,11 +1780,11 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1795,7 +1795,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_S – Change in entropy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1807,9 +1807,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1820,7 +1820,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_SoR – Change in entropy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1832,12 +1832,12 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1848,7 +1848,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_U – Change in internal energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1861,9 +1861,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1874,7 +1874,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_UoRT – Change in internal energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1886,9 +1886,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate partition function. See class docstring to see how to pass specific parameters to different @@ -1899,7 +1899,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_q – Change in partition function between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1912,21 +1912,21 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • initial_state (str) –

                  Thermodynamic state. Supported options:

                  +
                • initial_state (str) –

                  Thermodynamic state. Supported options:

                  • ’reactants’

                  • ’products’

                  • ’transition state’

                • -
                • final_state (str) –

                  Thermodynamic state. Supported options:

                  +
                • final_state (str) –

                  Thermodynamic state. Supported options:

                  • ’reactants’

                  • ’products’

                  • ’transition state’

                • -
                • method_name (str) – Name of method to use to calculate quantity. Calculates any +

                • method_name (str) – Name of method to use to calculate quantity. Calculates any quantity as long as the relevant objects have the same method name

                • kwargs (keyword arguments) – Arguments passed to evaluate the quantity of the reactants and @@ -1937,7 +1937,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_quantity – Change in thermodynamic quantity between particular states

                Return type:
                -

                float

                +

                float

                @@ -1950,9 +1950,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • include_ZPE (bool, optional) – If True, includes zero-point energy when calculating the +

                • include_ZPE (bool, optional) – If True, includes zero-point energy when calculating the value of the partition functions. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate partition function. See class docstring to see how to pass specific parameters to different @@ -1964,7 +1964,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -1976,7 +1976,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -2006,8 +2006,8 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • include_TS (bool, optional) – Whether transition states should be included. Default is True

                • -
                • key (str, optional) – Attribute to use as the key in the output dictionary. Default +

                • include_TS (bool, optional) – Whether transition states should be included. Default is True

                • +
                • key (str, optional) – Attribute to use as the key in the output dictionary. Default is name

                @@ -2015,7 +2015,7 @@

                pmutt.reaction.ChemkinReaction

                species – Unique species in the reaction

                Return type:
                -

                dict

                +

                dict

                @@ -2027,7 +2027,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  Thermodynamic state. Supported options:

                  +
                • state (str) –

                  Thermodynamic state. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -2036,7 +2036,7 @@

                    pmutt.reaction.ChemkinReactionstr) – Name of method to use to calculate quantity. Calculates any +
                  • method_name (str) – Name of method to use to calculate quantity. Calculates any quantity as long as the relevant objects have the same method name

                  • kwargs (keyword arguments) – Arguments required to calculate the thermodynamic quantity of @@ -2047,7 +2047,7 @@

                    pmutt.reaction.ChemkinReaction

                    state_quantity – Thermodynamic quantity of particular state

                Return type:
                -

                float

                +

                float

                @@ -2081,7 +2081,7 @@

                pmutt.reaction.ChemkinReaction

                obj_dict

                Return type:
                -

                dict

                +

                dict

                @@ -2093,21 +2093,21 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • species_delimiter (str, optional) – Separates species. Default is ‘+’

                • -
                • reaction_delimiter (str, optional) – Separates reaction states. Default is ‘=’

                • -
                • stoich_format (float, optional) – Format to write stoichiometric numbers. Default is ‘.2f’ (float +

                • species_delimiter (str, optional) – Separates species. Default is ‘+’

                • +
                • reaction_delimiter (str, optional) – Separates reaction states. Default is ‘=’

                • +
                • stoich_format (float, optional) – Format to write stoichiometric numbers. Default is ‘.2f’ (float rounded to 2 decimal places)

                • -
                • include_TS (bool, optional) – If True, includes transition states in output. Default is True

                • -
                • stoich_space (bool, optional) – If True, inserts a space between stoichiometric coefficients +

                • include_TS (bool, optional) – If True, includes transition states in output. Default is True

                • +
                • stoich_space (bool, optional) – If True, inserts a space between stoichiometric coefficients and the species name. Default is False

                • -
                • key (str, optional) – Attribute to use to print out species. Default is name

                • +
                • key (str, optional) – Attribute to use to print out species. Default is name

                Returns:

                reaction_str – Reaction string

                Return type:
                -

                str

                +

                str

                diff --git a/api/reactions/reaction/pmutt.reaction.Reaction.html b/api/reactions/reaction/pmutt.reaction.Reaction.html index 2983f332..bc62bb31 100644 --- a/api/reactions/reaction/pmutt.reaction.Reaction.html +++ b/api/reactions/reaction/pmutt.reaction.Reaction.html @@ -4,7 +4,7 @@ - pmutt.reaction.Reaction — pmutt 1.4.7 documentation + pmutt.reaction.Reaction — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
                - 1.4.7 + 1.4.9
                @@ -194,7 +194,7 @@

                pmutt.reaction.Reaction

                Other notes such as the source of the reaction. Default is None

                Type:
                -

                str or dict, optional

                +

                str or dict, optional

                @@ -439,7 +439,7 @@

                pmutt.reaction.Reaction
                Raises:
                -

                ValueError – Raised if the reactants, products and/or transition state +

                ValueError – Raised if the reactants, products and/or transition state element composition does not agree.

                @@ -451,7 +451,7 @@

                pmutt.reaction.Reaction

                Recreate an object from the JSON representation.

                Parameters:
                -

                json_obj (dict) – JSON representation

                +

                json_obj (dict) – JSON representation

                Returns:

                Reaction

                @@ -469,17 +469,17 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • reaction_str (str) – Reaction string.

                • -
                • species (dict or list) – Dictionary using the names as keys. If you have a list of +

                • reaction_str (str) – Reaction string.

                • +
                • species (dict or list) – Dictionary using the names as keys. If you have a list of species it will automatically be converted to a dictionary.

                • -
                • species_delimiter (str, optional) – Delimiter that separate species. Leading and trailing spaces +

                • species_delimiter (str, optional) – Delimiter that separate species. Leading and trailing spaces will be trimmed. Default is ‘+’

                • -
                • reaction_delimiter (str, optional) – Delimiter that separate states of the reaction. Leading and +

                • reaction_delimiter (str, optional) – Delimiter that separate states of the reaction. Leading and trailing spaces will be trimmed. Default is ‘=’

                • -
                • notes (str or dict, optional) – Other notes such as the source of the reaction. Default is None

                • -
                • raise_error (bool, optional) – If True, raises an error if the transition state is not located +

                • notes (str or dict, optional) – Other notes such as the source of the reaction. Default is None

                • +
                • raise_error (bool, optional) – If True, raises an error if the transition state is not located in species. Default is True

                • -
                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if the +

                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if the transition state is not located in species. If a warning is raised, the Reaction will try to be initialized without the transition state. Default is True

                • @@ -492,7 +492,7 @@

                  pmutt.reaction.Reaction

                  Reaction object

                Raises:
                -

                KeyError – Raised if species does not contain an entry for the +

                KeyError – Raised if species does not contain an entry for the reactants, products or transition state in reaction_str

                @@ -510,17 +510,17 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • T (float, optional) – Temperature in K. Default is standard temperature.

                • -
                • m (int, optional) – Molecularity of gas-phase species in the reaction. +

                • T (float, optional) – Temperature in K. Default is standard temperature.

                • +
                • m (int, optional) – Molecularity of gas-phase species in the reaction. Condensed-phase reactions and unimolecular gas-phase reactions should have a value of 1. Bimolecular gas-phase reactions should have a value of 2. If None specified, m will be calculated (assuming all species in the initial state arw gas phase). To get the transition-state estimate of the pre-exponential factor, set to 0 (default).

                • -
                • use_q (bool, optional) – If True, uses ratio of partition functions to calculate A +

                • use_q (bool, optional) – If True, uses ratio of partition functions to calculate A (Note: include_ZPE=False). If False, uses the entropy of activation to calculate A.

                • kwargs (keyword arguments) – Parameters required to calculate pre-exponential factor. See @@ -532,7 +532,7 @@

                  pmutt.reaction.Reaction

                  A – Pre-exponential factor

                Return type:
                -

                float

                +

                float

                @@ -545,9 +545,9 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -559,7 +559,7 @@

                  pmutt.reaction.Reaction

                Return type:
                -

                float

                +

                float

                @@ -571,7 +571,7 @@

                pmutt.reaction.Reaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -604,7 +604,7 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -616,7 +616,7 @@

                  pmutt.reaction.Reaction

                Return type:
                -

                float

                +

                float

                @@ -628,7 +628,7 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • state (str) –

                  state to calculate quantity. Supported options:

                  +
                • state (str) –

                  state to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -647,7 +647,7 @@

                    pmutt.reaction.Reaction

                Return type:
                -

                float

                +

                float

                @@ -660,9 +660,9 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -673,7 +673,7 @@

                  pmutt.reaction.Reaction

                  Cv_act – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -685,7 +685,7 @@

                pmutt.reaction.Reaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -718,7 +718,7 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -730,7 +730,7 @@

                  pmutt.reaction.Reaction

                Return type:
                -

                float

                +

                float

                @@ -742,7 +742,7 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • state (str) –

                  state to calculate quantity. Supported options:

                  +
                • state (str) –

                  state to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -761,7 +761,7 @@

                    pmutt.reaction.Reaction

                Return type:
                -

                float

                +

                float

                @@ -774,12 +774,12 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. +

                • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. Condensed-phase and unimolecular gas-phase reactions should have a value of 0. Bimolecular gas-phase reactions should have a value of -1. If None specified, m will be calculated @@ -796,7 +796,7 @@

                  pmutt.reaction.Reaction

                Return type:
                -

                float

                +

                float

                @@ -808,7 +808,7 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                • -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

                • +
                • T (float) – Temperature in K

                • +
                • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different species.

                • @@ -830,7 +830,7 @@

                  pmutt.reaction.Reaction

                  E – Electronic energy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -849,9 +849,9 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. +

                • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. Condensed-phase and unimolecular gas-phase reactions should have a value of 0. Bimolecular gas-phase reactions should have a value of -1. If None specified, m will be calculated @@ -867,7 +867,7 @@

                  pmutt.reaction.Reaction

                Return type:
                -

                float

                +

                float

                @@ -879,7 +879,7 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • state (str) –

                  state to calculate quantity. Supported options:

                  +
                • state (str) –

                  state to calculate quantity. Supported options:

                • -
                • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

                • +
                • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate dimensionless electronic energy. See class docstring to see how to pass specific parameters to different species.

                • @@ -898,7 +898,7 @@

                  pmutt.reaction.Reaction

                  EoRT – Dimensionless electronic energy of the reaction state.

                Return type:
                -

                float

                +

                float

                @@ -911,10 +911,10 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -926,7 +926,7 @@

                  pmutt.reaction.Reaction

                Return type:
                -

                float

                +

                float

                @@ -938,7 +938,7 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                • -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • +
                • T (float) – Temperature in K

                • kwargs (keyword arguments) – Parameters required to calculate Helholtz energy. See class docstring to see how to pass specific parameters to different species.

                • @@ -959,7 +959,7 @@

                  pmutt.reaction.Reaction

                  F – Helmholtz energy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -972,7 +972,7 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -984,7 +984,7 @@

                  pmutt.reaction.Reaction

                Return type:
                -

                float

                +

                float

                @@ -996,7 +996,7 @@

                pmutt.reaction.Reaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -1028,10 +1028,10 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1043,7 +1043,7 @@

                  pmutt.reaction.Reaction

                Return type:
                -

                float

                +

                float

                @@ -1055,7 +1055,7 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                • -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • +
                • T (float) – Temperature in K

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different species.

                • @@ -1076,7 +1076,7 @@

                  pmutt.reaction.Reaction

                  G – Gibbs energy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -1089,7 +1089,7 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1101,7 +1101,7 @@

                  pmutt.reaction.Reaction

                Return type:
                -

                float

                +

                float

                @@ -1113,7 +1113,7 @@

                pmutt.reaction.Reaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -1144,10 +1144,10 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different @@ -1159,7 +1159,7 @@

                  pmutt.reaction.Reaction

                Return type:
                -

                float

                +

                float

                @@ -1171,7 +1171,7 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                • -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • +
                • T (float) – Temperature in K

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different species.

                • @@ -1192,7 +1192,7 @@

                  pmutt.reaction.Reaction

                  H – Enthalpy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -1205,7 +1205,7 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different @@ -1217,7 +1217,7 @@

                  pmutt.reaction.Reaction

                Return type:
                -

                float

                +

                float

                @@ -1229,7 +1229,7 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • state (str) –

                  state to calculate quantity. Supported options:

                  +
                • state (str) –

                  state to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -1248,7 +1248,7 @@

                    pmutt.reaction.Reaction

                Return type:
                -

                float

                +

                float

                @@ -1260,9 +1260,9 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate equilibrium constant. See class docstring to see how to pass specific parameters to @@ -1273,7 +1273,7 @@

                  pmutt.reaction.Reaction

                  Keq – Equilibrium constant between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1286,9 +1286,9 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1300,7 +1300,7 @@

                  pmutt.reaction.Reaction

                Return type:
                -

                float

                +

                float

                @@ -1312,7 +1312,7 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                • -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to @@ -1332,7 +1332,7 @@

                  pmutt.reaction.Reaction

                  S – Entropy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -1345,7 +1345,7 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1357,7 +1357,7 @@

                  pmutt.reaction.Reaction

                Return type:
                -

                float

                +

                float

                @@ -1369,7 +1369,7 @@

                pmutt.reaction.Reaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -1400,10 +1400,10 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1415,7 +1415,7 @@

                  pmutt.reaction.Reaction

                Return type:
                -

                float

                +

                float

                @@ -1427,7 +1427,7 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                • -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • +
                • T (float) – Temperature in K

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different species.

                • @@ -1448,7 +1448,7 @@

                  pmutt.reaction.Reaction

                  U – Internal energy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -1461,7 +1461,7 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1473,7 +1473,7 @@

                  pmutt.reaction.Reaction

                Return type:
                -

                float

                +

                float

                @@ -1485,7 +1485,7 @@

                pmutt.reaction.Reaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -1516,11 +1516,11 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1531,7 +1531,7 @@

                  pmutt.reaction.Reaction

                  delta_Cp – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1544,9 +1544,9 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1557,7 +1557,7 @@

                  pmutt.reaction.Reaction

                  delta_CvoR – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1570,11 +1570,11 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1585,7 +1585,7 @@

                  pmutt.reaction.Reaction

                  delta_Cv – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1598,9 +1598,9 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1611,7 +1611,7 @@

                  pmutt.reaction.Reaction

                  delta_CvoR – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1623,12 +1623,12 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different @@ -1639,7 +1639,7 @@

                  pmutt.reaction.Reaction

                  delta_E – Change in electronic energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1652,9 +1652,9 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different @@ -1665,7 +1665,7 @@

                  pmutt.reaction.Reaction

                  delta_EoRT – Change in electronic energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1677,12 +1677,12 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -1693,7 +1693,7 @@

                  pmutt.reaction.Reaction

                  delta_F – Change in Helmholtz energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1706,9 +1706,9 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -1719,7 +1719,7 @@

                  pmutt.reaction.Reaction

                  delta_FoRT – Change in Helmholtz energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1731,12 +1731,12 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1747,7 +1747,7 @@

                  pmutt.reaction.Reaction

                  delta_G – Change in Gibbs energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1760,9 +1760,9 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1773,7 +1773,7 @@

                  pmutt.reaction.Reaction

                  delta_GoRT – Change in Gibbs energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1785,12 +1785,12 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different @@ -1801,7 +1801,7 @@

                  pmutt.reaction.Reaction

                  delta_H – Change in enthalpy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1813,9 +1813,9 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different @@ -1826,7 +1826,7 @@

                  pmutt.reaction.Reaction

                  delta_HoRT – Change in enthalpy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1838,11 +1838,11 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1853,7 +1853,7 @@

                  pmutt.reaction.Reaction

                  delta_S – Change in entropy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1865,9 +1865,9 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1878,7 +1878,7 @@

                  pmutt.reaction.Reaction

                  delta_SoR – Change in entropy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1890,12 +1890,12 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1906,7 +1906,7 @@

                  pmutt.reaction.Reaction

                  delta_U – Change in internal energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1919,9 +1919,9 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1932,7 +1932,7 @@

                  pmutt.reaction.Reaction

                  delta_UoRT – Change in internal energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1944,9 +1944,9 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate partition function. See class docstring to see how to pass specific parameters to different @@ -1957,7 +1957,7 @@

                  pmutt.reaction.Reaction

                  delta_q – Change in partition function between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1970,21 +1970,21 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • initial_state (str) –

                  Thermodynamic state. Supported options:

                  +
                • initial_state (str) –

                  Thermodynamic state. Supported options:

                  • ’reactants’

                  • ’products’

                  • ’transition state’

                • -
                • final_state (str) –

                  Thermodynamic state. Supported options:

                  +
                • final_state (str) –

                  Thermodynamic state. Supported options:

                  • ’reactants’

                  • ’products’

                  • ’transition state’

                • -
                • method_name (str) – Name of method to use to calculate quantity. Calculates any +

                • method_name (str) – Name of method to use to calculate quantity. Calculates any quantity as long as the relevant objects have the same method name

                • kwargs (keyword arguments) – Arguments passed to evaluate the quantity of the reactants and @@ -1995,7 +1995,7 @@

                  pmutt.reaction.Reaction

                  delta_quantity – Change in thermodynamic quantity between particular states

                Return type:
                -

                float

                +

                float

                @@ -2008,9 +2008,9 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • include_ZPE (bool, optional) – If True, includes zero-point energy when calculating the +

                • include_ZPE (bool, optional) – If True, includes zero-point energy when calculating the value of the partition functions. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate partition function. See class docstring to see how to pass specific parameters to different @@ -2022,7 +2022,7 @@

                  pmutt.reaction.Reaction

                Return type:
                -

                float

                +

                float

                @@ -2034,7 +2034,7 @@

                pmutt.reaction.Reaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -2064,8 +2064,8 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • include_TS (bool, optional) – Whether transition states should be included. Default is True

                • -
                • key (str, optional) – Attribute to use as the key in the output dictionary. Default +

                • include_TS (bool, optional) – Whether transition states should be included. Default is True

                • +
                • key (str, optional) – Attribute to use as the key in the output dictionary. Default is name

                @@ -2073,7 +2073,7 @@

                pmutt.reaction.Reaction

                species – Unique species in the reaction

                Return type:
                -

                dict

                +

                dict

                @@ -2085,7 +2085,7 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • state (str) –

                  Thermodynamic state. Supported options:

                  +
                • state (str) –

                  Thermodynamic state. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -2094,7 +2094,7 @@

                    pmutt.reaction.Reaction

                    ’ts’

                • -
                • method_name (str) – Name of method to use to calculate quantity. Calculates any +

                • method_name (str) – Name of method to use to calculate quantity. Calculates any quantity as long as the relevant objects have the same method name

                • kwargs (keyword arguments) – Arguments required to calculate the thermodynamic quantity of @@ -2105,7 +2105,7 @@

                  pmutt.reaction.Reaction

                  state_quantity – Thermodynamic quantity of particular state

                Return type:
                -

                float

                +

                float

                @@ -2139,7 +2139,7 @@

                pmutt.reaction.Reaction

                obj_dict

                Return type:
                -

                dict

                +

                dict

                @@ -2151,21 +2151,21 @@

                pmutt.reaction.Reaction
                Parameters:
                  -
                • species_delimiter (str, optional) – Separates species. Default is ‘+’

                • -
                • reaction_delimiter (str, optional) – Separates reaction states. Default is ‘=’

                • -
                • stoich_format (float, optional) – Format to write stoichiometric numbers. Default is ‘.2f’ (float +

                • species_delimiter (str, optional) – Separates species. Default is ‘+’

                • +
                • reaction_delimiter (str, optional) – Separates reaction states. Default is ‘=’

                • +
                • stoich_format (float, optional) – Format to write stoichiometric numbers. Default is ‘.2f’ (float rounded to 2 decimal places)

                • -
                • include_TS (bool, optional) – If True, includes transition states in output. Default is True

                • -
                • stoich_space (bool, optional) – If True, inserts a space between stoichiometric coefficients +

                • include_TS (bool, optional) – If True, includes transition states in output. Default is True

                • +
                • stoich_space (bool, optional) – If True, inserts a space between stoichiometric coefficients and the species name. Default is False

                • -
                • key (str, optional) – Attribute to use to print out species. Default is name

                • +
                • key (str, optional) – Attribute to use to print out species. Default is name

                Returns:

                reaction_str – Reaction string

                Return type:
                -

                str

                +

                str

                diff --git a/api/reactions/reactions.html b/api/reactions/reactions.html index 8be8f9f8..593eda9c 100644 --- a/api/reactions/reactions.html +++ b/api/reactions/reactions.html @@ -4,7 +4,7 @@ - Reactions — pmutt 1.4.7 documentation + Reactions — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
                - 1.4.7 + 1.4.9
                diff --git a/api/reactions/reactions/pmutt.omkm.reaction.SurfaceReaction.html b/api/reactions/reactions/pmutt.omkm.reaction.SurfaceReaction.html index d5934b6a..8021744b 100644 --- a/api/reactions/reactions/pmutt.omkm.reaction.SurfaceReaction.html +++ b/api/reactions/reactions/pmutt.omkm.reaction.SurfaceReaction.html @@ -4,7 +4,7 @@ - pmutt.omkm.reaction.SurfaceReaction — pmutt 1.4.7 documentation + pmutt.omkm.reaction.SurfaceReaction — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
                - 1.4.7 + 1.4.9
                @@ -128,7 +128,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Type:
                -

                str, optional

                +

                str, optional

                @@ -139,7 +139,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Type:
                -

                bool, optional

                +

                bool, optional

                @@ -151,7 +151,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Type:
                -

                float, optional

                +

                float, optional

                @@ -163,7 +163,7 @@

                pmutt.omkm.reaction.SurfaceReactionis_adsorption is False, 0 if is_adsorption is True.

                Type:
                -

                float, optional

                +

                float, optional

                @@ -175,7 +175,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Type:
                -

                float, optional

                +

                float, optional

                @@ -188,7 +188,7 @@

                pmutt.omkm.reaction.SurfaceReactionis_adsorption is False.

                Type:
                -

                float, optional

                +

                float, optional

                @@ -200,7 +200,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Type:
                -

                str, optional

                +

                str, optional

                @@ -213,7 +213,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Type:
                -

                bool, optional

                +

                bool, optional

                @@ -476,7 +476,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Raises:
                -

                ValueError – Raised if the reactants, products and/or transition state +

                ValueError – Raised if the reactants, products and/or transition state element composition does not agree.

                @@ -488,7 +488,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                -

                json_obj (dict) – JSON representation

                +

                json_obj (dict) – JSON representation

                Returns:

                Reaction

                @@ -506,27 +506,27 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • reaction_str (str) – Reaction string.

                • -
                • species (dict) – Dictionary using the names as keys. If you have a list of +

                • reaction_str (str) – Reaction string.

                • +
                • species (dict) – Dictionary using the names as keys. If you have a list of species, use pmutt.pmutt_list_to_dict to make a dict.

                • -
                • species_delimiter (str, optional) – Delimiter that separate species. Leading and trailing spaces +

                • species_delimiter (str, optional) – Delimiter that separate species. Leading and trailing spaces will be trimmed. Default is ‘+’

                • -
                • reaction_delimiter (str, optional) – Delimiter that separate states of the reaction. Leading and +

                • reaction_delimiter (str, optional) – Delimiter that separate states of the reaction. Leading and trailing spaces will be trimmed. Default is ‘=’

                • -
                • notes (str or dict, optional) – Other notes such as the source of the reaction. Default is None

                • -
                • A (float, optional) – Pre-exponential constant. If not specified, uses reaction to +

                • notes (str or dict, optional) – Other notes such as the source of the reaction. Default is None

                • +
                • A (float, optional) – Pre-exponential constant. If not specified, uses reaction to determine value.

