From 46458c16ad0ed8aa72369a539cd9c04af8e9102c Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:25:07 -0500 Subject: [PATCH 01/47] consistent formatting: prefix ``name`` --- docs/source_docs/user_guide/inputs/advanced.rst | 6 +++--- .../user_guide/inputs/boundary_conditions.rst | 4 ++-- .../user_guide/inputs/chemical_reactions.rst | 4 ++-- docs/source_docs/user_guide/inputs/domain.rst | 2 +- docs/source_docs/user_guide/inputs/fluid_model.rst | 4 ++-- docs/source_docs/user_guide/inputs/geometry.rst | 10 +++++----- .../user_guide/inputs/initial_conditions.rst | 10 +++++----- .../user_guide/inputs/mesh_and_gridding.rst | 10 +++++----- .../user_guide/inputs/model_options.rst | 14 +++++++------- docs/source_docs/user_guide/inputs/mpmd.rst | 2 +- .../user_guide/inputs/multigrid-solvers.rst | 10 +++++----- .../user_guide/inputs/output/ascent.rst | 5 +++-- .../user_guide/inputs/output/checkpointing.rst | 2 +- .../user_guide/inputs/output/monitors.rst | 2 +- .../user_guide/inputs/output/plotfiles.rst | 10 +++++----- .../user_guide/inputs/porous_media_defs.rst | 2 +- .../source_docs/user_guide/inputs/solids_model.rst | 2 +- .../source_docs/user_guide/inputs/species_defs.rst | 4 ++-- .../user_guide/inputs/time-stepping.rst | 4 ++-- 19 files changed, 54 insertions(+), 53 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/advanced.rst b/docs/source_docs/user_guide/inputs/advanced.rst index a1d2f7f..4431f83 100644 --- a/docs/source_docs/user_guide/inputs/advanced.rst +++ b/docs/source_docs/user_guide/inputs/advanced.rst @@ -35,7 +35,7 @@ The following inputs must be preceded by "amrex." GPU memory ---------- -The following inputs must be preceded by "amrex." +The following inputs must be preceded by the prefix ``amrex``: +----------------------------+-----------------------------------------------------------------------+-------------+---------------+ | | Description | Type | Default | @@ -58,7 +58,7 @@ the ``particles.max_grid_size`` (in each direction) have no meaning. Therefore t sizes should be set for particle load balancing. It may also be necessary to set the blocking factors to 1. -The following inputs must be preceded by ``mfix`` and determine how we load balance: +The following inputs must be preceded by the prefix ``mfix`` and control load balancing: +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ | | Description | Type | Default | @@ -88,7 +88,7 @@ To allow a user to verify the breakdown of fluid grids created before running a minimal memory to print the grid coverage report and exits immediately after that. -The following inputs are defined using the ``particles`` prefix. +The following inputs are defined using the prefix ``particles``: +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/boundary_conditions.rst b/docs/source_docs/user_guide/inputs/boundary_conditions.rst index bd5a0d2..e93d0d2 100644 --- a/docs/source_docs/user_guide/inputs/boundary_conditions.rst +++ b/docs/source_docs/user_guide/inputs/boundary_conditions.rst @@ -7,7 +7,7 @@ Boundary Conditions General boundary conditions --------------------------- -The following inputs are defined using the ``bc`` prefix. +The following inputs are defined using the prefix ``bc``: +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -36,7 +36,7 @@ Fluid settings ~~~~~~~~~~~~~~ For each boundary condition region, the fluid inputs are defined -using the ``bc.[region].[fluid]`` prefix. +using the prefix ``bc.[region].[fluid]``: +------------------------+------------------------------------------------------------------------+-------------+-----------+ diff --git a/docs/source_docs/user_guide/inputs/chemical_reactions.rst b/docs/source_docs/user_guide/inputs/chemical_reactions.rst index b72dd3d..64fff8e 100644 --- a/docs/source_docs/user_guide/inputs/chemical_reactions.rst +++ b/docs/source_docs/user_guide/inputs/chemical_reactions.rst @@ -1,7 +1,7 @@ Chemical Reactions ================== -The following inputs are defined using the ``chemistry`` prefix. +The following inputs are defined using the prefix ``chemistry``: +--------------------------+---------------------------------------------------------+----------+----------------+ | | Description | Type | Default | @@ -68,7 +68,7 @@ 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: + prefix ``chemistry.integrator``: +-----------------------+---------------------------------------------------------------------+--------+-----------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/domain.rst b/docs/source_docs/user_guide/inputs/domain.rst index fe18fc1..b62ac51 100644 --- a/docs/source_docs/user_guide/inputs/domain.rst +++ b/docs/source_docs/user_guide/inputs/domain.rst @@ -6,7 +6,7 @@ Defining the domain All simulations, whether using an embedded boundary (EB) or not, are specified on a simple cuboid domain. The low and high corners of the cuboid are defined by the ``prob_lo`` and ``prob_hi`` inputs. -The following inputs are defined using the ``geometry`` prefix. +The following inputs are defined using the prefix ``geometry``: .. _InputsTable_domain: diff --git a/docs/source_docs/user_guide/inputs/fluid_model.rst b/docs/source_docs/user_guide/inputs/fluid_model.rst index 1aef1ba..edc8259 100644 --- a/docs/source_docs/user_guide/inputs/fluid_model.rst +++ b/docs/source_docs/user_guide/inputs/fluid_model.rst @@ -3,7 +3,7 @@ Fluid model =========== -The following inputs are defined using the ``fluid`` prefix. +The following inputs are defined using the prefix ``fluid``: +--------------------------------------------+-------------------------------------------------------------+--------+----------+ | | Description | Type | Default | @@ -412,7 +412,7 @@ thermodynamic pressure for the system. bc.outlet.fluid0.pressure = 101325. -The following inputs are defined using the ``fluid`` prefix and control the convergence criteria +The following inputs are defined using the prefix ``fluid`` and control the convergence criteria of the damped Newton solver used to compute temperature from enthalpy and specific heat. +------------------------------------------+----------------------------------------------------------+--------+----------+ diff --git a/docs/source_docs/user_guide/inputs/geometry.rst b/docs/source_docs/user_guide/inputs/geometry.rst index c1aa586..d50d4d0 100644 --- a/docs/source_docs/user_guide/inputs/geometry.rst +++ b/docs/source_docs/user_guide/inputs/geometry.rst @@ -3,7 +3,7 @@ Specifying a geometry ===================== -The following inputs are defined using the ``mfix`` prefix. +The following inputs are defined using the prefix ``mfix``: +------------------------+-------------------------------------------------------------------------------+----------+---------------------+ | | Description | Type | Default | @@ -50,7 +50,7 @@ select the option to use a user-defined geometry constructed from native AMReX i ``box`` geometry ^^^^^^^^^^^^^^^^ -The following inputs are defined using the ``box`` prefix. +The following inputs are defined using the prefix ``box``: +------------------------+-------------------------------------------------------------------+----------+---------------------+ | | Description | Type | Default | @@ -147,7 +147,7 @@ the EB ``box`` are *covered* and thereby excluded from run-time calculations. ``cylinder`` geometry ^^^^^^^^^^^^^^^^^^^^^ -The following inputs are defined using the ``cylinder`` prefix. +The following inputs are defined using the prefix ``cylinder``: +------------------------+-------------------------------------------------------------------+----------+---------------------+ | | Description | Type | Default | @@ -339,7 +339,7 @@ Constructive solid geometry (CSG) * This option requires that the executable be built with CSG support. See the build documentation for for details. -The following inputs are defined using the ``csg`` prefix. +The following inputs are defined using the prefix ``csg``: +------------------------+-------------------------------------------------------------------+----------+---------------------+ | | Description | Type | Default | @@ -365,7 +365,7 @@ Standard triangle language (STL) * A standard triangle language (STL) geometry can be created using numerous CAD programs. -The following inputs are defined using the ``stl`` prefix. +The following inputs are defined using the prefix ``stl``: +------------------------+-------------------------------------------------------------------+----------+---------------------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/initial_conditions.rst b/docs/source_docs/user_guide/inputs/initial_conditions.rst index 12195a9..2070877 100644 --- a/docs/source_docs/user_guide/inputs/initial_conditions.rst +++ b/docs/source_docs/user_guide/inputs/initial_conditions.rst @@ -1,7 +1,7 @@ Initial Conditions ================== -The following inputs are defined using the ``ic`` prefix. +The following inputs are defined using the prefix ``ic``: +-----------------------+------------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -25,7 +25,7 @@ Fluid settings ~~~~~~~~~~~~~~ For each initial condition region, the fluid inputs are defined -using the ``ic.[region].[fluid]`` compound prefix. +using the compound prefix ``ic.[region].[fluid]``: +------------------------+------------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -48,7 +48,7 @@ Solids settings ~~~~~~~~~~~~~~~ For each initial condition region, general solids inputs are defined -using the ``ic.[region]`` compound prefix. +using the compound prefix ``ic.[region]``: +----------------------+------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -72,8 +72,8 @@ using the ``ic.[region]`` compound prefix. +----------------------+------------------------------------------------------------------+-------------+-----------+ For each initial condition region, the solid inputs are defined -using the ``ic.[region].[solid]`` compound prefix. -Note that diameter distributions must define a weighting type, +using the compound prefix ``ic.[region].[solid]``: +Note that diameter distributions must define a weighting type, please refer to :ref:`ReferenceParticleDistributions `. +---------------------+-----------------------------------------------------------------------+-------------+-----------+ 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 82fbc73..ecc8127 100644 --- a/docs/source_docs/user_guide/inputs/mesh_and_gridding.rst +++ b/docs/source_docs/user_guide/inputs/mesh_and_gridding.rst @@ -8,7 +8,7 @@ Mesh .. rubric:: Level-0 mesh -The following inputs are defined using the ``amr`` prefix. +The following inputs are defined using the prefix ``amr``: .. _InputsTable_mesh: @@ -76,7 +76,7 @@ The result is a uniform mesh spacing of :math:`0.125` *m* in all three direction .. rubric:: Mesh refinement -The following inputs are defined using the ``amr`` prefix. These inputs control the automatic +The following inputs are defined using the prefix ``amr``. These inputs control the automatic mesh refinement algorithm and are only applicable when ``amr.max_level > 0``. +----------------------+-----------------------------------------------------------------------+-------------+-----------+ @@ -103,7 +103,7 @@ for details on the adaptive mesh refinement algorithms. Grids ----- -The following inputs are defined using the ``amr`` prefix. +The following inputs are defined using the prefix ``amr``: +----------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -139,7 +139,7 @@ the grids will be sufficiently coarsenable for good multigrid performance; there Tiles ----- -The following inputs are defined using the ``fabarray`` prefix. +The following inputs are defined using the prefix ``fabarray``: +----------------------+-----------------------------------------------------------------------+----------+-------------+ | | Description | Type | Default | @@ -147,7 +147,7 @@ The following inputs are defined using the ``fabarray`` prefix. | mfiter_tile_size | Maximum number of cells in each direction for (logical) tiles | IntVect | 1024000,8,8 | +----------------------+-----------------------------------------------------------------------+----------+-------------+ -The following inputs are defined using the ``particles`` prefix. +The following inputs are defined using the prefix ``particles``: +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/model_options.rst b/docs/source_docs/user_guide/inputs/model_options.rst index 6eaf504..3072d64 100644 --- a/docs/source_docs/user_guide/inputs/model_options.rst +++ b/docs/source_docs/user_guide/inputs/model_options.rst @@ -2,7 +2,7 @@ Model options ============= -The following inputs are defined using the ``mfix`` prefix. +The following inputs are defined using the prefix ``mfix``: +------------------------+----------------------------------------------------------------------------+----------+---------------------+ | | Description | Type | Default | @@ -42,7 +42,7 @@ The following inputs are defined using the ``mfix`` prefix. Fluid discretization -------------------- -The following inputs are defined using the ``mfix`` prefix. +The following inputs are defined using the prefix ``mfix``: +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | Key | Description | Type | Default | @@ -97,7 +97,7 @@ Additional available constraints Additional constraints may be imposed on problems which are under-determined such as particle settling in a fully periodic domain. Currently, only particle constraints are supported. -The following inputs are defined using the ``particles`` prefix. +The following inputs are defined using the prefix ``particles``: +---------------------+---------------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -138,7 +138,7 @@ for the system is zero. Deposition scheme ----------------- -The following inputs are defined using the ``mfix`` prefix. +The following inputs are defined using the prefix ``mfix``: +----------------------------+--------------------------------------------------------------------+-----------+---------------+ | | Description | Type | Default | @@ -257,7 +257,7 @@ the *Y*-direction weights. The right image shows the resulting composite weights Deposition redistribution ------------------------- -The following inputs are defined using the ``mfix`` prefix. +The following inputs are defined using the prefix ``mfix``: +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | Key | Description | Type | Default | @@ -291,7 +291,7 @@ The following inputs are defined using the ``mfix`` prefix. Fluid-particle drag ------------------- -The following input is defined using the ``mfix.drag`` prefix. +The following input is defined using the prefix ``mfix.drag``: .. |VirtualMass_Eq| replace:: :math:`\mathbf{F}_p^{vm} = -C_p^{vm}\rho_f \left( \frac{D\mathbf{u}_f}{Dt} - \frac{d\mathbf{u}_p}{dt}\right)\mathcal{V}_p` @@ -349,7 +349,7 @@ The following input is defined using the ``mfix.drag`` prefix. Heat transfer coefficients -------------------------- -The following input is defined using the ``mfix.convection`` prefix. +The following input is defined using the prefix ``mfix.convection``: +-------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/mpmd.rst b/docs/source_docs/user_guide/inputs/mpmd.rst index 8954654..dd845ac 100644 --- a/docs/source_docs/user_guide/inputs/mpmd.rst +++ b/docs/source_docs/user_guide/inputs/mpmd.rst @@ -12,7 +12,7 @@ feature, the executable has to be built with ``-DMFIX_MPMD = yes``. * Cannot be used to send and receive particle data. -The following inputs are defined using the ``mfix`` prefix and control frequency and the data sent to the other program. +The following inputs are defined using the prefix ``mfix`` and control frequency and the data sent to the other program. +----------------------+-----------------------------------------------------------------------+-------------+-----------+ | | 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 4eea804..bdf4096 100644 --- a/docs/source_docs/user_guide/inputs/multigrid-solvers.rst +++ b/docs/source_docs/user_guide/inputs/multigrid-solvers.rst @@ -6,11 +6,11 @@ Multigrid solvers Nodal projection ---------------- -The following inputs are defined using the ``nodal_proj`` prefix. +The following inputs are defined using the prefix ``nodal_proj``: +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | -+-------------------------+-----------------------------------------------------------------------+-------------+--------------+ ++=========================+=======================================================================+=============+==============+ | verbose | Verbosity of multigrid solver in nodal projection | Int | 0 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bottom_verbose | Verbosity of BiCGStab solver in nodal projection | Int | 0 | @@ -43,7 +43,7 @@ The following inputs are defined using the ``nodal_proj`` prefix. MAC projection -------------- -The following inputs are defined using the ``mac_proj`` prefix. +The following inputs are defined using the prefix ``mac_proj``: +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | @@ -81,7 +81,7 @@ The following inputs are defined using the ``mac_proj`` prefix. Diffusion --------- -The following inputs are defined using the ``diffusion`` prefix. +The following inputs are defined using the prefix ``diffusion``: +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | @@ -113,7 +113,7 @@ Hypre Settings `hypre` settings are specified using the following inputs which are read directly by AMReX when `hypre` is used as the bottom solve for the MAC and/or nodal projections. By default, these inputs are defined using the -``hypre`` prefix, however different settings for the nodal and MAC projections can be used by specifying +prefix ``hypre``, however different settings for the nodal and MAC projections can be used by specifying a ``hpyre_namespace`` for each solver. .. warning:: diff --git a/docs/source_docs/user_guide/inputs/output/ascent.rst b/docs/source_docs/user_guide/inputs/output/ascent.rst index a2272c9..d30ae2a 100644 --- a/docs/source_docs/user_guide/inputs/output/ascent.rst +++ b/docs/source_docs/user_guide/inputs/output/ascent.rst @@ -1,7 +1,7 @@ Ascent ------ -The following inputs must be preceded by "mfix." and control frequency and naming of plotfile generation as well +The following inputs must be preceded by the prefix ``mfix`` and control frequency and naming of plotfile generation as well as whether the EB geometry or level set should be written out, and if the particles should be written out in Ascii format (for debugging). @@ -17,7 +17,8 @@ format (for debugging). `Ascent `_ has been integrated into MFIX-Exa for *in situ* visualization. -For codes that have been built with Ascent support, the following inputs must be preceded by "ascent." +For codes that have been built with Ascent support, the following input must be preceded by the prefix +``ascent``, and specifies the ascent actions for fluid and/or particles. The frequency which these are called is controlled by `ascent_int` or `ascent_per_approx`, see above. Note that if an ascent pipeline is being included in a GPU build/run, then you must enable managed memory, diff --git a/docs/source_docs/user_guide/inputs/output/checkpointing.rst b/docs/source_docs/user_guide/inputs/output/checkpointing.rst index 8e4c718..2f363ca 100644 --- a/docs/source_docs/user_guide/inputs/output/checkpointing.rst +++ b/docs/source_docs/user_guide/inputs/output/checkpointing.rst @@ -3,7 +3,7 @@ Checkpointing ============= -The following inputs must be preceded by "mfix." and control checkpoint/restart. +The following inputs must be preceded by the prefix ``mfix`` and control checkpoint/restart: +-------------------------+-----------------------------------------------------------------------+-------------+------------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/output/monitors.rst b/docs/source_docs/user_guide/inputs/output/monitors.rst index 5ff9dd7..66ee112 100644 --- a/docs/source_docs/user_guide/inputs/output/monitors.rst +++ b/docs/source_docs/user_guide/inputs/output/monitors.rst @@ -644,7 +644,7 @@ Flow rates For Lagrangian monitors of type FlowRate, the flow plane must be specified in the inputs and it must be defined by one of the regions defined in the regions inputs. The following input for a monitor [monitor] of type FlowRate can be -used, preceded by the "mfix.monitors" prefix. +used, preceded by the prefix ``mfix.monitors``: +------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/output/plotfiles.rst b/docs/source_docs/user_guide/inputs/output/plotfiles.rst index 1f524b1..175ba49 100644 --- a/docs/source_docs/user_guide/inputs/output/plotfiles.rst +++ b/docs/source_docs/user_guide/inputs/output/plotfiles.rst @@ -3,7 +3,7 @@ Plotfiles and Other Output ========================== -The following inputs must be preceded by "mfix." and control frequency and naming of plotfile generation as well +The following inputs must be preceded by the prefix ``mfix`` and control frequency and naming of plotfile generation as well as whether the EB geometry or level set should be written out, and if the particles should be written out in Ascii format (for debugging). @@ -86,7 +86,7 @@ The following inputs must be preceded by "mfix." and control what variables will +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -The following inputs must be preceded by "mfix." and control whether the EB geometry or level set should be written out. +The following inputs must be preceded by the prefix ``mfix`` and control whether the EB geometry or level set should be written out: +----------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -103,7 +103,8 @@ The following inputs must be preceded by "mfix." and control whether the EB geom `Ascent `_ has been integrated into MFIX-Exa for *in situ* visualization. -For codes that have been built with Ascent support, the following inputs must be preceded by "ascent." +For codes that have been built with Ascent support, the following input must be preceded by the prefix +``ascent`` and specifies the ascent actions for fluid and/or particles. The frequency which these are called is controlled by `ascent_int` or `ascent_per_approx`, see above. Note that if an ascent pipeline is being included in a GPU build/run, then you must enable managed memory, @@ -112,13 +113,12 @@ i.e., set `amrex.the_arena_is_managed = true`. +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +=====================+=======================================================================+=============+===========+ -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ | actions | yaml file of the ascent actions (ex. ascent_actions.yaml). If no file | String | | | | name is provided, then calls to Ascent are skipped. | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -The following inputs must be preceded by "mfix.solids." and allow to write additional plotfiles which +The following inputs must be preceded by the prefix ``mfix.solids`` and allow to write additional plotfiles which contain only solids variables in specific regions at fixed timesteps or approximated simulation times. All these parameters are user-defined. diff --git a/docs/source_docs/user_guide/inputs/porous_media_defs.rst b/docs/source_docs/user_guide/inputs/porous_media_defs.rst index 47d9e46..6d4b011 100644 --- a/docs/source_docs/user_guide/inputs/porous_media_defs.rst +++ b/docs/source_docs/user_guide/inputs/porous_media_defs.rst @@ -13,7 +13,7 @@ source term, :math:`\boldsymbol{S}_{pm}`, to the fluid momentum equation. :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. +The following inputs are defined using the prefix ``pm``: +--------------------------+------------------------------------------------------------------------------+----------+-----------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/solids_model.rst b/docs/source_docs/user_guide/inputs/solids_model.rst index 1fc5741..9ab66f7 100644 --- a/docs/source_docs/user_guide/inputs/solids_model.rst +++ b/docs/source_docs/user_guide/inputs/solids_model.rst @@ -5,7 +5,7 @@ Solids settings --------------- Enabling the SOLIDS solver and specifying options common to both DEM and PIC -models. The following inputs must be preceded by the "solids." root +models. The following inputs are defined with the prefix ``solids``: +------------------------------------------+-------------------------------------------------------------+----------+----------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/species_defs.rst b/docs/source_docs/user_guide/inputs/species_defs.rst index ad83fcf..c0b7619 100644 --- a/docs/source_docs/user_guide/inputs/species_defs.rst +++ b/docs/source_docs/user_guide/inputs/species_defs.rst @@ -3,7 +3,7 @@ Species definitions =================== -The following inputs are defined using the ``species`` prefix. +The following inputs are defined using the prefix ``species``: +--------------------------+------------------------------------------------------------------------+----------+-----------+ | | Description | Type | Default | @@ -58,7 +58,7 @@ The following inputs are defined using the ``species`` prefix. +--------------------------+------------------------------------------------------------------------+----------+-----------+ -The following inputs are for each species defined using the ``species.[species name]`` prefix. +The following inputs are for each species defined using the prefix ``species.[species name]``: +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/time-stepping.rst b/docs/source_docs/user_guide/inputs/time-stepping.rst index 97dc7ea..e2cff95 100644 --- a/docs/source_docs/user_guide/inputs/time-stepping.rst +++ b/docs/source_docs/user_guide/inputs/time-stepping.rst @@ -90,7 +90,7 @@ sub-time step is computed by dividing ``dt`` by ``nsubsteps``. } -The following inputs are defined using the ``mfix`` prefix. +The following inputs are defined using the prefix ``mfix``: +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | Key | Description | Type | Default | @@ -126,7 +126,7 @@ In the case of unsteady flow, the simulation will stop when either the number of reaches ``max_step`` or time reaches ``stop_time``. -The following inputs are defined using the ``mfix`` prefix and are only relevant if running a steady state simulation. +The following inputs are defined using the prefix ``mfix`` and are only relevant if running a steady state simulation. +-----------------------+-----------------------------------------------------------------------+-------------+------------+ | Key | Description | Type | Default | -- GitLab From 127c0debf73da44612ff07bd542e849ec9d414d5 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:25:51 -0500 Subject: [PATCH 02/47] default value --- docs/source_docs/user_guide/inputs/advanced.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/advanced.rst b/docs/source_docs/user_guide/inputs/advanced.rst index 4431f83..b0676aa 100644 --- a/docs/source_docs/user_guide/inputs/advanced.rst +++ b/docs/source_docs/user_guide/inputs/advanced.rst @@ -42,8 +42,8 @@ The following inputs must be preceded by the prefix ``amrex``: +============================+=======================================================================+=============+===============+ | the_arena_is_managed | Use managed memory for the main arena. | Int | 0 | +----------------------------+-----------------------------------------------------------------------+-------------+---------------+ -| the_arena_init_size | Main memory arena's initial size in bytes. | Int | 3/4 of system | -| | | | device memory | +| the_arena_init_size | Initial size of main memory arena (bytes). If not specified, use | Int | Unspecified | +| | 3/4 of system device memory. | | | +----------------------------+-----------------------------------------------------------------------+-------------+---------------+ | abort_on_out_of_gpu_memory | Abort if free device memory is less than the amount an arena is | Int | 0 | | | asked to allocate. | | | -- GitLab From c503131ed5a8c59c9a4f165f1237726c6d52a616 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:25:57 -0500 Subject: [PATCH 03/47] alignment --- docs/source_docs/user_guide/inputs/advanced.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/advanced.rst b/docs/source_docs/user_guide/inputs/advanced.rst index b0676aa..ffe3b0c 100644 --- a/docs/source_docs/user_guide/inputs/advanced.rst +++ b/docs/source_docs/user_guide/inputs/advanced.rst @@ -63,7 +63,7 @@ The following inputs must be preceded by the prefix ``mfix`` and control load ba +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ | | Description | Type | Default | +==================================+=======================================================================+=============+===================+ -| regrid_int | How often to regrid (in number of steps at level 0) | int | 0 | +| regrid_int | How often to regrid (in number of steps at level 0) | int | 0 | | | if regrid_int <= 0 then no regridding will occur | | | +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ | load_balance | * ``SingleGrid`` fluid and particles are co-located on the same grids | string | SingleGrid | -- GitLab From b2f67ca8ecabf153ff8ce09010fceef320d1f474 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:26:16 -0500 Subject: [PATCH 04/47] grammar --- docs/source_docs/user_guide/inputs/chemical_reactions.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/chemical_reactions.rst b/docs/source_docs/user_guide/inputs/chemical_reactions.rst index 64fff8e..76077f1 100644 --- a/docs/source_docs/user_guide/inputs/chemical_reactions.rst +++ b/docs/source_docs/user_guide/inputs/chemical_reactions.rst @@ -47,7 +47,7 @@ The following inputs are defined using the prefix ``chemistry``: 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 +chemical reactions. The ``StiffSolver`` class of integrators is inspired by the class of integrators in AMReX-Astro/Microphysics (https://github.com/AMReX-Astro/Microphysics) -- GitLab From d9b44e08ae3e137d5fe49e61bf25b19a04ac1e6b Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:26:55 -0500 Subject: [PATCH 05/47] grammar --- docs/source_docs/user_guide/inputs/fluid_model.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/fluid_model.rst b/docs/source_docs/user_guide/inputs/fluid_model.rst index edc8259..6c0a341 100644 --- a/docs/source_docs/user_guide/inputs/fluid_model.rst +++ b/docs/source_docs/user_guide/inputs/fluid_model.rst @@ -15,7 +15,7 @@ The following inputs are defined using the prefix ``fluid``: +--------------------------------------------+-------------------------------------------------------------+--------+----------+ -The root prefix for the following inputs use the name defined using the ``fluid.solve`` keyword. For example, if the fluid solver +The root prefix for the following inputs is the name defined using the ``fluid.solve`` keyword. For example, if the fluid solver 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. -- GitLab From 9cb61c30df7740ff210d181cc0aa3698a55fbbeb Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:27:02 -0500 Subject: [PATCH 06/47] remove punctuation --- docs/source_docs/user_guide/inputs/fluid_model.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/fluid_model.rst b/docs/source_docs/user_guide/inputs/fluid_model.rst index 6c0a341..5d7e4ca 100644 --- a/docs/source_docs/user_guide/inputs/fluid_model.rst +++ b/docs/source_docs/user_guide/inputs/fluid_model.rst @@ -70,9 +70,9 @@ a single fluid; therefore, it is common to name the fluid ``fluid``. This is ill | | | | | | | A value is required for ``Sutherland`` viscosity model. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ -| viscosity.molecular.Reid.A, | Reid model constants | Real | 0 | -| viscosity.molecular.Reid.B, | | | | -| viscosity.molecular.Reid.C, and | Values are required for ``Reid`` viscosity model. | | | +| viscosity.molecular.Reid.A | Reid model constants | Real | 0 | +| viscosity.molecular.Reid.B | | | | +| viscosity.molecular.Reid.C | Values are required for ``Reid`` viscosity model. | | | | viscosity.molecular.Reid.D | | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ | viscosity.eddy | Specify eddy viscosity model. | String | None | -- GitLab From cfa0f4179f669f7eab860edd1c17c02a5f6e3b70 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:27:12 -0500 Subject: [PATCH 07/47] remove empty row --- docs/source_docs/user_guide/inputs/multigrid-solvers.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/multigrid-solvers.rst b/docs/source_docs/user_guide/inputs/multigrid-solvers.rst index bdf4096..02f8d3d 100644 --- a/docs/source_docs/user_guide/inputs/multigrid-solvers.rst +++ b/docs/source_docs/user_guide/inputs/multigrid-solvers.rst @@ -127,7 +127,7 @@ and `GMRES` for the linear solver. +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ ++===================================+=======================================================================+=============+==============+ | hypre_preconditioner | Type of preconditioner | string | none | | | | | | | | Options are BoomerAMG or euclid | | | -- GitLab From 97e2ed4c26a039b09b497462246b70cc9cb0e953 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:27:21 -0500 Subject: [PATCH 08/47] remove empty row --- docs/source_docs/user_guide/inputs/multigrid-solvers.