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centralize some runtime parameters and their docs
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‎Docs/source/burn_cell.rst

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@@ -52,39 +52,17 @@ The parameters that affect the thermodynamics are:
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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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The composition can be set either by specifying individual mass fractions
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or setting ``unit_test.uniform_xn`` as described in :ref:`sec:defining_unit_test_composition`.
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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 either by setting each mass fraction explicitly via the
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parameters, ``unit_test.X1``, ``unit_test.X2``, ...,
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e.g.:
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::
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unit_test.X1 = 0.5
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unit_test.X2 = 0.2
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unit_test.X3 = 0.2
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unit_test.X4 = 0.1
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where parameters up to ``X35`` are available. If the values don't sum to ``1``
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initially, then the test will do a normalization. This normalization can be
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disabled by setting:
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If the values don't sum to ``1`` initially, then the test will do a
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normalization. This normalization can be disabled by setting:
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::
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unit_test.skip_initial_normalization = 1
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Alternately, the composition can be set automatically by initializing all
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of the mass fractions equally (to $1/N$, where $N$ is the number of species),
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by setting:
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::
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unit_test.uniform_xn = 1
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Controlling time
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----------------
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‎Docs/source/eos_cell.rst

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@@ -28,10 +28,6 @@ The parameters that affect the thermodynamics are:
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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

‎Docs/source/index.rst

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@@ -92,6 +92,7 @@ system.
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:hidden:
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unit_tests
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unit_test_runtime_parameters
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comprehensive_tests
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one_zone_tests
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‎Docs/source/jac_cell.rst

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@@ -38,10 +38,6 @@ The parameters that affect the thermodynamics are:
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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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While the mass fractions can be set individually (using
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``unit_test.X1``, ``unit_test.X2``, ...), it is recommended to use
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``unit_test.uniform_xn=1`` to initialize all the mass fractions to be

‎Docs/source/unit_test_runtime_parameters.rst

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***********************************
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Unit Test Common Runtime Parameters
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***********************************
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There are a number of runtime parameters that are common to all (or most) of the unit tests.
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These are defined in the top-level ``unit_test/_parameters`` file.
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Thermodynamics
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==============
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The equation of state enforces minimum density and temperatures, which must be set
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upon initialization. These are controlled by the following runtime parameters:
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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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.. _sec:defining_unit_test_composition:
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Defining composition
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====================
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Most of the unit tests require a composition to be defined (for the
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initial mass-fractions, $X_k$). There are a few ways this can be done
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(depending on the test).
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* One-zone (`*_cell`) tests usually do one of:
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* *Explicitly setting the individual mass fractions.* This is
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controlled by the parameters ``unit_test.X1``, ``unit_test.X2``, ..., ``unit_test.X35``,
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e.g.:
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::
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unit_test.X1 = 0.5
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unit_test.X2 = 0.2
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unit_test.X3 = 0.2
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unit_test.X4 = 0.1
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While many of the tests will renormalize the abundances, the user
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should take care to ensure that the mass fractions sum to unity.
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* *Setting the composition to be uniform.* This is controlled by
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``unit_test.uniform_xn``. If this is set to ``1``, then each mass fraction
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is initialized to ``1 / NumSpec``.
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* Comprehensive tests need many different compositions, since they are creating a cube
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of varying thermodynamic properties, and thus require a prescription
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to create the composition. This is done by setting ``unit_test.primary_species_1``,
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``unit_test.primary_species_2``, and ``unit_test.primary_species_3`` to one of the
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*names* of the species in the network.
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The function ``setup_composition()`` is then used to set limits on
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the species abundances (it takes a parameter which is the index into
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the cube of data that is being initialized) which is then used by
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``get_xn()`` to create the individual mass fractions. Both of these
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routines are contained in ``react_util.H``.

‎unit_test/_parameters

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@@ -40,5 +40,12 @@ X33 real 0.0e0
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X34 real 0.0e0
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X35 real 0.0e0
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# do we set all of the mass fractions equal (to 1/NumSpec)?
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uniform_xn bool 0
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# lowest temperature allowed in the EOS
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small_temp real 1.e5
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# lowest density allowed in the EOS
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small_dens real 1.e5
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‎unit_test/burn_cell/_parameters

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@namespace: unit_test
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small_temp real 1.e5
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small_dens real 1.e5
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# the final time to integrate to
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tmax real 1.e-2
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‎unit_test/burn_cell_metal_chem/_parameters

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run_prefix string "burn_cell_metal_chem"
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# floor values of temperature and density
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small_temp real 1.e1
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small_dens real 1.e-30
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small_temp real 1.e1 100
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small_dens real 1.e-30 100
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# the final time to integrate to
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tmax real 1.e20