                • -
                • beta (float, optional) – Power to raise the temperature in the rate expression. Default +

                • beta (float, optional) – Power to raise the temperature in the rate expression. Default is 1 if is_adsorption is False, 0 if is_adsorption is True.

                • -
                • Ea (float, optional) – Activation energy. If not specified, uses reaction to determine +

                • Ea (float, optional) – Activation energy. If not specified, uses reaction to determine value.

                • -
                • is_adsorption (bool, optional) – If True, the reaction represents an adsorption. Default is False

                • -
                • sticking_coeff (float, optional) – Sticking coefficient. Only relevant if is_adsorption is +

                • is_adsorption (bool, optional) – If True, the reaction represents an adsorption. Default is False

                • +
                • sticking_coeff (float, optional) – Sticking coefficient. Only relevant if is_adsorption is True. Default is 0.5

                • -
                • gas_phase (bool) – True if the reaction has only gas-phase species. This attribute +

                • gas_phase (bool) – True if the reaction has only gas-phase species. This attribute is determined based on the reactants and products

                • -
                • use_motz_wise (bool, optional) – Used when generating OpenMKM YAML file. If True, uses Motz-Wise +

                • use_motz_wise (bool, optional) – Used when generating OpenMKM YAML file. If True, uses Motz-Wise correction to sticking coefficient. Only applicable to adsorption reactions. Default is False.

                @@ -547,9 +547,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • sden_operation (str, optional) – Site density operation to use. Default is ‘min’

                • -
                • include_entropy (bool, optional) – If True, includes the entropy of activation. Default is True

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • sden_operation (str, optional) – Site density operation to use. Default is ‘min’

                • +
                • include_entropy (bool, optional) – If True, includes the entropy of activation. Default is True

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • units (str or Units, optional) – Units for A. If Units class specified, determines the units for A. Default is ‘molec/cm2’

                • kwargs (keyword arguments) – Parameters required to calculate pre-exponential factor

                • @@ -566,9 +566,9 @@

                  pmutt.omkm.reaction.SurfaceReaction
                  Parameters:
                    -
                  • units (str) – Units as string. See R() for accepted +

                  • units (str) – Units as string. See R() for accepted units.

                  • -
                  • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                  • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                  • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -580,7 +580,7 @@

                    pmutt.omkm.reaction.SurfaceReactionReturn type: -

                    float

                    +

                    float

                  @@ -592,7 +592,7 @@

                  pmutt.omkm.reaction.SurfaceReaction
                  Parameters:
                    -
                  • state (str) –

                    State to calculate quantity. Supported options:

                    +
                  • state (str) –

                    State to calculate quantity. Supported options:

                    • ’reactants’

                    • ’products’

                    • @@ -601,7 +601,7 @@

                      pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
                    • units (str) – Units as string. See R() for accepted units.

                    • kwargs (keyword arguments) – Parameters required to calculate heat capacity at constant pressure. See class docstring to see how to pass specific @@ -612,7 +612,7 @@

                      pmutt.omkm.reaction.SurfaceReaction

                      Cp – Heat capacity at constant pressure of the reaction state

                  Return type:
                  -

                  float

                  +

                  float

                @@ -625,7 +625,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -637,7 +637,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -649,7 +649,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  state to calculate quantity. Supported options:

                  +
                • state (str) –

                  state to calculate quantity. Supported options:

                @@ -681,9 +681,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -694,7 +694,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  Cv_act – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -706,7 +706,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -715,7 +715,7 @@

                    pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units.

                  • kwargs (keyword arguments) – Parameters required to calculate heat capacity at constant volume. See class docstring to see how to pass specific @@ -726,7 +726,7 @@

                    pmutt.omkm.reaction.SurfaceReaction

                    Cv – Heat capacity at constant volume of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -739,7 +739,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -751,7 +751,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -763,7 +763,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  state to calculate quantity. Supported options:

                  +
                • state (str) –

                  state to calculate quantity. Supported options:

                @@ -795,12 +795,12 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. +

                • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. Condensed-phase and unimolecular gas-phase reactions should have a value of 0. Bimolecular gas-phase reactions should have a value of -1. If None specified, m will be calculated @@ -817,7 +817,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -829,7 +829,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -838,10 +838,10 @@

                    pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                  • -
                  • T (float) – Temperature in K

                  • -
                  • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

                  • +
                  • T (float) – Temperature in K

                  • +
                  • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

                  • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -851,7 +851,7 @@

                    pmutt.omkm.reaction.SurfaceReaction

                    E – Electronic energy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -870,9 +870,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. +

                • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. Condensed-phase and unimolecular gas-phase reactions should have a value of 0. Bimolecular gas-phase reactions should have a value of -1. If None specified, m will be calculated @@ -888,7 +888,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -900,7 +900,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  state to calculate quantity. Supported options:

                  +
                • state (str) –

                  state to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -909,7 +909,7 @@

                    pmutt.omkm.reaction.SurfaceReactionbool, optional) – If True, includes the zero point energy. Default is False

                    +
                  • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

                  • kwargs (keyword arguments) – Parameters required to calculate dimensionless electronic energy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -919,7 +919,7 @@

                    pmutt.omkm.reaction.SurfaceReaction

                    EoRT – Dimensionless electronic energy of the reaction state.

                Return type:
                -

                float

                +

                float

                @@ -932,10 +932,10 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -947,7 +947,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -959,7 +959,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -968,9 +968,9 @@

                    pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                  • -
                  • T (float) – Temperature in K

                  • +
                  • T (float) – Temperature in K

                  • kwargs (keyword arguments) – Parameters required to calculate Helholtz energy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -980,7 +980,7 @@

                    pmutt.omkm.reaction.SurfaceReaction

                    F – Helmholtz energy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -993,7 +993,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -1005,7 +1005,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -1017,7 +1017,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -1049,10 +1049,10 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • T (float) – Temperature in K

                • -
                • P (float, optional) – Pressure in bar. Default is 1 bar

                • +
                • T (float) – Temperature in K

                • +
                • P (float, optional) – Pressure in bar. Default is 1 bar

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy of activation.

                @@ -1064,7 +1064,7 @@

                pmutt.omkm.reaction.SurfaceReactionReturn type: -

                float

                +

                float

                @@ -1076,7 +1076,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -1085,9 +1085,9 @@

                    pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                  • -
                  • T (float) – Temperature in K

                  • +
                  • T (float) – Temperature in K

                  • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -1097,7 +1097,7 @@

                    pmutt.omkm.reaction.SurfaceReaction

                    G – Gibbs energy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -1111,9 +1111,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy.

                @@ -1126,7 +1126,7 @@

                pmutt.omkm.reaction.SurfaceReactionReturn type: -

                float

                +

                float

                @@ -1138,7 +1138,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -1169,9 +1169,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • T (float) – Temperature in K

                • +
                • T (float) – Temperature in K

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy of activation.

                @@ -1183,7 +1183,7 @@

                pmutt.omkm.reaction.SurfaceReactionReturn type: -

                float

                +

                float

                @@ -1195,7 +1195,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -1204,9 +1204,9 @@

                    pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                  • -
                  • T (float) – Temperature in K

                  • +
                  • T (float) – Temperature in K

                  • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -1216,7 +1216,7 @@

                    pmutt.omkm.reaction.SurfaceReaction

                    H – Enthalpy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -1229,7 +1229,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy of activation.

                @@ -1242,7 +1242,7 @@

                pmutt.omkm.reaction.SurfaceReactionReturn type: -

                float

                +

                float

                @@ -1254,7 +1254,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  state to calculate quantity. Supported options:

                  +
                • state (str) –

                  state to calculate quantity. Supported options:

                @@ -1285,9 +1285,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate equilibrium constant. See class docstring to see how to pass specific parameters to @@ -1298,7 +1298,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  Keq – Equilibrium constant between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1311,9 +1311,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1325,7 +1325,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -1337,7 +1337,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -1346,7 +1346,7 @@

                    pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units.

                  • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to @@ -1357,7 +1357,7 @@

                    pmutt.omkm.reaction.SurfaceReaction

                    S – Entropy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -1370,7 +1370,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1382,7 +1382,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -1394,7 +1394,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -1425,10 +1425,10 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1440,7 +1440,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -1452,7 +1452,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -1461,9 +1461,9 @@

                    pmutt.omkm.reaction.SurfaceReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                  • -
                  • T (float) – Temperature in K

                  • +
                  • T (float) – Temperature in K

                  • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -1473,7 +1473,7 @@

                    pmutt.omkm.reaction.SurfaceReaction

                    U – Internal energy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -1486,7 +1486,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1498,7 +1498,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -1510,7 +1510,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -1541,11 +1541,11 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1556,7 +1556,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_Cp – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1569,9 +1569,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1582,7 +1582,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_CvoR – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1595,11 +1595,11 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1610,7 +1610,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_Cv – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1623,9 +1623,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1636,7 +1636,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_CvoR – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1648,12 +1648,12 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different @@ -1664,7 +1664,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_E – Change in electronic energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1677,9 +1677,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different @@ -1690,7 +1690,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_EoRT – Change in electronic energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1702,12 +1702,12 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -1718,7 +1718,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_F – Change in Helmholtz energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1731,9 +1731,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -1744,7 +1744,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_FoRT – Change in Helmholtz energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1756,12 +1756,12 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1772,7 +1772,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_G – Change in Gibbs energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1785,9 +1785,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1798,7 +1798,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_GoRT – Change in Gibbs energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1810,12 +1810,12 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different @@ -1826,7 +1826,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_H – Change in enthalpy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1838,9 +1838,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different @@ -1851,7 +1851,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_HoRT – Change in enthalpy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1863,11 +1863,11 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1878,7 +1878,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_S – Change in entropy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1890,9 +1890,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1903,7 +1903,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_SoR – Change in entropy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1915,12 +1915,12 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1931,7 +1931,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_U – Change in internal energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1944,9 +1944,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1957,7 +1957,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_UoRT – Change in internal energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1969,9 +1969,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate partition function. See class docstring to see how to pass specific parameters to different @@ -1982,7 +1982,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_q – Change in partition function between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1995,21 +1995,21 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • initial_state (str) –

                  Thermodynamic state. Supported options:

                  +
                • initial_state (str) –

                  Thermodynamic state. Supported options:

                  • ’reactants’

                  • ’products’

                  • ’transition state’

                • -
                • final_state (str) –

                  Thermodynamic state. Supported options:

                  +
                • final_state (str) –

                  Thermodynamic state. Supported options:

                  • ’reactants’

                  • ’products’

                  • ’transition state’

                • -
                • method_name (str) – Name of method to use to calculate quantity. Calculates any +

                • method_name (str) – Name of method to use to calculate quantity. Calculates any quantity as long as the relevant objects have the same method name

                • kwargs (keyword arguments) – Arguments passed to evaluate the quantity of the reactants and @@ -2020,7 +2020,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  delta_quantity – Change in thermodynamic quantity between particular states

                Return type:
                -

                float

                +

                float

                @@ -2033,9 +2033,9 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • include_ZPE (bool, optional) – If True, includes zero-point energy when calculating the +

                • include_ZPE (bool, optional) – If True, includes zero-point energy when calculating the value of the partition functions. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate partition function. See class docstring to see how to pass specific parameters to different @@ -2047,7 +2047,7 @@

                  pmutt.omkm.reaction.SurfaceReactionReturn type: -

                  float

                  +

                  float

                @@ -2059,7 +2059,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -2089,8 +2089,8 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • include_TS (bool, optional) – Whether transition states should be included. Default is True

                • -
                • key (str, optional) – Attribute to use as the key in the output dictionary. Default +

                • include_TS (bool, optional) – Whether transition states should be included. Default is True

                • +
                • key (str, optional) – Attribute to use as the key in the output dictionary. Default is name

                @@ -2098,7 +2098,7 @@

                pmutt.omkm.reaction.SurfaceReaction

                species – Unique species in the reaction

                Return type:
                -

                dict

                +

                dict

                @@ -2110,7 +2110,7 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • state (str) –

                  Thermodynamic state. Supported options:

                  +
                • state (str) –

                  Thermodynamic state. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -2119,7 +2119,7 @@

                    pmutt.omkm.reaction.SurfaceReactionstr) – Name of method to use to calculate quantity. Calculates any +
                  • method_name (str) – Name of method to use to calculate quantity. Calculates any quantity as long as the relevant objects have the same method name

                  • kwargs (keyword arguments) – Arguments required to calculate the thermodynamic quantity of @@ -2130,7 +2130,7 @@

                    pmutt.omkm.reaction.SurfaceReaction

                    state_quantity – Thermodynamic quantity of particular state

                Return type:
                -

                float

                +

                float

                @@ -2172,12 +2172,12 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • -
                • P (float, optional) – Pressure in bar. Default is 1 bar

                • -
                • quantity_unit (str, optional) – Quantity unit to calculate A. Default is ‘molec’

                • -
                • length_unit (str, optional) – Length unit to calculate A. Default is ‘cm’

                • -
                • act_energy_unit (str, optional) – Unit to use for activation energy. Default is ‘cal/mol’

                • -
                • ads_act_method (str, optional) – Activation method to use for adsorption reactions. Accepted +

                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • P (float, optional) – Pressure in bar. Default is 1 bar

                • +
                • quantity_unit (str, optional) – Quantity unit to calculate A. Default is ‘molec’

                • +
                • length_unit (str, optional) – Length unit to calculate A. Default is ‘cm’

                • +
                • act_energy_unit (str, optional) – Unit to use for activation energy. Default is ‘cal/mol’

                • +
                • ads_act_method (str, optional) – Activation method to use for adsorption reactions. Accepted options include ‘get_H_act’ and ‘get_G_act’. Default is ‘get_H_act’.

                • units (Units object) – If specified, quantity_unit, length_unit, and @@ -2188,7 +2188,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  cti_str – Surface reaction string in CTI format

                Return type:
                -

                str

                +

                str

                @@ -2202,7 +2202,7 @@

                pmutt.omkm.reaction.SurfaceReaction

                obj_dict

                Return type:
                -

                dict

                +

                dict

                @@ -2214,12 +2214,12 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • -
                • P (float, optional) – Pressure in bar. Default is 1 bar

                • -
                • quantity_unit (str, optional) – Quantity unit to calculate A. Default is ‘molec’

                • -
                • length_unit (str, optional) – Length unit to calculate A. Default is ‘cm’

                • -
                • act_energy_unit (str, optional) – Unit to use for activation energy. Default is ‘cal/mol’

                • -
                • ads_act_method (str, optional) – Activation method to use for adsorption reactions. Accepted +

                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • P (float, optional) – Pressure in bar. Default is 1 bar

                • +
                • quantity_unit (str, optional) – Quantity unit to calculate A. Default is ‘molec’

                • +
                • length_unit (str, optional) – Length unit to calculate A. Default is ‘cm’

                • +
                • act_energy_unit (str, optional) – Unit to use for activation energy. Default is ‘cal/mol’

                • +
                • ads_act_method (str, optional) – Activation method to use for adsorption reactions. Accepted options include ‘get_H_act’ and ‘get_G_act’. Default is ‘get_H_act’.

                • units (Units object) – If specified, quantity_unit, length_unit, and @@ -2230,7 +2230,7 @@

                  pmutt.omkm.reaction.SurfaceReaction

                  yaml_dict – Dictionary compatible with Cantera’s YAML format

                Return type:
                -

                dict

                +

                dict

                @@ -2242,21 +2242,21 @@

                pmutt.omkm.reaction.SurfaceReaction
                Parameters:
                  -
                • species_delimiter (str, optional) – Separates species. Default is ‘+’

                • -
                • reaction_delimiter (str, optional) – Separates reaction states. Default is ‘=’

                • -
                • stoich_format (float, optional) – Format to write stoichiometric numbers. Default is ‘.2f’ (float +

                • species_delimiter (str, optional) – Separates species. Default is ‘+’

                • +
                • reaction_delimiter (str, optional) – Separates reaction states. Default is ‘=’

                • +
                • stoich_format (float, optional) – Format to write stoichiometric numbers. Default is ‘.2f’ (float rounded to 2 decimal places)

                • -
                • include_TS (bool, optional) – If True, includes transition states in output. Default is True

                • -
                • stoich_space (bool, optional) – If True, inserts a space between stoichiometric coefficients +

                • include_TS (bool, optional) – If True, includes transition states in output. Default is True

                • +
                • stoich_space (bool, optional) – If True, inserts a space between stoichiometric coefficients and the species name. Default is False

                • -
                • key (str, optional) – Attribute to use to print out species. Default is name

                • +
                • key (str, optional) – Attribute to use to print out species. Default is name

                Returns:

                reaction_str – Reaction string

                Return type:
                -

                str

                +

                str

                diff --git a/api/reactions/reactions/pmutt.reaction.ChemkinReaction.html b/api/reactions/reactions/pmutt.reaction.ChemkinReaction.html index 3ae6e7db..6343861c 100644 --- a/api/reactions/reactions/pmutt.reaction.ChemkinReaction.html +++ b/api/reactions/reactions/pmutt.reaction.ChemkinReaction.html @@ -4,7 +4,7 @@ - pmutt.reaction.ChemkinReaction — pmutt 1.4.7 documentation + pmutt.reaction.ChemkinReaction — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
                - 1.4.7 + 1.4.9
                @@ -127,7 +127,7 @@

                pmutt.reaction.ChemkinReaction
                Type:
                -

                float, optional

                +

                float, optional

                @@ -138,7 +138,7 @@

                pmutt.reaction.ChemkinReaction
                Type:
                -

                bool, optional

                +

                bool, optional

                @@ -150,7 +150,7 @@

                pmutt.reaction.ChemkinReaction
                Type:
                -

                float, optional

                +

                float, optional

                @@ -162,7 +162,7 @@

                pmutt.reaction.ChemkinReaction
                Type:
                -

                bool

                +

                bool

                @@ -405,7 +405,7 @@

                pmutt.reaction.ChemkinReaction
                Raises:
                -

                ValueError – Raised if the reactants, products and/or transition state +

                ValueError – Raised if the reactants, products and/or transition state element composition does not agree.

                @@ -417,7 +417,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                -

                json_obj (dict) – JSON representation

                +

                json_obj (dict) – JSON representation

                Returns:

                Reaction

                @@ -435,20 +435,20 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • reaction_str (str) – Reaction string.

                • -
                • species (dict) – Dictionary using the names as keys. If you have a list of +

                • reaction_str (str) – Reaction string.

                • +
                • species (dict) – Dictionary using the names as keys. If you have a list of species, use pmutt.pmutt_list_to_dict to make a dict.

                • -
                • species_delimiter (str, optional) – Delimiter that separate species. Leading and trailing spaces +

                • species_delimiter (str, optional) – Delimiter that separate species. Leading and trailing spaces will be trimmed. Default is ‘+’

                • -
                • reaction_delimiter (str, optional) – Delimiter that separate states of the reaction. Leading and +

                • reaction_delimiter (str, optional) – Delimiter that separate states of the reaction. Leading and trailing spaces will be trimmed. Default is ‘=’

                • -
                • notes (str or dict, optional) – Other notes such as the source of the reaction. Default is None

                • -
                • beta (float, optional) – Power to raise the temperature in the rate expression. +

                • notes (str or dict, optional) – Other notes such as the source of the reaction. Default is None

                • +
                • beta (float, optional) – Power to raise the temperature in the rate expression. Default is 1

                • -
                • is_adsorption (bool, optional) – If True, the reaction represents an adsorption. Default is False

                • -
                • sticking_coeff (float, optional) – Sticking coefficient. Only relevant if is_adsorption is +

                • is_adsorption (bool, optional) – If True, the reaction represents an adsorption. Default is False

                • +
                • sticking_coeff (float, optional) – Sticking coefficient. Only relevant if is_adsorption is True. Default is 0.5

                • -
                • gas_phase (bool) – True if the reaction has only gas-phase species. This attribute +

                • gas_phase (bool) – True if the reaction has only gas-phase species. This attribute is determined based on the reactants and products

                @@ -468,9 +468,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • sden_operation (str, optional) – Site density operation to use. Default is ‘sum’

                • -
                • include_entropy (bool, optional) – If True, includes the act entropy. Default is True

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • sden_operation (str, optional) – Site density operation to use. Default is ‘sum’

                • +
                • include_entropy (bool, optional) – If True, includes the act entropy. Default is True

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters required to calculate pre-exponential factor

                @@ -485,9 +485,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -499,7 +499,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -511,7 +511,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -520,7 +520,7 @@

                    pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units.

                  • kwargs (keyword arguments) – Parameters required to calculate heat capacity at constant pressure. See class docstring to see how to pass specific @@ -531,7 +531,7 @@

                    pmutt.reaction.ChemkinReaction

                    Cp – Heat capacity at constant pressure of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -544,7 +544,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -556,7 +556,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -568,7 +568,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  state to calculate quantity. Supported options:

                  +
                • state (str) –

                  state to calculate quantity. Supported options:

                @@ -600,9 +600,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -613,7 +613,7 @@

                  pmutt.reaction.ChemkinReaction

                  Cv_act – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -625,7 +625,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -634,7 +634,7 @@

                    pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units.

                  • kwargs (keyword arguments) – Parameters required to calculate heat capacity at constant volume. See class docstring to see how to pass specific @@ -645,7 +645,7 @@

                    pmutt.reaction.ChemkinReaction

                    Cv – Heat capacity at constant volume of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -658,7 +658,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -670,7 +670,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -682,7 +682,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  state to calculate quantity. Supported options:

                  +
                • state (str) –

                  state to calculate quantity. Supported options:

                @@ -714,12 +714,12 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. +

                • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. Condensed-phase and unimolecular gas-phase reactions should have a value of 0. Bimolecular gas-phase reactions should have a value of -1. If None specified, m will be calculated @@ -736,7 +736,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -748,7 +748,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -757,10 +757,10 @@

                    pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                  • -
                  • T (float) – Temperature in K

                  • -
                  • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

                  • +
                  • T (float) – Temperature in K

                  • +
                  • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

                  • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -770,7 +770,7 @@

                    pmutt.reaction.ChemkinReaction

                    E – Electronic energy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -789,9 +789,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. +

                • del_m (int, optional) – Change in molecularity of gas-phase species in the reaction. Condensed-phase and unimolecular gas-phase reactions should have a value of 0. Bimolecular gas-phase reactions should have a value of -1. If None specified, m will be calculated @@ -807,7 +807,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -819,7 +819,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  state to calculate quantity. Supported options:

                  +
                • state (str) –

                  state to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -828,7 +828,7 @@

                    pmutt.reaction.ChemkinReactionbool, optional) – If True, includes the zero point energy. Default is False

                    +
                  • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

                  • kwargs (keyword arguments) – Parameters required to calculate dimensionless electronic energy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -838,7 +838,7 @@

                    pmutt.reaction.ChemkinReaction

                    EoRT – Dimensionless electronic energy of the reaction state.

