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Merge branch 'development' into jac_cell_display
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‎Docs/source/burn_cell.rst

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@@ -1,3 +1,5 @@
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.. _sec:burn_cell:
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13
*************
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``burn_cell``
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*************
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::
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unit_test.init_species_all_equal = 1
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unit_test.uniform_xn = 1
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Controlling time
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network or integrator.
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To run the code, enter the burn_cell directory and run::
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To run the code, in the ``burn_cell`` directory run::
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./main3d.gnu.ex inputs
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‎Docs/source/eos_cell.rst

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************
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``eos_cell``
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************
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.. index:: eos_cell
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``eos_cell`` simply calls the equation of state on an input density, temperature,
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and composition, and then outputs the full thermodynamic state. This is mainly
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used to understand the thermodynamics one might encounter in a simulation
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when using a particular EOS.
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Getting Started
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===============
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The ``eos_cell`` code is located in
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``Microphysics/unit_test/eos_cell``. An inputs file which sets the
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default parameters for your thermodynamic state is needed to run the
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test.
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Setting the thermodynamics
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--------------------------
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The parameters that affect the thermodynamics are:
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* ``unit_test.density`` : the initial density
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* ``unit_test.temperature`` : the initial temperature
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* ``unit_test.small_temp`` : the low temperature cutoff used in the equation of state
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* ``unit_test.small_dens`` : the low density cutoff used in the equation of state
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The composition can be set in the same way as in ``burn_cell``, either
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by setting each mass fraction explicitly via the parameters,
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``unit_test.X1``, ``unit_test.X2``, ..., or forcing them to be all
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equal via ``unit_test.uniform_xn=1``.
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Building and Running the Code
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=============================
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The code can be built simply as:
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.. prompt:: bash
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make
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.. note::
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Even though there are no reactions, a network is still required,
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and can be set via the ``NETWORK_DIR`` build variable. By default,
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the ``aprox13`` network is used.
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The network choice serves only to set the composition, and a
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``general_null`` network may also be used.
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The build process will automatically create links in the build
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directory to any required EOS table.
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To run the code, in the ``eos_cell`` directory run::
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./main3d.gnu.ex inputs_eos
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where ``inputs_eos`` is the provided inputs file. You may edit the
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thermodynamic state in that file prior to running.
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Output
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======
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All output is directed to ``stdout`` and simply lists the entries in the
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full ``eos_t`` datatype.

‎Docs/source/getting_started.rst

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Original file line numberDiff line numberDiff line change
@@ -58,17 +58,27 @@ one-zone burn. In ``Microphysics/`` do:
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cd unit_test/burn_cell
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make
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61-
This will create an executable called ``main3d.gnu.ex``. Then you can run it as:
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This will create an executable called ``main3d.gnu.ex``.
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By default, the test is built with the 13-isotope ``aprox13`` network,
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``helmholtz`` EOS, and VODE integrator.
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Then you can run it as:
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.. prompt:: bash
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./main3d.gnu.ex inputs_aprox13
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67-
By default, the test is built with the 13-isotope ``aprox13`` network,
68-
``helmholtz`` EOS, and VODE integrator.
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Here ``inputs_aprox13`` is the inputs file that sets options.
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This will output information about the starting and final state to the
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terminal and produce a file ``state_over_time.txt`` that contains the
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thermodynamic history at different points in time.
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.. note::
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See the :ref:`sec:burn_cell` documentation for more details on this
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unit test and how to visualize the output.
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Running with AMReX Application Code
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===================================

‎Docs/source/one_zone_tests.rst

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@@ -11,3 +11,4 @@ have analysis scripts, which we describe in the next sections.
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:hidden:
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burn_cell.rst
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eos_cell.rst

‎Docs/source/rp_intro.rst

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@@ -6,7 +6,7 @@ The behavior of the network and EOS are controlled by many runtime
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parameters. These parameters are defined in plain-text files
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``_parameters`` located in the different directories that hold the
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microphysics code. At compile time, a script in the AMReX build
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system, findparams.py, locates all of the ``_parameters`` files that
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system, ``findparams.py``, locates all of the ``_parameters`` files that
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are needed for the given choice of network, integrator, and EOS, and
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assembles all of the runtime parameters into a set of header files
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(using the ``write_probin.py`` script).
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.. toctree::
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runtime_parameters
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‎unit_test/_parameters

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@@ -39,3 +39,6 @@ X32 real 0.0e0
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X33 real 0.0e0
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X34 real 0.0e0
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X35 real 0.0e0
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uniform_xn bool 0
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‎unit_test/burn_cell/_parameters