‎unit_test/burn_cell_primordial_chem/_parameters

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run_prefix string "burn_cell_primordial_chem"
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# floor values of temperature and density
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small_temp real 1.e1
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small_dens real 1.e-30
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small_temp real 1.e1 100
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small_dens real 1.e-30 100
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# the final time to integrate to
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tmax real 1.e20

‎unit_test/burn_cell_sdc/_parameters

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@namespace: unit_test
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small_temp real 1.e5
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small_dens real 1.e5
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# the final time to integrate to
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tmax real 1.e-2
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‎unit_test/eos_cell/_parameters

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@namespace: unit_test
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small_temp real 1.e5
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small_dens real 1.e5
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density real 1.e7
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temperature real 3.e9

‎unit_test/jac_cell/_parameters

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@namespace: unit_test
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small_temp real 1.e5
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small_dens real 1.e5
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density real 1.e7
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temperature real 3.e9

‎unit_test/nse_net_cell/_parameters

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@@ -2,9 +2,6 @@
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run_prefix string ""
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small_temp real 1.e5
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small_dens real 1.e5
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density real 1.e7
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temperature real 3.e9

‎unit_test/nse_net_cell/make_table/_parameters

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@namespace: unit_test
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small_dens real 1.e5
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small_temp real 1.e5
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rho_min real 1.e6
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rho_max real 1.e10
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‎unit_test/nse_table_cell/_parameters

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@namespace: unit_test
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small_temp real 1.e5
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small_dens real 1.e5
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density real 1.23e9
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temperature real 5.18e9
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ye real 0.472

‎unit_test/part_func_cell/_parameters

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@namespace: unit_test
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small_temp real 1.e5
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small_dens real 1.e5
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density real 1.e9
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temperature real 5.e9
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‎unit_test/test_aprox_rates/_parameters

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@@ -6,6 +6,3 @@ temp_min real 1.e6
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temp_max real 1.e12
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metalicity_max real 0.1e0
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small_temp real 1.e4
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small_dens real 1.e-4

‎unit_test/test_conductivity/_parameters

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@@ -6,6 +6,3 @@ temp_min real 1.e6
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temp_max real 1.e12
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metalicity_max real 0.1e0
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small_temp real 1.e4
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small_dens real 1.e-4

‎unit_test/test_eos/_parameters

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@@ -6,6 +6,3 @@ temp_min real 1.e6
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temp_max real 1.e12
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metalicity_max real 0.1e0
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small_temp real 1.e4
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small_dens real 1.e-4

‎unit_test/test_jac/_parameters

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@@ -9,6 +9,3 @@ 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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small_dens real 1.e5
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‎unit_test/test_linear_algebra/_parameters

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@namespace: unit_test
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small_temp real 1.e5
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small_dens real 1.e5

‎unit_test/test_neutrino_cooling/_parameters

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@@ -6,6 +6,3 @@ temp_min real 1.e6
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temp_max real 1.e12
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metalicity_max real 0.1e0
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small_temp real 1.e4
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small_dens real 1.e-4

‎unit_test/test_nse_interp/_parameters

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@namespace: unit_test
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small_temp real 1.e5
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small_dens real 1.e5
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density real 1.23e9
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temperature real 5.18e9
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ye real 0.472

‎unit_test/test_parameters/_parameters

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@@ -5,7 +5,4 @@ dens_max real 1.e9
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temp_min real 1.e6
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temp_max real 1.e12
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small_temp real 1.e4
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small_dens real 1.e-4
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test_string string "test"

‎unit_test/test_react/_parameters

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@@ -7,6 +7,3 @@ temp_max real 1.e15
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tmax real 0.1e0
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small_temp real 1.e5
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small_dens real 1.e5
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‎unit_test/test_rhs/_parameters

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@@ -4,8 +4,3 @@ dens_min real 1.e6
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dens_max real 1.e9
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temp_min real 1.e6
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temp_max real 1.e15
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uniform_xn int 0
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small_temp real 1.e5
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small_dens real 1.e5

‎unit_test/test_screening_templated/_parameters

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@@ -7,7 +7,4 @@ temp_max real 1.e12
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metalicity_max real 0.1e0
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small_temp real 1.e4
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small_dens real 1.e-4
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loops int 1

‎unit_test/test_sdc/_parameters

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temp_min real 1.e6
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temp_max real 1.e15
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# uniform composition
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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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small_dens real 1.e3
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‎unit_test/test_sdc_vode_rhs/_parameters

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@namespace: unit_test
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small_temp real 1.e5
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small_dens real 1.e5
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density real 1.e7
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temperature real 3.e9

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