                Return type:
                -

                float

                +

                float

                @@ -851,10 +851,10 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -866,7 +866,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -878,7 +878,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -887,9 +887,9 @@

                    pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                  • -
                  • T (float) – Temperature in K

                  • +
                  • T (float) – Temperature in K

                  • kwargs (keyword arguments) – Parameters required to calculate Helholtz energy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -899,7 +899,7 @@

                    pmutt.reaction.ChemkinReaction

                    F – Helmholtz energy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -912,7 +912,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -924,7 +924,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -936,7 +936,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -968,10 +968,10 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -983,7 +983,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -995,7 +995,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -1004,9 +1004,9 @@

                    pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                  • -
                  • T (float) – Temperature in K

                  • +
                  • T (float) – Temperature in K

                  • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -1016,7 +1016,7 @@

                    pmutt.reaction.ChemkinReaction

                    G – Gibbs energy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -1029,9 +1029,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1043,7 +1043,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -1055,7 +1055,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -1086,10 +1086,10 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different @@ -1101,7 +1101,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -1113,7 +1113,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -1122,9 +1122,9 @@

                    pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                  • -
                  • T (float) – Temperature in K

                  • +
                  • T (float) – Temperature in K

                  • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -1134,7 +1134,7 @@

                    pmutt.reaction.ChemkinReaction

                    H – Enthalpy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -1147,7 +1147,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1159,7 +1159,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -1171,7 +1171,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  state to calculate quantity. Supported options:

                  +
                • state (str) –

                  state to calculate quantity. Supported options:

                @@ -1202,9 +1202,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate equilibrium constant. See class docstring to see how to pass specific parameters to @@ -1215,7 +1215,7 @@

                  pmutt.reaction.ChemkinReaction

                  Keq – Equilibrium constant between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1228,9 +1228,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1242,7 +1242,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -1254,7 +1254,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -1263,7 +1263,7 @@

                    pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units.

                  • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to @@ -1274,7 +1274,7 @@

                    pmutt.reaction.ChemkinReaction

                    S – Entropy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -1287,7 +1287,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1299,7 +1299,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -1311,7 +1311,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -1342,10 +1342,10 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1357,7 +1357,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -1369,7 +1369,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  State to calculate quantity. Supported options:

                  +
                • state (str) –

                  State to calculate quantity. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -1378,9 +1378,9 @@

                    pmutt.reaction.ChemkinReactionstr) – Units as string. See R() for accepted +
                  • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                  • -
                  • T (float) – Temperature in K

                  • +
                  • T (float) – Temperature in K

                  • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different species.

                  • @@ -1390,7 +1390,7 @@

                    pmutt.reaction.ChemkinReaction

                    U – Internal energy of the reaction state

                Return type:
                -

                float

                +

                float

                @@ -1403,7 +1403,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1415,7 +1415,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -1427,7 +1427,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -1458,11 +1458,11 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1473,7 +1473,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_Cp – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1486,9 +1486,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1499,7 +1499,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_CvoR – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1512,11 +1512,11 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1527,7 +1527,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_Cv – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1540,9 +1540,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different @@ -1553,7 +1553,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_CvoR – Change in heat capacity between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1565,12 +1565,12 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different @@ -1581,7 +1581,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_E – Change in electronic energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1594,9 +1594,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate electronic energy. See class docstring to see how to pass specific parameters to different @@ -1607,7 +1607,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_EoRT – Change in electronic energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1619,12 +1619,12 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -1635,7 +1635,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_F – Change in Helmholtz energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1648,9 +1648,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Helmholtz energy. See class docstring to see how to pass specific parameters to different @@ -1661,7 +1661,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_FoRT – Change in Helmholtz energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1673,12 +1673,12 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1689,7 +1689,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_G – Change in Gibbs energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1702,9 +1702,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate Gibbs energy. See class docstring to see how to pass specific parameters to different @@ -1715,7 +1715,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_GoRT – Change in Gibbs energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1727,12 +1727,12 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different @@ -1743,7 +1743,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_H – Change in enthalpy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1755,9 +1755,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate enthalpy. See class docstring to see how to pass specific parameters to different @@ -1768,7 +1768,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_HoRT – Change in enthalpy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1780,11 +1780,11 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1795,7 +1795,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_S – Change in entropy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1807,9 +1807,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate entropy. See class docstring to see how to pass specific parameters to different @@ -1820,7 +1820,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_SoR – Change in entropy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1832,12 +1832,12 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float) – Temperature in K

                • -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • T (float) – Temperature in K

                • +
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1848,7 +1848,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_U – Change in internal energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1861,9 +1861,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate internal energy. See class docstring to see how to pass specific parameters to different @@ -1874,7 +1874,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_UoRT – Change in internal energy between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1886,9 +1886,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • act (bool, optional) – If True, uses the transition state as the final state. Default +

                • act (bool, optional) – If True, uses the transition state as the final state. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate partition function. See class docstring to see how to pass specific parameters to different @@ -1899,7 +1899,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_q – Change in partition function between reactants and products

                Return type:
                -

                float

                +

                float

                @@ -1912,21 +1912,21 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • initial_state (str) –

                  Thermodynamic state. Supported options:

                  +
                • initial_state (str) –

                  Thermodynamic state. Supported options:

                  • ’reactants’

                  • ’products’

                  • ’transition state’

                • -
                • final_state (str) –

                  Thermodynamic state. Supported options:

                  +
                • final_state (str) –

                  Thermodynamic state. Supported options:

                  • ’reactants’

                  • ’products’

                  • ’transition state’

                • -
                • method_name (str) – Name of method to use to calculate quantity. Calculates any +

                • method_name (str) – Name of method to use to calculate quantity. Calculates any quantity as long as the relevant objects have the same method name

                • kwargs (keyword arguments) – Arguments passed to evaluate the quantity of the reactants and @@ -1937,7 +1937,7 @@

                  pmutt.reaction.ChemkinReaction

                  delta_quantity – Change in thermodynamic quantity between particular states

                Return type:
                -

                float

                +

                float

                @@ -1950,9 +1950,9 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • rev (bool, optional) – Reverse direction. If True, uses products as initial state +

                • rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False

                • -
                • include_ZPE (bool, optional) – If True, includes zero-point energy when calculating the +

                • include_ZPE (bool, optional) – If True, includes zero-point energy when calculating the value of the partition functions. Default is False

                • kwargs (keyword arguments) – Parameters required to calculate partition function. See class docstring to see how to pass specific parameters to different @@ -1964,7 +1964,7 @@

                  pmutt.reaction.ChemkinReactionReturn type: -

                  float

                  +

                  float

                @@ -1976,7 +1976,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                Return type:
                -

                float

                +

                float

                @@ -2006,8 +2006,8 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • include_TS (bool, optional) – Whether transition states should be included. Default is True

                • -
                • key (str, optional) – Attribute to use as the key in the output dictionary. Default +

                • include_TS (bool, optional) – Whether transition states should be included. Default is True

                • +
                • key (str, optional) – Attribute to use as the key in the output dictionary. Default is name

                @@ -2015,7 +2015,7 @@

                pmutt.reaction.ChemkinReaction

                species – Unique species in the reaction

                Return type:
                -

                dict

                +

                dict

                @@ -2027,7 +2027,7 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • state (str) –

                  Thermodynamic state. Supported options:

                  +
                • state (str) –

                  Thermodynamic state. Supported options:

                  • ’reactants’

                  • ’products’

                  • @@ -2036,7 +2036,7 @@

                    pmutt.reaction.ChemkinReactionstr) – Name of method to use to calculate quantity. Calculates any +
                  • method_name (str) – Name of method to use to calculate quantity. Calculates any quantity as long as the relevant objects have the same method name

                  • kwargs (keyword arguments) – Arguments required to calculate the thermodynamic quantity of @@ -2047,7 +2047,7 @@

                    pmutt.reaction.ChemkinReaction

                    state_quantity – Thermodynamic quantity of particular state

                Return type:
                -

                float

                +

                float

                @@ -2081,7 +2081,7 @@

                pmutt.reaction.ChemkinReaction

                obj_dict

                Return type:
                -

                dict

                +

                dict

                @@ -2093,21 +2093,21 @@

                pmutt.reaction.ChemkinReaction
                Parameters:
                  -
                • species_delimiter (str, optional) – Separates species. Default is ‘+’

                • -
                • reaction_delimiter (str, optional) – Separates reaction states. Default is ‘=’

                • -
                • stoich_format (float, optional) – Format to write stoichiometric numbers. Default is ‘.2f’ (float +

                • species_delimiter (str, optional) – Separates species. Default is ‘+’

                • +
                • reaction_delimiter (str, optional) – Separates reaction states. Default is ‘=’

                • +
                • stoich_format (float, optional) – Format to write stoichiometric numbers. Default is ‘.2f’ (float rounded to 2 decimal places)

                • -
                • include_TS (bool, optional) – If True, includes transition states in output. Default is True

                • -
                • stoich_space (bool, optional) – If True, inserts a space between stoichiometric coefficients +

                • include_TS (bool, optional) – If True, includes transition states in output. Default is True

                • +
                • stoich_space (bool, optional) – If True, inserts a space between stoichiometric coefficients and the species name. Default is False

                • -
                • key (str, optional) – Attribute to use to print out species. Default is name

                • +
                • key (str, optional) – Attribute to use to print out species. Default is name

                Returns:

                reaction_str – Reaction string

                Return type:
                -

                str

                +

                str

                diff --git a/api/reactions/reactions/pmutt.reaction.Reactions.html b/api/reactions/reactions/pmutt.reaction.Reactions.html index f395bc60..6d4ae682 100644 --- a/api/reactions/reactions/pmutt.reaction.Reactions.html +++ b/api/reactions/reactions/pmutt.reaction.Reactions.html @@ -4,7 +4,7 @@ - pmutt.reaction.Reactions — pmutt 1.4.7 documentation + pmutt.reaction.Reactions — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
                - 1.4.7 + 1.4.9
                @@ -165,7 +165,7 @@

                pmutt.reaction.Reactions
                Parameters:
                -

                json_obj (dict) – JSON representation

                +

                json_obj (dict) – JSON representation

                Returns:

                Reactions

                @@ -193,7 +193,7 @@

                pmutt.reaction.Reactions
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • kwargs (keyword arguments) – Parameters to evaluate Gibbs energy at each state.

                @@ -202,7 +202,7 @@

                pmutt.reaction.Reactions

                E_span – Energy span of the Reactions

                Return type:
                -

                float

                +

                float

                @@ -214,8 +214,8 @@

                pmutt.reaction.Reactions
                Parameters:
                  -
                • include_TS (bool, optional) – Whether transition states should be included. Default is True

                • -
                • key (str, optional) – Attribute to use as the key in the output dictionary. +

                • include_TS (bool, optional) – Whether transition states should be included. Default is True

                • +
                • key (str, optional) – Attribute to use as the key in the output dictionary. Default is name

                @@ -223,7 +223,7 @@

                pmutt.reaction.Reactions

                species – Unique species in the reactions

                Return type:
                -

                dict

                +

                dict

                @@ -235,13 +235,13 @@

                pmutt.reaction.Reactions
                Parameters:
                  -
                • method_name (str) – Name of method to use to calculate quantity. Calculates any +

                • method_name (str) – Name of method to use to calculate quantity. Calculates any quantity as long as the relevant objects have the same method name. Some examples include: get_HoRT, get_H, get_EoRT, get_E

                • -
                • ref_index (int, optional) – Reaction index to use to reference states. Default is the first +

                • ref_index (int, optional) – Reaction index to use to reference states. Default is the first reaction (i.e. ref_index = 0)

                • -
                • ref_state (str, optional) –

                  State of the reference to use. Supported options include:

                  +
                • ref_state (str, optional) –

                  State of the reference to use. Supported options include:

                  • reactants (default)

                  • products

                  • @@ -249,32 +249,32 @@

                    pmutt.reaction.Reactionsfloat, optional) – Spacing between reaction states. Shape of curve likely does not +
                  • x_offset (float, optional) – Spacing between reaction states. Shape of curve likely does not change with this parameter since the x axis would rescale appropriately

                  • -
                  • include_TS (bool, optional) – Whether transition states should be included. Default is True

                  • -
                  • x_scale_TS (float, optional) – Value between 0 and 1 that controls curvature of transition +

                  • include_TS (bool, optional) – Whether transition states should be included. Default is True

                  • +
                  • x_scale_TS (float, optional) – Value between 0 and 1 that controls curvature of transition state peaks. Higher values produce sharper peaks. Default is 0.5

                  • -
                  • y_scale_TS (float, optional) – Value between 0 and 1 that controls curvature of transition +

                  • y_scale_TS (float, optional) – Value between 0 and 1 that controls curvature of transition state peaks. Higher values produce sharper peaks. Default is 0.5

                  • -
                  • include_TS_labels (bool, optional) – If True, adds a label to the peaks indicating the difference +

                  • include_TS_labels (bool, optional) – If True, adds a label to the peaks indicating the difference between the reactants and the transition state. Default is True

                  • -
                  • y_TS_label_offset (float, optional) – Vertical value to offset TS_label from the TS position. This +

                  • y_TS_label_offset (float, optional) – Vertical value to offset TS_label from the TS position. This value scales with the difference between major ticks. Negative values will shift the label downwards. Default is 0.10

                  • -
                  • x_TS_label_offset (float, optional) – Horizontal value to offset TS_label from the TS_position. This +

                  • x_TS_label_offset (float, optional) – Horizontal value to offset TS_label from the TS_position. This value scales with the x_offset value. Negative values will shift the label rightward. Default is 0 (i.e. labels are directly above peaks by default)

                  • -
                  • TS_label_format (str, optional) – String format to print TS_labels. Uses the +

                  • TS_label_format (str, optional) – String format to print TS_labels. Uses the str.format syntax. Default is ‘.2f’ (i.e. a floating point value rounded to the second decimal place)

                  • figure (matplotlib.figure.Figure) – Add plot to this figure. If not specified, one will be generated

                  • axes (matplotlib.axes.Axes.axis, optional) – Adds plot to this axis. If not specified, one will be generated

                  • -
                  • plt_kwargs (dict, optional) – Extra arguments that will be fed to +

                  • plt_kwargs (dict, optional) – Extra arguments that will be fed to matplotlib.pyplot.subplots

                  • reaction_kwargs (keyword arguments) – Extra arguments that will be fed to the reactions

                  @@ -298,7 +298,7 @@

                  pmutt.reaction.Reactions

                  obj_dict

                Return type:
                -

                dict

                +

                dict

                diff --git a/api/statmech/elec/pmutt.statmech.elec.GroundStateElec.html b/api/statmech/elec/pmutt.statmech.elec.GroundStateElec.html index f8d762b8..31d01733 100644 --- a/api/statmech/elec/pmutt.statmech.elec.GroundStateElec.html +++ b/api/statmech/elec/pmutt.statmech.elec.GroundStateElec.html @@ -4,7 +4,7 @@ - pmutt.statmech.elec.GroundStateElec — pmutt 1.4.7 documentation + pmutt.statmech.elec.GroundStateElec — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
                - 1.4.7 + 1.4.9
                @@ -138,7 +138,7 @@

                pmutt.statmech.elec.GroundStateElec
                Type:
                -

                float, optional

                +

                float, optional

                @@ -154,7 +154,7 @@

                pmutt.statmech.elec.GroundStateElec
                Type:
                -

                float, optional

                +

                float, optional

                @@ -178,7 +178,7 @@

                pmutt.statmech.elec.GroundStateElec
                Type:
                -

                float, optional

                +

                float, optional

                @@ -261,7 +261,7 @@

                pmutt.statmech.elec.GroundStateElec
                Parameters:
                -

                json_obj (dict) – JSON representation

                +

                json_obj (dict) – JSON representation

                Returns:

                Obj

                @@ -279,7 +279,7 @@

                pmutt.statmech.elec.GroundStateElec
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CpoR

                @@ -288,7 +288,7 @@

                pmutt.statmech.elec.GroundStateElec

                Cp – Heat capacity (constant P) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -303,7 +303,7 @@

                pmutt.statmech.elec.GroundStateElec

                CpoR_elec – Electronic dimensionless heat capacity at constant pressure

                Return type:
                -

                float

                +

                float

                @@ -315,7 +315,7 @@

                pmutt.statmech.elec.GroundStateElec
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CvoR

                @@ -324,7 +324,7 @@

                pmutt.statmech.elec.GroundStateElec

                Cv – Heat capacity (constant V) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -339,7 +339,7 @@

                pmutt.statmech.elec.GroundStateElec

                CvoR_elec – electronic dimensionless heat capacity at constant volume

                Return type:
                -

                float

                +

                float

                @@ -351,9 +351,9 @@

                pmutt.statmech.elec.GroundStateElec
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_FoRT

                @@ -361,7 +361,7 @@

                pmutt.statmech.elec.GroundStateElec

                F – Hemholtz energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -373,13 +373,13 @@

                pmutt.statmech.elec.GroundStateElec\(\frac{A^{elec}}{RT}=\frac{U^{elec}}{RT}-\frac{S^{elec}}{R}\)

                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                FoRT_elec – Electronic dimensionless Helmholtz energy

                Return type:
                -

                float

                +

                float

                @@ -391,9 +391,9 @@

                pmutt.statmech.elec.GroundStateElec
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_GoRT

                @@ -401,7 +401,7 @@

                pmutt.statmech.elec.GroundStateElec

                G – Gibbs energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -413,13 +413,13 @@

                pmutt.statmech.elec.GroundStateElec\(\frac{G^{elec}}{RT}=\frac{H^{elec}}{RT}-\frac{S^{elec}}{R}\)

                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                GoRT_elec – Electronic dimensionless Gibbs energy

                Return type:
                -

                float

                +

                float

                @@ -431,9 +431,9 @@

                pmutt.statmech.elec.GroundStateElec
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_HoRT

                @@ -441,7 +441,7 @@

                pmutt.statmech.elec.GroundStateElec

                H – Enthalpy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -453,13 +453,13 @@

                pmutt.statmech.elec.GroundStateElec\(\frac{H^{elec}}{RT}=\frac{U^{elec}}{RT}\)

                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                HoRT_elec – Electronic dimensionless enthalpy

                Return type:
                -

                float

                +

                float

                @@ -471,7 +471,7 @@

                pmutt.statmech.elec.GroundStateElec
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_SoR

                @@ -480,7 +480,7 @@

                pmutt.statmech.elec.GroundStateElec

                S – Entropy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -495,7 +495,7 @@

                pmutt.statmech.elec.GroundStateElec

                SoR_elec – Electronic dimensionless entropy

                Return type:
                -

                float

                +

                float

                @@ -507,9 +507,9 @@

                pmutt.statmech.elec.GroundStateElec
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_UoRT

                @@ -517,7 +517,7 @@

                pmutt.statmech.elec.GroundStateElec

                U – Internal energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -529,13 +529,13 @@

                pmutt.statmech.elec.GroundStateElec\(\frac{U^{elec}}{RT}=\frac{E}{RT}\)

                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                UoRT_elec – Electronic dimensionless internal energy

                Return type:
                -

                float

                +

                float

                @@ -548,8 +548,8 @@

                pmutt.statmech.elec.GroundStateElec
                Parameters:
                  -
                • T (float) – Temperature in K

                • -
                • ignore_q_elec (bool, optional) – Ignore contribution of electronic mode to partition function +

                • T (float) – Temperature in K

                • +
                • ignore_q_elec (bool, optional) – Ignore contribution of electronic mode to partition function . Often necessary since DFT’s value for potentialenergy is very negative causing q_elec to go to infinity. Default is True

                @@ -558,7 +558,7 @@

                pmutt.statmech.elec.GroundStateElec

                q_elec – Electronic partition function

                Return type:
                -

                float

                +

                float

                @@ -577,7 +577,7 @@

                pmutt.statmech.elec.GroundStateElec

                obj_dict

                Return type:
                -

                dict

                +

                dict

                diff --git a/api/statmech/elec/pmutt.statmech.lsr.ExtendedLSR.html b/api/statmech/elec/pmutt.statmech.lsr.ExtendedLSR.html index 06c49250..ce01dec4 100644 --- a/api/statmech/elec/pmutt.statmech.lsr.ExtendedLSR.html +++ b/api/statmech/elec/pmutt.statmech.lsr.ExtendedLSR.html @@ -4,7 +4,7 @@ - pmutt.statmech.lsr.ExtendedLSR — pmutt 1.4.7 documentation + pmutt.statmech.lsr.ExtendedLSR — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
                - 1.4.7 + 1.4.9
                @@ -146,7 +146,7 @@

                pmutt.statmech.lsr.ExtendedLSR
                Type:
                -

                float

                +

                float

                @@ -201,7 +201,7 @@

                pmutt.statmech.lsr.ExtendedLSR
                Type:
                -

                str or dict, optional

                +

                str or dict, optional

                @@ -290,7 +290,7 @@

                pmutt.statmech.lsr.ExtendedLSR
                Parameters:
                -

                json_obj (dict) – JSON representation

                +

                json_obj (dict) – JSON representation

                Returns:

                LSR

                @@ -313,7 +313,7 @@

                pmutt.statmech.lsr.ExtendedLSR
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CpoR

                @@ -322,7 +322,7 @@

                pmutt.statmech.lsr.ExtendedLSR

                Cp – Heat capacity (constant P) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -341,7 +341,7 @@

                pmutt.statmech.lsr.ExtendedLSR
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CvoR

                @@ -350,7 +350,7 @@

                pmutt.statmech.lsr.ExtendedLSR

                Cv – Heat capacity (constant V) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -369,9 +369,9 @@

                pmutt.statmech.lsr.ExtendedLSR
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_FoRT

                @@ -379,7 +379,7 @@

                pmutt.statmech.lsr.ExtendedLSR

                F – Hemholtz energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -392,7 +392,7 @@

                pmutt.statmech.lsr.ExtendedLSR
                Parameters:
                  -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters to calculate reference binding energy, surface energy and gas-phase energy

                @@ -401,7 +401,7 @@

                pmutt.statmech.lsr.ExtendedLSR

                FoRT – Dimensionless Helmholtz energy

                Return type:
                -

                float

                +

                float

                @@ -413,9 +413,9 @@

                pmutt.statmech.lsr.ExtendedLSR
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_GoRT

                @@ -423,7 +423,7 @@

                pmutt.statmech.lsr.ExtendedLSR

                G – Gibbs energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -436,7 +436,7 @@

                pmutt.statmech.lsr.ExtendedLSR
                Parameters:
                  -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters to calculate reference binding energy, surface energy and gas-phase energy

                @@ -445,7 +445,7 @@

                pmutt.statmech.lsr.ExtendedLSR

                GoRT – Dimensionless Gibbs energy

                Return type:
                -

                float

                +

                float

                @@ -457,9 +457,9 @@

                pmutt.statmech.lsr.ExtendedLSR
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_HoRT

                @@ -467,7 +467,7 @@

                pmutt.statmech.lsr.ExtendedLSR

                H – Enthalpy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -480,7 +480,7 @@

                pmutt.statmech.lsr.ExtendedLSR
                Parameters:
                  -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters to calculate reference binding energy, surface energy and gas-phase energy

                @@ -489,7 +489,7 @@

                pmutt.statmech.lsr.ExtendedLSR

                HoRT – Dimensionless enthalpy

                Return type:
                -

                float

                +

                float

                @@ -501,7 +501,7 @@

                pmutt.statmech.lsr.ExtendedLSR
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_SoR

                @@ -510,7 +510,7 @@

                pmutt.statmech.lsr.ExtendedLSR

                S – Entropy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -526,7 +526,7 @@

                pmutt.statmech.lsr.ExtendedLSRReturn type: -

                float

                +

                float

                @@ -538,9 +538,9 @@

                pmutt.statmech.lsr.ExtendedLSR
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_UoRT

                @@ -548,7 +548,7 @@

                pmutt.statmech.lsr.ExtendedLSR

                U – Internal energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -561,7 +561,7 @@

                pmutt.statmech.lsr.ExtendedLSR
                Parameters:
                  -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters to calculate reference binding energy, surface energy and gas-phase energy

                @@ -570,7 +570,7 @@

                pmutt.statmech.lsr.ExtendedLSR

                UoRT – Dimensionless internal energy

                Return type:
                -

                float

                +

                float

                @@ -584,7 +584,7 @@

                pmutt.statmech.lsr.ExtendedLSR

                q – Returns 1

                Return type:
                -

                float

                +

                float

                @@ -608,7 +608,7 @@

                pmutt.statmech.lsr.ExtendedLSR

                obj_dict

                Return type:
                -

                dict

                +

                dict

                diff --git a/api/statmech/elec/pmutt.statmech.lsr.LSR.html b/api/statmech/elec/pmutt.statmech.lsr.LSR.html index 9e96f6f3..5f949916 100644 --- a/api/statmech/elec/pmutt.statmech.lsr.LSR.html +++ b/api/statmech/elec/pmutt.statmech.lsr.LSR.html @@ -4,7 +4,7 @@ - pmutt.statmech.lsr.LSR — pmutt 1.4.7 documentation + pmutt.statmech.lsr.LSR — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
                - 1.4.7 + 1.4.9
                @@ -170,7 +170,7 @@

                pmutt.statmech.lsr.LSR

                Slope of LSR relationship. Represents alpha in above equation

                Type:
                -

                float

                +

                float

                @@ -182,7 +182,7 @@

                pmutt.statmech.lsr.LSR
                Type:
                -

                float

                +

                float

                @@ -237,7 +237,7 @@

                pmutt.statmech.lsr.LSR

                Extra notes such as the source of the LSR. Default is None

                Type:
                -

                str or dict, optional

                +

                str or dict, optional

                @@ -335,7 +335,7 @@

                pmutt.statmech.lsr.LSR

                Recreate an object from the JSON representation.

