From 063e304ade90e63b83b49663acaf8bf6804b253a Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 31 Oct 2025 11:16:45 -0500 Subject: [PATCH] update documentation --- .../user_guide/inputs/advanced.rst | 10 +- .../user_guide/inputs/boundary_conditions.rst | 10 +- .../user_guide/inputs/chemical_reactions.rst | 32 ++-- .../user_guide/inputs/fluid_model.rst | 4 +- .../user_guide/inputs/geometry.rst | 14 +- .../user_guide/inputs/initial_conditions.rst | 158 +++++++++--------- .../user_guide/inputs/mesh_and_gridding.rst | 6 +- .../user_guide/inputs/model_options.rst | 2 +- .../user_guide/inputs/multigrid_solvers.rst | 5 +- .../inputs/output/checkpointing.rst | 8 +- .../user_guide/inputs/output/monitors.rst | 24 ++- .../user_guide/inputs/output/reports.rst | 2 +- .../user_guide/inputs/porous_media.rst | 2 +- .../source_docs/user_guide/inputs/regions.rst | 4 +- .../user_guide/inputs/solids_model.rst | 16 +- .../source_docs/user_guide/inputs/species.rst | 2 +- 16 files changed, 150 insertions(+), 149 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/advanced.rst b/docs/source_docs/user_guide/inputs/advanced.rst index 12cb5d3..f46b22c 100644 --- a/docs/source_docs/user_guide/inputs/advanced.rst +++ b/docs/source_docs/user_guide/inputs/advanced.rst @@ -70,8 +70,8 @@ The following inputs must be preceded by the prefix ``mfix`` and control load ba | | | | | | | Options: | | | | | | | | -| load_balance | * ``SingleGrid`` fluid and particles are co-located on the same grids | | | -| | * ``DualGrid`` fluid and particles live on different grids | | | +| load_balance | * ``SingleGrid`` - fluid and particles are co-located on the same grid| | | +| | * ``DualGrid`` - fluid and particles occupy different grids | | | +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ | load_balance.DualGrid.fluid | Regrid mesh (fluid) in addition to particles when using `DualGrid` | Int | 0 | +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ @@ -107,11 +107,11 @@ The following inputs are defined using the prefix ``particles``: | | Description | Type | Default | +======================+=======================================================================+=============+==============+ | max_grid_size_x | Maximum number of cells at level 0 in each grid in x-direction | Int | 32 | -| | for grids in the ParticleBoxArray if dual_grid is true | | | +| | for grids in the ParticleBoxArray if ``load_balance`` is ``DualGrid``.| | | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | max_grid_size_y | Maximum number of cells at level 0 in each grid in y-direction | Int | 32 | -| | for grids in the ParticleBoxArray if dual_grid is true | | | +| | for grids in the ParticleBoxArray if ``load_balance`` is ``DualGrid``.| | | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | max_grid_size_z | Maximum number of cells at level 0 in each grid in z-direction | Int | 32 | -| | for grids in the ParticleBoxArray if dual_grid is true. | | | +| | for grids in the ParticleBoxArray if ``load_balance`` is ``DualGrid``.| | | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ diff --git a/docs/source_docs/user_guide/inputs/boundary_conditions.rst b/docs/source_docs/user_guide/inputs/boundary_conditions.rst index 4d55603..20083b4 100644 --- a/docs/source_docs/user_guide/inputs/boundary_conditions.rst +++ b/docs/source_docs/user_guide/inputs/boundary_conditions.rst @@ -12,7 +12,7 @@ The following inputs are defined using the prefix ``bc``: +---------------------+--------------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +=====================+==========================================================================+=============+===========+ -| regions | Regions used to define boundary conditions. | String | None | +| regions | Regions used to define boundary conditions. | Strings | None | +---------------------+--------------------------------------------------------------------------+-------------+-----------+ | delp_dir | Direction for specified pressure drop. Note that this direction | Int | 0 | | | should also be periodic. | | | @@ -68,7 +68,7 @@ using the prefix ``bc.[region].[fluid]``: | massflow | Mass flow rate [required if bc_region_type='mi' | Real | 0 | | | and ``velocity`` or ``volflow`` not specified] | | | +------------------------+------------------------------------------------------------------------+-------------+-----------+ -| species.[species0] | Species 'species0' mass fraction [required if solve_species=1 | Real | 0 | +| species.[species_name] | Species 'species_name' mass fraction [required if solve_species=1 | Real | 0 | | | and bc_region_type='mi' or 'pi']. | | | +------------------------+------------------------------------------------------------------------+-------------+-----------+ @@ -135,7 +135,7 @@ tridimensional). We recall that, on the remaining part of the EBs, homogeneous Neumann boundary conditions are assumed by default. In the following table there is a list of the possible entries for EB boundary -conditions. Each entry must be preceded by `bc.[region0].` +conditions. Each entry must be preceded by the prefix ``bc.