Merge pull request #180 from sandialabs/wlc

WLC isotensional
sandialabs · May 8, 2023 · 64ff14a · 64ff14a · github-actions · May 8, 2023
2 parents 3feb915 + fda75f2
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diff --git a/Cargo.toml b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "polymers"
-version = "0.3.4"
+version = "0.3.5"
 edition = "2021"
 description = "Polymers Modeling Library"
 license = "BSD-3-Clause"

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "Polymers"
 uuid = "8aef037c-a721-4e8a-9d81-eb7093daef2c"
 authors = ["mrbuche <[email protected]>"]
-version = "0.3.4"
+version = "0.3.5"
 
 [deps]
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"

diff --git a/README.md b/README.md
@@ -17,16 +17,6 @@ The library can be installed as a Python package:
 pip install polymers
 ```
 
-If Rust is installed, the latest edition of the library can be installed from the GitHub repository:
-
-```shell
-git clone [email protected]:sandialabs/Polymers.git
-cd Polymers/
-pip install maturin
-maturin build --features python
-pip install target/wheels/*.whl
-```
-
 ## Julia
 
 [![docs (stable)](https://raw.githubusercontent.com/sandialabs/Polymers/main/pages/assets/images/julia-docs-stable.svg)](https://sandialabs.github.io/Polymers/julia/docs/stable)
@@ -40,30 +30,16 @@ using Pkg
 Pkg.add("Polymers")
 ```
 
-If Rust is installed, the latest edition of the library can be installed from the GitHub repository:
-
-```julia
-using Pkg
-Pkg.add(url="https://github.com/sandialabs/Polymers")
-```
-
 ## Rust
 
 [![docs (stable)](https://img.shields.io/badge/Docs-stable-e57300?logo=rust&logoColor=000000)](https://docs.rs/crate/polymers)
 [![docs (latest)](https://img.shields.io/badge/Docs-latest-e57300?logo=rust&logoColor=000000)](https://sandialabs.github.io/Polymers/rust/docs/latest)
 [![crates](https://img.shields.io/crates/v/polymers?logo=rust&logoColor=000000&label=Crates&color=32592f)](https://crates.io/crates/polymers)
 
-The library can be used in an existing Rust project by adding the `polymers` crate to Cargo.toml:
+The library can be added to an existing Rust project:
 
