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docs/source_docs/user_guide/inputs/chemical_reactions.rst
View file @ 29ec7d11
......@@ -3,14 +3,14 @@ Chemical Reactions
Enabling the Chemical Reactions solver and specifying model options.
+-------------------------+----------------------------------------------------------------------+----------+-----------+
| | Description | Type | Default |
+=========================+======================================================================+==========+===========+
| chemistry.solve | Specified name(s) of the chemical reactions types or None to disable | String | None |
| | the reactions solver. | | |
+-------------------------+----------------------------------------------------------------------+----------+-----------+
+----------------------------------+-------------------------------------------------------------+----------+-----------+
| | Description | Type | Default |
+==================================+=============================================================+==========+===========+
| chemistry.solve | Specified name(s) of the chemical reactions types or None | String | None |
| | to disable the reactions solver. | | |
+----------------------------------+-------------------------------------------------------------+----------+-----------+
The following inputs must be preceded by the "chemistry." prefix
The following inputs are defined using the ``chemistry`` prefix.
+------------------------+---------------------------------------------------------+----------+-----------+
| | Description | Type | Default |
......@@ -21,10 +21,99 @@ The following inputs must be preceded by the "chemistry." prefix
| | or '<--'. Chemical species phases must be defined as | | |
| | '(g)' for the fluid phase or '(s)' for the solid phase. | | |
+------------------------+---------------------------------------------------------+----------+-----------+
| mass_balance_tolerance | Tolerance used to test chemical formula conserves mass. | Real | 1e-12 |
| | | | |
| | abs( sum(products) - sum(reactants)) < tolerance | | |
| | | | |
+------------------------+---------------------------------------------------------+----------+-----------+
Choosing the integrator type for the chemistry ODE integration operation that is
performed to determine the fluid and solids phases transfer quantities due to
chemical reactions. The ``StiffSolver`` class of integrators is inspired to the
class of integrators in AMReX-Astro/Microphysics
(https://github.com/AMReX-Astro/Microphysics)
+-------------------------+----------------------------------------------------------------------+----------+---------------+
| | Description | Type | Default |
+=========================+======================================================================+==========+===============+
| chemistry.integrator | Specified name of the chemistry ODE integrator type. Available types | String | ForwardEuler |
| | are (case insensitive): | | |
| | | | |
| | * ``ForwardEuler`` | | |
| | * ``StiffSolver::ForwardEuler`` | | |
| | * ``StiffSolver::BackwardEuler`` | | |
| | * ``StiffSolver::VODE`` | | |
| | | | |
+-------------------------+----------------------------------------------------------------------+----------+---------------+
One can define the environment variable ``VODE_JACOBIAN_CACHING`` at compile
time to enable caching of the numerical approximation of the Jacobian matrix
(the derivative of the ODE right-hand side), applicable when the VODE integrator
is selected. The following inputs can be specified using the
``chemistry.integrator`` prefix:
+--------------------------------+---------------------------------------------------------------+----------+---------+
| | Description | Type | Default |
+================================+===============================================================+==========+=========+
| burner_verbose | Enables the printing on screen of some integration statistics | int | 0 |
+--------------------------------+---------------------------------------------------------------+----------+---------+
| ode_max_steps | The maximum number of substeps for the ODE integration | int | 150000 |
+--------------------------------+---------------------------------------------------------------+----------+---------+
| jacobian_type | Select how to compute the jacobian for the ODE iterative | int | 0 |
| | solver. Available choices are: | | |
| | | | |
| | * 0 for a first-order numerical approximation | | |
| | * 1 for the analytical jacobian (not available yet) | | |
+--------------------------------+---------------------------------------------------------------+----------+---------+
| atol | Absolute tolerance for the ODE integration error test between | Real | 1.e-6 |
| | the solution and the fine-step solution | | |
+--------------------------------+---------------------------------------------------------------+----------+---------+
| rtol | Relative tolerance for the ODE integration error test between | Real | 1.e-6 |
| | the solution and the fine-step solution | | |
+--------------------------------+---------------------------------------------------------------+----------+---------+
| retry_atol | Overwrites the absolute tolerance value atol in case the ODE | Real | -1 |
| | integration fails | | |
+--------------------------------+---------------------------------------------------------------+----------+---------+
| retry_rtol | Overwrites the relative tolerance value rtol in case the ODE | Real | -1 |
| | integration fails | | |
+--------------------------------+---------------------------------------------------------------+----------+---------+
| retry_swap_jacobian | Swaps the type of jacobian (from 1 to 0 or vice versa) in | int | 1 |
| | case the ODE integration fails | | |
+--------------------------------+---------------------------------------------------------------+----------+---------+
| ode_max_dt | Maximum timestep size for the ODE integration substeps | Real | 1.e30 |
+--------------------------------+---------------------------------------------------------------+----------+---------+
| maximum_timestep_change_factor | Only for StiffSolver::ForwardEuler, sets a maximum factor | Real | 1.001 |
| | for the change of the timestep for the internal substeps | | |
+--------------------------------+---------------------------------------------------------------+----------+---------+
| max_iter | Maximum number of iterations for the internal Newton solver | int | 100 |
+--------------------------------+---------------------------------------------------------------+----------+---------+
| linalg_do_pivoting | Only for StiffSolver::BackwardEuler and StiffSolver::VODE, | int | 1 |
| | switches on/off the pivoting when solving the linear algebra | | |
| | problem associated to the internal Newton solver | | |
+--------------------------------+---------------------------------------------------------------+----------+---------+
| rp_rtol | Relative tolerance for the convergence test of the internal | Real | 1.e-6 |
| | Newton solver. Valid only for StiffSolver::BackwardEuler | | |
+--------------------------------+---------------------------------------------------------------+----------+---------+
| use_jacobian_caching | Only for StiffSolver::VODE, enables caching the numerical | int | 1 |
| | jacobian | | |
+--------------------------------+---------------------------------------------------------------+----------+---------+
| X_reject_buffer | Only for StiffSolver::VODE, constrain species abundances | Real | 1.0 |
| | such that they don't change by more than a certain factor in | | |
| | a given step | | |
+--------------------------------+---------------------------------------------------------------+----------+---------+
Below is an example for specifying chemical reactions for MFIX-Exa.