[region]`` +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -158,8 +158,8 @@ In addition to the temperature, it is possible to set an inflow condition for fl on an embedeed boundary. We recall that, on the remaining part of the EBs, no slip velocity conditions are assumed by default. -In the following table there is a list of the possible entries for inflow EB boundary -conditions. Each entry must be preceded by `bc.[region0].` Like traditional mass +In the following table is a list of the possible entries for inflow EB boundary +conditions. Each entry must be preceded by the prefix ``bc.[region]``. Like traditional mass inflows, the fluid temperature, pressure, and species composition must be provided when appropriate. diff --git a/docs/source_docs/user_guide/inputs/chemical_reactions.rst b/docs/source_docs/user_guide/inputs/chemical_reactions.rst index 5cdfdf6..e1d7f09 100644 --- a/docs/source_docs/user_guide/inputs/chemical_reactions.rst +++ b/docs/source_docs/user_guide/inputs/chemical_reactions.rst @@ -8,15 +8,15 @@ The following inputs are defined using the prefix ``chemistry``: +--------------------------+---------------------------------------------------------+----------+----------------+ | | Description | Type | Default | +==========================+=========================================================+==========+================+ -| solve | Specify the name(s) of the chemical reactions or set | String | | +| solve | Specify the name(s) of the chemical reactions or set | Strings | | | | to None to disable the chemistry solver. The name(s) | | | | | assigned to the chemistry solver are used to specify | | | | | the chemical reactions equations. | | | +--------------------------+---------------------------------------------------------+----------+----------------+ -| [reaction0].reaction | Chemical formula for the given reaction. The string | String | | +| [reaction].reaction | Chemical formula for the given reaction. The string | String | | | | given as input must not contain white space and | | | -| | the reaction direction has to be specified as '\-\->' | | | -| | or '<\-\-'. Chemical species phases must be defined as | | | +| | the reaction direction must be specified as `\-\->` | | | +| | 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 | @@ -32,20 +32,20 @@ The following inputs are defined using the prefix ``chemistry``: | | * ``ConstantVolume`` - keep particle volume constant | | | | | * ``ConstantDensity`` - keep particle density constant | | | +--------------------------+---------------------------------------------------------+----------+----------------+ -| solids.mass_threshold | Sets a threshold value for the particles' mass. When | Real | 0 | -| | updating the solids quantities in chemistry, check | | | -| | whether the solids mass is below the threshold, and in | | | -| | that case set the particle as invalid and remove it. | | | +| solids.mass_threshold | Threshold value for the particle mass. When | Real | 0 | +| | updating the solids quantities in chemistry, if | | | +| | the particle solids mass is below the threshold, | | | +| | the particle is marked as invalid and removed. | | | +--------------------------+---------------------------------------------------------+----------+----------------+ -| solids.radius_threshold | Sets a threshold value for the particles' radius. When | Real | 0 | -| | updating the solids quantities in chemistry, check | | | -| | whether the solids radius is below the threshold, and | | | -| | in that case set the particle as invalid and remove it. | | | +| solids.radius_threshold | Threshold value for the particle radius. When | Real | 0 | +| | updating the solids quantities in chemistry, if | | | +| | the particle radius is below the threshold, | | | +| | the particle is marked as invalid and removed. | | | +--------------------------+---------------------------------------------------------+----------+----------------+ -| solids.density_threshold | Sets a threshold value for the particles' density. When | Real | 0 | -| | updating the solids quantities in chemistry, check | | | -| | whether the solids density is below the threshold, and | | | -| | in that case set the particle as invalid and remove it. | | | +| solids.density_threshold | Threshold value for the particle density. When | Real | 0 | +| | updating the solids quantities in chemistry, if | | | +| | the solids density is below the threshold, | | | +| | the particle is marked as invalid and removed. | | | +--------------------------+---------------------------------------------------------+----------+----------------+ Choosing the integrator type for the chemistry ODE integration operation that is diff --git a/docs/source_docs/user_guide/inputs/fluid_model.rst b/docs/source_docs/user_guide/inputs/fluid_model.rst index 98194ea..312fb52 100644 --- a/docs/source_docs/user_guide/inputs/fluid_model.rst +++ b/docs/source_docs/user_guide/inputs/fluid_model.rst @@ -19,7 +19,7 @@ The root prefix for the following inputs is the name defined using the ``fluid.s is named ``myfluid``, then the following keywords are preceded with ``myfluid`` and a period. Currently, MFIX-Exa only supports a single fluid; therefore, it is common to name the fluid ``fluid``. This is illustrated later in example input snippets. -.. |Sutherland_Eq| replace:: :math:`\mu(T) = \mu_{ref}\left(\frac{T}{T_{ref}}\right)^{3/2}\frac{T_{ref} + S}{T+S}` +.. |Sutherland_Eq| replace:: :math:`\mu(T) = \mu_{ref}\left(\frac{T}{T_{ref}}\right)^{3/2}\times\frac{(T_{ref} + S)}{(T+S)}` .. |Reid_4parm_Eq| replace:: :math:`\mu(T) = Ae^{\left(\frac{B}{T} + CT + DT^2 \right)}` @@ -156,7 +156,7 @@ a single fluid; therefore, it is common to name the fluid ``fluid``. This is ill | | :math:`\mu_{eff} < fac*\mu_{mol}`, where | | | | | |eff_visc| | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ -| species | Specify the species that constitute the fluid. | String | None | +| species | Specify the species that constitute the fluid. | Strings| None | | | | | | | | All listed species must be properly defined. See the | | | | | :ref:`species definition documentation` | | | diff --git a/docs/source_docs/user_guide/inputs/geometry.rst b/docs/source_docs/user_guide/inputs/geometry.rst index ac38cbf..8d9ae5a 100644 --- a/docs/source_docs/user_guide/inputs/geometry.rst +++ b/docs/source_docs/user_guide/inputs/geometry.rst @@ -8,7 +8,7 @@ The following inputs are defined using the prefix ``mfix``: +------------------------+-------------------------------------------------------------------------------+----------+---------------------+ | | Description | Type | Default | +========================+===============================================================================+==========+=====================+ -| geometry | Specify the simulation geometry. | String | '' | +| geometry | Simulation geometry type. | String | '' | | | Options (case-insensitive): | | | | | | | | | | * ``box`` - predefined :ref:`box geometry` | | | @@ -153,7 +153,7 @@ The following inputs are defined using the prefix ``cylinder``: +------------------------+-------------------------------------------------------------------+----------+---------------------+ | | Description | Type | Default | +========================+===================================================================+==========+=====================+ -| radius | Cylinder radius | Real | 0.0002 | +| radius | Cylinder radius. | Real | 0.0002 | +------------------------+-------------------------------------------------------------------+----------+---------------------+ | height | Height (length) of cylinder. If the height is not defined (-1), | Real | -1 | | | then the cylinder is made infinitely long to overhang the domain | | | @@ -162,7 +162,7 @@ The following inputs are defined using the prefix ``cylinder``: | direction | Axis the cylinder runs along. | Int | 0 | | | (``0``: *X*, ``1``: *Y*, ``2``: *Z*) | | | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -| center | Center of cylinder. For a cylinder with an undefined ``height``, | Reals | 0. 0. 0. | +| center | Center of cylinder. For a cylinder with an undefined ``height``, | Reals | 0 0 0 | | | the center value in the height ``direction`` can be any value. | | | +------------------------+-------------------------------------------------------------------+----------+---------------------+ | rotation | Rotation angle in degrees of cylinder. | Real | 0. | @@ -349,9 +349,9 @@ The following inputs are defined using the prefix ``csg``: +------------------------+-------------------------------------------------------------------+----------+---------------------+ | internal_flow | Indicates that flow is *inside* the box. | Bool | true | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -| scaling_factor | Scale the geometry. | Reals | 1. 1. 1. | +| scaling_factor | Scale the geometry. | Reals | 1 1 1 | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -| translation | Translate the geometry. | Reals | 0. 0. 0. | +| translation | Translate the geometry. | Reals | 0 0 0 | +------------------------+-------------------------------------------------------------------+----------+---------------------+ .. note:: @@ -373,9 +373,9 @@ The following inputs are defined using the prefix ``stl``: +========================+===================================================================+==========+=====================+ | geometry_filename | The STL file that defines the EB geometry. | String | '' | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -| scaling_factor | Scale the geometry. | Real | 1. | +| scaling_factor | Scale the geometry. | Real | 1 | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -| translation | Translate the geometry. | Reals | 0. 0. 0. | +| translation | Translate the geometry. | Reals | 0 0 0 | +------------------------+-------------------------------------------------------------------+----------+---------------------+ | use_bvh | Use bounding volume optimization. | Bool | true | +------------------------+-------------------------------------------------------------------+----------+---------------------+ diff --git a/docs/source_docs/user_guide/inputs/initial_conditions.rst b/docs/source_docs/user_guide/inputs/initial_conditions.rst index 5171d19..c29115a 100644 --- a/docs/source_docs/user_guide/inputs/initial_conditions.rst +++ b/docs/source_docs/user_guide/inputs/initial_conditions.rst @@ -6,7 +6,7 @@ The following inputs are defined using the prefix ``ic``: +-----------------------+------------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +=======================+========================================================================+=============+===========+ -| regions | Regions used to define initial conditions. | String | None | +| regions | Regions used to define initial conditions. | Strings | None | +-----------------------+------------------------------------------------------------------------+-------------+-----------+ | allow_regions_overlap | If enabled, particles will be generated/initialized more than once | Int | 1 | | | on areas where the IC regions intersect. | | | @@ -39,7 +39,7 @@ using the compound prefix ``ic.