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/multigrid-solvers.rst b/docs/source_docs/user_guide/inputs/multigrid-solvers.rst index 02f8d3d..71c20be 100644 --- a/docs/source_docs/user_guide/inputs/multigrid-solvers.rst +++ b/docs/source_docs/user_guide/inputs/multigrid-solvers.rst @@ -149,7 +149,7 @@ The following inputs are valid when using ``BoomerAMG`` as a preconditioner or s +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ ++===================================+=======================================================================+=============+==============+ | bamg_verbose | Set BoomerAMG verbosity | int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_logging | See HYPRE_BoomerAMGSetLogging | int | 0 | -- GitLab From 4bf0c708160ac8b819d34c39f708ce50ae4b828f Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:27:40 -0500 Subject: [PATCH 09/47] remove empty rows --- docs/source_docs/user_guide/inputs/multigrid-solvers.rst | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/multigrid-solvers.rst b/docs/source_docs/user_guide/inputs/multigrid-solvers.rst index 71c20be..6330643 100644 --- a/docs/source_docs/user_guide/inputs/multigrid-solvers.rst +++ b/docs/source_docs/user_guide/inputs/multigrid-solvers.rst @@ -164,34 +164,28 @@ The following inputs are valid when using ``BoomerAMG`` as a preconditioner or s +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_relax_order | See HYPRE_BoomerAMGSetRelaxOrder | int | 1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_relax_type | See HYPRE_BoomerAMGSetRelaxType | int | 6 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_down_relax_type | See HYPRE_BoomerAMGSetCycleRelaxType | int | 11 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_up_relax_type | See HYPRE_BoomerAMGSetCycleRelaxType | int | 11 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_coarse_relax_type | See HYPRE_BoomerAMGSetCycleRelaxType | int | 11 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_num_sweeps | See HYPRE_BoomerAMGSetNumSweeps | int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_num_down_sweeps | See HYPRE_BoomerAMGSetCycleNumSweeps | int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_num_up_sweeps | See HYPRE_BoomerAMGSetCycleNumSweeps | int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_num_coarse_sweeps | See HYPRE_BoomerAMGSetCycleNumSweeps | int | 1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_max_levels | See HYPRE_BoomerAMGSetMaxLevels | int | 20 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_strong_threshold | See HYPRE_BoomerAMGSetStrongThreshold | Real | 0.57 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_interp_type | See HYPRE_BoomerAMGSetInterpType | int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_variant | See HYPRE_BoomerAMGSetVariant | int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_keep_transpose | See HYPRE_BoomerAMGSetKeepTranspose | int | 0 | @@ -221,7 +215,7 @@ The following inputs are valid when using ``BoomerAMG`` as a preconditioner or s +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ ++===================================+=======================================================================+=============+==============+ | adjust_singular_matrix | Should be true if the problem to be solved has singular matrix | Bool | false | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | overwrite_existing_matrix_files | Over-write existing matrix files | Bool | false | -- GitLab From 6a49bea70191e11e2db498ecf7d4573239e4662a Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:27:53 -0500 Subject: [PATCH 10/47] spelling --- docs/source_docs/user_guide/inputs/solids_model.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/solids_model.rst b/docs/source_docs/user_guide/inputs/solids_model.rst index 9ab66f7..bad7706 100644 --- a/docs/source_docs/user_guide/inputs/solids_model.rst +++ b/docs/source_docs/user_guide/inputs/solids_model.rst @@ -36,11 +36,11 @@ models. The following inputs are defined with the prefix ``solids``: | | be a subset of the species.solve | | | | | arguments]. | | | +------------------------------------------+-------------------------------------------------------------+----------+----------+ -| newton_solver.absolute_tol | Define absolute tolerance for Damped-Newton solver | Real | 1.e-6 | +| newton_solver.absolute_tol | Define absolute tolerance for damped Newton solver | Real | 1.e-6 | +------------------------------------------+-------------------------------------------------------------+----------+----------+ -| newton_solver.relative_tol | Define relative tolerance for Damped-Newton solver | Real | 1.e-6 | +| newton_solver.relative_tol | Define relative tolerance for damped Newton solver | Real | 1.e-6 | +------------------------------------------+-------------------------------------------------------------+----------+----------+ -| newton_solver.max_iterations | Define max number of iterations for Damped-Newton solver | int | 100 | +| newton_solver.max_iterations | Define max number of iterations for damped Newton solver | int | 100 | +------------------------------------------+-------------------------------------------------------------+----------+----------+ Below is an example for specifying the solids solver model options. -- GitLab From 5dd4eb63f027298a483e70fe2ff6eda9f701dc96 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:28:08 -0500 Subject: [PATCH 11/47] factor out common "dem." prefix --- .../user_guide/inputs/solids_model.rst | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/solids_model.rst b/docs/source_docs/user_guide/inputs/solids_model.rst index bad7706..85ad2dc 100644 --- a/docs/source_docs/user_guide/inputs/solids_model.rst +++ b/docs/source_docs/user_guide/inputs/solids_model.rst @@ -64,43 +64,43 @@ DEM model settings .. |RollingFricModelB| replace:: :math:`\boldsymbol{\tau}_{ij}^{(r)} = -\mu_{r}\hat{r}_{ij} \left| f_{ij}^{(n)} \right| \boldsymbol{u}_{ij}^{\omega}` -Enabling the DEM solver and specifying model options. +Enabling the DEM solver and specifying model options. The following keys must be defined with the prefix ``dem``: +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ | | Description | Type | Default | +===============================+=========================================================================+==========+===========+ -| dem.solve | Specified name(s) of the DEM types or None to disable the DEM solver. | String | None | +| solve | Specified name(s) of the DEM types or None to disable the DEM solver. | String | None | | | The user defined names are used to specify DEM model inputs. | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.friction_coeff.pp | Friction coefficient :: particle to particle collisions [required] | Real | 0 | +| friction_coeff.pp | Friction coefficient :: particle to particle collisions [required] | Real | 0 | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.friction_coeff.pw | Friction coefficient :: particle to wall collisions [required] | Real | 0 | +| friction_coeff.pw | Friction coefficient :: particle to wall collisions [required] | Real | 0 | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.spring_const.pp | Normal spring constant :: particle to particle collisions [required] | Real | 0 | +| spring_const.pp | Normal spring constant :: particle to particle collisions [required] | Real | 0 | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.spring_const.pw | Normal spring constant :: particle to wall collisions [required] | Real | 0 | +| spring_const.pw | Normal spring constant :: particle to wall collisions [required] | Real | 0 | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.spring_tang_fac.pp | Tangential-to-normal spring constant factor :: particle to particle | Real | 0.2857 | +| spring_tang_fac.pp | Tangential-to-normal spring constant factor :: particle to particle | Real | 0.2857 | | | collisions | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.spring_tang_fac.pw | Tangential-to-normal spring constant factor :: particle to wall | Real | 0.2857 | +| spring_tang_fac.pw | Tangential-to-normal spring constant factor :: particle to wall | Real | 0.2857 | | | collisions | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.damping_tang_fac.pp | Factor relating the tangential damping coefficient to the normal | Real | 0.5 | +| damping_tang_fac.pp | Factor relating the tangential damping coefficient to the normal | Real | 0.5 | | | damping coefficient :: particle to particle collisions | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.damping_tang_fac.pw | Factor relating the tangential damping coefficient to the normal | Real | 0.5 | +| damping_tang_fac.pw | Factor relating the tangential damping coefficient to the normal | Real | 0.5 | | | damping coefficient :: particle to wall collisions | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.implicit_drag | Apply fluid-particle drag force by | int | 0 | +| implicit_drag | Apply fluid-particle drag force by | int | 0 | | | :ref:`implicit velocity update`. | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.tan_history | Include tangential history force in the collision model. | Bool | False | +| tan_history | Include tangential history force in the collision model. | Bool | False | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.tan_history.max_contacts | When tangential history is enabled, the maximum number of contacts | Int | 10 | +| tan_history.max_contacts | When tangential history is enabled, the maximum number of contacts | Int | 10 | | | per particle that are tracked at any point | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.rolling_friction | When tangential history is enabled, the rolling friction model | String | None | +| rolling_friction | When tangential history is enabled, the rolling friction model | String | None | | | to be used. :cite:p:`zhou1999,ai2011,wensrich2012,blais2019` | | | | | | | | | | * ``None`` | | | -- GitLab From aa47581b4204a16405c1ced7cfbac137fb216ea9 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:28:25 -0500 Subject: [PATCH 12/47] coeff -> coefficient --- docs/source_docs/user_guide/inputs/solids_model.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/solids_model.rst b/docs/source_docs/user_guide/inputs/solids_model.rst index 85ad2dc..034f19e 100644 --- a/docs/source_docs/user_guide/inputs/solids_model.rst +++ b/docs/source_docs/user_guide/inputs/solids_model.rst @@ -114,7 +114,7 @@ Enabling the DEM solver and specifying model options. The following keys must b | | |RollingFricModelB| | | | | | | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.rolling_friction_coeff | Rolling friction coefficient when using a rolling friction model | Real | 0 | +| rolling_friction_coefficient | Rolling friction coefficient when using a rolling friction model | Real | 0 | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -- GitLab From 39459ae1455e7c4a27cc1e06df3ebfaffecc4719 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:28:34 -0500 Subject: [PATCH 13/47] remove punctuation --- docs/source_docs/user_guide/inputs/species_defs.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/species_defs.rst b/docs/source_docs/user_guide/inputs/species_defs.rst index c0b7619..644147e 100644 --- a/docs/source_docs/user_guide/inputs/species_defs.rst +++ b/docs/source_docs/user_guide/inputs/species_defs.rst @@ -122,9 +122,9 @@ The following inputs are for each species defined using the prefix ``species.[sp | | | | | | | A value is required for ``Sutherland`` species viscosity model. | | | +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ -| viscosity.molecular.Reid.A, | Reid model constants for species. | Real | 0 | -| viscosity.molecular.Reid.B, | | | | -| viscosity.molecular.Reid.C, and | Values are required for ``Reid`` species viscosity model. | | | +| viscosity.molecular.Reid.A | Reid model constants for species. | Real | 0 | +| viscosity.molecular.Reid.B | | | | +| viscosity.molecular.Reid.C and | Values are required for ``Reid`` species viscosity model. | | | | viscosity.molecular.Reid.D | | | | +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ -- GitLab From 01bc02debce0ad22964bc4dcb43485787ff855f6 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:25:07 -0500 Subject: [PATCH 14/47] consistent formatting: prefix ``name`` --- docs/source_docs/user_guide/inputs/advanced.rst | 6 +++--- .../user_guide/inputs/boundary_conditions.rst | 4 ++-- .../user_guide/inputs/chemical_reactions.rst | 4 ++-- docs/source_docs/user_guide/inputs/domain.rst | 2 +- docs/source_docs/user_guide/inputs/fluid_model.rst | 4 ++-- docs/source_docs/user_guide/inputs/geometry.rst | 10 +++++----- .../user_guide/inputs/initial_conditions.rst | 10 +++++----- .../user_guide/inputs/mesh_and_gridding.rst | 10 +++++----- .../user_guide/inputs/model_options.rst | 14 +++++++------- docs/source_docs/user_guide/inputs/mpmd.rst | 2 +- .../user_guide/inputs/multigrid-solvers.rst | 10 +++++----- .../user_guide/inputs/output/ascent.rst | 5 +++-- .../user_guide/inputs/output/checkpointing.rst | 2 +- .../user_guide/inputs/output/monitors.rst | 2 +- .../user_guide/inputs/output/plotfiles.rst | 10 +++++----- .../user_guide/inputs/porous_media_defs.rst | 2 +- .../source_docs/user_guide/inputs/solids_model.rst | 2 +- .../source_docs/user_guide/inputs/species_defs.rst | 4 ++-- .../user_guide/inputs/time-stepping.rst | 4 ++-- 19 files changed, 54 insertions(+), 53 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/advanced.rst b/docs/source_docs/user_guide/inputs/advanced.rst index a1d2f7f..4431f83 100644 --- a/docs/source_docs/user_guide/inputs/advanced.rst +++ b/docs/source_docs/user_guide/inputs/advanced.rst @@ -35,7 +35,7 @@ The following inputs must be preceded by "amrex." GPU memory ---------- -The following inputs must be preceded by "amrex." +The following inputs must be preceded by the prefix ``amrex``: +----------------------------+-----------------------------------------------------------------------+-------------+---------------+ | | Description | Type | Default | @@ -58,7 +58,7 @@ the ``particles.max_grid_size`` (in each direction) have no meaning. Therefore t sizes should be set for particle load balancing. It may also be necessary to set the blocking factors to 1. -The following inputs must be preceded by ``mfix`` and determine how we load balance: +The following inputs must be preceded by the prefix ``mfix`` and control load balancing: +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ | | Description | Type | Default | @@ -88,7 +88,7 @@ To allow a user to verify the breakdown of fluid grids created before running a minimal memory to print the grid coverage report and exits immediately after that. -The following inputs are defined using the ``particles`` prefix. +The following inputs are defined using the prefix ``particles``: +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/boundary_conditions.rst b/docs/source_docs/user_guide/inputs/boundary_conditions.rst index bf097d4..d3a673f 100644 --- a/docs/source_docs/user_guide/inputs/boundary_conditions.rst +++ b/docs/source_docs/user_guide/inputs/boundary_conditions.rst @@ -7,7 +7,7 @@ Boundary Conditions General boundary conditions --------------------------- -The following inputs are defined using the ``bc`` prefix. +The following inputs are defined using the prefix ``bc``: +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -36,7 +36,7 @@ Fluid settings ~~~~~~~~~~~~~~ For each boundary condition region, the fluid inputs are defined -using the ``bc.[region].[fluid]`` prefix. +using the prefix ``bc.[region].