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temperature real 3.e9
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skip_initial_normalization bool 0
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init_species_all_equal bool 0

‎unit_test/burn_cell/burn_cell.H

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@@ -21,14 +21,10 @@ void burn_cell_c()
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// Make sure user set all the mass fractions to values in the interval [0, 1]
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for (int n = 1; n <= NumSpec; ++n) {
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if (unit_test_rp::init_species_all_equal) {
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massfractions[n-1] = 1.0_rt / static_cast<amrex::Real>(NumSpec);
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} else {
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massfractions[n-1] = get_xn(n);
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massfractions[n-1] = get_xn(n, unit_test_rp::uniform_xn);
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29-
if (massfractions[n-1] < 0 || massfractions[n-1] > 1) {
30-
amrex::Error("mass fraction for " + short_spec_names_cxx[n-1] + " not initialized in the interval [0,1]!");
31-
}
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if (massfractions[n-1] < 0 || massfractions[n-1] > 1) {
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amrex::Error("mass fraction for " + short_spec_names_cxx[n-1] + " not initialized in the interval [0,1]!");
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}
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}
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‎unit_test/burn_cell_sdc/burn_cell.H

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@@ -20,7 +20,7 @@ void burn_cell_c()
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// Make sure user set all the mass fractions to values in the interval [0, 1]
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for (int n = 1; n <= NumSpec; ++n) {
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23-
massfractions[n-1] = get_xn(n);
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massfractions[n-1] = get_xn(n, unit_test_rp::uniform_xn);
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2525
if (massfractions[n-1] < 0 || massfractions[n-1] > 1) {
2626
amrex::Error("mass fraction for " + short_spec_names_cxx[n-1] + " not initialized in the interval [0,1]!");

‎unit_test/eos_cell/eos_cell.H

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@@ -24,7 +24,7 @@ void eos_cell_c()
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// Make sure user set all the mass fractions to values in the interval [0, 1]
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for (int n = 1; n <= NumSpec; ++n) {
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27-
massfractions[n-1] = get_xn(n);
27+
massfractions[n-1] = get_xn(n, unit_test_rp::uniform_xn);
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2929
if (massfractions[n-1] < 0 || massfractions[n-1] > 1) {
3030
amrex::Error("mass fraction for " + short_spec_names_cxx[n-1] + " not initialized in the interval [0,1]!");

‎unit_test/jac_cell/jac_cell.H

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@@ -22,7 +22,7 @@ void jac_cell_c()
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// Make sure user set all the mass fractions to values in the interval [0, 1]
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for (int n = 1; n <= NumSpec; ++n) {
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25-
massfractions[n-1] = get_xn(n);
25+
massfractions[n-1] = get_xn(n, unit_test_rp::uniform_xn);
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2727
if (massfractions[n-1] < 0 || massfractions[n-1] > 1) {
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amrex::Error("mass fraction for " + short_spec_names_cxx[n-1] + " not initialized in the interval [0,1]!");
@@ -38,7 +38,9 @@ void jac_cell_c()
3838
burn_state.xn[n] = massfractions[n];
3939
}
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41-
normalize_abundances_burn(burn_state);
41+
if (! unit_test_rp::skip_initial_normalization) {
42+
normalize_abundances_burn(burn_state);
43+
}
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// get the energy
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‎unit_test/react_util.H

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@@ -88,7 +88,7 @@ init_t setup_composition(const int nz) {
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9090
AMREX_INLINE AMREX_GPU_HOST_DEVICE
91-
void get_xn(const int k, const init_t cd, amrex::Real *xn_zone, int uniform_composition = 0) {
91+
void get_xn(const int k, const init_t cd, amrex::Real *xn_zone, bool uniform_composition=false) {
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9393
for (int n = 0; n < NumSpec; n++) {
9494
xn_zone[n] = 0.0_rt;
@@ -167,10 +167,15 @@ void get_xn(const int k, const init_t cd, amrex::Real *xn_zone, int uniform_comp
167167
///
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169169
AMREX_INLINE AMREX_GPU_HOST_DEVICE
170-
amrex::Real get_xn(const int index) {
170+
amrex::Real get_xn(const int index, bool uniform_composition=false) {
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172172
amrex::Real mass_fraction{};
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174+
if (uniform_composition) {
175+
mass_fraction = 1.0_rt / NumSpec;
176+
return mass_fraction;
177+
}
178+
174179
switch (index) {
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176181
case 1:

‎unit_test/test_react/_parameters

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temp_min real 1.e6
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temp_max real 1.e15
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8-
uniform_xn int 0
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tmax real 0.1e0
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small_temp real 1.e5

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