[region].[fluid]``: +------------------------+------------------------------------------------------------------------+-------------+-----------+ | velocity | Velocity components | Reals | 0 0 0 | +------------------------+------------------------------------------------------------------------+-------------+-----------+ -| species.[species0] | Mass fraction of 'species0' | Reals | 0 0 0 | +| species.[species_name] | Mass fraction of 'species_name' | Real | 0 | +------------------------+------------------------------------------------------------------------+-------------+-----------+ @@ -78,83 +78,83 @@ using the compound prefix ``ic.[region].[solid]``: Note that diameter distributions must define a weighting type, please refer to :ref:`ReferenceParticleDistributions `. -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| | Description | Type | Default | -+=====================+=======================================================================+=============+===========+ -| volfrac | Volume fraction | Real | 0 | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| temperature | temperature | Real | 0 | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| species.[species0] | Mass fraction of 'species0' | Real | 0 | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| velocity | Velocity components | Reals | 0 0 0 | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| diameter | Method to specify particle diameter in the IC region. This is | String | None | -| | only used for auto-generated particles. | | | -| | | | | -| | Options: | | | -| | | | | -| | * ``constant`` - specified constant | | | -| | * ``uniform`` - uniform distribution | | | -| | * ``normal`` - normal distribution | | | -| | * ``custom`` - user-defined distribution | | | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| type | Distribution weighting. | String | N/A | -| | | | | -| | Options: | | | -| | | | | -| | * ``number-weighted`` | | | -| | * ``volume-weighted`` | | | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| bins | Number of bins used when discretizing the distribution to approximate | Int | 64 | -| | the number of particles within an initial condition region. | | | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| diameter.constant | Monodisperse (single valued) particle diameter. | Real | 0 | -| | Required for ``constant`` distributions. | | | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| diameter.mean | Distribution mean. | Real | 0 | -| | Required for ``normal`` distributions. | | | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| diameter.std | Distribution standard deviation. | Real | 0 | -| | Required for ``normal`` distributions. | | | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| diameter.min | Minimum diameter to clip distribution. | Real | 0 | -| | Required for ``normal`` distributions and ``uniform`` distributions. | | | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| diameter.max | Maximum diameter to clip distribution. | Real | 0 | -| | Required for ``normal`` distributions and ``uniform`` distributions. | | | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| diameter.custom | File name that specifies either the cumulative or probability | String | None | -| | distribution. Required for ``custom`` distributions. | | | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| density | Method to specify particle density in the IC region. This is | String | None | -| | only used for auto-generated particles. | | | -| | | | | -| | Options: | | | -| | | | | -| | * ``constant`` - specified constant | | | -| | * ``uniform`` - uniform distribution | | | -| | * ``normal`` - normal distribution | | | -| | * ``custom`` - user-defined distribution | | | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| density.constant | Monodisperse (single valued) particle density. | Real | 0 | -| | Required for ``constant`` distributions. | | | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| density.mean | Distribution mean. | Real | 0 | -| | Required for ``normal`` distributions. | | | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| density.std | Distribution standard deviation. | Real | 0 | -| | Required for ``normal`` distributions. | | | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| density.min | Minimum diameter to clip distribution. | Real | 0 | -| | Required for ``normal`` distributions and ``uniform`` distributions. | | | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| density.max | Maximum diameter to clip distribution. | Real | 0 | -| | Required for ``normal`` distributions and ``uniform`` distributions. | | | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| density.custom | File name that specifies either the cumulative or probability | String | None | -| | distribution. Required for ``custom`` distributions. | | | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ +| | Description | Type | Default | ++========================+=======================================================================+=============+===========+ +| volfrac | Volume fraction | Real | 0 | ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ +| temperature | temperature | Real | 0 | ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ +| species.