                Parameters:
                -

                json_obj (dict) – JSON representation

                +

                json_obj (dict) – JSON representation

                Returns:

                LSR

                @@ -358,7 +358,7 @@

                pmutt.statmech.lsr.LSR
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CpoR

                @@ -367,7 +367,7 @@

                pmutt.statmech.lsr.LSR

                Cp – Heat capacity (constant P) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -386,7 +386,7 @@

                pmutt.statmech.lsr.LSR
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CvoR

                @@ -395,7 +395,7 @@

                pmutt.statmech.lsr.LSR

                Cv – Heat capacity (constant V) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -414,9 +414,9 @@

                pmutt.statmech.lsr.LSR
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_FoRT

                @@ -424,7 +424,7 @@

                pmutt.statmech.lsr.LSR

                F – Hemholtz energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -437,7 +437,7 @@

                pmutt.statmech.lsr.LSR
                Parameters:
                  -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters to calculate reference binding energy, surface energy and gas-phase energy

                @@ -446,7 +446,7 @@

                pmutt.statmech.lsr.LSR

                FoRT – Dimensionless Helmholtz energy

                Return type:
                -

                float

                +

                float

                @@ -458,9 +458,9 @@

                pmutt.statmech.lsr.LSR
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_GoRT

                @@ -468,7 +468,7 @@

                pmutt.statmech.lsr.LSR

                G – Gibbs energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -481,7 +481,7 @@

                pmutt.statmech.lsr.LSR
                Parameters:
                  -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters to calculate reference binding energy, surface energy and gas-phase energy

                @@ -490,7 +490,7 @@

                pmutt.statmech.lsr.LSR

                GoRT – Dimensionless Gibbs energy

                Return type:
                -

                float

                +

                float

                @@ -502,9 +502,9 @@

                pmutt.statmech.lsr.LSR
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_HoRT

                @@ -512,7 +512,7 @@

                pmutt.statmech.lsr.LSR

                H – Enthalpy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -525,7 +525,7 @@

                pmutt.statmech.lsr.LSR
                Parameters:
                  -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters to calculate reference binding energy, surface energy and gas-phase energy

                @@ -534,7 +534,7 @@

                pmutt.statmech.lsr.LSR

                HoRT – Dimensionless enthalpy

                Return type:
                -

                float

                +

                float

                @@ -546,7 +546,7 @@

                pmutt.statmech.lsr.LSR
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_SoR

                @@ -555,7 +555,7 @@

                pmutt.statmech.lsr.LSR

                S – Entropy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -571,7 +571,7 @@

                pmutt.statmech.lsr.LSR
                Return type:
                -

                float

                +

                float

                @@ -583,9 +583,9 @@

                pmutt.statmech.lsr.LSR
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_UoRT

                @@ -593,7 +593,7 @@

                pmutt.statmech.lsr.LSR

                U – Internal energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -606,7 +606,7 @@

                pmutt.statmech.lsr.LSR
                Parameters:
                  -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters to calculate reference binding energy, surface energy and gas-phase energy

                @@ -615,7 +615,7 @@

                pmutt.statmech.lsr.LSR

                UoRT – Dimensionless internal energy

                Return type:
                -

                float

                +

                float

                @@ -629,7 +629,7 @@

                pmutt.statmech.lsr.LSR

                q – Returns 1

                Return type:
                -

                float

                +

                float

                @@ -653,7 +653,7 @@

                pmutt.statmech.lsr.LSR

                obj_dict

                Return type:
                -

                dict

                +

                dict

                diff --git a/api/statmech/misc/pmutt.statmech.ConstantMode.html b/api/statmech/misc/pmutt.statmech.ConstantMode.html index 5fc63b84..83826555 100644 --- a/api/statmech/misc/pmutt.statmech.ConstantMode.html +++ b/api/statmech/misc/pmutt.statmech.ConstantMode.html @@ -4,7 +4,7 @@ - pmutt.statmech.ConstantMode — pmutt 1.4.7 documentation + pmutt.statmech.ConstantMode — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
                - 1.4.7 + 1.4.9
                @@ -133,7 +133,7 @@

                pmutt.statmech.ConstantMode
                Type:
                -

                float, optional

                +

                float, optional

                @@ -144,7 +144,7 @@

                pmutt.statmech.ConstantMode
                Type:
                -

                float, optional

                +

                float, optional

                @@ -155,7 +155,7 @@

                pmutt.statmech.ConstantMode
                Type:
                -

                float, optional

                +

                float, optional

                @@ -166,7 +166,7 @@

                pmutt.statmech.ConstantMode
                Type:
                -

                float, optional

                +

                float, optional

                @@ -177,7 +177,7 @@

                pmutt.statmech.ConstantMode
                Type:
                -

                float, optional

                +

                float, optional

                @@ -188,7 +188,7 @@

                pmutt.statmech.ConstantMode
                Type:
                -

                float, optional

                +

                float, optional

                @@ -199,7 +199,7 @@

                pmutt.statmech.ConstantMode
                Type:
                -

                float, optional

                +

                float, optional

                @@ -210,7 +210,7 @@

                pmutt.statmech.ConstantMode
                Type:
                -

                float, optional

                +

                float, optional

                @@ -222,7 +222,7 @@

                pmutt.statmech.ConstantMode
                Type:
                -

                str or dict, optional

                +

                str or dict, optional

                @@ -297,7 +297,7 @@

                pmutt.statmech.ConstantMode
                Parameters:
                -

                json_obj (dict) – JSON representation

                +

                json_obj (dict) – JSON representation

                Returns:

                Obj

                @@ -315,7 +315,7 @@

                pmutt.statmech.ConstantMode
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CpoR

                @@ -324,7 +324,7 @@

                pmutt.statmech.ConstantMode

                Cp – Heat capacity (constant P) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -338,7 +338,7 @@

                pmutt.statmech.ConstantMode

                CpoR – Dimensionless heat capacity (constant pressure)

                Return type:
                -

                float

                +

                float

                @@ -350,7 +350,7 @@

                pmutt.statmech.ConstantMode
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CvoR

                @@ -359,7 +359,7 @@

                pmutt.statmech.ConstantMode

                Cv – Heat capacity (constant V) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -373,7 +373,7 @@

                pmutt.statmech.ConstantMode

                CvoR – Dimensionless heat capacity (constant volume)

                Return type:
                -

                float

                +

                float

                @@ -385,9 +385,9 @@

                pmutt.statmech.ConstantMode
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_FoRT

                @@ -395,7 +395,7 @@

                pmutt.statmech.ConstantMode

                F – Hemholtz energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -406,13 +406,13 @@

                pmutt.statmech.ConstantMode
                Parameters:
                -

                T (float, optional) – Temperature in K. Default is 298.15 K

                +

                T (float, optional) – Temperature in K. Default is 298.15 K

                Returns:

                FoRT – Dimensionless Helmholtz energy

                Return type:
                -

                float

                +

                float

                @@ -424,9 +424,9 @@

                pmutt.statmech.ConstantMode
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_GoRT

                @@ -434,7 +434,7 @@

                pmutt.statmech.ConstantMode

                G – Gibbs energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -445,13 +445,13 @@

                pmutt.statmech.ConstantMode
                Parameters:
                -

                T (float, optional) – Temperature in K. Default is 298.15 K

                +

                T (float, optional) – Temperature in K. Default is 298.15 K

                Returns:

                GoRT – Dimensionless Gibbs energy

                Return type:
                -

                float

                +

                float

                @@ -463,9 +463,9 @@

                pmutt.statmech.ConstantMode
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_HoRT

                @@ -473,7 +473,7 @@

                pmutt.statmech.ConstantMode

                H – Enthalpy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -484,13 +484,13 @@

                pmutt.statmech.ConstantMode
                Parameters:
                -

                T (float, optional) – Temperature in K. Default is 298.15 K

                +

                T (float, optional) – Temperature in K. Default is 298.15 K

                Returns:

                HoRT – Dimensionless enthalpy

                Return type:
                -

                float

                +

                float

                @@ -502,7 +502,7 @@

                pmutt.statmech.ConstantMode
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_SoR

                @@ -511,7 +511,7 @@

                pmutt.statmech.ConstantMode

                S – Entropy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -525,7 +525,7 @@

                pmutt.statmech.ConstantMode

                SoR – Dimensionless entropy

                Return type:
                -

                float

                +

                float

                @@ -537,9 +537,9 @@

                pmutt.statmech.ConstantMode
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_UoRT

                @@ -547,7 +547,7 @@

                pmutt.statmech.ConstantMode

                U – Internal energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -558,13 +558,13 @@

                pmutt.statmech.ConstantMode
                Parameters:
                -

                T (float, optional) – Temperature in K. Default is 298.15 K

                +

                T (float, optional) – Temperature in K. Default is 298.15 K

                Returns:

                UoRT – Dimensionless internal energy

                Return type:
                -

                float

                +

                float

                @@ -578,7 +578,7 @@

                pmutt.statmech.ConstantMode

                q – Partition function

                Return type:
                -

                float

                +

                float

                @@ -592,7 +592,7 @@

                pmutt.statmech.ConstantMode

                obj_dict

                Return type:
                -

                dict

                +

                dict

                diff --git a/api/statmech/misc/pmutt.statmech.EmptyMode.html b/api/statmech/misc/pmutt.statmech.EmptyMode.html index cbed01e3..eb7c780c 100644 --- a/api/statmech/misc/pmutt.statmech.EmptyMode.html +++ b/api/statmech/misc/pmutt.statmech.EmptyMode.html @@ -4,7 +4,7 @@ - pmutt.statmech.EmptyMode — pmutt 1.4.7 documentation + pmutt.statmech.EmptyMode — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
                - 1.4.7 + 1.4.9
                @@ -196,7 +196,7 @@

                pmutt.statmech.EmptyMode
                Parameters:
                -

                json_obj (dict) – JSON representation

                +

                json_obj (dict) – JSON representation

                Returns:

                Obj

                @@ -214,7 +214,7 @@

                pmutt.statmech.EmptyMode
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CpoR

                @@ -223,7 +223,7 @@

                pmutt.statmech.EmptyMode

                Cp – Heat capacity (constant P) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -238,7 +238,7 @@

                pmutt.statmech.EmptyMode

                CpoR – Returns 0

                Return type:
                -

                float

                +

                float

                @@ -250,7 +250,7 @@

                pmutt.statmech.EmptyMode
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CvoR

                @@ -259,7 +259,7 @@

                pmutt.statmech.EmptyMode

                Cv – Heat capacity (constant V) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -274,7 +274,7 @@

                pmutt.statmech.EmptyMode

                CvoR – Returns 0

                Return type:
                -

                float

                +

                float

                @@ -286,9 +286,9 @@

                pmutt.statmech.EmptyMode
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_FoRT

                @@ -296,7 +296,7 @@

                pmutt.statmech.EmptyMode

                F – Hemholtz energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -313,7 +313,7 @@

                pmutt.statmech.EmptyMode

                FoRT – Dimensionless Helmholtz energy

                Return type:
                -

                float

                +

                float

                @@ -325,9 +325,9 @@

                pmutt.statmech.EmptyMode
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_GoRT

                @@ -335,7 +335,7 @@

                pmutt.statmech.EmptyMode

                G – Gibbs energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -352,7 +352,7 @@

                pmutt.statmech.EmptyMode

                GoRT – Dimensionless Gibbs free energy

                Return type:
                -

                float

                +

                float

                @@ -364,9 +364,9 @@

                pmutt.statmech.EmptyMode
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_HoRT

                @@ -374,7 +374,7 @@

                pmutt.statmech.EmptyMode

                H – Enthalpy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -388,7 +388,7 @@

                pmutt.statmech.EmptyMode

                HoRT – Returns 0

                Return type:
                -

                float

                +

                float

                @@ -400,7 +400,7 @@

                pmutt.statmech.EmptyMode
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_SoR

                @@ -409,7 +409,7 @@

                pmutt.statmech.EmptyMode

                S – Entropy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -423,7 +423,7 @@

                pmutt.statmech.EmptyMode

                SoR – Returns 0

                Return type:
                -

                float

                +

                float

                @@ -435,9 +435,9 @@

                pmutt.statmech.EmptyMode
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_UoRT

                @@ -445,7 +445,7 @@

                pmutt.statmech.EmptyMode

                U – Internal energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -459,7 +459,7 @@

                pmutt.statmech.EmptyMode

                UoRT – Returns 0

                Return type:
                -

                float

                +

                float

                @@ -473,7 +473,7 @@

                pmutt.statmech.EmptyMode

                q – Returns 1

                Return type:
                -

                float

                +

                float

                @@ -487,7 +487,7 @@

                pmutt.statmech.EmptyMode

                obj_dict

                Return type:
                -

                dict

                +

                dict

                diff --git a/api/statmech/nucl/pmutt.statmech.nucl.EmptyNucl.html b/api/statmech/nucl/pmutt.statmech.nucl.EmptyNucl.html index d647af90..36a87bfe 100644 --- a/api/statmech/nucl/pmutt.statmech.nucl.EmptyNucl.html +++ b/api/statmech/nucl/pmutt.statmech.nucl.EmptyNucl.html @@ -4,7 +4,7 @@ - pmutt.statmech.nucl.EmptyNucl — pmutt 1.4.7 documentation + pmutt.statmech.nucl.EmptyNucl — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
                - 1.4.7 + 1.4.9
                @@ -195,7 +195,7 @@

                pmutt.statmech.nucl.EmptyNucl
                Parameters:
                -

                json_obj (dict) – JSON representation

                +

                json_obj (dict) – JSON representation

                Returns:

                Obj

                @@ -213,7 +213,7 @@

                pmutt.statmech.nucl.EmptyNucl
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CpoR

                @@ -222,7 +222,7 @@

                pmutt.statmech.nucl.EmptyNucl

                Cp – Heat capacity (constant P) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -236,7 +236,7 @@

                pmutt.statmech.nucl.EmptyNucl

                CpoR_nucl – Nuclear dimensionless heat capacity at constant pressure

                Return type:
                -

                float

                +

                float

                @@ -248,7 +248,7 @@

                pmutt.statmech.nucl.EmptyNucl
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CvoR

                @@ -257,7 +257,7 @@

                pmutt.statmech.nucl.EmptyNucl

                Cv – Heat capacity (constant V) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -271,7 +271,7 @@

                pmutt.statmech.nucl.EmptyNucl

                CvoR_nucl – Nuclear dimensionless heat capacity at constant volume

                Return type:
                -

                float

                +

                float

                @@ -283,9 +283,9 @@

                pmutt.statmech.nucl.EmptyNucl
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_FoRT

                @@ -293,7 +293,7 @@

                pmutt.statmech.nucl.EmptyNucl

                F – Hemholtz energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -307,7 +307,7 @@

                pmutt.statmech.nucl.EmptyNucl

                FoRT_nucl – Nuclear dimensionless Helmholtz energy

                Return type:
                -

                float

                +

                float

                @@ -319,9 +319,9 @@

                pmutt.statmech.nucl.EmptyNucl
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_GoRT

                @@ -329,7 +329,7 @@

                pmutt.statmech.nucl.EmptyNucl

                G – Gibbs energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -343,7 +343,7 @@

                pmutt.statmech.nucl.EmptyNucl

                GoRT_nucl – Nuclear dimensionless Gibbs energy

                Return type:
                -

                float

                +

                float

                @@ -355,9 +355,9 @@

                pmutt.statmech.nucl.EmptyNucl
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_HoRT

                @@ -365,7 +365,7 @@

                pmutt.statmech.nucl.EmptyNucl

                H – Enthalpy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -379,7 +379,7 @@

                pmutt.statmech.nucl.EmptyNucl

                HoRT_nucl – Nuclear dimensionless enthalpy

                Return type:
                -

                float

                +

                float

                @@ -391,7 +391,7 @@

                pmutt.statmech.nucl.EmptyNucl
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_SoR

                @@ -400,7 +400,7 @@

                pmutt.statmech.nucl.EmptyNucl

                S – Entropy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -414,7 +414,7 @@

                pmutt.statmech.nucl.EmptyNucl

                SoR_nucl – Nuclear dimensionless entropy

                Return type:
                -

                float

                +

                float

                @@ -426,9 +426,9 @@

                pmutt.statmech.nucl.EmptyNucl
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_UoRT

                @@ -436,7 +436,7 @@

                pmutt.statmech.nucl.EmptyNucl

                U – Internal energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -450,7 +450,7 @@

                pmutt.statmech.nucl.EmptyNucl

                UoRT_nucl – Nuclear dimensionless internal energy

                Return type:
                -

                float

                +

                float

                @@ -464,7 +464,7 @@

                pmutt.statmech.nucl.EmptyNucl

                q_nucl – Nuclear partition function

                Return type:
                -

                float

                +

                float

                @@ -478,7 +478,7 @@

                pmutt.statmech.nucl.EmptyNucl

                obj_dict

                Return type:
                -

                dict

                +

                dict

                diff --git a/api/statmech/rot/pmutt.statmech.rot.RigidRotor.html b/api/statmech/rot/pmutt.statmech.rot.RigidRotor.html index c275ed4d..4f1aa5ef 100644 --- a/api/statmech/rot/pmutt.statmech.rot.RigidRotor.html +++ b/api/statmech/rot/pmutt.statmech.rot.RigidRotor.html @@ -4,7 +4,7 @@ - pmutt.statmech.rot.RigidRotor — pmutt 1.4.7 documentation + pmutt.statmech.rot.RigidRotor — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
                - 1.4.7 + 1.4.9
                @@ -185,7 +185,7 @@

                pmutt.statmech.rot.RigidRotor
                Type:
                -

                float or str

                +

                float or str

                @@ -212,7 +212,7 @@

                pmutt.statmech.rot.RigidRotor
                Type:
                -

                str

                +

                str

                @@ -236,7 +236,7 @@

                pmutt.statmech.rot.RigidRotor
                Type:
                -

                float

                +

                float

                @@ -311,7 +311,7 @@

                pmutt.statmech.rot.RigidRotor
                Parameters:
                -

                json_obj (dict) – JSON representation

                +

                json_obj (dict) – JSON representation

                Returns:

                Obj

                @@ -329,7 +329,7 @@

                pmutt.statmech.rot.RigidRotor
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CpoR

                @@ -338,7 +338,7 @@

                pmutt.statmech.rot.RigidRotor

                Cp – Heat capacity (constant P) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -353,7 +353,7 @@

                pmutt.statmech.rot.RigidRotor

                CpoR_rot – Rotational dimensionless heat capacity at constant pressure

                Return type:
                -

                float

                +

                float

                @@ -365,7 +365,7 @@

                pmutt.statmech.rot.RigidRotor
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CvoR

                @@ -374,7 +374,7 @@

                pmutt.statmech.rot.RigidRotor

                Cv – Heat capacity (constant V) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -391,7 +391,7 @@

                pmutt.statmech.rot.RigidRotor

                CvoR_rot – Rotational dimensionless heat capacity at constant volume

                Return type:
                -

                float

                +

                float

                @@ -403,9 +403,9 @@

                pmutt.statmech.rot.RigidRotor
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_FoRT

                @@ -413,7 +413,7 @@

                pmutt.statmech.rot.RigidRotor

                F – Hemholtz energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -425,13 +425,13 @@

                pmutt.statmech.rot.RigidRotor\(\frac{A^{rot}}{RT}=\frac{U^{rot}}{RT}-\frac{S^{rot}}{R}\)

                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                FoRT_rot – Rotational dimensionless Helmholtz energy

                Return type:
                -

                float

                +

                float

                @@ -443,9 +443,9 @@

                pmutt.statmech.rot.RigidRotor
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_GoRT

                @@ -453,7 +453,7 @@

                pmutt.statmech.rot.RigidRotor

                G – Gibbs energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -465,13 +465,13 @@

                pmutt.statmech.rot.RigidRotor\(\frac{G^{rot}}{RT}=\frac{H^{rot}}{RT}-\frac{S^{rot}}{R}\)

                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                GoRT_rot – Rotational dimensionless Gibbs energy

                Return type:
                -

                float

                +

                float

                @@ -483,9 +483,9 @@

                pmutt.statmech.rot.RigidRotor
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_HoRT

                @@ -493,7 +493,7 @@

                pmutt.statmech.rot.RigidRotor

                H – Enthalpy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -508,7 +508,7 @@

                pmutt.statmech.rot.RigidRotor

                HoRT_rot – Rotational dimensionless enthalpy

                Return type:
                -

                float

                +

                float

                @@ -520,7 +520,7 @@

                pmutt.statmech.rot.RigidRotor
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_SoR

                @@ -529,7 +529,7 @@

                pmutt.statmech.rot.RigidRotor

                S – Entropy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -546,13 +546,13 @@

                pmutt.statmech.rot.RigidRotor
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                SoR_rot – Rotational dimensionless entropy

                Return type:
                -

                float

                +

                float

                @@ -564,9 +564,9 @@

                pmutt.statmech.rot.RigidRotor
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_UoRT

                @@ -574,7 +574,7 @@

                pmutt.statmech.rot.RigidRotor

                U – Internal energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -591,7 +591,7 @@

                pmutt.statmech.rot.RigidRotor

                UoRT_rot – Rotational dimensionless internal energy

                Return type:
                -

                float

                +

                float

                @@ -606,13 +606,13 @@

                pmutt.statmech.rot.RigidRotor
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                q_rot – Rotational partition function

                Return type:
                -

                float

                +

                float

                @@ -626,7 +626,7 @@

                pmutt.statmech.rot.RigidRotor

                obj_dict

                Return type:
                -

                dict

                +

                dict

                diff --git a/api/statmech/statmech.html b/api/statmech/statmech.html index d4d1614d..a24858ec 100644 --- a/api/statmech/statmech.html +++ b/api/statmech/statmech.html @@ -4,7 +4,7 @@ - Statistical Thermodynamic Models — pmutt 1.4.7 documentation + Statistical Thermodynamic Models — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
                - 1.4.7 + 1.4.9
                diff --git a/api/statmech/statmech/pmutt.statmech.StatMech.html b/api/statmech/statmech/pmutt.statmech.StatMech.html index 4e2d7dd0..fe365414 100644 --- a/api/statmech/statmech/pmutt.statmech.StatMech.html +++ b/api/statmech/statmech/pmutt.statmech.StatMech.html @@ -4,7 +4,7 @@ - pmutt.statmech.StatMech — pmutt 1.4.7 documentation + pmutt.statmech.StatMech — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
                - 1.4.7 + 1.4.9
                @@ -132,7 +132,7 @@

                pmutt.statmech.StatMech

                Name of the specie. Default is None

                Type:
                -

                str, optional

                +

                str, optional

                @@ -207,7 +207,7 @@

                pmutt.statmech.StatMech
                Type:
                -

                dict, optional

                +

                dict, optional

                @@ -242,7 +242,7 @@

                pmutt.statmech.StatMech

                Smiles representation of species

                Type:
                -

                str, optional

                +

                str, optional

                @@ -254,7 +254,7 @@

                pmutt.statmech.StatMech
                Type:
                -

                str, optional

                +

                str, optional

                @@ -341,7 +341,7 @@

                pmutt.statmech.StatMech

                Recreate an object from the JSON representation.