-```toml
-[dependencies]
-polymers = "*"
-```
-To use the latest edition of the library, add the GitHub repository to Cargo.toml:
-
-```toml
-[dependencies]
-regex = { git = "https://github.com/sandialabs/polymers" }
+```shell
+cargo add polymers
 ```
 
 ## Citation

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -16,16 +16,6 @@ The library can be installed as a Python package:
 
    pip install polymers
 
-If Rust is installed, the latest edition of the library can be installed from the GitHub repository:
-
-.. code-block:: sh
-
-   git clone [email protected]:sandialabs/Polymers.git
-   cd Polymers/
-   pip install maturin
-   maturin build --features python
-   pip install target/wheels/*.whl
-
 Citation
 --------
 

diff --git a/docs/source/physics/single_chain/wlc/thermodynamics.rst b/docs/source/physics/single_chain/wlc/thermodynamics.rst
@@ -5,6 +5,7 @@ WLC model thermodynamics
    :maxdepth: 1
 
    Isometric <thermodynamics/isometric>
+   Isometric <thermodynamics/isotensional>
 
 .. autoclass:: polymers.physics.single_chain.wlc.thermodynamics::WLC(number_of_links, link_length, hinge_mass, persistance_length)
 
@@ -13,3 +14,4 @@ WLC model thermodynamics
    .. autoattribute:: hinge_mass
    .. autoattribute:: persistance_length
    .. autoattribute:: isometric
+   .. autoattribute:: isotensional
diff --git a/docs/source/physics/single_chain/wlc/thermodynamics/isotensional.rst b/docs/source/physics/single_chain/wlc/thermodynamics/isotensional.rst
@@ -0,0 +1,34 @@
+WLC model thermodynamics (isotensional)
+=======================================
+
+.. toctree::
+   :maxdepth: 1
+
+   Legendre <isotensional/legendre>
+
+.. autoclass:: polymers.physics.single_chain.wlc.thermodynamics.isotensional::WLC(number_of_links, link_length, hinge_mass, persistance_length)
+
+   .. autoattribute:: number_of_links
+   .. autoattribute:: link_length
+   .. autoattribute:: hinge_mass
+   .. autoattribute:: persistance_length
+   .. autoattribute:: legendre
+   .. automethod:: end_to_end_length(force, temperature)
+   .. automethod:: end_to_end_length_per_link(force, temperature)
+   .. automethod:: nondimensional_end_to_end_length(nondimensional_force)
+   .. automethod:: nondimensional_end_to_end_length_per_link(nondimensional_force)
+   .. automethod:: gibbs_free_energy(force, temperature)
+   .. automethod:: gibbs_free_energy_per_link(force, temperature)
+   .. automethod:: relative_gibbs_free_energy(force, temperature)
+   .. automethod:: relative_gibbs_free_energy_per_link(force, temperature)
+   .. automethod:: nondimensional_gibbs_free_energy(nondimensional_force, temperature)
+   .. automethod:: nondimensional_gibbs_free_energy_per_link(nondimensional_force, temperature)
+   .. automethod:: nondimensional_relative_gibbs_free_energy(nondimensional_force)
+   .. automethod:: nondimensional_relative_gibbs_free_energy_per_link(nondimensional_force)
+
+.. raw::
+ html
+
+   <hr>
+
+.. footbibliography::
diff --git a/docs/source/physics/single_chain/wlc/thermodynamics/isotensional/legendre.rst b/docs/source/physics/single_chain/wlc/thermodynamics/isotensional/legendre.rst
@@ -0,0 +1,17 @@
+WLC model thermodynamics (isotensional/legendre)
+================================================
+
+.. autoclass:: polymers.physics.single_chain.wlc.thermodynamics.isotensional.legendre::WLC(number_of_links, link_length, hinge_mass, persistance_length)
+
+   .. autoattribute:: number_of_links
+   .. autoattribute:: link_length
+   .. autoattribute:: hinge_mass
+   .. autoattribute:: persistance_length
+   .. automethod:: helmholtz_free_energy(force, temperature)
+   .. automethod:: helmholtz_free_energy_per_link(force, temperature)
+   .. automethod:: relative_helmholtz_free_energy(force, temperature)
+   .. automethod:: relative_helmholtz_free_energy_per_link(force, temperature)
+   .. automethod:: nondimensional_helmholtz_free_energy(nondimensional_force, temperature)
+   .. automethod:: nondimensional_helmholtz_free_energy_per_link(nondimensional_force, temperature)
+   .. automethod:: nondimensional_relative_helmholtz_free_energy(nondimensional_force)
+   .. automethod:: nondimensional_relative_helmholtz_free_energy_per_link(nondimensional_force)
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -16,13 +16,6 @@ using Pkg
 Pkg.add("Polymers")
 ```
 
-If Rust is installed, the latest edition of the library can be installed from the GitHub repository:
-
-```julia
-using Pkg
-Pkg.add(url="https://github.com/sandialabs/Polymers")
-```
-
 ## Citation
 
 [![doi](https://img.shields.io/badge/Zenodo-10.5281%2Fzenodo.7041983-blue)](https://doi.org/10.5281/zenodo.7041983)

diff --git a/docs/src/physics/single_chain/wlc.md b/docs/src/physics/single_chain/wlc.md
@@ -3,5 +3,5 @@
   * [WLC model thermodynamics](../../thermodynamics)
 
 ```@autodocs
-Modules = [Polymers.Physics.SingleChain.WLC]
+Modules = [Polymers.Physics.SingleChain.Wlc]
 ```
diff --git a/docs/src/physics/single_chain/wlc/thermodynamics.md b/docs/src/physics/single_chain/wlc/thermodynamics.md
@@ -1,7 +1,8 @@
 # WLC model thermodynamics
 