[species_name] | Mass fraction of 'species_name' | Real | 0 | ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ +| velocity | Velocity components | Reals | 0 0 0 | ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ +| diameter | Method to specify particle diameter in the IC region. This is | String | None | +| | only used for auto-generated particles. | | | +| | | | | +| | Options: | | | +| | | | | +| | * ``constant`` - specified constant | | | +| | * ``uniform`` - uniform distribution | | | +| | * ``normal`` - normal distribution | | | +| | * ``custom`` - user-defined distribution | | | ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ +| type | Distribution weighting. | String | N/A | +| | | | | +| | Options: | | | +| | | | | +| | * ``number-weighted`` | | | +| | * ``volume-weighted`` | | | ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ +| bins | Number of bins used when discretizing the distribution to approximate | Int | 64 | +| | the number of particles within an initial condition region. | | | ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ +| diameter.constant | Monodisperse (single valued) particle diameter. | Real | 0 | +| | Required for ``constant`` distributions. | | | ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ +| diameter.mean | Distribution mean. | Real | 0 | +| | Required for ``normal`` distributions. | | | ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ +| diameter.std | Distribution standard deviation. | Real | 0 | +| | Required for ``normal`` distributions. | | | ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ +| diameter.min | Minimum diameter to clip distribution. | Real | 0 | +| | Required for ``normal`` distributions and ``uniform`` distributions. | | | ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ +| diameter.max | Maximum diameter to clip distribution. | Real | 0 | +| | Required for ``normal`` distributions and ``uniform`` distributions. | | | ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ +| diameter.custom | File name that specifies either the cumulative or probability | String | None | +| | distribution. Required for ``custom`` distributions. | | | ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ +| density | Method to specify particle density in the IC region. This is | String | None | +| | only used for auto-generated particles. | | | +| | | | | +| | Options: | | | +| | | | | +| | * ``constant`` - specified constant | | | +| | * ``uniform`` - uniform distribution | | | +| | * ``normal`` - normal distribution | | | +| | * ``custom`` - user-defined distribution | | | ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ +| density.constant | Monodisperse (single valued) particle density. | Real | 0 | +| | Required for ``constant`` distributions. | | | ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ +| density.mean | Distribution mean. | Real | 0 | +| | Required for ``normal`` distributions. | | | ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ +| density.std | Distribution standard deviation. | Real | 0 | +| | Required for ``normal`` distributions. | | | ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ +| density.min | Minimum diameter to clip distribution. | Real | 0 | +| | Required for ``normal`` distributions and ``uniform`` distributions. | | | ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ +| density.max | Maximum diameter to clip distribution. | Real | 0 | +| | Required for ``normal`` distributions and ``uniform`` distributions. | | | ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ +| density.custom | File name that specifies either the cumulative or probability | String | None | +| | distribution. Required for ``custom`` distributions. | | | ++------------------------+-----------------------------------------------------------------------+-------------+-----------+ The following inputs must be preceded by the prefix ``mfix``: diff --git a/docs/source_docs/user_guide/inputs/mesh_and_gridding.rst b/docs/source_docs/user_guide/inputs/mesh_and_gridding.rst index 7f8186c..e63d163 100644 --- a/docs/source_docs/user_guide/inputs/mesh_and_gridding.rst +++ b/docs/source_docs/user_guide/inputs/mesh_and_gridding.rst @@ -144,7 +144,7 @@ The following inputs are defined using the prefix ``fabarray``: +----------------------+-----------------------------------------------------------------------+----------+-------------+ | | Description | Type | Default | +======================+=======================================================================+==========+=============+ -| mfiter_tile_size | Maximum number of cells in each direction for (logical) tiles | IntVect | 1024000,8,8 | +| mfiter_tile_size | Maximum number of cells in each direction for (logical) tiles. | Ints | 1024000 8 8 | +----------------------+-----------------------------------------------------------------------+----------+-------------+ The following inputs are defined using the prefix ``particles``: @@ -152,8 +152,8 @@ The following inputs are defined using the prefix ``particles``: +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +======================+=======================================================================+=============+==============+ -| tile_size | Maximum number of cells in each direction for (logical) tiles | IntVect | 1024000,8,8 | -| | in the ParticleBoxArray if dual_grid is true. | | | +| tile_size | Maximum number of cells in each direction for (logical) tiles | Ints | 1024000 8 8 | +| | in the ParticleBoxArray if ``load_balance`` is ``DualGrid`` | | | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ When running on shared memory machines using an OpenMP enabled executable, *grids* are subdivided into diff --git a/docs/source_docs/user_guide/inputs/model_options.rst b/docs/source_docs/user_guide/inputs/model_options.rst index 6679ff9..d137449 100644 --- a/docs/source_docs/user_guide/inputs/model_options.rst +++ b/docs/source_docs/user_guide/inputs/model_options.rst @@ -113,7 +113,7 @@ The following inputs are defined using the prefix ``particles``: | | | | | +---------------------+---------------------------------------------------------------------------+-------------+-----------+ -For the `mean_velocity` constraint, the following inputs can be defined. +For the `mean_velocity` constraint, the following inputs can be defined using the prefix ``particles.constraint``: +------------------------+------------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/multigrid_solvers.rst b/docs/source_docs/user_guide/inputs/multigrid_solvers.rst index 188d2ec..03c42c8 100644 --- a/docs/source_docs/user_guide/inputs/multigrid_solvers.rst +++ b/docs/source_docs/user_guide/inputs/multigrid_solvers.rst @@ -189,7 +189,8 @@ and `GMRES` for the linear solver. +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -The following inputs are valid when using ``BoomerAMG`` as a preconditioner or solver. +The following inputs are valid when using ``BoomerAMG`` as a preconditioner or solver. They must be defined using the +prefix ``hypre``: +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | @@ -230,7 +231,7 @@ The following inputs are valid when using ``BoomerAMG`` as a preconditioner or s +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_num_sweeps | See ``HYPRE_BoomerAMGSetNumSweeps``. | Int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_num_sweeps | See ``HYPRE_BoomerAMGSetNumSweeps``. | int | 2 | +| bamg_num_sweeps | See ``HYPRE_BoomerAMGSetNumSweeps``. | Int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_num_up_sweeps | See ``HYPRE_BoomerAMGSetCycleNumSweeps``. | Int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ diff --git a/docs/source_docs/user_guide/inputs/output/checkpointing.rst b/docs/source_docs/user_guide/inputs/output/checkpointing.rst index e571458..30fe4fb 100644 --- a/docs/source_docs/user_guide/inputs/output/checkpointing.rst +++ b/docs/source_docs/user_guide/inputs/output/checkpointing.rst @@ -20,12 +20,12 @@ The following inputs must be preceded by the prefix ``mfix`` and control checkpo +-------------------------+-----------------------------------------------------------------------+-------------+------------+ | check_file | Prefix to use for checkpoint output | String | chk | +-------------------------+-----------------------------------------------------------------------+-------------+------------+ -| geom_chk_write | When enabled, write the EB geometry data into geom_chk_file | Bool | false | -| | and additionally, geom_levelset_chk_file, if levelset | | | +| geom_chk_write | When enabled, write the EB geometry data into ``geom_chk_file`` | Bool | false | +| | and additionally, ``geom_levelset_chk_file`` if levelset | | | | | refinement is enabled. | | | +-------------------------+-----------------------------------------------------------------------+-------------+------------+ -| geom_chk_read | When true, read the EB geometry data from geom_chk_file | Bool | false | -| | and additionally, geom_levelset_chk_file, if levelset | | | +| geom_chk_read | When true, read the EB geometry data from ``geom_chk_file`` | Bool | false | +| | and additionally, ``geom_levelset_chk_file`` if levelset | | | | | refinement is enabled. | | | +-------------------------+-----------------------------------------------------------------------+-------------+------------+ | geom_chk_file | Name of the EB checkpoint file that is used to store or read | String | geom_chk | diff --git a/docs/source_docs/user_guide/inputs/output/monitors.rst b/docs/source_docs/user_guide/inputs/output/monitors.rst index 835437d..302af84 100644 --- a/docs/source_docs/user_guide/inputs/output/monitors.rst +++ b/docs/source_docs/user_guide/inputs/output/monitors.rst @@ -10,7 +10,7 @@ To define monitors, the following inputs must be preceded by the prefix ``mfix`` +--------------------+------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +====================+======================================================+=============+===========+ -| monitors | Names of the monitors to be computed | String | None | +| monitors | Names of the monitors to be computed | Strings | None | +--------------------+------------------------------------------------------+-------------+-----------+ | monitors.