                Parameters:
                -

                json_obj (dict) – JSON representation

                +

                json_obj (dict) – JSON representation

                Returns:

                StatMech

                @@ -359,16 +359,16 @@

                pmutt.statmech.StatMech
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • verbose (bool, optional) – If False, returns the total heat capacity. If True, returns +

                • verbose (bool, optional) – If False, returns the total heat capacity. If True, returns contribution of each mode.

                • -
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

                • -
                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

                • -
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • +
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • kwargs (key-word arguments) – Parameters passed to each mode

                @@ -390,14 +390,14 @@

                pmutt.statmech.StatMech
                Parameters:
                  -
                • verbose (bool, optional) – If False, returns the total heat capacity. If True, returns +

                • verbose (bool, optional) – If False, returns the total heat capacity. If True, returns contribution of each mode.

                • -
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

                • -
                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

                • -
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • +
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • kwargs (key-word arguments) – Parameters passed to each mode

                @@ -420,16 +420,16 @@

                pmutt.statmech.StatMech
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • verbose (bool, optional) – If False, returns the total heat capacity. If True, returns +

                • verbose (bool, optional) – If False, returns the total heat capacity. If True, returns contribution of each mode.

                • -
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

                • -
                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

                • -
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • +
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • kwargs (key-word arguments) – Parameters passed to each mode

                @@ -451,14 +451,14 @@

                pmutt.statmech.StatMech
                Parameters:
                  -
                • verbose (bool, optional) – If False, returns the total heat capacity. If True, returns +

                • verbose (bool, optional) – If False, returns the total heat capacity. If True, returns contribution of each mode.

                • -
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

                • -
                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

                • -
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • +
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • kwargs (key-word arguments) – Parameters passed to each mode

                @@ -481,15 +481,15 @@

                pmutt.statmech.StatMech
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. If the electronic mode is +

                • T (float, optional) – Temperature in K. If the electronic mode is GroundStateElec, then the output is insensitive to this input. Default is 298.15 K

                • -
                • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

                • -
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

                • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

                • +
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

                • -
                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

                • kwargs (key-word arguments) – Parameters passed to each mode

                • @@ -499,7 +499,7 @@

                  pmutt.statmech.StatMech

                  E – Electronic energy

                Return type:
                -

                float

                +

                float

                @@ -511,13 +511,13 @@

                pmutt.statmech.StatMech
                Parameters:
                  -
                • T (float, optional) – Temperature in K. If the electronic mode is +

                • T (float, optional) – Temperature in K. If the electronic mode is GroundStateElec, then the output is insensitive to this input. Default is 298.15 K

                • -
                • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

                • -
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

                • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

                • +
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

                • -
                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

                • kwargs (key-word arguments) – Parameters passed to electronic mode

                • @@ -527,7 +527,7 @@

                  pmutt.statmech.StatMech

                  EoRT – Dimensionless electronic energy

                Return type:
                -

                float

                +

                float

                @@ -539,18 +539,18 @@

                pmutt.statmech.StatMech
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • -
                • verbose (bool, optional) – If False, returns the Helmholtz energy. If True, returns +

                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • verbose (bool, optional) – If False, returns the Helmholtz energy. If True, returns contribution of each mode.

                • -
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

                • -
                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

                • -
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • -
                • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of +

                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • +
                • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

                • kwargs (key-word arguments) – Parameters passed to each mode

                @@ -573,15 +573,15 @@

                pmutt.statmech.StatMech
                Parameters:
                  -
                • verbose (bool, optional) – If False, returns the total Helmholtz energy. If True, returns +

                • verbose (bool, optional) – If False, returns the total Helmholtz energy. If True, returns contribution of each mode.

                • -
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

                • -
                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

                • -
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • -
                • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of +

                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • +
                • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

                • kwargs (key-word arguments) – Parameters passed to each mode

                @@ -605,17 +605,17 @@

                pmutt.statmech.StatMech
                Parameters:
                  -
                • verbose (bool, optional) – If False, returns the Gibbs energy. If True, returns +

                • verbose (bool, optional) – If False, returns the Gibbs energy. If True, returns contribution of each mode.

                • -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • -
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

                • -
                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

                • -
                • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of +

                • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

                • kwargs (key-word arguments) – Parameters passed to each mode

                @@ -638,15 +638,15 @@

                pmutt.statmech.StatMech
                Parameters:
                  -
                • verbose (bool, optional) – If False, returns the total Gibbs energy. If True, returns +

                • verbose (bool, optional) – If False, returns the total Gibbs energy. If True, returns contribution of each mode.

                • -
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

                • -
                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

                • -
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • -
                • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of +

                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • +
                • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

                • kwargs (key-word arguments) – Parameters passed to each mode

                @@ -670,17 +670,17 @@

                pmutt.statmech.StatMech
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • -
                • verbose (bool, optional) – If False, returns the enthalpy. If True, returns +

                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • verbose (bool, optional) – If False, returns the enthalpy. If True, returns contribution of each mode.

                • -
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

                • -
                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

                • -
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • +
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • kwargs (key-word arguments) – Parameters passed to each mode

                @@ -702,14 +702,14 @@

                pmutt.statmech.StatMech
                Parameters:
                  -
                • verbose (bool, optional) – If False, returns the total enthalpy. If True, returns +

                • verbose (bool, optional) – If False, returns the total enthalpy. If True, returns contribution of each mode.

                • -
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

                • -
                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

                • -
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • +
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • kwargs (key-word arguments) – Parameters passed to each mode

                @@ -732,17 +732,17 @@

                pmutt.statmech.StatMech
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • -
                • verbose (bool, optional) – If False, returns the entropy. If True, returns +

                • verbose (bool, optional) – If False, returns the entropy. If True, returns contribution of each mode.

                • -
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

                • -
                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

                • -
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • -
                • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of +

                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • +
                • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

                • kwargs (key-word arguments) – Parameters passed to each mode

                @@ -770,7 +770,7 @@

                pmutt.statmech.StatMech

                SoR – Entropy

                Return type:
                -

                float

                +

                float

                @@ -782,16 +782,16 @@

                pmutt.statmech.StatMech
                Parameters:
                  -
                • verbose (bool, optional) – If False, returns the total entropy. If True, returns +

                • verbose (bool, optional) – If False, returns the total entropy. If True, returns contribution of each mode.

                • kwargs (key-word arguments) – Parameters passed to each mode

                • -
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

                • -
                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

                • -
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • -
                • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of +

                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • +
                • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

                @@ -813,17 +813,17 @@

                pmutt.statmech.StatMech
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • -
                • verbose (bool, optional) – If False, returns the internal energy. If True, returns +

                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • verbose (bool, optional) – If False, returns the internal energy. If True, returns contribution of each mode.

                • -
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

                • -
                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

                • -
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • +
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • kwargs (key-word arguments) – Parameters passed to each mode

                @@ -845,14 +845,14 @@

                pmutt.statmech.StatMech
                Parameters:
                  -
                • verbose (bool, optional) – If False, returns the total internal energy. If True, returns +

                • verbose (bool, optional) – If False, returns the total internal energy. If True, returns contribution of each mode.

                • -
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

                • -
                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

                • -
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • +
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • kwargs (key-word arguments) – Parameters passed to each mode

                @@ -875,14 +875,14 @@

                pmutt.statmech.StatMech
                Parameters:
                  -
                • verbose (bool, optional) – If False, returns the product of partition functions. If True, +

                • verbose (bool, optional) – If False, returns the product of partition functions. If True, returns contributions of each mode

                • -
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

                • -
                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

                • -
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • +
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • kwargs (key-word arguments) – Parameters passed to each mode

                @@ -904,23 +904,23 @@

                pmutt.statmech.StatMech
                Parameters:
                  -
                • method_name (str) – Name of method to use to calculate quantity. Calculates any +

                • method_name (str) – Name of method to use to calculate quantity. Calculates any quantity as long as the relevant objects have the same method name

                • -
                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the +

                • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

                • -
                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any +

                • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

                • -
                • operation (str, optional) –

                  Operation to apply when combining the modes. Supported options +

                • operation (str, optional) –

                  Operation to apply when combining the modes. Supported options include:

                  • sum (Default)

                  • prod

                • -
                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • -
                • verbose (bool, optional) – If False, returns the total Gibbs energy. If True, returns +

                • use_references (bool, optional) – If True, adds contribution from references. Default is True

                • +
                • verbose (bool, optional) – If False, returns the total Gibbs energy. If True, returns contribution of each mode.

                • kwargs (key-word arguments) – Parameters passed to each mode

                @@ -945,7 +945,7 @@

                pmutt.statmech.StatMech

                obj_dict

                Return type:
                -

                dict

                +

                dict

                diff --git a/api/statmech/trans/pmutt.statmech.trans.FreeTrans.html b/api/statmech/trans/pmutt.statmech.trans.FreeTrans.html index 0e8cc82c..1d404b0d 100644 --- a/api/statmech/trans/pmutt.statmech.trans.FreeTrans.html +++ b/api/statmech/trans/pmutt.statmech.trans.FreeTrans.html @@ -4,7 +4,7 @@ - pmutt.statmech.trans.FreeTrans — pmutt 1.4.7 documentation + pmutt.statmech.trans.FreeTrans — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
                - 1.4.7 + 1.4.9
                @@ -135,7 +135,7 @@

                pmutt.statmech.trans.FreeTrans
                Type:
                -

                int, optional

                +

                int, optional

                @@ -146,7 +146,7 @@

                pmutt.statmech.trans.FreeTrans
                Type:
                -

                float

                +

                float

                @@ -236,7 +236,7 @@

                pmutt.statmech.trans.FreeTrans
                Parameters:
                -

                json_obj (dict) – JSON representation

                +

                json_obj (dict) – JSON representation

                Returns:

                Obj

                @@ -254,7 +254,7 @@

                pmutt.statmech.trans.FreeTrans
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CpoR

                @@ -263,7 +263,7 @@

                pmutt.statmech.trans.FreeTrans

                Cp – Heat capacity (constant P) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -278,7 +278,7 @@

                pmutt.statmech.trans.FreeTrans

                CpoR_trans – Translational dimensionless heat capacity at constant P

                Return type:
                -

                float

                +

                float

                @@ -290,7 +290,7 @@

                pmutt.statmech.trans.FreeTrans
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CvoR

                @@ -299,7 +299,7 @@

                pmutt.statmech.trans.FreeTrans

                Cv – Heat capacity (constant V) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -314,7 +314,7 @@

                pmutt.statmech.trans.FreeTrans

                CvoR_trans – Translational dimensionless heat capacity at constant V

                Return type:
                -

                float

                +

                float

                @@ -326,9 +326,9 @@

                pmutt.statmech.trans.FreeTrans
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_FoRT

                @@ -336,7 +336,7 @@

                pmutt.statmech.trans.FreeTrans

                F – Hemholtz energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -349,8 +349,8 @@

                pmutt.statmech.trans.FreeTrans
                Parameters:
                  -
                • T (float) – Temperature in K

                • -
                • P (float, optional) – Pressure (bar) or pressure-like quantity. +

                • T (float) – Temperature in K

                • +
                • P (float, optional) – Pressure (bar) or pressure-like quantity. Default is atmospheric pressure

                @@ -358,7 +358,7 @@

                pmutt.statmech.trans.FreeTrans

                FoRT_trans – Translational dimensionless Helmholtz energy

                Return type:
                -

                float

                +

                float

                @@ -370,9 +370,9 @@

                pmutt.statmech.trans.FreeTrans
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_GoRT

                @@ -380,7 +380,7 @@

                pmutt.statmech.trans.FreeTrans

                G – Gibbs energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -393,8 +393,8 @@

                pmutt.statmech.trans.FreeTrans
                Parameters:
                  -
                • T (float) – Temperature in K

                • -
                • P (float, optional) – Pressure (bar) or pressure-like quantity. +

                • T (float) – Temperature in K

                • +
                • P (float, optional) – Pressure (bar) or pressure-like quantity. Default is atmospheric pressure

                @@ -402,7 +402,7 @@

                pmutt.statmech.trans.FreeTrans

                GoR_trans – Translational dimensionless Gibbs energy

                Return type:
                -

                float

                +

                float

                @@ -414,9 +414,9 @@

                pmutt.statmech.trans.FreeTrans
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_HoRT

                @@ -424,7 +424,7 @@

                pmutt.statmech.trans.FreeTrans

                H – Enthalpy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -439,7 +439,7 @@

                pmutt.statmech.trans.FreeTrans

                HoRT_trans – Translational enthalpy

                Return type:
                -

                float

                +

                float

                @@ -451,7 +451,7 @@

                pmutt.statmech.trans.FreeTrans
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_SoR

                @@ -460,7 +460,7 @@

                pmutt.statmech.trans.FreeTrans

                S – Entropy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -474,8 +474,8 @@

                pmutt.statmech.trans.FreeTrans
                Parameters:
                  -
                • T (float) – Temperature in K

                • -
                • P (float, optional) – Pressure (bar) or pressure-like quantity. +

                • T (float) – Temperature in K

                • +
                • P (float, optional) – Pressure (bar) or pressure-like quantity. Default is atmospheric pressure

                @@ -483,7 +483,7 @@

                pmutt.statmech.trans.FreeTrans

                SoR_trans – Translational dimensionless entropy

                Return type:
                -

                float

                +

                float

                @@ -495,9 +495,9 @@

                pmutt.statmech.trans.FreeTrans
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_UoRT

                @@ -505,7 +505,7 @@

                pmutt.statmech.trans.FreeTrans

                U – Internal energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -520,7 +520,7 @@

                pmutt.statmech.trans.FreeTrans

                UoRT_trans – Translational internal energy

                Return type:
                -

                float

                +

                float

                @@ -533,15 +533,15 @@

                pmutt.statmech.trans.FreeTrans
                Parameters:
                  -
                • T (float) – Temperature in K

                • -
                • P (float) – Pressure in bar

                • +
                • T (float) – Temperature in K

                • +
                • P (float) – Pressure in bar

                Returns:

                V – Molar volume in m3

                Return type:
                -

                float

                +

                float

                @@ -555,8 +555,8 @@

                pmutt.statmech.trans.FreeTrans
                Parameters:
                  -
                • T (float) – Temperature in K

                • -
                • P (float, optional) – Pressure (bar) or pressure-like quantity. +

                • T (float) – Temperature in K

                • +
                • P (float, optional) – Pressure (bar) or pressure-like quantity. Default is atmospheric pressure

                @@ -564,7 +564,7 @@

                pmutt.statmech.trans.FreeTrans

                q_trans – Translational partition function

                Return type:
                -

                float

                +

                float

                @@ -578,7 +578,7 @@

                pmutt.statmech.trans.FreeTrans

                obj_dict

                Return type:
                -

                dict

                +

                dict

                diff --git a/api/statmech/vib/pmutt.statmech.vib.DebyeVib.html b/api/statmech/vib/pmutt.statmech.vib.DebyeVib.html index 6b0f67e8..dc479d14 100644 --- a/api/statmech/vib/pmutt.statmech.vib.DebyeVib.html +++ b/api/statmech/vib/pmutt.statmech.vib.DebyeVib.html @@ -4,7 +4,7 @@ - pmutt.statmech.vib.DebyeVib — pmutt 1.4.7 documentation + pmutt.statmech.vib.DebyeVib — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
                - 1.4.7 + 1.4.9
                @@ -138,7 +138,7 @@

                pmutt.statmech.vib.DebyeVib\(\Theta_D\)) in K

                Type:
                -

                float

                +

                float

                @@ -149,7 +149,7 @@

                pmutt.statmech.vib.DebyeVib\(u\)) per atom in eV. Default is 0 eV

                Type:
                -

                float, optional

                +

                float, optional

                @@ -227,7 +227,7 @@

                pmutt.statmech.vib.DebyeVib
                Parameters:
                -

                json_obj (dict) – JSON representation

                +

                json_obj (dict) – JSON representation

                Returns:

                Obj

                @@ -245,7 +245,7 @@

                pmutt.statmech.vib.DebyeVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CpoR

                @@ -254,7 +254,7 @@

                pmutt.statmech.vib.DebyeVib

                Cp – Heat capacity (constant P) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -268,13 +268,13 @@

                pmutt.statmech.vib.DebyeVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                CpoR – Dimensionless heat capacity (constant P)

                Return type:
                -

                float

                +

                float

                @@ -286,7 +286,7 @@

                pmutt.statmech.vib.DebyeVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CvoR

                @@ -295,7 +295,7 @@

                pmutt.statmech.vib.DebyeVib

                Cv – Heat capacity (constant V) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -309,13 +309,13 @@

                pmutt.statmech.vib.DebyeVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                CvoR – Dimensionless heat capacity (constant V)

                Return type:
                -

                float

                +

                float

                @@ -327,9 +327,9 @@

                pmutt.statmech.vib.DebyeVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_FoRT

                @@ -337,7 +337,7 @@

                pmutt.statmech.vib.DebyeVib

                F – Hemholtz energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -349,13 +349,13 @@

                pmutt.statmech.vib.DebyeVib\(\frac{F^{vib}}{RT}=\frac{U^{vib}}{RT}-\frac{S^{vib}}{R}\)

                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                FoRT – Dimensionless Helmholtz energy

                Return type:
                -

                float

                +

                float

                @@ -367,9 +367,9 @@

                pmutt.statmech.vib.DebyeVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_GoRT

                @@ -377,7 +377,7 @@

                pmutt.statmech.vib.DebyeVib

                G – Gibbs energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -389,13 +389,13 @@

                pmutt.statmech.vib.DebyeVib\(\frac{G^{vib}}{RT}=\frac{H^{vib}}{RT}-\frac{S^{vib}}{R}\)

                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                GoRT – Dimensionless Gibbs energy

                Return type:
                -

                float

                +

                float

                @@ -407,9 +407,9 @@

                pmutt.statmech.vib.DebyeVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_HoRT

                @@ -417,7 +417,7 @@

                pmutt.statmech.vib.DebyeVib

                H – Enthalpy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -433,13 +433,13 @@

                pmutt.statmech.vib.DebyeVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                HoRT – Dimensionless enthalpy

                Return type:
                -

                float

                +

                float

                @@ -451,7 +451,7 @@

                pmutt.statmech.vib.DebyeVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_SoR

                @@ -460,7 +460,7 @@

                pmutt.statmech.vib.DebyeVib

                S – Entropy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -479,13 +479,13 @@

                pmutt.statmech.vib.DebyeVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                SoR – Dimensionless entropy

                Return type:
                -

                float

                +

                float

                @@ -497,9 +497,9 @@

                pmutt.statmech.vib.DebyeVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_UoRT

                @@ -507,7 +507,7 @@

                pmutt.statmech.vib.DebyeVib

                U – Internal energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -523,13 +523,13 @@

                pmutt.statmech.vib.DebyeVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                UoRT – Dimensionless internal energy

                Return type:
                -

                float

                +

                float

                @@ -544,7 +544,7 @@

                pmutt.statmech.vib.DebyeVib

                zpe – Zero point energy in eV

                Return type:
                -

                float

                +

                float

                @@ -560,13 +560,13 @@

                pmutt.statmech.vib.DebyeVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                q – Partition function

                Return type:
                -

                float

                +

                float

                @@ -580,7 +580,7 @@

                pmutt.statmech.vib.DebyeVib

                obj_dict

                Return type:
                -

                dict

                +

                dict

                diff --git a/api/statmech/vib/pmutt.statmech.vib.EinsteinVib.html b/api/statmech/vib/pmutt.statmech.vib.EinsteinVib.html index debf6ce3..01cc148b 100644 --- a/api/statmech/vib/pmutt.statmech.vib.EinsteinVib.html +++ b/api/statmech/vib/pmutt.statmech.vib.EinsteinVib.html @@ -4,7 +4,7 @@ - pmutt.statmech.vib.EinsteinVib — pmutt 1.4.7 documentation + pmutt.statmech.vib.EinsteinVib — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
                - 1.4.7 + 1.4.9
                @@ -138,7 +138,7 @@

                pmutt.statmech.vib.EinsteinVib\(\Theta_E\)) in K

                Type:
                -

                float

                +

                float

                @@ -149,7 +149,7 @@

                pmutt.statmech.vib.EinsteinVib\(u\)) per atom in eV. Default is 0 eV

                Type:
                -

                float, optional

                +

                float, optional

                @@ -227,7 +227,7 @@

                pmutt.statmech.vib.EinsteinVib
                Parameters:
                -

                json_obj (dict) – JSON representation

                +

                json_obj (dict) – JSON representation

                Returns:

                Obj

                @@ -245,7 +245,7 @@

                pmutt.statmech.vib.EinsteinVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CpoR

                @@ -254,7 +254,7 @@

                pmutt.statmech.vib.EinsteinVib

                Cp – Heat capacity (constant P) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -268,13 +268,13 @@

                pmutt.statmech.vib.EinsteinVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                CpoR_vib – Vibrational dimensionless heat capacity at constant pressure

                Return type:
                -

                float

                +

                float

                @@ -286,7 +286,7 @@

                pmutt.statmech.vib.EinsteinVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CvoR

                @@ -295,7 +295,7 @@

                pmutt.statmech.vib.EinsteinVib

                Cv – Heat capacity (constant V) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -309,13 +309,13 @@

                pmutt.statmech.vib.EinsteinVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                CvoR_vib – Vibrational dimensionless heat capacity at constant volume

                Return type:
                -

                float

                +

                float

                @@ -327,9 +327,9 @@

                pmutt.statmech.vib.EinsteinVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_FoRT

                @@ -337,7 +337,7 @@

                pmutt.statmech.vib.EinsteinVib

                F – Hemholtz energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -349,13 +349,13 @@

                pmutt.statmech.vib.EinsteinVib\(\frac{A^{vib}}{RT}=\frac{U^{vib}}{RT}-\frac{S^{vib}}{R}\)

                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                FoRT_vib – Vibrational dimensionless Helmholtz energy

                Return type:
                -

                float

                +

                float

                @@ -367,9 +367,9 @@

                pmutt.statmech.vib.EinsteinVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_GoRT

                @@ -377,7 +377,7 @@

                pmutt.statmech.vib.EinsteinVib

                G – Gibbs energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -389,13 +389,13 @@

                pmutt.statmech.vib.EinsteinVib\(\frac{G^{vib}}{RT}=\frac{H^{vib}}{RT}-\frac{S^{vib}}{R}\)

                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                GoRT_vib – Vibrational dimensionless Gibbs energy

                Return type:
                -

                float

                +

                float

                @@ -407,9 +407,9 @@

                pmutt.statmech.vib.EinsteinVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_HoRT

                @@ -417,7 +417,7 @@

                pmutt.statmech.vib.EinsteinVib

                H – Enthalpy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -431,13 +431,13 @@

                pmutt.statmech.vib.EinsteinVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                HoRT_vib – Vibrational dimensionless enthalpy

                Return type:
                -

                float

                +

                float

                @@ -449,7 +449,7 @@

                pmutt.statmech.vib.EinsteinVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_SoR

                @@ -458,7 +458,7 @@

                pmutt.statmech.vib.EinsteinVib

                S – Entropy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -472,13 +472,13 @@

                pmutt.statmech.vib.EinsteinVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                SoR_vib – Vibrational dimensionless entropy