[fluid]``: +------------------------+------------------------------------------------------------------------+-------------+-----------+ diff --git a/docs/source_docs/user_guide/inputs/chemical_reactions.rst b/docs/source_docs/user_guide/inputs/chemical_reactions.rst index b72dd3d..64fff8e 100644 --- a/docs/source_docs/user_guide/inputs/chemical_reactions.rst +++ b/docs/source_docs/user_guide/inputs/chemical_reactions.rst @@ -1,7 +1,7 @@ Chemical Reactions ================== -The following inputs are defined using the ``chemistry`` prefix. +The following inputs are defined using the prefix ``chemistry``: +--------------------------+---------------------------------------------------------+----------+----------------+ | | Description | Type | Default | @@ -68,7 +68,7 @@ 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: + prefix ``chemistry.integrator``: +-----------------------+---------------------------------------------------------------------+--------+-----------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/domain.rst b/docs/source_docs/user_guide/inputs/domain.rst index fe18fc1..b62ac51 100644 --- a/docs/source_docs/user_guide/inputs/domain.rst +++ b/docs/source_docs/user_guide/inputs/domain.rst @@ -6,7 +6,7 @@ Defining the domain All simulations, whether using an embedded boundary (EB) or not, are specified on a simple cuboid domain. The low and high corners of the cuboid are defined by the ``prob_lo`` and ``prob_hi`` inputs. -The following inputs are defined using the ``geometry`` prefix. +The following inputs are defined using the prefix ``geometry``: .. _InputsTable_domain: diff --git a/docs/source_docs/user_guide/inputs/fluid_model.rst b/docs/source_docs/user_guide/inputs/fluid_model.rst index 1aef1ba..edc8259 100644 --- a/docs/source_docs/user_guide/inputs/fluid_model.rst +++ b/docs/source_docs/user_guide/inputs/fluid_model.rst @@ -3,7 +3,7 @@ Fluid model =========== -The following inputs are defined using the ``fluid`` prefix. +The following inputs are defined using the prefix ``fluid``: +--------------------------------------------+-------------------------------------------------------------+--------+----------+ | | Description | Type | Default | @@ -412,7 +412,7 @@ thermodynamic pressure for the system. bc.outlet.fluid0.pressure = 101325. -The following inputs are defined using the ``fluid`` prefix and control the convergence criteria +The following inputs are defined using the prefix ``fluid`` and control the convergence criteria of the damped Newton solver used to compute temperature from enthalpy and specific heat. +------------------------------------------+----------------------------------------------------------+--------+----------+ diff --git a/docs/source_docs/user_guide/inputs/geometry.rst b/docs/source_docs/user_guide/inputs/geometry.rst index c1aa586..d50d4d0 100644 --- a/docs/source_docs/user_guide/inputs/geometry.rst +++ b/docs/source_docs/user_guide/inputs/geometry.rst @@ -3,7 +3,7 @@ Specifying a geometry ===================== -The following inputs are defined using the ``mfix`` prefix. +The following inputs are defined using the prefix ``mfix``: +------------------------+-------------------------------------------------------------------------------+----------+---------------------+ | | Description | Type | Default | @@ -50,7 +50,7 @@ select the option to use a user-defined geometry constructed from native AMReX i ``box`` geometry ^^^^^^^^^^^^^^^^ -The following inputs are defined using the ``box`` prefix. +The following inputs are defined using the prefix ``box``: +------------------------+-------------------------------------------------------------------+----------+---------------------+ | | Description | Type | Default | @@ -147,7 +147,7 @@ the EB ``box`` are *covered* and thereby excluded from run-time calculations. ``cylinder`` geometry ^^^^^^^^^^^^^^^^^^^^^ -The following inputs are defined using the ``cylinder`` prefix. +The following inputs are defined using the prefix ``cylinder``: +------------------------+-------------------------------------------------------------------+----------+---------------------+ | | Description | Type | Default | @@ -339,7 +339,7 @@ Constructive solid geometry (CSG) * This option requires that the executable be built with CSG support. See the build documentation for for details. -The following inputs are defined using the ``csg`` prefix. +The following inputs are defined using the prefix ``csg``: +------------------------+-------------------------------------------------------------------+----------+---------------------+ | | Description | Type | Default | @@ -365,7 +365,7 @@ Standard triangle language (STL) * A standard triangle language (STL) geometry can be created using numerous CAD programs. -The following inputs are defined using the ``stl`` prefix. +The following inputs are defined using the prefix ``stl``: +------------------------+-------------------------------------------------------------------+----------+---------------------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/initial_conditions.rst b/docs/source_docs/user_guide/inputs/initial_conditions.rst index 12195a9..2070877 100644 --- a/docs/source_docs/user_guide/inputs/initial_conditions.rst +++ b/docs/source_docs/user_guide/inputs/initial_conditions.rst @@ -1,7 +1,7 @@ Initial Conditions ================== -The following inputs are defined using the ``ic`` prefix. +The following inputs are defined using the prefix ``ic``: +-----------------------+------------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -25,7 +25,7 @@ Fluid settings ~~~~~~~~~~~~~~ For each initial condition region, the fluid inputs are defined -using the ``ic.[region].[fluid]`` compound prefix. +using the compound prefix ``ic.[region].[fluid]``: +------------------------+------------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -48,7 +48,7 @@ Solids settings ~~~~~~~~~~~~~~~ For each initial condition region, general solids inputs are defined -using the ``ic.[region]`` compound prefix. +using the compound prefix ``ic.[region]``: +----------------------+------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -72,8 +72,8 @@ using the ``ic.[region]`` compound prefix. +----------------------+------------------------------------------------------------------+-------------+-----------+ For each initial condition region, the solid inputs are defined -using the ``ic.[region].[solid]`` compound prefix. -Note that diameter distributions must define a weighting type, +using the compound prefix ``ic.[region].[solid]``: +Note that diameter distributions must define a weighting type, please refer to :ref:`ReferenceParticleDistributions `. +---------------------+-----------------------------------------------------------------------+-------------+-----------+ 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 82fbc73..ecc8127 100644 --- a/docs/source_docs/user_guide/inputs/mesh_and_gridding.rst +++ b/docs/source_docs/user_guide/inputs/mesh_and_gridding.rst @@ -8,7 +8,7 @@ Mesh .. rubric:: Level-0 mesh -The following inputs are defined using the ``amr`` prefix. +The following inputs are defined using the prefix ``amr``: .. _InputsTable_mesh: @@ -76,7 +76,7 @@ The result is a uniform mesh spacing of :math:`0.125` *m* in all three direction .. rubric:: Mesh refinement -The following inputs are defined using the ``amr`` prefix. These inputs control the automatic +The following inputs are defined using the prefix ``amr``. These inputs control the automatic mesh refinement algorithm and are only applicable when ``amr.max_level > 0``. +----------------------+-----------------------------------------------------------------------+-------------+-----------+ @@ -103,7 +103,7 @@ for details on the adaptive mesh refinement algorithms. Grids ----- -The following inputs are defined using the ``amr`` prefix. +The following inputs are defined using the prefix ``amr``: +----------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -139,7 +139,7 @@ the grids will be sufficiently coarsenable for good multigrid performance; there Tiles ----- -The following inputs are defined using the ``fabarray`` prefix. +The following inputs are defined using the prefix ``fabarray``: +----------------------+-----------------------------------------------------------------------+----------+-------------+ | | Description | Type | Default | @@ -147,7 +147,7 @@ The following inputs are defined using the ``fabarray`` prefix. | mfiter_tile_size | Maximum number of cells in each direction for (logical) tiles | IntVect | 1024000,8,8 | +----------------------+-----------------------------------------------------------------------+----------+-------------+ -The following inputs are defined using the ``particles`` prefix. +The following inputs are defined using the prefix ``particles``: +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/model_options.rst b/docs/source_docs/user_guide/inputs/model_options.rst index 6eaf504..3072d64 100644 --- a/docs/source_docs/user_guide/inputs/model_options.rst +++ b/docs/source_docs/user_guide/inputs/model_options.rst @@ -2,7 +2,7 @@ Model options ============= -The following inputs are defined using the ``mfix`` prefix. +The following inputs are defined using the prefix ``mfix``: +------------------------+----------------------------------------------------------------------------+----------+---------------------+ | | Description | Type | Default | @@ -42,7 +42,7 @@ The following inputs are defined using the ``mfix`` prefix. Fluid discretization -------------------- -The following inputs are defined using the ``mfix`` prefix. +The following inputs are defined using the prefix ``mfix``: +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | Key | Description | Type | Default | @@ -97,7 +97,7 @@ Additional available constraints Additional constraints may be imposed on problems which are under-determined such as particle settling in a fully periodic domain. Currently, only particle constraints are supported. -The following inputs are defined using the ``particles`` prefix. +The following inputs are defined using the prefix ``particles``: +---------------------+---------------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -138,7 +138,7 @@ for the system is zero. Deposition scheme ----------------- -The following inputs are defined using the ``mfix`` prefix. +The following inputs are defined using the prefix ``mfix``: +----------------------------+--------------------------------------------------------------------+-----------+---------------+ | | Description | Type | Default | @@ -257,7 +257,7 @@ the *Y*-direction weights. The right image shows the resulting composite weights Deposition redistribution ------------------------- -The following inputs are defined using the ``mfix`` prefix. +The following inputs are defined using the prefix ``mfix``: +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | Key | Description | Type | Default | @@ -291,7 +291,7 @@ The following inputs are defined using the ``mfix`` prefix. Fluid-particle drag ------------------- -The following input is defined using the ``mfix.drag`` prefix. +The following input is defined using the prefix ``mfix.drag``: .. |VirtualMass_Eq| replace:: :math:`\mathbf{F}_p^{vm} = -C_p^{vm}\rho_f \left( \frac{D\mathbf{u}_f}{Dt} - \frac{d\mathbf{u}_p}{dt}\right)\mathcal{V}_p` @@ -349,7 +349,7 @@ The following input is defined using the ``mfix.drag`` prefix. Heat transfer coefficients -------------------------- -The following input is defined using the ``mfix.convection`` prefix. +The following input is defined using the prefix ``mfix.convection``: +-------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/mpmd.rst b/docs/source_docs/user_guide/inputs/mpmd.rst index 8954654..dd845ac 100644 --- a/docs/source_docs/user_guide/inputs/mpmd.rst +++ b/docs/source_docs/user_guide/inputs/mpmd.rst @@ -12,7 +12,7 @@ feature, the executable has to be built with ``-DMFIX_MPMD = yes``. * Cannot be used to send and receive particle data. -The following inputs are defined using the ``mfix`` prefix and control frequency and the data sent to the other program. +The following inputs are defined using the prefix ``mfix`` and control frequency and the data sent to the other program. +----------------------+-----------------------------------------------------------------------+-------------+-----------+ | | 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 4eea804..bdf4096 100644 --- a/docs/source_docs/user_guide/inputs/multigrid-solvers.rst +++ b/docs/source_docs/user_guide/inputs/multigrid-solvers.rst @@ -6,11 +6,11 @@ Multigrid solvers Nodal projection ---------------- -The following inputs are defined using the ``nodal_proj`` prefix. +The following inputs are defined using the prefix ``nodal_proj``: +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | -+-------------------------+-----------------------------------------------------------------------+-------------+--------------+ ++=========================+=======================================================================+=============+==============+ | verbose | Verbosity of multigrid solver in nodal projection | Int | 0 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bottom_verbose | Verbosity of BiCGStab solver in nodal projection | Int | 0 | @@ -43,7 +43,7 @@ The following inputs are defined using the ``nodal_proj`` prefix. MAC projection -------------- -The following inputs are defined using the ``mac_proj`` prefix. +The following inputs are defined using the prefix ``mac_proj``: +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | @@ -81,7 +81,7 @@ The following inputs are defined using the ``mac_proj`` prefix. Diffusion --------- -The following inputs are defined using the ``diffusion`` prefix. +The following inputs are defined using the prefix ``diffusion``: +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | @@ -113,7 +113,7 @@ Hypre Settings `hypre` settings are specified using the following inputs which are read directly by AMReX when `hypre` is used as the bottom solve for the MAC and/or nodal projections. By default, these inputs are defined using the -``hypre`` prefix, however different settings for the nodal and MAC projections can be used by specifying +prefix ``hypre``, however different settings for the nodal and MAC projections can be used by specifying a ``hpyre_namespace`` for each solver. .. warning:: diff --git a/docs/source_docs/user_guide/inputs/output/ascent.rst b/docs/source_docs/user_guide/inputs/output/ascent.rst index a2272c9..d30ae2a 100644 --- a/docs/source_docs/user_guide/inputs/output/ascent.rst +++ b/docs/source_docs/user_guide/inputs/output/ascent.rst @@ -1,7 +1,7 @@ Ascent ------ -The following inputs must be preceded by "mfix." and control frequency and naming of plotfile generation as well +The following inputs must be preceded by the prefix ``mfix`` and control frequency and naming of plotfile generation as well as whether the EB geometry or level set should be written out, and if the particles should be written out in Ascii format (for debugging). @@ -17,7 +17,8 @@ format (for debugging). `Ascent `_ has been integrated into MFIX-Exa for *in situ* visualization. -For codes that have been built with Ascent support, the following inputs must be preceded by "ascent." +For codes that have been built with Ascent support, the following input must be preceded by the prefix +``ascent``, and specifies the ascent actions for fluid and/or particles. The frequency which these are called is controlled by `ascent_int` or `ascent_per_approx`, see above. Note that if an ascent pipeline is being included in a GPU build/run, then you must enable managed memory, diff --git a/docs/source_docs/user_guide/inputs/output/checkpointing.rst b/docs/source_docs/user_guide/inputs/output/checkpointing.rst index 8e4c718..2f363ca 100644 --- a/docs/source_docs/user_guide/inputs/output/checkpointing.rst +++ b/docs/source_docs/user_guide/inputs/output/checkpointing.rst @@ -3,7 +3,7 @@ Checkpointing ============= -The following inputs must be preceded by "mfix." and control checkpoint/restart. +The following inputs must be preceded by the prefix ``mfix`` and control checkpoint/restart: +-------------------------+-----------------------------------------------------------------------+-------------+------------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/output/monitors.rst b/docs/source_docs/user_guide/inputs/output/monitors.rst index 5ff9dd7..66ee112 100644 --- a/docs/source_docs/user_guide/inputs/output/monitors.rst +++ b/docs/source_docs/user_guide/inputs/output/monitors.rst @@ -644,7 +644,7 @@ Flow rates For Lagrangian monitors of type FlowRate, the flow plane must be specified in the inputs and it must be defined by one of the regions defined in the regions inputs. The following input for a monitor [monitor] of type FlowRate can be -used, preceded by the "mfix.monitors" prefix. +used, preceded