Merge branch 'development' into jac_cell_display

Docs/source/burn_cell.rst

@@ -1,3 +1,5 @@
+.. _sec:burn_cell:
+
 *************
 ``burn_cell``
 *************
@@ -80,7 +82,7 @@ by setting:
 
 ::
 
-    unit_test.init_species_all_equal = 1
+    unit_test.uniform_xn = 1
 
 
 Controlling time
@@ -139,7 +141,7 @@ choice of network.
    network or integrator.
 
 
-To run the code, enter the burn_cell directory and run::
+To run the code, in the ``burn_cell`` directory run::
 
    ./main3d.gnu.ex inputs
 

Docs/source/eos_cell.rst

@@ -0,0 +1,72 @@
+************
+``eos_cell``
+************
+
+.. index:: eos_cell
+
+``eos_cell`` simply calls the equation of state on an input density, temperature,
+and composition, and then outputs the full thermodynamic state.  This is mainly
+used to understand the thermodynamics one might encounter in a simulation
+when using a particular EOS.
+
+Getting Started
+===============
+
+The ``eos_cell`` code is located in
+``Microphysics/unit_test/eos_cell``.  An inputs file which sets the
+default parameters for your thermodynamic state is needed to run the
+test.
+
+Setting the thermodynamics
+--------------------------
+
+The parameters that affect the thermodynamics are:
+
+* ``unit_test.density`` : the initial density
+
+* ``unit_test.temperature`` : the initial temperature
+
+* ``unit_test.small_temp`` : the low temperature cutoff used in the equation of state
+
+* ``unit_test.small_dens`` : the low density cutoff used in the equation of state
+
+The composition can be set in the same way as in ``burn_cell``, either
+by setting each mass fraction explicitly via the parameters,
+``unit_test.X1``, ``unit_test.X2``, ..., or forcing them to be all
+equal via ``unit_test.uniform_xn=1``.
+
+
+Building and Running the Code
+=============================
+
+The code can be built simply as:
+
+.. prompt:: bash
+
+   make
+
+.. note::
+
+   Even though there are no reactions, a network is still required,
+   and can be set via the ``NETWORK_DIR`` build variable.  By default,
+   the ``aprox13`` network is used.
+
+   The network choice serves only to set the composition, and a
+   ``general_null`` network may also be used.
+
+The build process will automatically create links in the build
+directory to any required EOS table.
+
+To run the code, in the ``eos_cell`` directory run::
+
+   ./main3d.gnu.ex inputs_eos
+
+where ``inputs_eos`` is the provided inputs file.  You may edit the
+thermodynamic state in that file prior to running.
+
+
+Output
+======
+
+All output is directed to ``stdout`` and simply lists the entries in the
+full ``eos_t`` datatype.

Docs/source/getting_started.rst

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

Docs/source/one_zone_tests.rst

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

Docs/source/rp_intro.rst

@@ -6,7 +6,7 @@ The behavior of the network and EOS are controlled by many runtime
 parameters. These parameters are defined in plain-text files
 ``_parameters`` located in the different directories that hold the
 microphysics code. At compile time, a script in the AMReX build
-system, findparams.py, locates all of the ``_parameters`` files that
+system, ``findparams.py``, locates all of the ``_parameters`` files that
 are needed for the given choice of network, integrator, and EOS, and
 assembles all of the runtime parameters into a set of header files
 (using the ``write_probin.py`` script).
@@ -32,4 +32,3 @@ noted in separate tables.
 .. toctree::
 
    runtime_parameters
-

unit_test/_parameters

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

unit_test/burn_cell/_parameters

@@ -17,5 +17,3 @@ density       real       1.e7
 temperature   real       3.e9
 
 skip_initial_normalization    bool    0
-
-init_species_all_equal        bool    0

unit_test/burn_cell/burn_cell.H

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

unit_test/burn_cell_sdc/burn_cell.H

@@ -20,7 +20,7 @@ void burn_cell_c()
     // Make sure user set all the mass fractions to values in the interval [0, 1]
     for (int n = 1; n <= NumSpec; ++n) {
 
-        massfractions[n-1] = get_xn(n);
+        massfractions[n-1] = get_xn(n, unit_test_rp::uniform_xn);
 
         if (massfractions[n-1] < 0 || massfractions[n-1] > 1) {
             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

@@ -24,7 +24,7 @@ void eos_cell_c()
     // Make sure user set all the mass fractions to values in the interval [0, 1]
     for (int n = 1; n <= NumSpec; ++n) {
 
-        massfractions[n-1] = get_xn(n);
+        massfractions[n-1] = get_xn(n, unit_test_rp::uniform_xn);
 
         if (massfractions[n-1] < 0 || massfractions[n-1] > 1) {
             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

@@ -22,7 +22,7 @@ void jac_cell_c()
     // Make sure user set all the mass fractions to values in the interval [0, 1]
     for (int n = 1; n <= NumSpec; ++n) {
 
-        massfractions[n-1] = get_xn(n);
+        massfractions[n-1] = get_xn(n, unit_test_rp::uniform_xn);
 
         if (massfractions[n-1] < 0 || massfractions[n-1] > 1) {
             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()
         burn_state.xn[n] = massfractions[n];
     }
 
-    normalize_abundances_burn(burn_state);
+    if (! unit_test_rp::skip_initial_normalization) {
+        normalize_abundances_burn(burn_state);
+    }
 
     // get the energy
 

unit_test/react_util.H

@@ -88,7 +88,7 @@ init_t setup_composition(const int nz) {
 
 
 AMREX_INLINE AMREX_GPU_HOST_DEVICE
-void get_xn(const int k, const init_t cd, amrex::Real *xn_zone, int uniform_composition = 0) {
+void get_xn(const int k, const init_t cd, amrex::Real *xn_zone, bool uniform_composition=false) {
 
     for (int n = 0; n < NumSpec; n++) {
         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
 ///
 
 AMREX_INLINE AMREX_GPU_HOST_DEVICE
-amrex::Real get_xn(const int index) {
+amrex::Real get_xn(const int index, bool uniform_composition=false) {
 
     amrex::Real mass_fraction{};
 
+    if (uniform_composition) {
+        mass_fraction = 1.0_rt / NumSpec;
+        return mass_fraction;
+    }
+
     switch (index) {
 
     case 1:

unit_test/test_react/_parameters

@@ -5,8 +5,6 @@ dens_max      real       1.e9
 temp_min      real       1.e6
 temp_max      real       1.e15
 
-uniform_xn    int        0
-
 tmax          real       0.1e0
 
 small_temp    real       1.e5