                Return type:
                -

                float

                +

                float

                @@ -490,9 +490,9 @@

                pmutt.statmech.vib.EinsteinVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_UoRT

                @@ -500,7 +500,7 @@

                pmutt.statmech.vib.EinsteinVib

                U – Internal energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -514,13 +514,13 @@

                pmutt.statmech.vib.EinsteinVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                UoRT_vib – Vibrational dimensionless internal energy

                Return type:
                -

                float

                +

                float

                @@ -535,7 +535,7 @@

                pmutt.statmech.vib.EinsteinVib

                zpe – Zero point energy in eV

                Return type:
                -

                float

                +

                float

                @@ -548,13 +548,13 @@

                pmutt.statmech.vib.EinsteinVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                q_vib – Vibrational partition function

                Return type:
                -

                float

                +

                float

                @@ -568,7 +568,7 @@

                pmutt.statmech.vib.EinsteinVib

                obj_dict

                Return type:
                -

                dict

                +

                dict

                diff --git a/api/statmech/vib/pmutt.statmech.vib.HarmonicVib.html b/api/statmech/vib/pmutt.statmech.vib.HarmonicVib.html index f74af985..5c4a1697 100644 --- a/api/statmech/vib/pmutt.statmech.vib.HarmonicVib.html +++ b/api/statmech/vib/pmutt.statmech.vib.HarmonicVib.html @@ -4,7 +4,7 @@ - pmutt.statmech.vib.HarmonicVib — pmutt 1.4.7 documentation + pmutt.statmech.vib.HarmonicVib — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
                - 1.4.7 + 1.4.9
                @@ -152,7 +152,7 @@

                pmutt.statmech.vib.HarmonicVib
                Type:
                -

                float, optional

                +

                float, optional

                @@ -241,7 +241,7 @@

                pmutt.statmech.vib.HarmonicVib
                Parameters:
                -

                json_obj (dict) – JSON representation

                +

                json_obj (dict) – JSON representation

                Returns:

                HarmonicVib

                @@ -259,7 +259,7 @@

                pmutt.statmech.vib.HarmonicVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CpoR

                @@ -268,7 +268,7 @@

                pmutt.statmech.vib.HarmonicVib

                Cp – Heat capacity (constant P) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -282,13 +282,13 @@

                pmutt.statmech.vib.HarmonicVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                CpoR_vib – Vibrational dimensionless heat capacity at constant pressure

                Return type:
                -

                float

                +

                float

                @@ -300,7 +300,7 @@

                pmutt.statmech.vib.HarmonicVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CvoR

                @@ -309,7 +309,7 @@

                pmutt.statmech.vib.HarmonicVib

                Cv – Heat capacity (constant V) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -322,13 +322,13 @@

                pmutt.statmech.vib.HarmonicVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                CvoR_vib – Vibrational dimensionless heat capacity at constant volume

                Return type:
                -

                float

                +

                float

                @@ -340,9 +340,9 @@

                pmutt.statmech.vib.HarmonicVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_FoRT

                @@ -350,7 +350,7 @@

                pmutt.statmech.vib.HarmonicVib

                F – Hemholtz energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -362,13 +362,13 @@

                pmutt.statmech.vib.HarmonicVib\(\frac{A^{vib}}{RT}=\frac{U^{vib}}{RT}-\frac{S^{vib}}{R}\)

                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                FoRT_vib – Vibrational dimensionless Helmholtz energy

                Return type:
                -

                float

                +

                float

                @@ -380,9 +380,9 @@

                pmutt.statmech.vib.HarmonicVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_GoRT

                @@ -390,7 +390,7 @@

                pmutt.statmech.vib.HarmonicVib

                G – Gibbs energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -402,13 +402,13 @@

                pmutt.statmech.vib.HarmonicVib\(\frac{G^{vib}}{RT}=\frac{H^{vib}}{RT}-\frac{S^{vib}}{R}\)

                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                GoRT_vib – Vibrational dimensionless Gibbs energy

                Return type:
                -

                float

                +

                float

                @@ -420,9 +420,9 @@

                pmutt.statmech.vib.HarmonicVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_HoRT

                @@ -430,7 +430,7 @@

                pmutt.statmech.vib.HarmonicVib

                H – Enthalpy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -445,13 +445,13 @@

                pmutt.statmech.vib.HarmonicVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                HoRT_vib – Vibrational dimensionless enthalpy

                Return type:
                -

                float

                +

                float

                @@ -463,7 +463,7 @@

                pmutt.statmech.vib.HarmonicVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_SoR

                @@ -472,7 +472,7 @@

                pmutt.statmech.vib.HarmonicVib

                S – Entropy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -487,13 +487,13 @@

                pmutt.statmech.vib.HarmonicVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                SoR_vib – Vibrational dimensionless entropy

                Return type:
                -

                float

                +

                float

                @@ -505,9 +505,9 @@

                pmutt.statmech.vib.HarmonicVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_UoRT

                @@ -515,7 +515,7 @@

                pmutt.statmech.vib.HarmonicVib

                U – Internal energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -529,13 +529,13 @@

                pmutt.statmech.vib.HarmonicVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                UoRT_vib – Vibrational dimensionless internal energy

                Return type:
                -

                float

                +

                float

                @@ -550,7 +550,7 @@

                pmutt.statmech.vib.HarmonicVib

                zpe – Zero point energy in eV

                Return type:
                -

                float

                +

                float

                @@ -566,15 +566,15 @@

                pmutt.statmech.vib.HarmonicVib
                Parameters:
                  -
                • T (float) – Temperature in K

                • -
                • include_ZPE (bool, optional) – If True, includes the zero-point energy term

                • +
                • T (float) – Temperature in K

                • +
                • include_ZPE (bool, optional) – If True, includes the zero-point energy term

                Returns:

                q_vib – Vibrational partition function

                Return type:
                -

                float

                +

                float

                @@ -597,7 +597,7 @@

                pmutt.statmech.vib.HarmonicVib

                obj_dict

                Return type:
                -

                dict

                +

                dict

                diff --git a/api/statmech/vib/pmutt.statmech.vib.QRRHOVib.html b/api/statmech/vib/pmutt.statmech.vib.QRRHOVib.html index e909090e..c4071eb5 100644 --- a/api/statmech/vib/pmutt.statmech.vib.QRRHOVib.html +++ b/api/statmech/vib/pmutt.statmech.vib.QRRHOVib.html @@ -4,7 +4,7 @@ - pmutt.statmech.vib.QRRHOVib — pmutt 1.4.7 documentation + pmutt.statmech.vib.QRRHOVib — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
                - 1.4.7 + 1.4.9
                @@ -152,7 +152,7 @@

                pmutt.statmech.vib.QRRHOVib
                Type:
                -

                float, optional

                +

                float, optional

                @@ -163,7 +163,7 @@

                pmutt.statmech.vib.QRRHOVib
                Type:
                -

                float, optional

                +

                float, optional

                @@ -174,7 +174,7 @@

                pmutt.statmech.vib.QRRHOVib
                Type:
                -

                int, optional

                +

                int, optional

                @@ -187,7 +187,7 @@

                pmutt.statmech.vib.QRRHOVib
                Type:
                -

                float, optional

                +

                float, optional

                @@ -276,7 +276,7 @@

                pmutt.statmech.vib.QRRHOVib
                Parameters:
                -

                json_obj (dict) – JSON representation

                +

                json_obj (dict) – JSON representation

                Returns:

                QRRHOVib

                @@ -294,7 +294,7 @@

                pmutt.statmech.vib.QRRHOVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CpoR

                @@ -303,7 +303,7 @@

                pmutt.statmech.vib.QRRHOVib

                Cp – Heat capacity (constant P) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -315,13 +315,13 @@

                pmutt.statmech.vib.QRRHOVib\(\frac{C_{P}^{qRRHO}} {R} = \frac{C_{V}^{qRRHO}} {R}\)

                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                CpoR_vib – Vibrational dimensionless heat capacity at constant pressure

                Return type:
                -

                float

                +

                float

                @@ -333,7 +333,7 @@

                pmutt.statmech.vib.QRRHOVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_CvoR

                @@ -342,7 +342,7 @@

                pmutt.statmech.vib.QRRHOVib

                Cv – Heat capacity (constant V) in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -358,13 +358,13 @@

                pmutt.statmech.vib.QRRHOVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                CvoR_vib – Vibrational dimensionless heat capacity at constant volume

                Return type:
                -

                float

                +

                float

                @@ -376,9 +376,9 @@

                pmutt.statmech.vib.QRRHOVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_FoRT

                @@ -386,7 +386,7 @@

                pmutt.statmech.vib.QRRHOVib

                F – Hemholtz energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -399,13 +399,13 @@

                pmutt.statmech.vib.QRRHOVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                FoRT_vib – Vibrational dimensionless Helmholtz energy

                Return type:
                -

                float

                +

                float

                @@ -417,9 +417,9 @@

                pmutt.statmech.vib.QRRHOVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_GoRT

                @@ -427,7 +427,7 @@

                pmutt.statmech.vib.QRRHOVib

                G – Gibbs energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -440,13 +440,13 @@

                pmutt.statmech.vib.QRRHOVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                GoRT_vib – Vibrational dimensionless Gibbs energy

                Return type:
                -

                float

                +

                float

                @@ -458,9 +458,9 @@

                pmutt.statmech.vib.QRRHOVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_HoRT

                @@ -468,7 +468,7 @@

                pmutt.statmech.vib.QRRHOVib

                H – Enthalpy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -480,13 +480,13 @@

                pmutt.statmech.vib.QRRHOVib\(\frac{H^{qRRHO}} {RT} = \frac{U^{qRRHO}} {RT}\)

                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                HoRT_vib – Vibrational dimensionless enthalpy

                Return type:
                -

                float

                +

                float

                @@ -498,7 +498,7 @@

                pmutt.statmech.vib.QRRHOVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units.

                • kwargs (keyword arguments) – Parameters needed by get_SoR

                @@ -507,7 +507,7 @@

                pmutt.statmech.vib.QRRHOVib

                S – Entropy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -525,13 +525,13 @@

                pmutt.statmech.vib.QRRHOVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                SoR_vib – Vibrational dimensionless entropy

                Return type:
                -

                float

                +

                float

                @@ -543,9 +543,9 @@

                pmutt.statmech.vib.QRRHOVib
                Parameters:
                  -
                • units (str) – Units as string. See R() for accepted +

                • units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).

                • -
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • +
                • T (float, optional) – Temperature in K. Default is 298.15 K

                • kwargs (keyword arguments) – Parameters needed by get_UoRT

                @@ -553,7 +553,7 @@

                pmutt.statmech.vib.QRRHOVib

                U – Internal energy in appropriate units

                Return type:
                -

                float

                +

                float

                @@ -569,13 +569,13 @@

                pmutt.statmech.vib.QRRHOVib
                Parameters:
                -

                T (float) – Temperature in K

                +

                T (float) – Temperature in K

                Returns:

                UoRT_vib – Vibrational dimensionless internal energy

                Return type:
                -

                float

                +

                float

                @@ -590,7 +590,7 @@

                pmutt.statmech.vib.QRRHOVib

                zpe – Zero point energy in eV

                Return type:
                -

                float

                +

                float

                @@ -604,7 +604,7 @@

                pmutt.statmech.vib.QRRHOVib

                q_vib – Vibrational partition function

                Return type:
                -

                float

                +

                float

                @@ -627,7 +627,7 @@

                pmutt.statmech.vib.QRRHOVib

                obj_dict

                Return type:
                -

                dict

                +

                dict

                diff --git a/api/visualization/visual.html b/api/visualization/visual.html index 10096ec7..b444bc92 100644 --- a/api/visualization/visual.html +++ b/api/visualization/visual.html @@ -4,7 +4,7 @@ - Visualization — pmutt 1.4.7 documentation + Visualization — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
                - 1.4.7 + 1.4.9
                @@ -125,12 +125,12 @@

                Plot_1DParameters:
                • obj (Any model, species, or reaction object) – pMuTT object to evaluate

                • -
                • x_name (str) – Name of variable to vary

                • +
                • x_name (str) – Name of variable to vary

                • x_values (iterable object) – x values to use

                • -
                • methods (tuple of str or str) – Methods to use

                • -
                • nrows (int, optional) – Number of rows of the subplot grid. It not specified, defaults +

                • methods (tuple of str or str) – Methods to use

                • +
                • nrows (int, optional) – Number of rows of the subplot grid. It not specified, defaults to length of methods

                • -
                • ncols (int, optional) – Number of columns of the subplot grid. If not specified, +

                • ncols (int, optional) – Number of columns of the subplot grid. If not specified, defaults to 1

                • figure (matplotlib.figure.Figure, optional) – Add plot to this figure. If not specified, one will be generated

                • @@ -201,14 +201,14 @@

                  Plot_2DParameters:
                  • obj (Any model, species, or reaction object) – pMuTT object to evaluate

                  • -
                  • x1_name (str) – Name of first variable to vary

                  • +
                  • x1_name (str) – Name of first variable to vary

                  • x1_values (iterable object) – x1 values to use

                  • -
                  • x2_name (str) – Name of second variable to vary

                  • +
                  • x2_name (str) – Name of second variable to vary

                  • x2_values (iterable object) – x2 values to use

                  • -
                  • methods (tuple of str or str) – Methods to use

                  • -
                  • nrows (int, optional) – Number of rows of the subplot grid. It not specified, defaults +

                  • methods (tuple of str or str) – Methods to use

                  • +
                  • nrows (int, optional) – Number of rows of the subplot grid. It not specified, defaults to length of methods

                  • -
                  • ncols (int, optional) – Number of columns of the subplot grid. If not specified, +

                  • ncols (int, optional) – Number of columns of the subplot grid. If not specified, defaults to 1

                  • kwargs (keyword arguments) –

                    Other variables to use in the calculation. Method specific arguments can be passed by having a key that corresponds to diff --git a/examples_jupyter/examples.html b/examples_jupyter/examples.html index acb02e09..999e1fa3 100644 --- a/examples_jupyter/examples.html +++ b/examples_jupyter/examples.html @@ -4,7 +4,7 @@ - Examples — pmutt 1.4.7 documentation + Examples — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@

                    - 1.4.7 + 1.4.9
                    diff --git a/genindex.html b/genindex.html index 2ba54be8..5f36cf4a 100644 --- a/genindex.html +++ b/genindex.html @@ -3,7 +3,7 @@ - Index — pmutt 1.4.7 documentation + Index — pmutt 1.4.9 documentation @@ -35,7 +35,7 @@
                    - 1.4.7 + 1.4.9
                    diff --git a/includeme.html b/includeme.html index 4688b609..4b58a4ac 100644 --- a/includeme.html +++ b/includeme.html @@ -4,7 +4,7 @@ - Python Multiscale Thermochemistry Toolbox (pMuTT) — pmutt 1.4.7 documentation + Python Multiscale Thermochemistry Toolbox (pMuTT) — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
                    - 1.4.7 + 1.4.9
                    diff --git a/index.html b/index.html index 99d781d9..4fc07db6 100644 --- a/index.html +++ b/index.html @@ -4,7 +4,7 @@ - Welcome to pmutt’s documentation! — pmutt 1.4.7 documentation + Welcome to pmutt’s documentation! — pmutt 1.4.9 documentation @@ -37,7 +37,7 @@
                    - 1.4.7 + 1.4.9
                    @@ -239,6 +239,7 @@

                    Welcome to pmutt’s documentation!Release Notes
                    • Development Branch
                    • +
                    • Version 1.4.9
                    • Version 1.4.7
                    • Version 1.4.6
                    • Version 1.4.5
                    • diff --git a/install.html b/install.html index ef86fb9e..ae9c6c7d 100644 --- a/install.html +++ b/install.html @@ -4,7 +4,7 @@ - Installation — pmutt 1.4.7 documentation + Installation — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
                      - 1.4.7 + 1.4.9
                      diff --git a/objects.inv b/objects.inv index da5a526b..af2dd17e 100644 Binary files a/objects.inv and b/objects.inv differ diff --git a/publications.html b/publications.html index ab572aef..3d4cbed4 100644 --- a/publications.html +++ b/publications.html @@ -4,7 +4,7 @@ - Publications — pmutt 1.4.7 documentation + Publications — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
                      - 1.4.7 + 1.4.9
                      diff --git a/referencing.html b/referencing.html index e9e2777b..8bcc4ab1 100644 --- a/referencing.html +++ b/referencing.html @@ -4,7 +4,7 @@ - Referencing — pmutt 1.4.7 documentation + Referencing — pmutt 1.4.9 documentation @@ -39,7 +39,7 @@
                      - 1.4.7 + 1.4.9
                      diff --git a/release_notes.html b/release_notes.html index af8a0089..5e38664f 100644 --- a/release_notes.html +++ b/release_notes.html @@ -4,7 +4,7 @@ - Release Notes — pmutt 1.4.7 documentation + Release Notes — pmutt 1.4.9 documentation @@ -37,7 +37,7 @@
                      - 1.4.7 + 1.4.9
                      @@ -72,6 +72,7 @@
                    • Helper Functions
                    • Release Notes
                      • Development Branch
                      • +
                      • Version 1.4.9
                      • Version 1.4.7
                      • Version 1.4.6
                      • Version 1.4.5
                      • @@ -155,6 +156,14 @@

                        Development Branch

                        Development Branch

                        +
                        +

                        Version 1.4.9

                        +

                        October 25, 2023

                        +
                          +
                        • Fixed deprecated numpy function impacting nasa.py and shomate.py +Conversion of an array with ndim > 0 to a scalar