by the prefix ``mfix.monitors``: +------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/output/plotfiles.rst b/docs/source_docs/user_guide/inputs/output/plotfiles.rst index 1f524b1..175ba49 100644 --- a/docs/source_docs/user_guide/inputs/output/plotfiles.rst +++ b/docs/source_docs/user_guide/inputs/output/plotfiles.rst @@ -3,7 +3,7 @@ Plotfiles and Other Output ========================== -The following inputs must be preceded by "mfix." and control frequency and naming of plotfile generation as well +The following inputs must be preceded by the prefix ``mfix`` and control frequency and naming of plotfile generation as well as whether the EB geometry or level set should be written out, and if the particles should be written out in Ascii format (for debugging). @@ -86,7 +86,7 @@ The following inputs must be preceded by "mfix." and control what variables will +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -The following inputs must be preceded by "mfix." and control whether the EB geometry or level set should be written out. +The following inputs must be preceded by the prefix ``mfix`` and control whether the EB geometry or level set should be written out: +----------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -103,7 +103,8 @@ The following inputs must be preceded by "mfix." and control whether the EB geom `Ascent `_ has been integrated into MFIX-Exa for *in situ* visualization. -For codes that have been built with Ascent support, the following inputs must be preceded by "ascent." +For codes that have been built with Ascent support, the following input must be preceded by the prefix +``ascent`` and specifies the ascent actions for fluid and/or particles. The frequency which these are called is controlled by `ascent_int` or `ascent_per_approx`, see above. Note that if an ascent pipeline is being included in a GPU build/run, then you must enable managed memory, @@ -112,13 +113,12 @@ i.e., set `amrex.the_arena_is_managed = true`. +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +=====================+=======================================================================+=============+===========+ -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ | actions | yaml file of the ascent actions (ex. ascent_actions.yaml). If no file | String | | | | name is provided, then calls to Ascent are skipped. | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -The following inputs must be preceded by "mfix.solids." and allow to write additional plotfiles which +The following inputs must be preceded by the prefix ``mfix.solids`` and allow to write additional plotfiles which contain only solids variables in specific regions at fixed timesteps or approximated simulation times. All these parameters are user-defined. diff --git a/docs/source_docs/user_guide/inputs/porous_media_defs.rst b/docs/source_docs/user_guide/inputs/porous_media_defs.rst index 47d9e46..6d4b011 100644 --- a/docs/source_docs/user_guide/inputs/porous_media_defs.rst +++ b/docs/source_docs/user_guide/inputs/porous_media_defs.rst @@ -13,7 +13,7 @@ source term, :math:`\boldsymbol{S}_{pm}`, to the fluid momentum equation. :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. +The following inputs are defined using the prefix ``pm``: +--------------------------+------------------------------------------------------------------------------+----------+-----------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/solids_model.rst b/docs/source_docs/user_guide/inputs/solids_model.rst index 1fc5741..9ab66f7 100644 --- a/docs/source_docs/user_guide/inputs/solids_model.rst +++ b/docs/source_docs/user_guide/inputs/solids_model.rst @@ -5,7 +5,7 @@ Solids settings --------------- Enabling the SOLIDS solver and specifying options common to both DEM and PIC -models. The following inputs must be preceded by the "solids." root +models. The following inputs are defined with the prefix ``solids``: +------------------------------------------+-------------------------------------------------------------+----------+----------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/species_defs.rst b/docs/source_docs/user_guide/inputs/species_defs.rst index ad83fcf..c0b7619 100644 --- a/docs/source_docs/user_guide/inputs/species_defs.rst +++ b/docs/source_docs/user_guide/inputs/species_defs.rst @@ -3,7 +3,7 @@ Species definitions =================== -The following inputs are defined using the ``species`` prefix. +The following inputs are defined using the prefix ``species``: +--------------------------+------------------------------------------------------------------------+----------+-----------+ | | Description | Type | Default | @@ -58,7 +58,7 @@ The following inputs are defined using the ``species`` prefix. +--------------------------+------------------------------------------------------------------------+----------+-----------+ -The following inputs are for each species defined using the ``species.[species name]`` prefix. +The following inputs are for each species defined using the prefix ``species.[species name]``: +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/time-stepping.rst b/docs/source_docs/user_guide/inputs/time-stepping.rst index 97dc7ea..e2cff95 100644 --- a/docs/source_docs/user_guide/inputs/time-stepping.rst +++ b/docs/source_docs/user_guide/inputs/time-stepping.rst @@ -90,7 +90,7 @@ sub-time step is computed by dividing ``dt`` by ``nsubsteps``. } -The following inputs are defined using the ``mfix`` prefix. +The following inputs are defined using the prefix ``mfix``: +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | Key | Description | Type | Default | @@ -126,7 +126,7 @@ In the case of unsteady flow, the simulation will stop when either the number of reaches ``max_step`` or time reaches ``stop_time``. -The following inputs are defined using the ``mfix`` prefix and are only relevant if running a steady state simulation. +The following inputs are defined using the prefix ``mfix`` and are only relevant if running a steady state simulation. +-----------------------+-----------------------------------------------------------------------+-------------+------------+ | Key | Description | Type | Default | -- GitLab From 508fef741901519aa5335872b2ff9c6ef1f4c4ee Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:25:51 -0500 Subject: [PATCH 15/47] default value --- docs/source_docs/user_guide/inputs/advanced.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/advanced.rst b/docs/source_docs/user_guide/inputs/advanced.rst index 4431f83..b0676aa 100644 --- a/docs/source_docs/user_guide/inputs/advanced.rst +++ b/docs/source_docs/user_guide/inputs/advanced.rst @@ -42,8 +42,8 @@ The following inputs must be preceded by the prefix ``amrex``: +============================+=======================================================================+=============+===============+ | the_arena_is_managed | Use managed memory for the main arena. | Int | 0 | +----------------------------+-----------------------------------------------------------------------+-------------+---------------+ -| the_arena_init_size | Main memory arena's initial size in bytes. | Int | 3/4 of system | -| | | | device memory | +| the_arena_init_size | Initial size of main memory arena (bytes). If not specified, use | Int | Unspecified | +| | 3/4 of system device memory. | | | +----------------------------+-----------------------------------------------------------------------+-------------+---------------+ | abort_on_out_of_gpu_memory | Abort if free device memory is less than the amount an arena is | Int | 0 | | | asked to allocate. | | | -- GitLab From 85b527340138a8ade1a1111546165c473693382c Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:25:57 -0500 Subject: [PATCH 16/47] alignment --- docs/source_docs/user_guide/inputs/advanced.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/advanced.rst b/docs/source_docs/user_guide/inputs/advanced.rst index b0676aa..ffe3b0c 100644 --- a/docs/source_docs/user_guide/inputs/advanced.rst +++ b/docs/source_docs/user_guide/inputs/advanced.rst @@ -63,7 +63,7 @@ The following inputs must be preceded by the prefix ``mfix`` and control load ba +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ | | Description | Type | Default | +==================================+=======================================================================+=============+===================+ -| regrid_int | How often to regrid (in number of steps at level 0) | int | 0 | +| regrid_int | How often to regrid (in number of steps at level 0) | int | 0 | | | if regrid_int <= 0 then no regridding will occur | | | +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ | load_balance | * ``SingleGrid`` fluid and particles are co-located on the same grids | string | SingleGrid | -- GitLab From 66581090f50cd998574032862c57c715dd055c32 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:26:16 -0500 Subject: [PATCH 17/47] grammar --- docs/source_docs/user_guide/inputs/chemical_reactions.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/chemical_reactions.rst b/docs/source_docs/user_guide/inputs/chemical_reactions.rst index 64fff8e..76077f1 100644 --- a/docs/source_docs/user_guide/inputs/chemical_reactions.rst +++ b/docs/source_docs/user_guide/inputs/chemical_reactions.rst @@ -47,7 +47,7 @@ The following inputs are defined using the prefix ``chemistry``: 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 +chemical reactions. The ``StiffSolver`` class of integrators is inspired by the class of integrators in AMReX-Astro/Microphysics (https://github.com/AMReX-Astro/Microphysics) -- GitLab From 4a9bdaf3723e43e47449be26ec87659f0ca3bae9 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:26:55 -0500 Subject: [PATCH 18/47] grammar --- docs/source_docs/user_guide/inputs/fluid_model.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/fluid_model.rst b/docs/source_docs/user_guide/inputs/fluid_model.rst index edc8259..6c0a341 100644 --- a/docs/source_docs/user_guide/inputs/fluid_model.rst +++ b/docs/source_docs/user_guide/inputs/fluid_model.rst @@ -15,7 +15,7 @@ The following inputs are defined using the prefix ``fluid``: +--------------------------------------------+-------------------------------------------------------------+--------+----------+ -The root prefix for the following inputs use the name defined using the ``fluid.solve`` keyword. For example, if the fluid solver +The root prefix for the following inputs is the name defined using the ``fluid.solve`` keyword. For example, if the fluid solver 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. -- GitLab From 817f14c21cee2020f57d9dd09a647ce53b204546 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:27:02 -0500 Subject: [PATCH 19/47] remove punctuation --- docs/source_docs/user_guide/inputs/fluid_model.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/fluid_model.rst b/docs/source_docs/user_guide/inputs/fluid_model.rst index 6c0a341..5d7e4ca 100644 --- a/docs/source_docs/user_guide/inputs/fluid_model.rst +++ b/docs/source_docs/user_guide/inputs/fluid_model.rst @@ -70,9 +70,9 @@ a single fluid; therefore, it is common to name the fluid ``fluid``. This is ill | | | | | | | A value is required for ``Sutherland`` viscosity model. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ -| viscosity.molecular.Reid.A, | Reid model constants | Real | 0 | -| viscosity.molecular.Reid.B, | | | | -| viscosity.molecular.Reid.C, and | Values are required for ``Reid`` viscosity model. | | | +| viscosity.molecular.Reid.A | Reid model constants | Real | 0 | +| viscosity.molecular.Reid.B | | | | +| viscosity.molecular.Reid.C | Values are required for ``Reid`` viscosity model. | | | | viscosity.molecular.Reid.D | | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ | viscosity.eddy | Specify eddy viscosity model. | String | None | -- GitLab From 8ab97b2344e69f131b5f0a9a876771350febcaa5 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:27:12 -0500 Subject: [PATCH 20/47] remove empty row --- docs/source_docs/user_guide/inputs/multigrid-solvers.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/multigrid-solvers.rst b/docs/source_docs/user_guide/inputs/multigrid-solvers.rst index bdf4096..02f8d3d 100644 --- a/docs/source_docs/user_guide/inputs/multigrid-solvers.rst +++ b/docs/source_docs/user_guide/inputs/multigrid-solvers.rst @@ -127,7 +127,7 @@ and `GMRES` for the linear solver. +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ ++===================================+=======================================================================+=============+==============+ | hypre_preconditioner | Type of preconditioner | string | none | | | | | | | | Options are BoomerAMG or euclid | | | -- GitLab From 0da518a98c7dd9619c4bb2f1146f313d13c1a224 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:27:21 -0500 Subject: [PATCH 21/47] remove empty row --- docs/source_docs/user_guide/inputs/multigrid-solvers.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/multigrid-solvers.rst b/docs/source_docs/user_guide/inputs/multigrid-solvers.rst index 02f8d3d..71c20be 100644 --- a/docs/source_docs/user_guide/inputs/multigrid-solvers.rst +++ b/docs/source_docs/user_guide/inputs/multigrid-solvers.rst @@ -149,7 +149,7 @@ The following inputs are valid when using ``BoomerAMG`` as a preconditioner or s +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ ++===================================+=======================================================================+=============+==============+ | bamg_verbose | Set BoomerAMG verbosity | int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_logging | See HYPRE_BoomerAMGSetLogging | int | 0 | -- GitLab From 4a2505f1c17f9599bed0762b79ef63af067a03dd Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:27:40 -0500 Subject: [PATCH 22/47] remove empty rows --- docs/source_docs/user_guide/inputs/multigrid-solvers.rst | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/multigrid-solvers.rst b/docs/source_docs/user_guide/inputs/multigrid-solvers.rst index 71c20be..6330643 100644 --- a/docs/source_docs/user_guide/inputs/multigrid-solvers.rst +++ b/docs/source_docs/user_guide/inputs/multigrid-solvers.rst @@ -164,34 +164,28 @@ The following inputs are valid when using ``BoomerAMG`` as a preconditioner or s +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_relax_order | See HYPRE_BoomerAMGSetRelaxOrder | int | 1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_relax_type | See HYPRE_BoomerAMGSetRelaxType | int | 6 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_down_relax_type | See HYPRE_BoomerAMGSetCycleRelaxType | int | 11 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_up_relax_type | See HYPRE_BoomerAMGSetCycleRelaxType | int | 11 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_coarse_relax_type | See HYPRE_BoomerAMGSetCycleRelaxType | int | 11 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_num_sweeps | See HYPRE_BoomerAMGSetNumSweeps | int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_num_down_sweeps | See HYPRE_BoomerAMGSetCycleNumSweeps | int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_num_up_sweeps | See HYPRE_BoomerAMGSetCycleNumSweeps | int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_num_coarse_sweeps | See HYPRE_BoomerAMGSetCycleNumSweeps | int | 1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_max_levels | See HYPRE_BoomerAMGSetMaxLevels | int | 20 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_strong_threshold | See HYPRE_BoomerAMGSetStrongThreshold | Real | 0.57 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_interp_type | See HYPRE_BoomerAMGSetInterpType | int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_variant | See HYPRE_BoomerAMGSetVariant | int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_keep_transpose | See HYPRE_BoomerAMGSetKeepTranspose | int | 0 | @@ -221,7 +215,7 @@ The following inputs are valid when using ``BoomerAMG`` as a preconditioner or s +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ ++===================================+=======================================================================+=============+==============+ | adjust_singular_matrix | Should be true if the problem to be solved has singular matrix | Bool | false | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | overwrite_existing_matrix_files | Over-write existing matrix files | Bool | false | -- GitLab From f48e87a5c0da8b2f9f9bc5df4537db7e903f6a78 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:27:53 -0500 Subject: [PATCH 23/47] spelling --- docs/source_docs/user_guide/inputs/solids_model.