   * [WLC model thermodynamics (isometric)](../../../isometric)
+  * [WLC model thermodynamics (isotensional)](../../../isotensional)
 
 ```@autodocs
-Modules = [Polymers.Physics.SingleChain.WLC.Thermodynamics]
+Modules = [Polymers.Physics.SingleChain.Wlc.Thermodynamics]
 ```
diff --git a/docs/src/physics/single_chain/wlc/thermodynamics/isometric.md b/docs/src/physics/single_chain/wlc/thermodynamics/isometric.md
@@ -3,5 +3,5 @@
   * [WLC model thermodynamics (isometric/legendre)](../../../../legendre)
 
 ```@autodocs
-Modules = [Polymers.Physics.SingleChain.WLC.Thermodynamics.Isometric]
+Modules = [Polymers.Physics.SingleChain.Wlc.Thermodynamics.Isometric]
 ```
diff --git a/docs/src/physics/single_chain/wlc/thermodynamics/isometric/legendre.md b/docs/src/physics/single_chain/wlc/thermodynamics/isometric/legendre.md
@@ -1,5 +1,5 @@
 # WLC model thermodynamics (isometric/legendre)
 
 ```@autodocs
-Modules = [Polymers.Physics.SingleChain.WLC.Thermodynamics.Isometric.Legendre]
+Modules = [Polymers.Physics.SingleChain.Wlc.Thermodynamics.Isometric.Legendre]
 ```
diff --git a/docs/src/physics/single_chain/wlc/thermodynamics/isotensional.md b/docs/src/physics/single_chain/wlc/thermodynamics/isotensional.md
@@ -0,0 +1,7 @@
+# WLC model thermodynamics (isotensional)
+
+  * [WLC model thermodynamics (isotensional/legendre)](../../../../legendre)
+
+```@autodocs
+Modules = [Polymers.Physics.SingleChain.Wlc.Thermodynamics.Isotensional]
+```
diff --git a/docs/src/physics/single_chain/wlc/thermodynamics/isotensional/legendre.md b/docs/src/physics/single_chain/wlc/thermodynamics/isotensional/legendre.md
@@ -0,0 +1,5 @@
+# WLC model thermodynamics (isotensional/legendre)
+
+```@autodocs
+Modules = [Polymers.Physics.SingleChain.Wlc.Thermodynamics.Isotensional.Legendre]
+```
diff --git a/src/physics/single_chain/mod.jl b/src/physics/single_chain/mod.jl
@@ -36,6 +36,7 @@ struct Parameters
     link_stiffness_scale::Float64
     link_energy_reference::Float64
     link_energy_scale::Float64
+    nondimensional_persistance_length_small::Float64
     nondimensional_link_stiffness_large::Float64
     nondimensional_link_stiffness_big::Float64
     nondimensional_link_stiffness_medium::Float64
@@ -80,6 +81,7 @@ parameters = Parameters(
     99e4,
     5e4,
     99e3,
+    2e-2,
     1e4,
     1e3,
     1e1,

diff --git a/src/physics/single_chain/test.py b/src/physics/single_chain/test.py
@@ -39,6 +39,7 @@ def __init__(self):
         self.link_stiffness_scale = 99e4
         self.link_energy_reference = 5e4
         self.link_energy_scale = 99e3
+        self.nondimensional_persistance_length_small = 2e-2
         self.nondimensional_link_stiffness_large = 1e4
         self.nondimensional_link_stiffness_big = 1e3
         self.nondimensional_link_stiffness_medium = 1e1

diff --git a/src/physics/single_chain/test.rs b/src/physics/single_chain/test.rs
@@ -26,6 +26,7 @@ pub struct Parameters
     pub link_stiffness_scale: f64,
     pub link_energy_reference: f64,
     pub link_energy_scale: f64,
+    pub nondimensional_persistance_length_small: f64,
     pub nondimensional_link_stiffness_large: f64,
     pub nondimensional_link_stiffness_big: f64,
     pub nondimensional_link_stiffness_medium: f64,
@@ -74,6 +75,7 @@ impl Default for Parameters
             link_stiffness_scale: 99e4,
             link_energy_reference: 5e4,
             link_energy_scale: 99e3,
+            nondimensional_persistance_length_small: 2e-2,
             nondimensional_link_stiffness_large: 1e4,
             nondimensional_link_stiffness_big: 1e3,
             nondimensional_link_stiffness_medium: 1e1,

diff --git a/src/physics/single_chain/wlc/thermodynamics/isometric/legendre/mod.jl b/src/physics/single_chain/wlc/thermodynamics/isometric/legendre/mod.jl
@@ -64,7 +64,7 @@ end
 