[monitor] | Monitor type | String | None | +--------------------+------------------------------------------------------+-------------+-----------+ @@ -48,7 +48,7 @@ Monitor output -------------- The monitor data will be output to a file with name given by the input -"plot_file", and the extension ``.csv`` is automatically added. The monitor +``plot_file``, and the extension ``.csv`` is automatically added. The monitor output file is in Comma Separated Value (CSV) format. The first line of the file provides header information. The following inputs must be preceded by the prefix ``mfix.monitors``: @@ -56,34 +56,32 @@ the prefix ``mfix.monitors``: +-------------------------------+----------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +===============================+==========================================================+=============+===========+ -| [monitor].plot_file | Define the name of the plotfile where monitor output | String | None | -| | will be saved | | | +| [monitor].plot_file | Name of the plot file for monitor output. | String | None | +-------------------------------+----------------------------------------------------------+-------------+-----------+ -| [monitor].plot_int | Define the timestep frequency for saving monitored data | Int | -1 | -| | to file | | | +| [monitor].plot_int | Frequency for saving monitored data to output file. | Int | -1 | +-------------------------------+----------------------------------------------------------+-------------+-----------+ | [monitor].plot_per_approx | Define the approximated simulation time at which saving | Real | 0 | | | monitored data | | | +-------------------------------+----------------------------------------------------------+-------------+-----------+ -| [monitor].output.openmode | Sets the open mode for the monitor output file. | String | app | +| [monitor].output.openmode | Select open mode for the monitor output file. | String | app | | | | | | | | Options: | | | | | | | | | | * ``app`` - append to the file if it already exists | | | | | * ``trunc`` - overwrite the output file if it exists | | | +-------------------------------+----------------------------------------------------------+-------------+-----------+ -| [monitor].output.setw | Sets the field width to be used on output file | Int | 0 | +| [monitor].output.setw | Field width for output file. | Int | 0 | +-------------------------------+----------------------------------------------------------+-------------+-----------+ -| [monitor].output.setfill | Sets the filling character for the output file | Char | '' | +| [monitor].output.setfill | Fill character for output file. | Char | '' | +-------------------------------+----------------------------------------------------------+-------------+-----------+ | [monitor].output.setprecision | Sets the decimal precision to be used to format | Int | 0 | | | floating-point values in the output file | | | +-------------------------------+----------------------------------------------------------+-------------+-----------+ -| [monitor].output.format | Sets the format flags. Admissible values are: | String | "" | +| [monitor].output.format | Sets the format flags. Options: | String | "" | | | | | | -| | * "defaultfloat" | | | -| | * "fixed" | | | -| | * "scientific" | | | +| | * ``defaultfloat`` | | | +| | * ``fixed`` | | | +| | * ``scientific`` | | | +-------------------------------+----------------------------------------------------------+-------------+-----------+ .. code-block:: none diff --git a/docs/source_docs/user_guide/inputs/output/reports.rst b/docs/source_docs/user_guide/inputs/output/reports.rst index f69ade8..c722d11 100644 --- a/docs/source_docs/user_guide/inputs/output/reports.rst +++ b/docs/source_docs/user_guide/inputs/output/reports.rst @@ -15,7 +15,7 @@ The following inputs are defined using the prefix ``mfix.reports``: +--------------------+------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +====================+======================================================+=============+===========+ -| diameter | Names of the PSD reports | String | None | +| diameter | Names of the PSD reports | Strings | None | +--------------------+------------------------------------------------------+-------------+-----------+ diff --git a/docs/source_docs/user_guide/inputs/porous_media.rst b/docs/source_docs/user_guide/inputs/porous_media.rst index bed06fa..871ac65 100644 --- a/docs/source_docs/user_guide/inputs/porous_media.rst +++ b/docs/source_docs/user_guide/inputs/porous_media.rst @@ -18,7 +18,7 @@ The following inputs are defined using the prefix ``pm``: +--------------------------+------------------------------------------------------------------------------+----------+-----------+ | | Description | Type | Default | +==========================+==============================================================================+==========+===========+ -| regions | Regions used to define porous media. | String | None | +| regions | Regions used to define porous media. | Strings | None | +--------------------------+------------------------------------------------------------------------------+----------+-----------+ | [region].volfrac | Solids volume fraction of the porous media region. | Real | None | +--------------------------+------------------------------------------------------------------------------+----------+-----------+ diff --git a/docs/source_docs/user_guide/inputs/regions.rst b/docs/source_docs/user_guide/inputs/regions.rst index d57bd97..67d8c82 100644 --- a/docs/source_docs/user_guide/inputs/regions.rst +++ b/docs/source_docs/user_guide/inputs/regions.rst @@ -3,12 +3,12 @@ Regions definitions =================== -Regions are used to define sections of the domain. They may be either boxes, planes or points. They are used in building initial condition regions. +Regions are used to define sections of the domain. They may be either boxes, planes or points. They are used in defining initial and boundary conditions. +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +=====================+=======================================================================+=============+===========+ -| mfix.regions | Names given to regions. | String | None | +| mfix.regions | Names given to regions. | Strings | None | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | regions.[region].lo | Low corner of physical region (physical, not index space) | Reals | 0 0 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ diff --git a/docs/source_docs/user_guide/inputs/solids_model.rst b/docs/source_docs/user_guide/inputs/solids_model.rst index 1c09682..7316954 100644 --- a/docs/source_docs/user_guide/inputs/solids_model.rst +++ b/docs/source_docs/user_guide/inputs/solids_model.rst @@ -10,8 +10,8 @@ models. The following inputs are defined with the prefix ``solids``: +------------------------------------------+-------------------------------------------------------------+----------+----------+ | | Description | Type | Default | +==========================================+=============================================================+==========+==========+ -| types | Specified name(s) of the SOLIDS types or None to disable | String | None | -| | the SOLIDS solver. The user-defined names are used to | | | +| types | Specified name(s) of the solids types or None to disable | Strings | None | +| | the solids solver. The user-defined names are used to | | | | | specify DEM and/or PIC model inputs. | | | +------------------------------------------+-------------------------------------------------------------+----------+----------+ | molecular_weight | Value of constant solid molecular weight. | Real | 0 | @@ -28,7 +28,7 @@ models. The following inputs are defined with the prefix ``solids``: +------------------------------------------+-------------------------------------------------------------+----------+----------+ | reference_temperature | Reference temperature used for specific enthalpy. | Real | 0 | +------------------------------------------+-------------------------------------------------------------+----------+----------+ -| species | Specify which species can constitute | String | None | +| species | Specify which species can constitute | Strings | None | | | the fluid phase [defined species must | | | | | be a subset of the species.solve | | | | | arguments]. | | | @@ -94,11 +94,13 @@ Enabling the DEM solver and specifying model options. The following keys must b +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ | tan_history | Include tangential history force in the collision model. | Bool | false | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| tan_history.max_contacts | When tangential history is enabled, the maximum number of contacts | Int | 10 | -| | per particle that are tracked at any point | | | +| tan_history.max_contacts | Maximum number of contacts per particle tracked at any point when | Int | 10 | +| | tangential history is enabled. | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| rolling_friction | When tangential history is enabled, the rolling friction model | String | None | -| | to be used. :cite:p:`zhou1999,ai2011,wensrich2012,blais2019` | | | +| rolling_friction | Rolling friction model to use when tangential history is enabled. | String | None | +| | :cite:p:`zhou1999,ai2011,wensrich2012,blais2019` | | | +| | | | | +| | Options: | | | | | | | | | | * ``None`` | | | | | | | | diff --git a/docs/source_docs/user_guide/inputs/species.rst b/docs/source_docs/user_guide/inputs/species.rst index dd04b4c..e1fd83b 100644 --- a/docs/source_docs/user_guide/inputs/species.rst +++ b/docs/source_docs/user_guide/inputs/species.rst @@ -8,7 +8,7 @@ The following inputs are defined using the prefix ``species``: +--------------------------+------------------------------------------------------------------------+----------+-----------+ | | Description | Type | Default | +==========================+========================================================================+==========+===========+ -| solve | Specified name(s) of the species or None to disable the | String | None | +| solve | Specified name(s) of the species or None to disable the | Strings | None | | | species solver. The name assigned to the species | | | | | solver is used to specify species inputs. | | | +--------------------------+------------------------------------------------------------------------+----------+-----------+ -- GitLab