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/solids_model.rst b/docs/source_docs/user_guide/inputs/solids_model.rst index 9ab66f7..bad7706 100644 --- a/docs/source_docs/user_guide/inputs/solids_model.rst +++ b/docs/source_docs/user_guide/inputs/solids_model.rst @@ -36,11 +36,11 @@ models. The following inputs are defined with the prefix ``solids``: | | be a subset of the species.solve | | | | | arguments]. | | | +------------------------------------------+-------------------------------------------------------------+----------+----------+ -| newton_solver.absolute_tol | Define absolute tolerance for Damped-Newton solver | Real | 1.e-6 | +| newton_solver.absolute_tol | Define absolute tolerance for damped Newton solver | Real | 1.e-6 | +------------------------------------------+-------------------------------------------------------------+----------+----------+ -| newton_solver.relative_tol | Define relative tolerance for Damped-Newton solver | Real | 1.e-6 | +| newton_solver.relative_tol | Define relative tolerance for damped Newton solver | Real | 1.e-6 | +------------------------------------------+-------------------------------------------------------------+----------+----------+ -| newton_solver.max_iterations | Define max number of iterations for Damped-Newton solver | int | 100 | +| newton_solver.max_iterations | Define max number of iterations for damped Newton solver | int | 100 | +------------------------------------------+-------------------------------------------------------------+----------+----------+ Below is an example for specifying the solids solver model options. -- GitLab From b990b80926f87b5761319f181c0eb3a9d9f1ba15 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:28:08 -0500 Subject: [PATCH 24/47] factor out common "dem." prefix --- .../user_guide/inputs/solids_model.rst | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/solids_model.rst b/docs/source_docs/user_guide/inputs/solids_model.rst index bad7706..85ad2dc 100644 --- a/docs/source_docs/user_guide/inputs/solids_model.rst +++ b/docs/source_docs/user_guide/inputs/solids_model.rst @@ -64,43 +64,43 @@ DEM model settings .. |RollingFricModelB| replace:: :math:`\boldsymbol{\tau}_{ij}^{(r)} = -\mu_{r}\hat{r}_{ij} \left| f_{ij}^{(n)} \right| \boldsymbol{u}_{ij}^{\omega}` -Enabling the DEM solver and specifying model options. +Enabling the DEM solver and specifying model options. The following keys must be defined with the prefix ``dem``: +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ | | Description | Type | Default | +===============================+=========================================================================+==========+===========+ -| dem.solve | Specified name(s) of the DEM types or None to disable the DEM solver. | String | None | +| solve | Specified name(s) of the DEM types or None to disable the DEM solver. | String | None | | | The user defined names are used to specify DEM model inputs. | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.friction_coeff.pp | Friction coefficient :: particle to particle collisions [required] | Real | 0 | +| friction_coeff.pp | Friction coefficient :: particle to particle collisions [required] | Real | 0 | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.friction_coeff.pw | Friction coefficient :: particle to wall collisions [required] | Real | 0 | +| friction_coeff.pw | Friction coefficient :: particle to wall collisions [required] | Real | 0 | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.spring_const.pp | Normal spring constant :: particle to particle collisions [required] | Real | 0 | +| spring_const.pp | Normal spring constant :: particle to particle collisions [required] | Real | 0 | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.spring_const.pw | Normal spring constant :: particle to wall collisions [required] | Real | 0 | +| spring_const.pw | Normal spring constant :: particle to wall collisions [required] | Real | 0 | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.spring_tang_fac.pp | Tangential-to-normal spring constant factor :: particle to particle | Real | 0.2857 | +| spring_tang_fac.pp | Tangential-to-normal spring constant factor :: particle to particle | Real | 0.2857 | | | collisions | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.spring_tang_fac.pw | Tangential-to-normal spring constant factor :: particle to wall | Real | 0.2857 | +| spring_tang_fac.pw | Tangential-to-normal spring constant factor :: particle to wall | Real | 0.2857 | | | collisions | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.damping_tang_fac.pp | Factor relating the tangential damping coefficient to the normal | Real | 0.5 | +| damping_tang_fac.pp | Factor relating the tangential damping coefficient to the normal | Real | 0.5 | | | damping coefficient :: particle to particle collisions | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.damping_tang_fac.pw | Factor relating the tangential damping coefficient to the normal | Real | 0.5 | +| damping_tang_fac.pw | Factor relating the tangential damping coefficient to the normal | Real | 0.5 | | | damping coefficient :: particle to wall collisions | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.implicit_drag | Apply fluid-particle drag force by | int | 0 | +| implicit_drag | Apply fluid-particle drag force by | int | 0 | | | :ref:`implicit velocity update`. | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.tan_history | Include tangential history force in the collision model. | Bool | False | +| tan_history | Include tangential history force in the collision model. | Bool | False | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.tan_history.max_contacts | When tangential history is enabled, the maximum number of contacts | Int | 10 | +| tan_history.max_contacts | When tangential history is enabled, the maximum number of contacts | Int | 10 | | | per particle that are tracked at any point | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.rolling_friction | When tangential history is enabled, the rolling friction model | String | None | +| rolling_friction | When tangential history is enabled, the rolling friction model | String | None | | | to be used. :cite:p:`zhou1999,ai2011,wensrich2012,blais2019` | | | | | | | | | | * ``None`` | | | -- GitLab From 18e2d8dc8df9a78e953aff6aef863369a5403e90 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:28:25 -0500 Subject: [PATCH 25/47] coeff -> coefficient --- docs/source_docs/user_guide/inputs/solids_model.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/solids_model.rst b/docs/source_docs/user_guide/inputs/solids_model.rst index 85ad2dc..034f19e 100644 --- a/docs/source_docs/user_guide/inputs/solids_model.rst +++ b/docs/source_docs/user_guide/inputs/solids_model.rst @@ -114,7 +114,7 @@ Enabling the DEM solver and specifying model options. The following keys must b | | |RollingFricModelB| | | | | | | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| dem.rolling_friction_coeff | Rolling friction coefficient when using a rolling friction model | Real | 0 | +| rolling_friction_coefficient | Rolling friction coefficient when using a rolling friction model | Real | 0 | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -- GitLab From 81f89c90f8815e436702b522ca0ecd40b0503e61 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:28:34 -0500 Subject: [PATCH 26/47] remove punctuation --- docs/source_docs/user_guide/inputs/species_defs.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/species_defs.rst b/docs/source_docs/user_guide/inputs/species_defs.rst index c0b7619..644147e 100644 --- a/docs/source_docs/user_guide/inputs/species_defs.rst +++ b/docs/source_docs/user_guide/inputs/species_defs.rst @@ -122,9 +122,9 @@ The following inputs are for each species defined using the prefix ``species.[sp | | | | | | | A value is required for ``Sutherland`` species viscosity model. | | | +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ -| viscosity.molecular.Reid.A, | Reid model constants for species. | Real | 0 | -| viscosity.molecular.Reid.B, | | | | -| viscosity.molecular.Reid.C, and | Values are required for ``Reid`` species viscosity model. | | | +| viscosity.molecular.Reid.A | Reid model constants for species. | Real | 0 | +| viscosity.molecular.Reid.B | | | | +| viscosity.molecular.Reid.C and | Values are required for ``Reid`` species viscosity model. | | | | viscosity.molecular.Reid.D | | | | +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ -- GitLab From 824d1d5ddc4b3f600b35b444c6bc8fae581763b8 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:40:42 -0500 Subject: [PATCH 27/47] quoting --- docs/source_docs/user_guide/inputs/boundary_conditions.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/boundary_conditions.rst b/docs/source_docs/user_guide/inputs/boundary_conditions.rst index d3a673f..4a2fb3a 100644 --- a/docs/source_docs/user_guide/inputs/boundary_conditions.rst +++ b/docs/source_docs/user_guide/inputs/boundary_conditions.rst @@ -51,13 +51,13 @@ using the prefix ``bc.[region].[fluid]``: | temperature | Fluid temperature [required if bc_region_type='mi' or 'pi'] | Real | 0 | +------------------------+------------------------------------------------------------------------+-------------+-----------+ | velocity | Velocity components [required if bc_region_type='mi' | Reals | 0 0 0 | -| | and volflow or massflow not specified] | | | +| | and ``volflow`` or ``massflow`` not specified] | | | +------------------------+------------------------------------------------------------------------+-------------+-----------+ | volflow | Volumetric flow rate [required if bc_region_type='mi' | Real | 0 | -| | and velocity or massflow not specified] | | | +| | and ``velocity`` or ``massflow`` not specified] | | | +------------------------+------------------------------------------------------------------------+-------------+-----------+ | massflow | Mass flow rate [required if bc_region_type='mi' | Real | 0 | -| | and velocity or volflow not specified] | | | +| | and ``velocity`` or ``volflow`` not specified] | | | +------------------------+------------------------------------------------------------------------+-------------+-----------+ | delp_dir | Direction for specified pressure drop. Note that this direction | Int | 0 | | | should also be periodic. | | | -- GitLab From d98867027cd9fb7ce4c03f9a08476a5949c22e00 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 15:04:36 -0500 Subject: [PATCH 28/47] remove 'and' --- docs/source_docs/user_guide/inputs/species_defs.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/species_defs.rst b/docs/source_docs/user_guide/inputs/species_defs.rst index 644147e..95aa51a 100644 --- a/docs/source_docs/user_guide/inputs/species_defs.rst +++ b/docs/source_docs/user_guide/inputs/species_defs.rst @@ -124,7 +124,7 @@ The following inputs are for each species defined using the prefix ``species.[sp +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ | viscosity.molecular.Reid.A | Reid model constants for species. | Real | 0 | | viscosity.molecular.Reid.B | | | | -| viscosity.molecular.Reid.C and | Values are required for ``Reid`` species viscosity model. | | | +| viscosity.molecular.Reid.C | Values are required for ``Reid`` species viscosity model. | | | | viscosity.molecular.Reid.D | | | | +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ -- GitLab From ba25b9bdac88cbb8267a0d24eb47486f7d209e09 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 15:04:46 -0500 Subject: [PATCH 29/47] grammar --- docs/source_docs/user_guide/inputs/species_defs.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/species_defs.rst b/docs/source_docs/user_guide/inputs/species_defs.rst index 95aa51a..14d0081 100644 --- a/docs/source_docs/user_guide/inputs/species_defs.rst +++ b/docs/source_docs/user_guide/inputs/species_defs.rst @@ -58,7 +58,7 @@ The following inputs are defined using the prefix ``species``: +--------------------------+------------------------------------------------------------------------+----------+-----------+ -The following inputs are for each species defined using the prefix ``species.[species name]``: +The following inputs are defined for each species using the prefix ``species.[species name]``: +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ | | Description | Type | Default | -- GitLab From 78201223fc44ec7c09fe87f74e21366f83b8b097 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 15:05:00 -0500 Subject: [PATCH 30/47] explain split temperature is Tsplit --- docs/source_docs/user_guide/inputs/species_defs.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/species_defs.rst b/docs/source_docs/user_guide/inputs/species_defs.rst index 14d0081..44959f9 100644 --- a/docs/source_docs/user_guide/inputs/species_defs.rst +++ b/docs/source_docs/user_guide/inputs/species_defs.rst @@ -83,11 +83,11 @@ The following inputs are defined for each species using the prefix ``species.[sp | | | | | | | * By default, two sets of coefficients are required. The coefficients | | | | | define two polynomials used to compute the specific heat and | | | -| | enthalpy across low and high temperatures. The *split temperature* | | | -| | defines the transition from low-to-high polynomials. | | | +| | enthalpy across low and high temperatures. The split temperature | | | +| | (Tsplit) defines the transition from low-to-high polynomials. | | | | | | | | | | * A single polynomial can be used for all temperatures by setting the | | | -| | *split temperature* to -1. | | | +| | split temperature to -1. | | | | | | | | | | * Three or more polynomials can be used by defining multiple split | | | | | temperatures. | | | -- GitLab From 934ca2f1f9a32a2c04606af6bd7d0fec87c3eddf Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 25 Aug 2025 10:31:22 -0500 Subject: [PATCH 31/47] fix indentation --- docs/source_docs/user_guide/inputs/chemical_reactions.