rework the unit test docs

sphinx_docs/source/comprehensive_tests.rst

@@ -0,0 +1,119 @@
+************************
+Comprehensive Unit Tests
+************************
+
+Generally, for each test, you simply type ``make`` in the test
+directory.  There are a number of runtime parameters that can
+control the behavior.  These are specified (along with defaults)
+in ``_parameters`` files in each test directory and can be
+overridden in an inputs file or on the commandline.
+
+Some additional details on a few of the comprehensive unit tests
+are given below.
+
+EOS test (``test_eos``)
+=======================
+
+``Microphysics/unit_test/test_eos/`` is a unit test for the equations
+of state in Microphysics. It sets up a cube of data, with
+:math:`\rho`, :math:`T`, and :math:`X_k` varying along the three
+dimensions, and then calls the EOS in each zone. Calls are done to
+exercise all modes of calling the EOS, in order:
+
+- ``eos_input_rt``: We call the EOS using :math:`\rho, T`. this is the
+  reference call, and we save the :math:`h`, :math:`e`, :math:`p`, and
+  :math:`s` from here to use in subsequent calls.
+
+- ``eos_input_rh``: We call the EOS using :math:`\rho, h`, to recover
+  the original :math:`T`. To give the root finder some work to do, we
+  perturb the initial temperature.
+
+  We store the relative error in :math:`T` in the output file.
+
+- ``eos_input_tp``: We call the EOS using :math:`T, p`, to recover the
+  original :math:`\rho`. To give the root finder some work to do, we
+  perturb the initial density.
+
+  We store the relative error in :math:`\rho` in the output file.
+
+- ``eos_input_rp``: We call the EOS using :math:`\rho, p`, to recover
+  the original :math:`T`. To give the root finder some work to do, we
+  perturb the initial temperature.
+
+  We store the relative error in :math:`T` in the output file.
+
+- ``eos_input_re``: We call the EOS using :math:`\rho, e`, to recover
+  the original :math:`T`. To give the root finder some work to do, we
+  perturb the initial temperature.
+
+  We store the relative error in :math:`T` in the output file.
+
+- ``eos_input_ps``: We call the EOS using :math:`p, s`, to recover the
+  original :math:`\rho, T`. To give the root finder some work to do,
+  we perturb the initial density and temperature.
+
+  Note: entropy is not well-defined for some EOSs, so we only attempt
+  the root find if :math:`s > 0`.
+
+  We store the relative error in :math:`\rho, T` in the output file.
+
+- ``eos_input_ph``: We call the EOS using :math:`p, h`, to recover the
+  original :math:`\rho, T`. To give the root finder some work to do,
+  we perturb the initial density and temperature.
+
+  We store the relative error in :math:`\rho, T` in the output file.
+
+- ``eos_input_th``: We call the EOS using :math:`T, h`, to recover the
+  original :math:`\rho`. To give the root finder some work to do, we
+  perturb the initial density.
+
+  Note: for some EOSs, :math:`h = h(\rho)` (e.g., an ideal gas), so there
+  is no temperature dependence, and we do not do this test.
+
+  We store the relative error in :math:`\rho` in the output file.
+
+This unit test is marked up with OpenMP directives and therefore also
+tests whether the EOS is threadsafe.
+
+To compile for a specific EOS, e.g., helmholtz, do::
+
+    make EOS_DIR=helmholtz -j 4
+
+Examining the output (an AMReX plotfile) will show you how big the
+errors are. You can use the ``amrex/Tools/Plotfile/`` tool
+``fextrema`` to display the maximum error for each variable.
+
+
+Network test (``test_react``)
+=============================
+
+``Microphysics/unit_test/test_react/`` is a unit test for the nuclear
+reaction networks in Microphysics. It sets up a cube of data, with
+:math:`\rho`, :math:`T`, and :math:`X_k` varying along the three
+dimensions (as a :math:`16^3` domain), and then calls the EOS in each
+zone.  This test does the entire ODE integration of the network for
+each zone.
+
+The state in each zone of our data cube is determined by the runtime
+parameters ``dens_min``, ``dens_max``, ``temp_min``, and ``temp_max``
+for :math:`(\rho, T)`. Because each network carries different
+compositions, we specify the composition through runtime parameters in
+the ``&extern`` namelist: ``primary_species_1``,
+``primary_species_2``, ``primary_species_3``. These primary species
+will vary from X = 0.2 to X = 0.7 to 0.9 (depending on the number).
+Only one primary species varies at a time. The non-primary species
+will be set equally to share whatever fraction of 1 is not accounted
+for by the primary species mass fractions.
+
+This test calls the network on each zone, running for a time
+``tmax``. The full state, including new mass fractions and energy
+release is output to a AMReX plotfile.
+
+You can compile for a specific integrator (e.g., ``VODE``) or
+network (e.g., ``aprox13``) as::
+
+    make NETWORK_DIR=aprox13 INTEGRATOR_DIR=VODE -j 4
+
+The loop over the burner is marked up for OpenMP and CUDA and
+therefore this test can be used to assess threadsafety of the burners
+as well as to optimize the GPU performance of the burners.

sphinx_docs/source/index.rst

@@ -24,7 +24,6 @@ for astrophysical simulation codes.
    data_structures
    autodiff
    rp_intro
-   unit_tests
 
 .. toctree::
    :maxdepth: 1
@@ -53,7 +52,15 @@ for astrophysical simulation codes.
 