 """
 The Gibbs free energy ``\\varphi`` as a function of the applied end-to-end length ``\\xi`` and temperature ``T``,
-parameterized by the number of links ``N_b``, link length ``\\ell_b``, and hinge mass ``m``,
+parameterized by the number of links ``N_b``, link length ``\\ell_b``, hinge mass ``m``, and persistance length ``\\ell_p``,
 
 ```math
 \\varphi(\\xi, T) \\sim \\psi(\\xi, T) - \\xi f(\\xi, T) \\quad \\text{for } N_b\\gg 1,
@@ -115,7 +115,7 @@ end
 
 """
 The Gibbs free energy per link ``\\varphi/N_b`` as a function of the applied end-to-end length ``\\xi`` and temperature ``T``,
-parameterized by the number of links ``N_b``, link length ``\\ell_b``, and hinge mass ``m``.
+parameterized by the number of links ``N_b``, link length ``\\ell_b``, hinge mass ``m``, and persistance length ``\\ell_p``.
 
 $(TYPEDSIGNATURES)
 """
@@ -160,7 +160,7 @@ end
 
 """
 The relative Helmholtz free energy ``\\Delta\\varphi\\equiv\\varphi(\\xi,T)-\\varphi(0,T)`` as a function of the applied end-to-end length ``\\xi`` and temperature ``T``,
-parameterized by the number of links ``N_b`` and link length ``\\ell_b``.
+parameterized by the number of links ``N_b``, link length ``\\ell_b``, and persistance length ``\\ell_p``.
 
 $(TYPEDSIGNATURES)
 """
@@ -201,7 +201,7 @@ end
 
 """
 The relative Gibbs free energy per link ``\\Delta\\varphi/N_b`` as a function of the applied end-to-end length ``\\xi`` and temperature ``T``,
-parameterized by the number of links ``N_b`` and link length ``\\ell_b``.
+parameterized by the number of links ``N_b``, link length ``\\ell_b``, and persistance length ``\\ell_p``.
 
 $(TYPEDSIGNATURES)
 """
@@ -242,7 +242,7 @@ end
 
 """
 The nondimensional Gibbs free energy ``N_b\\varrho=\\beta\\varphi`` as a function of the applied nondimensional end-to-end length per link ``\\gamma`` and temperature ``T``,
-parameterized by the number of links ``N_b``, link length ``\\ell_b``, and hinge mass ``m``.
+parameterized by the number of links ``N_b``, link length ``\\ell_b``, hinge mass ``m``, and nondimensional persistance length ``\\zeta``.
 
 $(TYPEDSIGNATURES)
 """
@@ -287,7 +287,7 @@ end
 
 """
 The nondimensional Gibbs free energy per link ``\\varrho\\equiv\\beta\\varphi/N_b`` as a function of the applied nondimensional end-to-end length per link ``\\gamma`` and temperature ``T``,
-parameterized by the number of links ``N_b``, link length ``\\ell_b``, and hinge mass ``m``.
+parameterized by the number of links ``N_b``, link length ``\\ell_b``, hinge mass ``m``, and nondimensional persistance length ``\\zeta``.
 
 $(TYPEDSIGNATURES)
 """
@@ -332,7 +332,7 @@ end
 
 """
 The nondimensional relative Gibbs free energy ``N_b\\Delta\\varrho=\\beta\\Delta\\varphi`` as a function of the applied nondimensional end-to-end length per link ``\\gamma`` and temperature ``T``,
-parameterized by the number of links ``N_b``.
+parameterized by the number of links ``N_b`` and nondimensional persistance length ``\\zeta``.
 
 $(TYPEDSIGNATURES)
 """
@@ -365,7 +365,7 @@ end
 
 """
 The nondimensional relative Helmholtz free energy per link ``\\Delta\\varrho\\equiv\\beta\\Delta\\varphi/N_b`` as a function of the applied nondimensional end-to-end length per link ``\\gamma`` and temperature ``T``,
-parameterized by the number of links ``N_b``.
+parameterized by the number of links ``N_b`` and nondimensional persistance length ``\\zeta``.
 
 $(TYPEDSIGNATURES)
 """