                        • +
                        +

                        Version 1.4.7

                        August 23, 2023

                        diff --git a/search.html b/search.html index 3d0d8b57..cce8c9cf 100644 --- a/search.html +++ b/search.html @@ -3,7 +3,7 @@ - Search — pmutt 1.4.7 documentation + Search — pmutt 1.4.9 documentation @@ -38,7 +38,7 @@
                        - 1.4.7 + 1.4.9
                        diff --git a/searchindex.js b/searchindex.js index c02f215f..487ffbdd 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["api/constants/constants", "api/constants/constants/pmutt.constants.Na", "api/constants/constants/pmutt.constants.P0", "api/constants/constants/pmutt.constants.R", "api/constants/constants/pmutt.constants.T0", "api/constants/constants/pmutt.constants.V0", "api/constants/constants/pmutt.constants.c", "api/constants/constants/pmutt.constants.e", "api/constants/constants/pmutt.constants.h", "api/constants/constants/pmutt.constants.kb", "api/constants/constants/pmutt.constants.m_e", "api/constants/constants/pmutt.constants.m_p", "api/constants/misc/pmutt.constants.atomic_weight", "api/constants/misc/pmutt.constants.prefixes", "api/constants/misc/pmutt.constants.symmetry_dict", "api/constants/misc/pmutt.constants.type_dict", "api/constants/unit_conv/pmutt.constants.convert_unit", 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104, 105, 107, 108, 110, 113, 116, 120, 137], "a2": [15, 16], "area": [15, 16, 50, 77, 85, 102, 113], "temp": [15, 20, 23, 26, 27, 28], "energi": [15, 16, 19, 20, 21, 22, 26, 29, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 52, 70, 76, 93, 95, 106, 107, 108, 109, 110, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 139, 144], "amount": [15, 16, 58], "particl": [15, 44], "cm2": [15, 16, 94, 104, 107, 116, 120], "dai": [15, 16, 79], "time": [15, 16, 59, 85, 93, 102, 108, 143], "ft": [15, 16], "ft2": [15, 16], "ft3": [15, 16], "hr": [15, 16], "inch2": [15, 16], "inch3": [15, 16], "km": [15, 16], "km2": [15, 16], "lb": [15, 16], "m2": [15, 16, 25, 31, 125, 136], "mile": [15, 16], "min": [15, 16, 52, 107, 116, 120], "molec": [15, 16, 93, 103, 104, 105, 107, 108, 116, 120], "ms": [15, 16], "nm": [15, 16], "ns": [15, 16], "ps": [15, 16], "num": 16, "none": [16, 34, 36, 37, 38, 39, 40, 41, 48, 49, 50, 51, 52, 53, 55, 79, 83, 84, 85, 87, 90, 91, 92, 95, 100, 101, 102, 103, 104, 105, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 129, 131, 132, 135, 136, 137], "initi": [16, 37, 45, 53, 54, 83, 85, 90, 91, 92, 95, 100, 102, 104, 106, 107, 114, 115, 116, 117, 118, 120, 121, 138, 144], "final": [16, 95, 107, 116, 117, 118, 120, 121, 139, 144], "convert": [16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 47, 54, 77, 78, 85, 89, 95, 102, 107, 116, 117, 118, 120, 121, 124, 125, 138, 139], "between": [16, 33, 34, 36, 37, 38, 39, 40, 41, 44, 85, 95, 102, 103, 105, 107, 108, 109, 110, 113, 116, 117, 118, 120, 121, 122, 144], "two": [16, 110, 113, 123, 130], "set": [16, 34, 85, 90, 91, 92, 95, 102, 104, 107, 113, 116, 117, 118, 120, 121, 122, 126, 130, 131, 135, 136, 144, 146], "specifi": [16, 34, 36, 37, 38, 39, 40, 41, 45, 47, 49, 50, 51, 52, 53, 54, 59, 79, 84, 85, 87, 90, 92, 95, 101, 102, 103, 104, 105, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 130, 131, 137, 138, 144], "convers": [16, 138, 140, 144], "factor": [16, 35, 52, 95, 107, 113, 116, 117, 118, 120, 121, 143, 144], "current": [16, 77, 85, 90, 92, 102, 103, 104, 105, 108, 130, 144], "you": [16, 34, 54, 77, 79, 95, 107, 116, 117, 118, 120, 121, 125, 126, 130, 131, 139, 141, 142, 144, 146], "would": [16, 34, 79, 110, 113, 122, 126, 131, 139, 141, 142, 144], "like": [16, 33, 34, 35, 54, 79, 85, 102, 113, 122, 126, 131, 132, 138, 139, 142, 143, 144], "conversion_num": 16, "valueerror": [16, 79, 95, 107, 110, 116, 117, 118, 120, 121], "consist": [16, 79, 113, 143], "picosecond": 16, "nanosecond": 16, "millisecond": 16, "minut": 16, "hour": 16, "yr": 16, "year": 16, "nanomet": 16, "anstrom": 16, "kilomet": 16, "foot": 16, "feet": 16, "millilmet": 16, "debye_temperatur": [17, 18, 133], "deby": [17, 18, 133], "einstein": [17, 18, 134], "einstein_temperatur": [17, 18, 134], "frequenc": [19, 22, 23, 24, 27, 30, 54, 65, 69, 71, 88, 135, 136, 144], "freq": [19, 22, 23, 24, 27, 30], "hz": [19, 22, 23, 24, 27, 30], "wavenumb": [21, 24, 28, 29, 30, 31, 32, 130, 135, 136, 144], "inertia": [25, 31, 109, 136, 144], "moment": [25, 31, 136], "rotat": [25, 28, 64, 74, 75, 129, 131, 140, 144], "rot_temperatur": [25, 54, 65, 129, 130], "vibrat": [28, 65, 68, 69, 88, 131, 134, 135, 136, 140, 144], "correspond": [29, 32, 36, 37, 39, 40, 41, 56, 73, 80, 83, 97, 100, 113, 137], "predict": [33, 46], "thermodynam": [33, 34, 36, 37, 38, 39, 41, 45, 46, 48, 66, 95, 107, 109, 111, 116, 117, 118, 120, 121, 123, 126, 127, 128, 129, 132, 133, 134, 135, 136, 138, 139, 140, 143, 144], "properti": [33, 34, 36, 37, 41, 48, 90, 91, 92, 95, 103, 104, 105, 107, 110, 111, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 130, 135, 136, 138, 139, 144], "speci": [33, 34, 36, 37, 39, 40, 41, 45, 47, 48, 51, 52, 53, 80, 82, 83, 84, 85, 87, 90, 91, 92, 94, 95, 97, 99, 100, 101, 102, 103, 104, 105, 107, 109, 110, 111, 113, 115, 116, 117, 118, 120, 121, 122, 124, 125, 130, 131, 137, 138, 143, 144], "us": [33, 34, 36, 37, 38, 39, 40, 41, 42, 45, 47, 49, 51, 52, 54, 55, 61, 62, 77, 79, 83, 84, 85, 86, 87, 89, 90, 91, 92, 93, 95, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 129, 131, 132, 134, 135, 136, 137, 138, 139, 142, 143, 144, 145, 146, 147], "simpl": [33, 77, 115], "polynomi": [33, 34, 36, 37, 38, 41, 45, 48, 86, 138, 144], "These": [33, 111, 113, 119, 139], "evalu": [33, 37, 49, 95, 107, 113, 116, 117, 118, 120, 121, 122, 130, 137, 144], "more": [33, 129, 138, 139, 141, 144], "quickli": 33, "than": [33, 54, 88, 141, 143, 144], "statist": [33, 34, 36, 37, 38, 39, 41, 109, 123, 129, 131, 132, 133, 134, 135, 140, 144], "mechan": [33, 34, 36, 41, 51, 131, 143, 144], "equat": [33, 43, 44, 113, 122, 123, 124, 125, 129, 132, 133, 134, 135, 136, 139, 140, 143, 144], "tend": 33, "kinet": [33, 90, 91, 103, 104, 138, 139, 140, 142, 146], "softwar": [33, 119, 142, 146], "when": 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95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 119, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 139, 143, 144], "format": [33, 36, 37, 38, 40, 41, 45, 48, 49, 50, 52, 53, 61, 62, 77, 79, 84, 85, 86, 87, 89, 90, 92, 93, 95, 101, 102, 103, 104, 105, 106, 107, 108, 110, 113, 114, 116, 117, 118, 119, 120, 121, 122, 131, 138, 139, 142, 143, 144], "howev": 33, "from": [33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 47, 48, 54, 56, 60, 70, 71, 72, 73, 74, 75, 76, 77, 79, 88, 90, 91, 92, 94, 95, 103, 104, 106, 107, 109, 110, 111, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 144, 146], "dft": [33, 39, 40, 123, 138, 139, 143], "base": [33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 79, 90, 91, 92, 93, 94, 95, 103, 104, 105, 106, 107, 108, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 139, 140], "mai": [33, 96, 118, 125, 130, 138, 141, 142, 143, 144, 146], "differ": [33, 77, 95, 103, 105, 107, 108, 113, 116, 117, 118, 120, 121, 122, 139, 143, 144], "see": [33, 34, 35, 36, 37, 38, 39, 40, 41, 66, 85, 95, 102, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 139, 141], "inform": [33, 41, 53, 85, 102, 109], "bridg": 33, "gap": 33, "ab": [33, 138, 139], "initio": [33, 138, 139], "code": [33, 138, 139, 140, 141, 144, 146], "miscellan": [33, 144], "associ": [33, 91, 104, 106, 114, 130, 144], "locat": [33, 54, 55, 118, 141], "here": [33, 103, 105, 108, 141, 142, 145, 146, 147, 148], "class": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 57, 63, 64, 66, 67, 68, 78, 79, 90, 91, 92, 93, 94, 95, 103, 104, 105, 106, 107, 108, 109, 110, 111, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 140, 144], "phase": [34, 35, 44, 49, 51, 52, 53, 77, 80, 81, 82, 83, 84, 85, 95, 97, 98, 99, 100, 101, 102, 107, 113, 116, 117, 118, 119, 120, 121, 124, 125, 140, 144], "model": [34, 36, 37, 38, 39, 41, 45, 57, 63, 64, 66, 67, 68, 77, 85, 90, 91, 92, 102, 104, 109, 110, 113, 118, 119, 122, 131, 133, 134, 137, 138, 140, 144, 146], "misc_model": [34, 77, 106, 114, 115, 131, 144], "smile": [34, 77, 131, 144], "note": [34, 35, 54, 59, 77, 85, 87, 90, 91, 92, 95, 96, 102, 103, 104, 105, 107, 115, 116, 117, 118, 120, 121, 124, 125, 126, 131, 140, 141, 146], "add_gas_p_adj": [34, 35, 144], "kwarg": [34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 54, 89, 95, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 137], "_modelbas": [34, 35, 40, 90, 91, 92, 104, 110, 115, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "parent": [34, 91, 122, 140], "hold": [34, 40], "surfac": [34, 49, 51, 52, 85, 102, 106, 107, 113, 114, 116, 120, 124, 125, 143, 144], "composit": [34, 36, 37, 40, 41, 45, 46, 47, 95, 107, 115, 116, 117, 118, 120, 121, 131, 143, 144], "dictionari": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 47, 49, 53, 54, 56, 77, 78, 79, 80, 81, 82, 83, 85, 86, 90, 91, 93, 94, 95, 97, 98, 99, 100, 102, 103, 104, 105, 106, 107, 108, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 138, 144], "stoichiometr": [34, 36, 37, 41, 47, 49, 52, 59, 92, 95, 105, 107, 115, 116, 117, 118, 120, 121, 125, 131], "formula": [34, 36, 37, 40, 41, 47, 54, 58, 59, 115, 131], "ch3oh": [34, 36, 37, 41, 59, 115, 131], "repres": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 85, 88, 90, 92, 93, 94, 95, 102, 103, 104, 105, 106, 107, 108, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 143, 144], "object": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 47, 48, 49, 51, 52, 53, 54, 55, 61, 62, 77, 78, 79, 80, 81, 82, 83, 84, 85, 89, 90, 91, 92, 93, 94, 95, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 112, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 137, 138, 140, 144], "which": [34, 79, 123, 141], "wa": [34, 139, 141, 144, 146], "should": [34, 40, 41, 49, 53, 54, 56, 58, 60, 77, 78, 79, 84, 85, 87, 88, 95, 101, 102, 107, 110, 112, 113, 116, 117, 118, 120, 121, 122, 130, 141, 144], "follow": [34, 36, 40, 41, 54, 95, 107, 116, 117, 118, 120, 121, 125, 130, 131, 141, 142], "method": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 49, 52, 77, 79, 80, 81, 82, 83, 84, 90, 91, 92, 93, 94, 95, 97, 98, 99, 100, 101, 103, 104, 105, 106, 107, 108, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 141, 143, 144], "get_cpor": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "get_hort": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 113, 114, 115, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 144], "get_sor": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 144], "get_gort": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "extra": [34, 113, 122, 124, 125, 131, 144], "add": [34, 40, 77, 103, 105, 108, 113, 122, 131, 137, 138, 139, 144], "function": [34, 49, 52, 56, 60, 77, 79, 89, 93, 95, 96, 107, 108, 110, 116, 117, 118, 120, 121, 123, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 140, 144], "commonli": [34, 131], "mixtur": [34, 36, 37, 41, 131, 140], "list": [34, 36, 37, 38, 39, 40, 41, 45, 47, 48, 49, 50, 51, 53, 54, 60, 71, 73, 75, 77, 79, 80, 81, 82, 83, 84, 85, 86, 87, 90, 91, 92, 95, 97, 98, 99, 100, 101, 102, 104, 106, 107, 109, 110, 112, 113, 114, 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92, 93, 94, 95, 103, 104, 105, 106, 107, 108, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136], "compare_cpor": [34, 36, 37, 38, 39, 41, 109], "compar": [34, 36, 37, 38, 39, 41, 79, 109], "dimensionless": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136], "heat": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 139], "capac": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 139], "numpi": [34, 35, 36, 37, 38, 39, 40, 41, 45, 77, 109, 113, 130, 131, 137, 139], "ndarrai": [34, 35, 36, 37, 38, 39, 40, 41, 45, 77, 109, 113, 124, 131], "calcul": [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 49, 52, 95, 103, 104, 105, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 143, 144], "cpor": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 126, 127, 131, 133, 144], "gener": [34, 36, 37, 38, 39, 41, 56, 60, 84, 85, 101, 102, 107, 109, 113, 116, 120, 122, 131, 137, 138, 139, 144], "self": [34, 36, 37, 38, 39, 41, 77, 79, 109, 110, 135, 136], "t_low": [34, 36, 37, 38, 39, 41, 77, 109], "t_high": [34, 36, 37, 38, 39, 41, 77, 109], "cpor_model": [34, 36, 37, 38, 39, 41, 109], "cpor_empir": [34, 36, 37, 38, 39, 41, 109], "compare_gort": [34, 36, 37, 38, 39, 41, 109], "gibb": [34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 95, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 139, 144], "compare_hort": [34, 36, 37, 38, 39, 41, 109], "compare_sor": [34, 36, 37, 38, 39, 41, 109], "entropi": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 139, 144], "classmethod": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 77, 94, 95, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136], "from_dict": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 77, 94, 95, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "json_obj": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 77, 78, 94, 95, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136], "recreat": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 94, 95, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136], "json": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 94, 95, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 138, 140, 144], "get_cp": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136], "constant": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 138, 140, 144], "string": [34, 35, 36, 37, 38, 39, 40, 41, 45, 47, 49, 50, 51, 52, 53, 54, 55, 58, 77, 79, 80, 81, 82, 85, 87, 90, 92, 93, 95, 97, 98, 99, 102, 103, 104, 105, 106, 107, 108, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 138, 144], "accept": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 84, 94, 95, 101, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 144], "keyword": [34, 35, 36, 37, 38, 39, 40, 41, 52, 54, 83, 89, 95, 100, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 132, 133, 134, 135, 136, 137], "argument": [34, 35, 36, 37, 38, 39, 40, 41, 52, 54, 83, 85, 89, 95, 100, 102, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 137, 144], "need": [34, 35, 36, 37, 38, 39, 40, 41, 52, 87, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 130, 132, 133, 134, 135, 136], "cp": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "get_cv": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "get_cvor": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "cv": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "cvor": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 126, 127, 131, 133], "get_f": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136], "helmholtz": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "omit": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136], "get_fort": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "hemholtz": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 132, 133, 134, 135, 136], "get_uort": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "fort": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 124, 125, 126, 127, 131, 133], "get_g": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 137], "free": [34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 109, 113, 123, 127, 144], "gort": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 124, 125, 126, 127, 131, 133], "get_h": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 113, 114, 115, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 137], "hort": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 124, 125, 126, 127, 131, 133], "get_": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 113, 114, 115, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 144], "sor": [34, 35, 36, 37, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 124, 125, 126, 127, 131, 133], "get_u": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "intern": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "uort": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 124, 125, 126, 127, 131, 133], "get_q": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "partit": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 144], "coeffici": [34, 35, 36, 37, 38, 39, 40, 41, 47, 52, 61, 62, 84, 95, 101, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 127, 144], "q": [34, 35, 36, 37, 38, 39, 40, 41, 50, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 129, 130, 131, 133, 134, 135, 144], "plot_empir": [34, 36, 37, 38, 39, 41, 109], "cp_unit": [34, 36, 37, 38, 39, 41, 109], "h_unit": [34, 36, 37, 38, 39, 41, 109], "s_unit": [34, 36, 37, 38, 39, 41, 109], "g_unit": [34, 36, 37, 38, 39, 41, 109, 113], "plot": [34, 36, 37, 38, 39, 41, 109, 113, 122, 137, 138, 139, 144], "profil": [34, 36, 37, 38, 39, 41, 109], "lower": [34, 36, 37, 38, 39, 41, 109, 144], "attribut": [34, 36, 37, 38, 39, 40, 41, 45, 47, 77, 79, 85, 86, 87, 90, 91, 92, 95, 102, 103, 104, 105, 106, 107, 109, 113, 114, 116, 117, 118, 120, 121, 122, 123, 124, 125, 130, 131, 135, 136, 144], "upper": [34, 36, 37, 38, 39, 41, 109], "figur": [34, 36, 37, 38, 39, 41, 109, 113, 122, 137], "matplotlib": [34, 36, 37, 38, 39, 41, 109, 113, 122, 137, 139], "ax": [34, 36, 37, 38, 39, 41, 109, 113, 122, 137], "tupl": [34, 36, 37, 38, 39, 40, 41, 77, 79, 86, 109, 113, 122, 137, 144], "axi": [34, 36, 37, 38, 39, 41, 109, 113, 122, 137], "plot_statmech": [34, 36, 37, 38, 39, 41, 109], "use_refer": [34, 36, 37, 38, 39, 41, 109, 131], "plot_statmech_and_empir": [34, 36, 37, 38, 39, 41, 109], "to_dict": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 77, 79, 94, 95, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "datatyp": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 94, 95, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 144], "obj_dict": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 94, 95, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136], "effect": [35, 110, 140, 144], "thi": [35, 47, 51, 77, 78, 79, 85, 86, 90, 95, 96, 102, 103, 104, 105, 107, 108, 110, 113, 116, 117, 118, 120, 121, 122, 123, 125, 130, 131, 135, 136, 137, 138, 139, 141, 143, 144, 146], "adjust": [35, 36, 39, 40, 41, 131, 138], "onli": [35, 36, 37, 41, 49, 51, 54, 79, 88, 95, 107, 116, 117, 118, 120, 121, 129, 131, 141, 144, 146], "valid": [35, 55], "nasa": [35, 41, 45, 48, 51, 53, 54, 61, 62, 77, 83, 84, 86, 87, 100, 101, 109, 111, 138, 140, 144], "nasa9": [35, 38, 83, 84, 100, 101, 111, 144], "shomat": [35, 77, 83, 84, 100, 101, 111, 138, 140, 144], "been": [35, 106, 114, 115], "ad": [35, 119, 143, 144], "unless": 35, "obj": [35, 40, 43, 44, 78, 85, 89, 94, 102, 106, 114, 115, 123, 126, 127, 128, 129, 132, 133, 134, 137], "dimesionless": 35, "frac": [35, 36, 37, 41, 44, 95, 107, 116, 117, 118, 120, 121, 123, 124, 125, 129, 130, 132, 133, 134, 135, 136], "ln": [35, 36, 37, 41, 133, 134, 135], "bigg": [35, 41, 44, 118, 123, 129, 132, 133, 134, 135, 136], "p_0": 35, "p0": 35, "t_mid": [36, 37, 144], "a_low": [36, 54, 62], "a_high": [36, 54, 61], "cat_sit": 36, "n_site": [36, 37, 41, 77, 144], "empiricalbas": [36, 37, 38, 39, 41, 80, 82, 85, 97, 99, 102, 109, 110, 144], "store": [36, 37, 38, 41, 109, 130, 132], "inherit": [36, 37, 38, 41, 90, 92, 104, 106, 107, 109, 113, 114, 115, 116, 120, 130], "form": [36, 41, 77, 85, 95, 102, 107, 116, 117, 118, 120, 121], "a_": [36, 37], "rt": [36, 37, 41, 44, 95, 107, 116, 117, 118, 120, 121, 123, 129, 130, 132, 133, 134, 135, 136], "bound": [36, 37, 38, 41], "middl": 36, "high": [36, 37, 38, 41, 142], "catalyst": [36, 50, 85, 94, 102, 138], "site": [36, 94, 95, 104, 107, 116, 117, 120, 121, 138], "adsorpt": [36, 49, 52, 84, 95, 101, 107, 116, 117, 120, 121, 144], "chemkin": [36, 86, 87, 95, 117, 121, 140, 144], "input": [36, 37, 48, 84, 85, 86, 95, 101, 102, 117, 121, 125, 129, 131, 138, 139, 140, 144], "output": [36, 79, 85, 86, 87, 95, 102, 107, 113, 116, 117, 118, 120, 121, 122, 131, 138, 139, 140, 141], "catsit": 36, "occupi": [36, 144], "int": [36, 37, 41, 54, 58, 73, 74, 79, 85, 89, 90, 92, 93, 95, 102, 103, 104, 105, 107, 108, 113, 116, 117, 118, 120, 121, 122, 130, 132, 136, 137], "from_data": [36, 37, 41], "t_ref": [36, 37, 39, 40, 41, 144], "hort_ref": [36, 37, 39, 40, 41], "sor_ref": [36, 37, 41], "iter": [36, 37, 79, 113, 137], "guess": [36, 37, 47, 54, 129], "find": [36, 37, 53, 54, 61, 62, 139, 143, 146], "best": [36, 37, 139, 146], "each": [36, 37, 40, 45, 48, 49, 53, 79, 83, 85, 87, 100, 102, 113, 122, 130, 131, 138, 143], "rang": [36, 37, 90, 103, 139], "screen": [36, 37], "6th": [36, 37], "lowest": [36, 37], "highest": [36, 37], "term": [36, 37, 41, 135], "from_model": [36, 37, 41, 144], "n_t": [36, 37, 41], "pass": [36, 37, 41, 47, 79, 85, 89, 95, 102, 107, 116, 117, 118, 120, 121, 130, 131, 137, 144], "must": [36, 37, 41, 45, 77, 78, 79, 87, 115, 126, 144], "contain": [36, 37, 41, 45, 47, 48, 52, 58, 77, 79, 106, 114, 118, 122, 131, 137, 138, 144], "limit": [36, 37, 41, 136], "temeratur": [36, 37, 41], "higher": [36, 37, 41, 113, 122], "point": [36, 41, 50, 53, 70, 76, 95, 107, 113, 116, 117, 118, 120, 121, 122, 129, 131, 133, 134, 135, 136, 144], "init": [36, 37, 41], "from_statmech": [36, 41, 144], "statmech_model": [36, 41, 54], "deprec": [36, 41, 144], "version": [36, 41, 79, 96, 140, 146], "pleas": [36, 41, 96, 139, 142, 146], "instead": [36, 41, 85, 95, 102, 106, 107, 114, 115, 116, 117, 118, 120, 121, 144], "statmech": [36, 41, 45, 47, 66, 77, 111, 138, 140, 144], "raise_error": [36, 37, 41, 118, 131, 144], "raise_warn": [36, 37, 41, 118, 131, 144], "error": [36, 37, 41, 118, 131, 144], "mode": [36, 37, 41, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 135, 136, 138, 144], "do": [36, 37, 41, 85, 102, 130, 131, 139, 144, 146], "quantiti": [36, 37, 41, 49, 84, 85, 93, 95, 101, 102, 103, 104, 105, 107, 108, 110, 113, 116, 117, 118, 120, 121, 122, 128, 130, 131, 132, 144], "interest": [36, 37, 41, 95, 107, 116, 117, 118, 120, 121, 125, 131, 141, 146], "relev": [36, 37, 41, 44, 49, 95, 107, 113, 115, 116, 117, 118, 120, 121, 122, 131], "warn": [36, 37, 41, 118, 131, 144], "word": [36, 37, 41, 131], "s_element": [36, 37, 41, 131, 144], "defauli": [36, 37, 41, 131], "get_sel": [36, 37, 41, 131], "get_a": [36, 95, 107, 116, 117, 118, 120, 121], "correct": [36, 52, 107, 116, 120, 143, 144], "to_cti": [36, 37, 38, 41, 89, 90, 92, 93, 103, 104, 105, 106, 107, 108, 110, 114, 116, 120], "write": [36, 37, 38, 41, 49, 50, 51, 52, 53, 77, 79, 84, 85, 87, 90, 92, 93, 95, 96, 101, 102, 103, 104, 105, 106, 107, 108, 110, 114, 116, 117, 118, 120, 121, 138, 139, 144], "cantera": [36, 37, 38, 41, 103, 104, 105, 106, 107, 108, 110, 114, 116, 120, 140, 144], "cti": [36, 37, 38, 41, 84, 85, 89, 90, 92, 93, 101, 102, 103, 104, 105, 106, 107, 108, 110, 114, 116, 120, 138, 144], "cti_str": [36, 37, 38, 41, 89, 90, 92, 93, 103, 104, 105, 106, 107, 108, 114, 116, 