 .. toctree::
    :maxdepth: 1
-   :caption: references
+   :caption: Unit tests
+
+   unit_tests
+   comprehensive_tests
+   one_zone_tests
+
+.. toctree::
+   :maxdepth: 1
+   :caption: References
 
    zreferences
 

sphinx_docs/source/one_zone_tests.rst

@@ -0,0 +1,103 @@
+**************
+One Zone Tests
+**************
+
+There are several tests that let you call the EOS or reaction network
+on a single zone to inspect the output directly.
+
+
+``burn_cell``
+=============
+
+``burn_cell`` is a simple one-zone burn that will evolve a state with
+a network for a specified amount of time.  This can be used to
+understand the timescales involved in a reaction sequence or to
+determine the needed ODE tolerances.
+
+
+Getting Started
+---------------
+
+The ``burn_cell`` code are located in
+``Microphysics/unit_test/burn_cell``. To run a simulation, ensure that
+both an input file and an initial conditions file have been created
+and are in the same directory as the executable.
+
+Input File
+----------
+
+These files are typically named as ``inputs_burn_network`` where network
+is the network you wish to use for your testing.
+
+The structure of this file is is fairly self-explanatory.  The run
+prefix defined should be unique to the tests that will be run as they
+will be used to identify all of the output files. Typically, the run
+prefix involves the name of the network being tested.  The ``atol``
+variables define absolute tolerances of the ordinary differential
+equations and the ``rtol`` variables define the relative tolerances.  The
+second section of the input file collects the inputs that ``main.f90``
+asks for so that the user does not have to input all 5+
+parameters that are required every time the test is run.  Each input
+required is defined and initialized on the lines following
+``&cellparams``.  The use of the parameters is show below:
+
+.. table:: The definition of parameters used in the burn_cell unit tests and specified in the second half of each inputs file.
+
+   +-----------------------+----------------------------------------+
+   | ``tmax``              | Maximum Time (s)                       |
+   +-----------------------+----------------------------------------+
+   | ``nsteps``            | Number of time subdivisions            |
+   +-----------------------+----------------------------------------+
+   | ``density``           | State Density (:math:`\frac{g}{cm^3}`) |
+   +-----------------------+----------------------------------------+
+   | ``temperature``       | State Temperature (K)                  |
+   +-----------------------+----------------------------------------+
+   | ``massfractions(i)``  | Mass Fraction for element i            |
+   +-----------------------+----------------------------------------+
+
+Running the Code
+----------------
+
+To run the code, enter the burn_cell directory and run::
+
+   ./main3d.gnu.ex inputs
+
+where ``inputs`` is the name of your inputs file.
+
+For each of the ``numsteps`` steps defined in the inputs
+file, the code will output a files into a new directory titled
+``run_prefix_output`` where ``run_prefix`` is the run prefix defined in the
+inputs file.  Each output file will be named using the run prefix
+defined in the inputs file and the corresponding timestep.
+
+Next, run ``burn_cell.py`` using python 3.x, giving the defined run prefix as an argument.
+For example::
+
+    python3 burn_cell.py react_aprox13
+
+The ``burn_cell.py`` code will gather information from all of the
+output files and compile them into three graphs explained below.
+
+Graphs Output by ``burn_cell.py``
+---------------------------------
+
+The file ``run-prefix_logX.png`` and ``run-prefix_logX.eps`` will display a
+graph of the chemical abundances as a function of the time, both on
+logarithmic scales, for all species involved in the simulation.  An
+example of this graph is shown below.
+
+.. figure:: react_aprox13_logX.png
+   :alt: An example of a plot output by the burn_cell unit test. This is the logX output corresponding to the network aprox13.
+   :width: 4.5in
+
+   An example of a plot output by the burn_cell unit test. This is the
+   logX output corresponding to the network aprox13.
+
+
+
+The file ``run-prefix_ydot.png`` and ``run-prefix_ydot.eps`` will display the
+molar fraction (mass fraction / atomic weight) as a function of time,
+both on logarithmic scales, for all species involved in the code.
+
+The file ``run-prefix_T-edot.png`` and ``run-prefix_T-edot.eps`` will display
+the temperature and the energy generation rate as a function of time.