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/chemical_reactions.rst b/docs/source_docs/user_guide/inputs/chemical_reactions.rst index 76077f1..51e554e 100644 --- a/docs/source_docs/user_guide/inputs/chemical_reactions.rst +++ b/docs/source_docs/user_guide/inputs/chemical_reactions.rst @@ -68,7 +68,7 @@ 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 - prefix ``chemistry.integrator``: +prefix ``chemistry.integrator``: +-----------------------+---------------------------------------------------------------------+--------+-----------+ | | Description | Type | Default | -- GitLab From 662a311f6cfe56557571ce7388852e14cc358c25 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 25 Aug 2025 12:11:36 -0500 Subject: [PATCH 32/47] rename --- .../{multigrid-solvers.rst => multigrid_solvers.rst} | 0 .../inputs/{time-stepping.rst => time_stepping.rst} | 0 docs/source_docs/user_guide/run-time_inputs.rst | 8 +++----- 3 files changed, 3 insertions(+), 5 deletions(-) rename docs/source_docs/user_guide/inputs/{multigrid-solvers.rst => multigrid_solvers.rst} (100%) rename docs/source_docs/user_guide/inputs/{time-stepping.rst => time_stepping.rst} (100%) diff --git a/docs/source_docs/user_guide/inputs/multigrid-solvers.rst b/docs/source_docs/user_guide/inputs/multigrid_solvers.rst similarity index 100% rename from docs/source_docs/user_guide/inputs/multigrid-solvers.rst rename to docs/source_docs/user_guide/inputs/multigrid_solvers.rst diff --git a/docs/source_docs/user_guide/inputs/time-stepping.rst b/docs/source_docs/user_guide/inputs/time_stepping.rst similarity index 100% rename from docs/source_docs/user_guide/inputs/time-stepping.rst rename to docs/source_docs/user_guide/inputs/time_stepping.rst diff --git a/docs/source_docs/user_guide/run-time_inputs.rst b/docs/source_docs/user_guide/run-time_inputs.rst index 17e22db..2448226 100644 --- a/docs/source_docs/user_guide/run-time_inputs.rst +++ b/docs/source_docs/user_guide/run-time_inputs.rst @@ -36,16 +36,15 @@ values for setting up a problem. Pay special attention to any prefixes for the keywords such as ``mfix``, ``amr``, ``geometry``, ``nodal_proj`` etc. .. toctree:: - :maxdepth: 0 - :hidden: + :maxdepth: 1 :titlesonly: inputs/initialization - inputs/time-stepping + inputs/time_stepping inputs/domain inputs/geometry inputs/mesh_and_gridding - inputs/multigrid-solvers + inputs/multigrid_solvers inputs/model_options inputs/fluid_model inputs/solids_model @@ -58,4 +57,3 @@ keywords such as ``mfix``, ``amr``, ``geometry``, ``nodal_proj`` etc. inputs/output inputs/advanced inputs/mpmd - -- GitLab From 1304891687d144329a45e9d9a4f4c0b77f3024c3 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Tue, 9 Sep 2025 09:17:39 -0500 Subject: [PATCH 33/47] update docs for doc_scanner --- docs/source_docs/tools/pic2dem.rst | 4 +- .../user_guide/inputs/advanced.rst | 41 +++-- .../user_guide/inputs/boundary_conditions.rst | 63 ++++--- .../user_guide/inputs/chemical_reactions.rst | 81 ++++---- docs/source_docs/user_guide/inputs/domain.rst | 2 +- .../user_guide/inputs/fluid_model.rst | 67 +++---- .../user_guide/inputs/geometry.rst | 33 ++-- .../user_guide/inputs/initial_conditions.rst | 83 +++++---- .../user_guide/inputs/initialization.rst | 19 +- .../user_guide/inputs/mesh_and_gridding.rst | 18 +- .../user_guide/inputs/model_options.rst | 79 ++++---- .../user_guide/inputs/multigrid_solvers.rst | 173 +++++++++++------- docs/source_docs/user_guide/inputs/output.rst | 2 +- .../user_guide/inputs/output/ascent.rst | 2 +- .../inputs/output/checkpointing.rst | 12 +- .../user_guide/inputs/output/monitors.rst | 63 +++---- .../output/{plotfiles.rst => plotting.rst} | 110 +++++------ ...porous_media_defs.rst => porous_media.rst} | 6 +- .../inputs/{regions_defs.rst => regions.rst} | 0 .../user_guide/inputs/solids_model.rst | 33 ++-- .../inputs/{species_defs.rst => species.rst} | 34 ++-- .../user_guide/inputs/time_stepping.rst | 22 +-- .../user_guide/run-time_inputs.rst | 6 +- 23 files changed, 516 insertions(+), 437 deletions(-) rename docs/source_docs/user_guide/inputs/output/{plotfiles.rst => plotting.rst} (73%) rename docs/source_docs/user_guide/inputs/{porous_media_defs.rst => porous_media.rst} (95%) rename docs/source_docs/user_guide/inputs/{regions_defs.rst => regions.rst} (100%) rename docs/source_docs/user_guide/inputs/{species_defs.rst => species.rst} (89%) diff --git a/docs/source_docs/tools/pic2dem.rst b/docs/source_docs/tools/pic2dem.rst index 494d291..ccdd9bf 100644 --- a/docs/source_docs/tools/pic2dem.rst +++ b/docs/source_docs/tools/pic2dem.rst @@ -50,10 +50,10 @@ The following inputs must be preceded by "pic2dem.": | | geometry for the DEM refined case will be read or | | | | | written | | | +------------------------+---------------------------------------------------+--------+---------+ -| geom_chk_write | Flag to turn on/off writing the EB geometry | bool | false | +| geom_chk_write | Enable writing the EB geometry | bool | false | | | checkpoint file for the DEM refined case | | | +------------------------+---------------------------------------------------+--------+---------+ -| geom_chk_read | Flag to turn on/off reading the EB geometry | bool | false | +| geom_chk_read | Enable reading the EB geometry | bool | false | | | checkpoint file for the DEM refined case | | | +------------------------+---------------------------------------------------+--------+---------+ | geometry_filename | CSG filename that will be used for generating the | string | "" | diff --git a/docs/source_docs/user_guide/inputs/advanced.rst b/docs/source_docs/user_guide/inputs/advanced.rst index ffe3b0c..9e94245 100644 --- a/docs/source_docs/user_guide/inputs/advanced.rst +++ b/docs/source_docs/user_guide/inputs/advanced.rst @@ -6,21 +6,21 @@ Advanced Testing / debugging ------------------- -The following inputs must be preceded by "mfix." +The following inputs must be preceded by the prefix ``mfix``: +------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +========================+=======================================================================+=============+==============+ | verbose | Verbosity in MFIX-Exa routines | Int | 0 | +------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| ooo_debug | If true then print the name of the routine we are in | Bool | False | +| ooo_debug | If true, print the name of the current routine. | Bool | false | +------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| only_print_grid_report | Do not time-march the simulation. Simply generate the grid report | Bool | False | +| only_print_grid_report | Do not time-march the simulation. Simply generate the grid report | Bool | false | | | and exit. | | | +------------------------+-----------------------------------------------------------------------+-------------+--------------+ -The following inputs must be preceded by "amrex." +The following inputs must be preceded by the prefix ``amrex``: +------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | @@ -63,23 +63,36 @@ The following inputs must be preceded by the prefix ``mfix`` and control load ba +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ | | Description | Type | Default | +==================================+=======================================================================+=============+===================+ -| regrid_int | How often to regrid (in number of steps at level 0) | int | 0 | -| | if regrid_int <= 0 then no regridding will occur | | | +| regrid_int | How often to regrid (in number of steps at level 0). | Int | 0 | +| | If regrid_int <= 0 then no regridding will occur. | | | +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ -| load_balance | * ``SingleGrid`` fluid and particles are co-located on the same grids | string | SingleGrid | +| | Grid type. | String | SingleGrid | +| | | | | +| | Options: | | | +| | | | | +| load_balance | * ``SingleGrid`` fluid and particles are co-located on the same grids | | | | | * ``DualGrid`` fluid and particles live on different grids | | | +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ -| load_balance.DualGrid.fluid | Regrid mesh (fluid) in addition to particles when using `DualGrid` | int | 0 | +| load_balance.DualGrid.fluid | Regrid mesh (fluid) in addition to particles when using `DualGrid` | Int | 0 | +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ -| load_balance.strategy | What strategy to use for load balancing | string | KnapSack | -| | Options are ``KnapSack`` and ``SFC`` | | | +| load_balance.strategy | Strategy to use for dynamic load balancing. | String | KnapSack | +| | | | | +| | Options (case-insensitive): | | | +| | | | | +| | * ``KnapSack`` - FIXME | | | +| | * ``SFC`` - FIXME | | | +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ -| load_balance.weighting | What weighting function to use if using Knapsack load balancing | string | ParticleRunTime | -| | Options are ``ParticleRunTime``, ``ParticleCount`` and ``CellCount`` | | | +| load_balance.weighting | Weighting function to use if using ``KnapSack`` load balancing | String | ParticleRunTime | +| | | | | +| | Options: | | | +| | | | | +| | * ``ParticleRunTime`` - FIXME | | | +| | * ``ParticleCount`` | | | +| | * ``CellCount`` | | | +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ -| knapsack_nmax | Maximum number of grids per MPI process if using knapsack algorithm | int | 128 | +| knapsack_nmax | Maximum number of grids per MPI process if using knapsack algorithm | Int | 128 | +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ -| grid_pruning | Remove all covered grids from the base mesh; this may result in | bool | False | +| grid_pruning | Remove all covered grids from the base mesh; this may result in | Bool | false | | | disjoined grids | | | +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ diff --git a/docs/source_docs/user_guide/inputs/boundary_conditions.rst b/docs/source_docs/user_guide/inputs/boundary_conditions.rst index 4a2fb3a..1c950c4 100644 --- a/docs/source_docs/user_guide/inputs/boundary_conditions.rst +++ b/docs/source_docs/user_guide/inputs/boundary_conditions.rst @@ -1,6 +1,6 @@ .. _InputsBoundaryConditions: -Boundary Conditions +Boundary conditions =================== @@ -9,29 +9,38 @@ General boundary conditions The following inputs are defined using the prefix ``bc``: -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| | Description | Type | Default | -+=====================+=======================================================================+=============+===========+ -| regions | Regions used to define boundary conditions. | String | None | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ - -The type of the boundary conditions in the BC region must be defined. ++---------------------+--------------------------------------------------------------------------+-------------+-----------+ +| | Description | Type | Default | ++=====================+==========================================================================+=============+===========+ +| regions | Regions used to define boundary conditions. | String | None | ++---------------------+--------------------------------------------------------------------------+-------------+-----------+ +| delp_dir | Direction for specified pressure drop. Note that this direction | Int | 0 | +| | should also be periodic. | | | ++---------------------+--------------------------------------------------------------------------+-------------+-----------+ +| delp | Pressure drop (Pa) | Real | 0 | ++---------------------+--------------------------------------------------------------------------+-------------+-----------+ +| po_no_par_out | Force particles to bounce back rather than exiting at pressure outflows. | Int | 0 | ++---------------------+--------------------------------------------------------------------------+-------------+-----------+ + +The type of the boundary conditions in the BC region must be defined with the prefix ``bc``: +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +=====================+=======================================================================+=============+===========+ -| [region] | Used to define boundary condition type. Available options include: | String | None | +| [region] | Specify boundary condition type. | String | None | | | | | | -| | * 'pi' for pressure inflow BC type | | | -| | * 'po' for pressure outflow BC type | | | -| | * 'mi' for mass inflow BC type | | | -| | * 'nsw' for no-slip wall BC type | | | -| | * 'eb' for inhomogeneous Dirichlet BCs of temperature or fluid | | | -| | velocity (mass inflow) on the contained EBs | | | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| po_no_par_out | Let particles exit (default) or bounce-back at pressure outflows | Int | 0 | +| | Options: | | | +| | | | | +| | * ``pi`` - pressure inflow | | | +| | * ``po`` - pressure outflow | | | +| | * ``mi`` - mass inflow | | | +| | * ``nsw`` - no-slip wall | | | +| | * ``eb`` - embedded boundary - for inhomogeneous Dirichlet BCs | | | +| | of temperature or fluid velocity (mass inflow) on the | | | +| | contained EBs | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ + Fluid settings ~~~~~~~~~~~~~~ @@ -59,11 +68,6 @@ using the prefix ``bc.[region].[fluid]``: | massflow | Mass flow rate [required if bc_region_type='mi' | Real | 0 | | | and ``velocity`` or ``volflow`` not specified] | | | +------------------------+------------------------------------------------------------------------+-------------+-----------+ -| delp_dir | Direction for specified pressure drop. Note that this direction | Int | 0 | -| | should also be periodic. | | | -+------------------------+------------------------------------------------------------------------+-------------+-----------+ -| delp | Pressure drop (Pa) | Real | 0 | -+------------------------+------------------------------------------------------------------------+-------------+-----------+ | species.[species0] | Species 'species0' mass fraction [required if solve_species=1 | Real | 0 | | | and bc_region_type='mi' or 'pi']. | | | +------------------------+------------------------------------------------------------------------+-------------+-----------+ @@ -162,28 +166,29 @@ provided when appropriate. +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +=====================+=======================================================================+=============+===========+ -| fluid.velocity | (Required if not `volflow` or `massflow`) | | | +| fluid.velocity | [Required if not `volflow` or `massflow`] | | | | | Inflow fluid velocity on EB faces | Reals | 0 0 0 | | | contained in the (tridimensional) region. | | | | | Note that if only one value is specified, that is assumed to | | | | | be the magnitude in the direction of the EB face's normal. | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| fluid.volflow | (Required if not `velocity` or `massflow`) | | | +| fluid.volflow | [Required if not `velocity` or `massflow`] | | | | | Inflow BC for fluid volumetric flow | Real | 0 | | | rate in the (tridimensional) region. The flow is assumed to be | | | | | normal to the EB surface in the region. | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| fluid.massflow | (Required if not `velocity` or `volflow`) | | | +| fluid.massflow | [Required if not `velocity` or `volflow`] | | | | | Inflow BC for fluid mass flow rate in the (tridimensional) region. | Real | 0 | | | The flow is assumed to be normal to the EB surface in the region. | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| fluid.volfrac | (Required) Volume fraction. | Real | 0 | +| fluid.volfrac | [Required] Volume fraction. | Real | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| eb.normal | (Optional) When specified, only cells with EB face normal that is | Reals | 0 0 0 | +| eb.normal | [Optional] When specified, only cells with EB face normal that is | Reals | 0 0 0 | | | parallel and opposite in direction to the specified values | | | -| | are imposed with the inflow velocity. | | | +| | are imposed with the inflow velocity. FIXME what does OPTIONAL mean | | | +| | with a default value of 0? | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| eb.normal_tol | (Optional) Used in conjunction with `eb.normal`. It determines the | Real | 0 | +| eb.normal_tol | [Optional] Used in conjunction with `eb.normal`. It determines the | Real | 0 | | | tolerance (in degrees) for choosing cells with a specific normal. | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ diff --git a/docs/source_docs/user_guide/inputs/chemical_reactions.rst b/docs/source_docs/user_guide/inputs/chemical_reactions.rst index 51e554e..5cdfdf6 100644 --- a/docs/source_docs/user_guide/inputs/chemical_reactions.rst +++ b/docs/source_docs/user_guide/inputs/chemical_reactions.rst @@ -1,48 +1,51 @@ -Chemical Reactions -================== +Defining chemical reactions +=========================== + +.. |tol_eq| replace:: :math:`\left|\sum\text{products - \sum\text{reactants}\right| < \text{tolerance}` The following inputs are defined using the prefix ``chemistry``: +--------------------------+---------------------------------------------------------+----------+----------------+ | | Description | Type | Default | +==========================+=========================================================+==========+================+ -| solve | Specify the name(s) of the chemical reactions or set | String | None | +| solve | Specify the name(s) of the chemical reactions or set | String | | | | 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 | None | -| | given as input must not contain white spaces and | | | +| [reaction0].