120], "to_omkm_yaml": [36, 37, 41, 90, 93, 103, 104, 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"api\\statmech\\nucl\\pmutt.statmech.nucl.EmptyNucl.rst", "api\\statmech\\rot\\pmutt.statmech.rot.RigidRotor.rst", "api\\statmech\\statmech.rst", "api\\statmech\\statmech\\pmutt.statmech.StatMech.rst", "api\\statmech\\trans\\pmutt.statmech.trans.FreeTrans.rst", "api\\statmech\\vib\\pmutt.statmech.vib.DebyeVib.rst", "api\\statmech\\vib\\pmutt.statmech.vib.EinsteinVib.rst", "api\\statmech\\vib\\pmutt.statmech.vib.HarmonicVib.rst", "api\\statmech\\vib\\pmutt.statmech.vib.QRRHOVib.rst", "api\\visualization\\visual.rst", "examples_jupyter\\examples.rst", "includeme.rst", "index.rst", "install.rst", "publications.rst", "referencing.rst", "release_notes.rst", "workshops\\aiche_2019.rst", "workshops\\nam_2019.rst", "workshops\\polimi_2020.rst", "workshops\\workshops.rst"], "titles": ["Constants", "pmutt.constants.Na", "pmutt.constants.P0", "pmutt.constants.R", "pmutt.constants.T0", "pmutt.constants.V0", "pmutt.constants.c", "pmutt.constants.e", "pmutt.constants.h", "pmutt.constants.kb", "pmutt.constants.m_e", "pmutt.constants.m_p", "pmutt.constants.atomic_weight", "pmutt.constants.prefixes", "pmutt.constants.symmetry_dict", "pmutt.constants.type_dict", "pmutt.constants.convert_unit", "pmutt.constants.debye_to_einstein", "pmutt.constants.einstein_to_debye", "pmutt.constants.energy_to_freq", "pmutt.constants.energy_to_temp", "pmutt.constants.energy_to_wavenumber", "pmutt.constants.freq_to_energy", "pmutt.constants.freq_to_temp", "pmutt.constants.freq_to_wavenumber", "pmutt.constants.inertia_to_temp", "pmutt.constants.temp_to_energy", "pmutt.constants.temp_to_freq", "pmutt.constants.temp_to_wavenumber", "pmutt.constants.wavenumber_to_energy", "pmutt.constants.wavenumber_to_freq", "pmutt.constants.wavenumber_to_inertia", "pmutt.constants.wavenumber_to_temp", "Empirical Models", "pmutt.empirical.EmpiricalBase", "pmutt.empirical.GasPressureAdj", "pmutt.empirical.nasa.Nasa", "pmutt.empirical.nasa.Nasa9", "pmutt.empirical.nasa.SingleNasa9", 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45, 53, 54, 83, 85, 90, 91, 92, 95, 100, 102, 104, 106, 107, 114, 115, 116, 117, 118, 120, 121, 138, 144], "final": [16, 95, 107, 116, 117, 118, 120, 121, 139, 144], "convert": [16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 47, 54, 77, 78, 85, 89, 95, 102, 107, 116, 117, 118, 120, 121, 124, 125, 138, 139], "between": [16, 33, 34, 36, 37, 38, 39, 40, 41, 44, 85, 95, 102, 103, 105, 107, 108, 109, 110, 113, 116, 117, 118, 120, 121, 122, 144], "two": [16, 110, 113, 123, 130], "set": [16, 34, 85, 90, 91, 92, 95, 102, 104, 107, 113, 116, 117, 118, 120, 121, 122, 126, 130, 131, 135, 136, 144, 146], "specifi": [16, 34, 36, 37, 38, 39, 40, 41, 45, 47, 49, 50, 51, 52, 53, 54, 59, 79, 84, 85, 87, 90, 92, 95, 101, 102, 103, 104, 105, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 130, 131, 137, 138, 144], "convers": [16, 138, 140, 144], "factor": [16, 35, 52, 95, 107, 113, 116, 117, 118, 120, 121, 143, 144], "current": [16, 77, 85, 90, 92, 102, 103, 104, 105, 108, 130, 144], "you": [16, 34, 54, 77, 79, 95, 107, 116, 117, 118, 120, 121, 125, 126, 130, 131, 139, 141, 142, 144, 146], "would": [16, 34, 79, 110, 113, 122, 126, 131, 139, 141, 142, 144], "like": [16, 33, 34, 35, 54, 79, 85, 102, 113, 122, 126, 131, 132, 138, 139, 142, 143, 144], "conversion_num": 16, "valueerror": [16, 79, 95, 107, 110, 116, 117, 118, 120, 121], "consist": [16, 79, 113, 143], "picosecond": 16, "nanosecond": 16, "millisecond": 16, "minut": 16, "hour": 16, "yr": 16, "year": 16, "nanomet": 16, "anstrom": 16, "kilomet": 16, "foot": 16, "feet": 16, "millilmet": 16, "debye_temperatur": [17, 18, 133], "deby": [17, 18, 133], "einstein": [17, 18, 134], "einstein_temperatur": [17, 18, 134], "frequenc": [19, 22, 23, 24, 27, 30, 54, 65, 69, 71, 88, 135, 136, 144], "freq": [19, 22, 23, 24, 27, 30], "hz": [19, 22, 23, 24, 27, 30], "wavenumb": [21, 24, 28, 29, 30, 31, 32, 130, 135, 136, 144], "inertia": [25, 31, 109, 136, 144], "moment": [25, 31, 136], 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41, 106, 107, 109, 114, 115, 116, 119, 120, 124, 125, 138, 144], "mind": 33, "result": [33, 37, 77, 85, 102, 130], "have": [33, 34, 36, 37, 40, 41, 53, 77, 78, 79, 85, 95, 102, 106, 107, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 130, 131, 137, 139, 141, 142, 143, 144, 146], "same": [33, 95, 107, 110, 112, 113, 116, 117, 118, 120, 121, 122, 130, 131, 141], "state": [33, 43, 44, 77, 85, 95, 102, 106, 107, 113, 114, 115, 116, 117, 118, 120, 121, 122, 130, 140, 141, 144], "origin": [33, 34, 36, 37, 38, 39, 41, 109, 139, 144], "data": [33, 36, 37, 39, 40, 41, 45, 47, 54, 77, 79, 83, 89, 100, 112, 113, 126, 139, 140, 144], "databas": [33, 139, 144], "nist": 33, "chemistri": 33, "webbook": 33, "burcat": 33, "pure": [33, 52, 143], "natur": 33, "enthalpi": [33, 34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 119, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 139, 143, 144], "format": [33, 36, 37, 38, 40, 41, 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39, 40, 41, 66, 85, 95, 102, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 139, 141], "inform": [33, 41, 53, 85, 102, 109], "bridg": 33, "gap": 33, "ab": [33, 138, 139], "initio": [33, 138, 139], "code": [33, 138, 139, 140, 141, 144, 146], "miscellan": [33, 144], "associ": [33, 91, 104, 106, 114, 130, 144], "locat": [33, 54, 55, 118, 141], "here": [33, 103, 105, 108, 141, 142, 145, 146, 147, 148], "class": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 57, 63, 64, 66, 67, 68, 78, 79, 90, 91, 92, 93, 94, 95, 103, 104, 105, 106, 107, 108, 109, 110, 111, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 140, 144], "phase": [34, 35, 44, 49, 51, 52, 53, 77, 80, 81, 82, 83, 84, 85, 95, 97, 98, 99, 100, 101, 102, 107, 113, 116, 117, 118, 119, 120, 121, 124, 125, 140, 144], "model": [34, 36, 37, 38, 39, 41, 45, 57, 63, 64, 66, 67, 68, 77, 85, 90, 91, 92, 102, 104, 109, 110, 113, 118, 119, 122, 131, 133, 134, 137, 138, 140, 144, 146], "misc_model": [34, 77, 106, 114, 115, 131, 144], "smile": [34, 77, 131, 144], "note": [34, 35, 54, 59, 77, 85, 87, 90, 91, 92, 95, 96, 102, 103, 104, 105, 107, 115, 116, 117, 118, 120, 121, 124, 125, 126, 131, 140, 141, 146], "add_gas_p_adj": [34, 35, 144], "kwarg": [34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 54, 89, 95, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 137], "_modelbas": [34, 35, 40, 90, 91, 92, 104, 110, 115, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "parent": [34, 91, 122, 140], "hold": [34, 40], "surfac": [34, 49, 51, 52, 85, 102, 106, 107, 113, 114, 116, 120, 124, 125, 143, 144], "composit": [34, 36, 37, 40, 41, 45, 46, 47, 95, 107, 115, 116, 117, 118, 120, 121, 131, 143, 144], "dictionari": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 47, 49, 53, 54, 56, 77, 78, 79, 80, 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132, 133, 134, 135, 136, 137, 138, 140, 144], "which": [34, 79, 123, 141], "wa": [34, 139, 141, 144, 146], "should": [34, 40, 41, 49, 53, 54, 56, 58, 60, 77, 78, 79, 84, 85, 87, 88, 95, 101, 102, 107, 110, 112, 113, 116, 117, 118, 120, 121, 122, 130, 141, 144], "follow": [34, 36, 40, 41, 54, 95, 107, 116, 117, 118, 120, 121, 125, 130, 131, 141, 142], "method": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 49, 52, 77, 79, 80, 81, 82, 83, 84, 90, 91, 92, 93, 94, 95, 97, 98, 99, 100, 101, 103, 104, 105, 106, 107, 108, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 141, 143, 144], "get_cpor": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "get_hort": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 113, 114, 115, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 144], "get_sor": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 144], "get_gort": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "extra": [34, 113, 122, 124, 125, 131, 144], "add": [34, 40, 77, 103, 105, 108, 113, 122, 131, 137, 138, 139, 144], "function": [34, 49, 52, 56, 60, 77, 79, 89, 93, 95, 96, 107, 108, 110, 116, 117, 118, 120, 121, 123, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 140, 144], "commonli": [34, 131], "mixtur": [34, 36, 37, 41, 131, 140], "list": [34, 36, 37, 38, 39, 40, 41, 45, 47, 48, 49, 50, 51, 53, 54, 60, 71, 73, 75, 77, 79, 80, 81, 82, 83, 84, 85, 86, 87, 90, 91, 92, 95, 97, 98, 99, 100, 101, 102, 104, 106, 107, 109, 110, 112, 113, 114, 116, 117, 118, 120, 121, 122, 124, 129, 130, 131, 135, 136, 137, 138, 144, 148], "represent": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 79, 94, 95, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136], "ani": [34, 36, 37, 41, 78, 85, 90, 95, 102, 104, 107, 113, 116, 117, 118, 120, 121, 122, 126, 128, 131, 137, 138, 141, 144], "addit": [34, 84, 87, 91, 95, 101, 117, 119, 121, 126, 131, 144], "detail": [34, 126, 129, 131, 139], "includ": [34, 35, 36, 37, 41, 45, 49, 54, 83, 84, 85, 87, 88, 95, 100, 101, 102, 107, 113, 116, 117, 118, 120, 121, 122, 126, 131, 135, 144], "comput": [34, 36, 37, 41, 45, 131, 138, 139, 142, 143, 144], "up": [34, 85, 102, 131, 144, 146], "automat": [34, 35, 84, 101, 110, 118, 144], "assign": [34, 35, 36, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 84, 88, 101, 110, 144], "gaspressureadj": [34, 77, 144], "__init__": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 79, 90, 91, 92, 93, 94, 95, 103, 104, 105, 106, 107, 108, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136], "compare_cpor": [34, 36, 37, 38, 39, 41, 109], "compar": [34, 36, 37, 38, 39, 41, 79, 109], "dimensionless": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136], "heat": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 139], "capac": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 139], "numpi": [34, 35, 36, 37, 38, 39, 40, 41, 45, 77, 109, 113, 130, 131, 137, 139, 144], "ndarrai": [34, 35, 36, 37, 38, 39, 40, 41, 45, 77, 109, 113, 124, 131], "calcul": [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 49, 52, 95, 103, 104, 105, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 143, 144], 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138, 140, 144], "get_cp": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136], "constant": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 138, 140, 144], "string": [34, 35, 36, 37, 38, 39, 40, 41, 45, 47, 49, 50, 51, 52, 53, 54, 55, 58, 77, 79, 80, 81, 82, 85, 87, 90, 92, 93, 95, 97, 98, 99, 102, 103, 104, 105, 106, 107, 108, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 138, 144], "accept": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 84, 94, 95, 101, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 144], "keyword": [34, 35, 36, 37, 38, 39, 40, 41, 52, 54, 83, 89, 95, 100, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 132, 133, 134, 135, 136, 137], "argument": [34, 35, 36, 37, 38, 39, 40, 41, 52, 54, 83, 85, 89, 95, 100, 102, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 137, 144], "need": [34, 35, 36, 37, 38, 39, 40, 41, 52, 87, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 130, 132, 133, 134, 135, 136], "cp": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "get_cv": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "get_cvor": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "cv": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "cvor": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 126, 127, 131, 133], "get_f": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136], "helmholtz": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "omit": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136], "get_fort": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "hemholtz": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 132, 133, 134, 135, 136], "get_uort": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "fort": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 124, 125, 126, 127, 131, 133], "get_g": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 137], "free": [34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 109, 113, 123, 127, 144], "gort": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 124, 125, 126, 127, 131, 133], "get_h": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 113, 114, 115, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 137], "hort": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 124, 125, 126, 127, 131, 133], "get_": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 113, 114, 115, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 144], "sor": [34, 35, 36, 37, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 124, 125, 126, 127, 131, 133], "get_u": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "intern": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "uort": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 124, 125, 126, 127, 131, 133], "get_q": [34, 35, 36, 37, 38, 39, 40, 41, 106, 109, 110, 114, 115, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "partit": [34, 35, 36, 37, 38, 39, 40, 41, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 144], "coeffici": [34, 35, 36, 37, 38, 39, 40, 41, 47, 52, 61, 62, 84, 95, 101, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 127, 144], "q": [34, 35, 36, 37, 38, 39, 40, 41, 50, 95, 106, 107, 109, 110, 114, 115, 116, 117, 118, 120, 121, 123, 124, 125, 126, 127, 129, 130, 131, 133, 134, 135, 144], "plot_empir": [34, 36, 37, 38, 39, 41, 109], "cp_unit": [34, 36, 37, 38, 39, 41, 109], "h_unit": [34, 36, 37, 38, 39, 41, 109], "s_unit": [34, 36, 37, 38, 39, 41, 109], "g_unit": [34, 36, 37, 38, 39, 41, 109, 113], "plot": [34, 36, 37, 38, 39, 41, 109, 113, 122, 137, 138, 139, 144], "profil": [34, 36, 37, 38, 39, 41, 109], "lower": [34, 36, 37, 38, 39, 41, 109, 144], "attribut": [34, 36, 37, 38, 39, 40, 41, 45, 47, 77, 79, 85, 86, 87, 90, 91, 92, 95, 102, 103, 104, 105, 106, 107, 109, 113, 114, 116, 117, 118, 120, 121, 122, 123, 124, 125, 130, 131, 135, 136, 144], "upper": [34, 36, 37, 38, 39, 41, 109], "figur": [34, 36, 37, 38, 39, 41, 109, 113, 122, 137], "matplotlib": [34, 36, 37, 38, 39, 41, 109, 113, 122, 137, 139], "ax": [34, 36, 37, 38, 39, 41, 109, 113, 122, 137], "tupl": [34, 36, 37, 38, 39, 40, 41, 77, 79, 86, 109, 113, 122, 137, 144], "axi": [34, 36, 37, 38, 39, 41, 109, 113, 122, 137], "plot_statmech": [34, 36, 37, 38, 39, 41, 109], "use_refer": [34, 36, 37, 38, 39, 41, 109, 131], "plot_statmech_and_empir": [34, 36, 37, 38, 39, 41, 109], "to_dict": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 77, 79, 94, 95, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "datatyp": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 94, 95, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 144], "obj_dict": [34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 94, 95, 106, 107, 109, 110, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136], "effect": [35, 110, 140, 144], "thi": [35, 47, 51, 77, 78, 79, 85, 86, 90, 95, 96, 102, 103, 104, 105, 107, 108, 110, 113, 116, 117, 118, 120, 121, 122, 123, 125, 130, 131, 135, 136, 137, 138, 139, 141, 143, 144, 146], "adjust": [35, 36, 39, 40, 41, 131, 138], "onli": [35, 36, 37, 41, 49, 51, 54, 79, 88, 95, 107, 116, 117, 118, 120, 121, 129, 131, 141, 144, 146], "valid": [35, 55], "nasa": [35, 41, 45, 48, 51, 53, 54, 61, 62, 77, 83, 84, 86, 87, 100, 101, 109, 111, 138, 140, 144], "nasa9": [35, 38, 83, 84, 100, 101, 111, 144], "shomat": [35, 77, 83, 84, 100, 101, 111, 138, 140, 144], "been": [35, 106, 114, 115], "ad": [35, 119, 143, 144], "unless": 35, "obj": [35, 40, 43, 44, 78, 85, 89, 94, 102, 106, 114, 115, 123, 126, 127, 128, 129, 132, 133, 134, 137], "dimesionless": 35, "frac": [35, 36, 37, 41, 44, 95, 107, 116, 117, 118, 120, 121, 123, 124, 125, 129, 130, 132, 133, 134, 135, 136], "ln": [35, 36, 37, 41, 133, 134, 135], "bigg": [35, 41, 44, 118, 123, 129, 132, 133, 134, 135, 136], "p_0": 35, "p0": 35, "t_mid": [36, 37, 144], "a_low": [36, 54, 62], "a_high": [36, 54, 61], "cat_sit": 36, "n_site": [36, 37, 41, 77, 144], "empiricalbas": [36, 37, 38, 39, 41, 80, 82, 85, 97, 99, 102, 109, 110, 144], "store": [36, 37, 38, 41, 109, 130, 132], "inherit": [36, 37, 38, 41, 90, 92, 104, 106, 107, 109, 113, 114, 115, 116, 120, 130], "form": [36, 41, 77, 85, 95, 102, 107, 116, 117, 118, 120, 121], "a_": [36, 37], "rt": [36, 37, 41, 44, 95, 107, 116, 117, 118, 120, 121, 123, 129, 130, 132, 133, 134, 135, 136], "bound": [36, 37, 38, 41], "middl": 36, "high": [36, 37, 38, 41, 142], "catalyst": [36, 50, 85, 94, 102, 138], "site": [36, 94, 95, 104, 107, 116, 117, 120, 121, 138], "adsorpt": [36, 49, 52, 84, 95, 101, 107, 116, 117, 120, 121, 144], "chemkin": [36, 86, 87, 95, 117, 121, 140, 144], "input": [36, 37, 48, 84, 85, 86, 95, 101, 102, 117, 121, 125, 129, 131, 138, 139, 140, 144], "output": [36, 79, 85, 86, 87, 95, 102, 107, 113, 116, 117, 118, 120, 121, 122, 131, 138, 139, 140, 141], "catsit": 36, "occupi": [36, 144], "int": [36, 37, 41, 54, 58, 73, 74, 79, 85, 89, 90, 92, 93, 95, 102, 103, 104, 105, 107, 108, 113, 116, 117, 118, 120, 121, 122, 130, 132, 136, 137], "from_data": [36, 37, 41], "t_ref": [36, 37, 39, 40, 41, 144], "hort_ref": [36, 37, 39, 40, 41], "sor_ref": [36, 37, 41], "iter": [36, 37, 79, 113, 137], "guess": [36, 37, 47, 54, 129], "find": [36, 37, 53, 54, 61, 62, 139, 143, 146], "best": [36, 37, 139, 146], "each": [36, 37, 40, 45, 48, 49, 53, 79, 83, 85, 87, 100, 102, 113, 122, 130, 131, 138, 143], "rang": [36, 37, 90, 103, 139], "screen": [36, 37], "6th": [36, 37], "lowest": [36, 37], "highest": [36, 37], "term": [36, 37, 41, 135], "from_model": [36, 37, 41, 144], "n_t": [36, 37, 41], "pass": [36, 37, 41, 47, 79, 85, 89, 95, 102, 107, 116, 117, 118, 120, 121, 130, 131, 137, 144], "must": [36, 37, 41, 45, 77, 78, 79, 87, 115, 126, 144], "contain": [36, 37, 41, 45, 47, 48, 52, 58, 77, 79, 106, 114, 118, 122, 131, 137, 138, 144], "limit": [36, 37, 41, 136], "temeratur": [36, 37, 41], "higher": [36, 37, 41, 113, 122], "point": [36, 41, 50, 53, 70, 76, 95, 107, 113, 116, 117, 118, 120, 121, 122, 129, 131, 133, 134, 135, 136, 144], "init": [36, 37, 41], "from_statmech": [36, 41, 144], "statmech_model": [36, 41, 54], "deprec": [36, 41, 144], "version": [36, 41, 79, 96, 140, 146], "pleas": [36, 41, 96, 139, 142, 146], "instead": [36, 41, 85, 95, 102, 106, 107, 114, 115, 116, 117, 118, 120, 121, 144], "statmech": [36, 41, 45, 47, 66, 77, 111, 138, 140, 144], "raise_error": [36, 37, 41, 118, 131, 144], "raise_warn": [36, 37, 41, 118, 131, 144], "error": [36, 37, 41, 118, 131, 144], "mode": [36, 37, 41, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 135, 136, 138, 144], "do": [36, 37, 41, 85, 102, 130, 131, 139, 144, 146], "quantiti": [36, 37, 41, 49, 84, 85, 93, 95, 101, 102, 103, 104, 105, 107, 108, 110, 113, 116, 117, 118, 120, 121, 122, 128, 130, 131, 132, 144], "interest": [36, 37, 41, 95, 107, 116, 117, 118, 120, 121, 125, 131, 141, 146], "relev": [36, 37, 41, 44, 49, 95, 107, 113, 115, 116, 117, 118, 120, 121, 122, 131], "warn": [36, 37, 41, 118, 131, 144], "word": [36, 37, 41, 131], "s_element": [36, 37, 41, 131, 144], "defauli": [36, 37, 41, 131], "get_sel": [36, 37, 41, 131], "get_a": [36, 95, 107, 116, 117, 118, 120, 121], "correct": [36, 52, 107, 116, 120, 143, 144], "to_cti": [36, 37, 38, 41, 89, 90, 92, 93, 103, 104, 105, 106, 107, 108, 110, 114, 116, 120], "write": [36, 37, 38, 41, 49, 50, 51, 52, 53, 77, 79, 84, 85, 87, 90, 92, 93, 95, 96, 101, 102, 103, 104, 105, 106, 107, 108, 110, 114, 116, 117, 118, 120, 121, 138, 139, 144], "cantera": [36, 37, 38, 41, 103, 104, 105, 106, 107, 108, 110, 114, 116, 120, 140, 144], "cti": [36, 37, 38, 41, 84, 85, 89, 90, 92, 93, 101, 102, 103, 104, 105, 106, 107, 108, 110, 114, 116, 120, 138, 144], "cti_str": [36, 37, 38, 41, 89, 90, 92, 93, 103, 104, 105, 106, 107, 108, 114, 116, 120], "to_omkm_yaml": [36, 37, 41, 90, 93, 103, 104, 105, 106, 107, 108, 110, 114, 116, 120], "compat": [36, 37, 41, 77, 90, 93, 103, 104, 105, 106, 107, 108, 110, 114, 116, 120, 139, 144], "yaml": [36, 37, 41, 85, 90, 93, 102, 103, 104, 105, 106, 107, 108, 110, 114, 116, 120, 139, 140, 144], "yaml_dict": [36, 37, 41, 90, 93, 103, 104, 105, 106, 107, 108, 110, 114, 116, 120], "a_2": 37, "interv": [37, 38, 110], "singlenasa9": [37, 144], "determin": [37, 61, 62, 89, 95, 107, 113, 116, 117, 120, 121, 122, 141], "fit_t_mid": 37, "n_interv": 37, "behavior": [37, 79, 144], "creat": [37, 40, 44, 95, 107, 112, 116, 117, 118, 120, 121, 138, 140, 144, 146], "larger": [37, 44, 144], "better": 37, "take": [37, 61, 62, 79, 85, 102, 144], "longer": 37, "run": [37, 85, 102, 138, 139, 140, 146], "chang": [37, 95, 103, 105, 107, 108, 110, 113, 115, 116, 117, 118, 119, 120, 121, 122, 128, 130, 139, 141, 144], "defin": [38, 40, 77], "line_ind": 38, "first": [38, 73, 87, 110, 113, 122, 130, 137], "line": [38, 49, 50, 51, 52, 53, 86, 87, 89, 90, 92, 93, 103, 104, 105, 108], "indent": [38, 77, 79, 85, 89, 102], "space": [38, 49, 52, 95, 107, 113, 116, 117, 118, 120, 121, 122, 138, 144], "singl": [39, 119, 123, 124, 125, 144], "experiment": [39, 40, 140, 143], "offset": [40, 113, 122], "descriptor": [40, 106, 114, 115, 144], "member": [40, 79], "append": [40, 141], "clear_offset": 40, "remov": [40, 56, 60, 110, 144], "all": [40, 45, 48, 77, 79, 85, 90, 95, 102, 104, 107, 113, 116, 117, 118, 120, 121, 123, 127, 130, 138, 144], "entri": [40, 77, 78, 87, 118, 130, 144], "extend": [40, 124], "seq": 40, "fit_hort_offset": 40, "get_aort": 40, "due": [40, 130, 141, 144], "hort_": 40, "exp": [40, 118, 123, 133, 134, 135, 136], "where": [40, 41, 55, 80, 81, 82, 85, 95, 97, 98, 99, 102, 107, 116, 117, 118, 120, 121, 125, 126, 130, 143, 144], "decriptor": 40, "potentialenergi": [40, 109, 123, 130, 144], "get_descriptor": 40, "uniqu": [40, 95, 107, 113, 116, 117, 118, 120, 121, 122], "get_descriptors_matrix": 40, "matrix": [40, 85, 102, 139, 143], "requir": [40, 54, 85, 95, 102, 106, 107, 114, 115, 116, 117, 118, 120, 121, 129, 130, 138, 144], "sort": [40, 79, 110], "alphabet": 40, "order": [40, 110, 143], "row": [40, 54, 137, 143], "column": [40, 49, 50, 52, 53, 54, 137, 143], "index": [40, 54, 61, 62, 110, 113, 122, 140], "insert": [40, 79, 95, 107, 110, 116, 117, 118, 120, 121], "pop": [40, 110], "individu": [41, 109, 144], "c_p": [41, 123, 129, 130, 133, 134, 135], "bt": 41, "ct": 41, "dt": 41, "d": [41, 139, 142], "2t": [41, 134, 135], "_pmuttbas": [43, 44, 94, 118, 122], "pv": 43, "nrt": 43, "get_p": [43, 44], "0247895618937": [43, 44], "get_t": [43, 44], "get_v": [43, 44, 132], "get_n": [43, 44], "van": 44, "der": 44, "waal": 44, "big": [44, 132, 133, 134, 135], "measur": 44, "averag": [44, 136], "attract": 44, "m6": 44, "exclud": [44, 144], "from_crit": 44, "pc": 44, "critic": [44, 144], "get_pc": 44, "get_tc": 44, "critcial": 44, "gas_phas": [44, 95, 107, 116, 117, 120, 121], "system": [44, 85, 102, 130], "vapor": 44, "liquid": 44, "equilibrium": [44, 95, 107, 116, 117, 118, 120, 121, 140, 144], "smaller": 44, "get_vc": 44, "vc": 44, "get_vm": 44, "vm": 44, "network": [45, 46, 139, 144], "reaction": [45, 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    Unit