.. code-block:: none
chemistry.solve = my_reaction0 my_reaction1
my_reaction0.reaction = Fe2O3(s)+CO(g)-->2.FeO(s)+CO2(g)
my_reaction1.reaction = FeO(s)+0.25O2(g)-->0.5Fe2O3(s)
chemistry.my_reaction0.reaction = Fe2O3(s)+CO(g)-->2.FeO(s)+CO2(g)
chemistry.my_reaction1.reaction = FeO(s)+0.25O2(g)-->0.5Fe2O3(s)
chemistry.mass_balance_tolerance = 1.e-5
chemistry.integrator = StiffSolver::BackwardEuler
chemistry.integrator.atol = 1.e-8
chemistry.integrator.rtol = 1.e-9
docs/source_docs/user_guide/inputs/output/plotfiles.rst
View file @ 29ec7d11
......@@ -28,6 +28,9 @@ format (for debugging).
| par_ascii_per_approx | Time period of the ascii particle output (approximate); | Real | -1 |
| | if -1 then particle ascii files will not be written at this frequency | | |
+----------------------+-----------------------------------------------------------------------+-------------+-----------+
| file_digits | Number of digits to use in plotfile (plt[0-9]+) and checkpoint | Int | 5 |
| | (chk[0-9]+) filenames. | | |
+----------------------+-----------------------------------------------------------------------+-------------+-----------+
| ascent_int | Frequency of ascent pipeline; | Int | -1 |
| | if -1 then ascent will not be called. | | |
+----------------------+-----------------------------------------------------------------------+-------------+-----------+
......@@ -51,7 +54,9 @@ The following inputs must be preceded by "mfix." and control what variables will
+---------------------+-----------------------------------------------------------------------+-------------+-----------+
| plt_ro_g | Save fluid density to plot file | Int | 0 |
+---------------------+-----------------------------------------------------------------------+-------------+-----------+
| plt_mu_g | Save fluid viscosity to plot file | Int | 0 |
| plt_mu_g | Save fluid molecular viscosity to plot file | Int | 0 |
+---------------------+-----------------------------------------------------------------------+-------------+-----------+
| plt_mu_g_eff | Save fluid effective viscosity to plot file | Int | 0 |
+---------------------+-----------------------------------------------------------------------+-------------+-----------+
| plt_diveu | Save div(ep_g . u) to plot file | Int | 0 |
+---------------------+-----------------------------------------------------------------------+-------------+-----------+
......
docs/source_docs/user_guide/inputs/porous_media_defs.rst 0 → 100644
View file @ 29ec7d11
.. _InputsPorousMediaDefs:
Porous media
============
Homogeneous porous media are modeled by the addition of a momentum
source term, :math:`\boldsymbol{S}_{pm}`, to the fluid momentum equation.
.. math::
\boldsymbol{S}_{pm} =-\frac{\mu_f}{C_1} \boldsymbol{u}_f - C_2\frac{1}{2}\rho_f\lvert \boldsymbol{u}_f \rvert \boldsymbol{u}_f
:math:`\mu_f`, :math:`\rho_f`, and :math:`\boldsymbol{u}_f` are the fluid viscosity, density, and velocity and
:math:`C_1` and :math:`C_2` are user defined constants.
The following inputs are defined using the ``pm`` prefix.
+--------------------------+------------------------------------------------------------------------------+----------+-----------+
| | Description | Type | Default |
+==========================+==============================================================================+==========+===========+
| regions | Regions used to define porous media. | String | None |
+--------------------------+------------------------------------------------------------------------------+----------+-----------+
| [region].volfrac | Solids volume fraction of the porous media region. | Real | None |
+--------------------------+------------------------------------------------------------------------------+----------+-----------+
| [region].c1 | Porous media permeabilty constant for the source term in fluid | Real | None |
| | momentum equation. | | |
+--------------------------+------------------------------------------------------------------------------+----------+-----------+
| [region].c2 | Porous media inertial resistance factor for the source term in fluid | Real | None |
| | momentum equation. | | |
+--------------------------+------------------------------------------------------------------------------+----------+-----------+
| [region].allow_particles | Allow particles to flow through the porous media region. | Int | 0 |
+--------------------------+------------------------------------------------------------------------------+----------+-----------+
docs/source_docs/user_guide/run-time_inputs.rst
View file @ 29ec7d11
......@@ -50,6 +50,7 @@ keywords such as ``mfix``, ``amr``, ``geometry``, ``nodal_proj`` etc.
inputs/fluid_model
inputs/solids_model
inputs/species_defs
inputs/porous_media_defs
inputs/chemical_reactions
inputs/regions_defs
inputs/initial_conditions
......