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 | | | | | '(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 | | | +| | |tol_eq| | | | | | | | | +--------------------------+---------------------------------------------------------+----------+----------------+ -| solids.update_type | When updating the solids quantities in chemistry due to | String | ConstantVolume | -| | chemical reactions, choose the update type among: | | | +| solids.update_type | How to update solids quantities due to chemical | | ConstantVolume | +| | reactions. | | | | | | | | -| | * ``ConstantVolume`` keep particles' volume constant | | | -| | * ``ConstantDensity`` keep particles' density constant | | | +| | Options: | | | | | | | | +| | * ``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 | | | +| | that case set the particle as invalid and remove it. | | | +--------------------------+---------------------------------------------------------+----------+----------------+ | 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 | | | +| | in that case set the particle as invalid and remove it. | | | +--------------------------+---------------------------------------------------------+----------+----------------+ | 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 | | | +| | in that case set the particle as invalid and remove it. | | | +--------------------------+---------------------------------------------------------+----------+----------------+ Choosing the integrator type for the chemistry ODE integration operation that is @@ -54,8 +57,8 @@ class of integrators in AMReX-Astro/Microphysics +-------------------------+----------------------------------------------------------------------+----------+---------------+ | | Description | Type | Default | +=========================+======================================================================+==========+===============+ -| chemistry.integrator | Specified name of the chemistry ODE integrator type. Available types | String | ForwardEuler | -| | are (case insensitive): | | | +| chemistry.integrator | Specified name of the chemistry ODE integrator type. Options | String | ForwardEuler | +| | (case-insensitive): | | | | | | | | | | * ``ForwardEuler`` | | | | | * ``StiffSolver::ForwardEuler`` | | | @@ -73,52 +76,54 @@ prefix ``chemistry.integrator``: +-----------------------+---------------------------------------------------------------------+--------+-----------+ | | Description | Type | Default | +=======================+=====================================================================+========+===========+ -| burner_verbose | Enables the printing on screen of some integration statistics | int | 0 | +| burner_verbose | Enable printing of some integration statistics. | Int | 0 | +-----------------------+---------------------------------------------------------------------+--------+-----------+ -| ode_max_steps | The maximum number of substeps for the ODE integration | int | 150000 | +| 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 solver. | string | Numerical | +| jacobian_type | Select how to compute the Jacobian for the ODE iterative solver. | String | Numerical | | | This option is available for ``StiffSolver::BackwardEuler`` and | | | -| | ``StiffSolver::VODE``. Available choices are: | | | +| | ``StiffSolver::VODE``. | | | +| | | | | +| | Options (case-insensitive): | | | | | | | | -| | * ``Numerical`` for a first-order numerical approximation | | | -| | * ``Broyden`` for Broyden's method (only for BackwardEuler) | | | +| | * ``Numerical`` - first-order numerical approximation | | | +| | * ``Broyden`` - Broyden's method (only for ``BackwardEuler``) | | | +-----------------------+---------------------------------------------------------------------+--------+-----------+ | atol | Absolute tolerance for the ODE integration error test between | Real | 1.e-6 | -| | the solution and the fine-step solution | | | +| | 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 | | | +| | the solution and the fine-step solution. | | | +-----------------------+---------------------------------------------------------------------+--------+-----------+ | retry_atol | Overwrites the absolute tolerance value atol in case the ODE | Real | -1 | -| | integration fails | | | +| | integration fails. | | | +-----------------------+---------------------------------------------------------------------+--------+-----------+ | retry_rtol | Overwrites the relative tolerance value rtol in case the ODE | Real | -1 | -| | integration fails | | | +| | 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 | | | +| 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 | +| ode_max_dt | Maximum timestep size for the ODE integration substeps. | Real | 1.e30 | +-----------------------+---------------------------------------------------------------------+--------+-----------+ | max_dt_change_factor | Only for StiffSolver::ForwardEuler, sets a maximum factor | Real | 1.001 | -| | for the change of the timestep for the internal substeps | | | +| | for the change of the timestep for the internal substeps. | | | +-----------------------+---------------------------------------------------------------------+--------+-----------+ -| max_iter | Maximum number of iterations for the internal Newton solver | int | 100 | +| 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 | | | +| linalg_do_pivoting | Only for ``StiffSolver::BackwardEuler`` and ``StiffSolver::VODE``, | Int | 1 | +| | enables 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 | | | +| | Newton solver. Valid only for ``StiffSolver::BackwardEuler``. | | | +-----------------------+---------------------------------------------------------------------+--------+-----------+ -| use_jacobian_caching | Only for StiffSolver::VODE, enables caching the numerical | int | 1 | -| | jacobian | | | +| use_jacobian_caching | Only for ``StiffSolver::VODE``, enable caching the numerical | Int | 1 | +| | Jacobian. | | | +-----------------------+---------------------------------------------------------------------+--------+-----------+ -| X_reject_buffer | Only for StiffSolver::VODE, constrain species abundances | Real | 1.0 | +| 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 | | | +| | a given step. | | | +-----------------------+---------------------------------------------------------------------+--------+-----------+ diff --git a/docs/source_docs/user_guide/inputs/domain.rst b/docs/source_docs/user_guide/inputs/domain.rst index b62ac51..f49b9c8 100644 --- a/docs/source_docs/user_guide/inputs/domain.rst +++ b/docs/source_docs/user_guide/inputs/domain.rst @@ -16,7 +16,7 @@ The following inputs are defined using the prefix ``geometry``: | coord_sys | Coordinate system used in simulation. Only Cartesian coordinates | Int | 0 | | | (``coord_sys = 0``) are supported. | | | +-----------------+-----------------------------------------------------------------------+-------------+-----------+ -| is_periodic | 1 for true, 0 for false (one value for each coordinate direction) | Int | 0 0 0 | +| is_periodic | 1 for true, 0 for false (one value for each coordinate direction) | Ints | 0 0 0 | +-----------------+-----------------------------------------------------------------------+-------------+-----------+ | prob_lo | Low corner of physical domain (physical not index space) | Reals | 0 0 0 | +-----------------+-----------------------------------------------------------------------+-------------+-----------+ diff --git a/docs/source_docs/user_guide/inputs/fluid_model.rst b/docs/source_docs/user_guide/inputs/fluid_model.rst index 5d7e4ca..9c7d51d 100644 --- a/docs/source_docs/user_guide/inputs/fluid_model.rst +++ b/docs/source_docs/user_guide/inputs/fluid_model.rst @@ -1,4 +1,4 @@ -.. _InputsFluidModel: +. _InputsFluidModel: Fluid model =========== @@ -11,7 +11,7 @@ The following inputs are defined using the prefix ``fluid``: | solve | Specify the name of the fluid or set to ``None`` to disable | String | ``None`` | | | the fluid solver. The name assigned to the fluid solver is | | | | | used to specify fluid properties and initial and boundary | | | -| | conditions. | | | +| | conditions. It is common to use the name ``fluid``. | | | +--------------------------------------------+-------------------------------------------------------------+--------+----------+ @@ -34,55 +34,56 @@ a single fluid; therefore, it is common to name the fluid ``fluid``. This is ill +============================================+============================================================+========+==========+ | viscosity.molecular | Specify which molecular viscosity model to use. | String | None | | | | | | -| | Available options include: | | | +| | Options: | | | | | | | | -| | * ``constant`` constant viscosity | | | -| | * ``Sutherland`` :cite:p:`suth1893` | | | +| | * ``None`` - no viscosity model. | | | +| | * ``constant`` - constant viscosity | | | +| | * ``Sutherland`` :cite:p:`suth1893` - | | | | | | | | | | |Sutherland_Eq| | | | | | | | | -| | * ``Reid`` :cite:p:`reid87` | | | +| | * ``Reid`` :cite:p:`reid87` - | | | | | | | | | | |Reid_4parm_Eq| | | | | | | | | -| | * ``mixture`` a mixture viscosity is computed from | | | +| | * ``mixture`` - a mixture viscosity is computed from | | | | | :ref:`species viscosities` | | | | | and local species mass fractions :cite:p:`bird06` | | | | | | | | | | |mix_Eq| | | | | | | | | | | A viscosity model is required if the fluid solver is | | | -| | enabled. | | | +| | enabled. FIXME NEED A DEFAULT | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ | viscosity.molecular.constant | Constant fluid viscosity. | Real | 0 | | | | | | | | A value is required for ``constant`` viscosity model. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ -| viscosity.molecular.Sutherland.T_ref | Sutherland model reference temperature | Real | 0 | +| viscosity.molecular.Sutherland.T_ref | Sutherland model reference temperature. | Real | 0 | | | | | | | | A value is required for ``Sutherland`` viscosity model. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ -| viscosity.molecular.Sutherland.mu_ref | Sutherland model reference viscosity at T_ref | Real | 0 | +| viscosity.molecular.Sutherland.mu_ref | Sutherland model reference viscosity at T_ref. | Real | 0 | | | | | | | | A value is required for ``Sutherland`` viscosity model. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ -| viscosity.molecular.Sutherland.S | Sutherland model temperature | Real | 0 | +| viscosity.molecular.Sutherland.S | Sutherland model temperature. | Real | 0 | | | | | | | | A value is required for ``Sutherland`` viscosity model. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ -| viscosity.molecular.Reid.A | Reid model constants | Real | 0 | +| viscosity.molecular.Reid.A | Reid model constants. | Real | 0 | | viscosity.molecular.Reid.B | | | | | viscosity.molecular.Reid.C | Values are required for ``Reid`` viscosity model. | | | | viscosity.molecular.Reid.D | | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ -| viscosity.eddy | Specify eddy viscosity model. | String | None | +| viscosity.eddy | Specify eddy viscosity model. | | | | | | | | -| | Available options include: | | | -| | | | | -| | * ``None`` No eddy viscosity model | | | +| | Options: | | | +| | |String | None | +| | * ``None`` - No eddy viscosity model | | | | | * ``Smagorinsky-Lilly`` :cite:p:`Smag63,Lilly66` | | | | | * ``WALE`` :cite:p:`ducros98` | | | -| | | | | +| | * ``usr`` -- FIXME | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ | viscosity.eddy.Smagorinsky-Lilly.constant | Smagorinsky-Lilly constant which usually has values | Real | None | | | between 0.1 and 0.2. | | | @@ -94,29 +95,29 @@ a single fluid; therefore, it is common to name the fluid ``fluid``. This is ill +--------------------------------------------+------------------------------------------------------------+--------+----------+ | viscosity.suspension | Specify suspension viscosity model of the form | String | None | | | | | | -| | :math:`\mu_{susp}=\mu_{mol}(\mu^* - 1)` | | | +| | :math:`\mu_{susp} = \mu_{mol}(\mu^* - 1)` | | | | | | | | -| | Available options include: | | | +| | Options: | | | | | | | | -| | * ``None`` No eddy suspension model | | | +| | * ``None`` - No eddy suspension model | | | | | | | | -| | :math:`\mu^*=1` | | | +| | :math:`\mu^* = 1` | | | | | | | | | | * ``Einstein`` :cite:p:`einstein11` | | | | | | | | -| | :math:`\mu^*=1 + 2.5\varepsilon_s` | | | +| | :math:`\mu^* = 1 + 2.5\varepsilon_s` | | | | | | | | | | * ``Brinkman`` :cite:p:`brinkman52,gibilaro07` | | | | | | | | -| | :math:`\mu^*=(1-\varepsilon_s)^{-c}` | | | +| | :math:`\mu^* = (1-\varepsilon_s)^{-c}` | | | | | | | | | | * ``Roscoe`` :cite:p:`roscoe52,krieger59,maron56` | | | | | | | | -| | :math:`\mu^*=(1-\varepsilon_s/c_1)^{-c_2}` | | | +| | :math:`\mu^* = (1-\varepsilon_s/c_1)^{-c_2}` | | | | | | | | | | * ``ChengLaw`` :cite:p:`cheng03` | | | | | | | | -| | :math:`\mu^*=e^{2.5(1/(1-\varepsilon_s)^c-1)/c}` | | | +| | :math:`\mu^* = e^{2.5(1/(1-\varepsilon_s)^c-1)/c}` | | | | | | | | | | * ``Sato`` :cite:p:`sato81` | | | | | | | | @@ -129,19 +130,19 @@ a single fluid; therefore, it is common to name the fluid ``fluid``. This is ill +--------------------------------------------+------------------------------------------------------------+--------+----------+ | viscosity.suspension.Brinkman.constant | Constant for exponent in Brinkman suspension expression. | Real | None | | | | | | -| | A value is required when using the model ``Brinkman``. | | | +| | A value is required when using the ``Brinkman`` model. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ | viscosity.suspension.Roscoe.c1 | Constant for max packing in Roscoe suspension expression. | Real | None | | | | | | -| | A value is required when using the model ``Roscoe``. | | | +| | A value is required when using the ``Roscoe`` model. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ | viscosity.suspension.Roscoe.c2 | Constant for exponent in Roscoe suspension expression. | Real | None | | | | | | -| | A value is required when using the model ``Roscoe``. | | | +| | A value is required when using the ``Roscoe`` model. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ | viscosity.suspension.ChengLaw.constant | Constant for exponent in ChengLaw suspension expression. | Real | None | | | | | | -| | A value is required when using the model ``ChengLaw``. | | | +| | A value is required when using the ``ChengLaw`` model. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ | viscosity.suspension.Sato.constant | Constant for Sato suspension expression. | Real | 0.65 | | | | | | @@ -168,12 +169,12 @@ a single fluid; therefore, it is common to name the fluid ``fluid``. This is ill | | are not solved. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ | specific_heat | Specify which specific heat model to use for the fluid. | String | None | -| | Available options include: | | | +| | Options: | | | | | | | | | | * ``constant`` - the fluid has a constant specific heat | | | | | | | | | | * ``NASA7-poly`` the fluid specific heat is defined by | | | -| | NASA-7 polynomails. | | | +| | NASA-7 polynomials. | | | | | | | | | | NASA7 polynomial format: | | | | | | | | @@ -206,7 +207,7 @@ a single fluid; therefore, it is common to name the fluid ``fluid``. This is ill | | | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ | thermal_conductivity | Specify which thermal conductivity model to use for | String | None | -| | fluid. Available options include: | | | +| | fluid. Options: : | | | | | | | | | | * ``constant`` - the fluid has a constant thermal | | | | | conductivity model | | | @@ -422,5 +423,5 @@ of the damped Newton solver used to compute temperature from enthalpy and specif +------------------------------------------+----------------------------------------------------------+--------+----------+ | newton_solver.relative_tol | Define relative tolerance for the Newton solver | Real | 1.e-8 | +------------------------------------------+----------------------------------------------------------+--------+----------+ -| newton_solver.max_iterations | Define max number of iterations for the Newton solver | int | 500 | +| newton_solver.max_iterations | Define max number of iterations for the Newton solver | Int | 500 | +------------------------------------------+----------------------------------------------------------+--------+----------+ diff --git a/docs/source_docs/user_guide/inputs/geometry.rst b/docs/source_docs/user_guide/inputs/geometry.rst index d50d4d0..90a7b5a 100644 --- a/docs/source_docs/user_guide/inputs/geometry.rst +++ b/docs/source_docs/user_guide/inputs/geometry.rst @@ -9,12 +9,13 @@ The following inputs are defined using the prefix ``mfix``: | | Description | Type | Default | +========================+===============================================================================+==========+=====================+ | geometry | Specify the simulation geometry. | String | '' | +| | Options (case-insensitive): | | | | | | | | | | * ``box`` - predefined :ref:`box geometry` | | | | | * ``cylinder`` - predefined :ref:`cylinder geometry` | | | | | * ``generic`` - :ref:`user-defined geometry` | | | -| | * ``csg`` - use :ref:`Constructive Solid Geometry` file | | | -| | * ``stl`` - use :ref:`Standard Triangle Language` file | | | +| | * ``CSG`` - use :ref:`Constructive Solid Geometry` file | | | +| | * ``STL`` - use :ref:`Standard Triangle Language` file | | | | | | | | | | If left undefined, then the system should be fully periodic, or | | | | | :ref:`planar regions` should be used to | | | @@ -59,7 +60,7 @@ The following inputs are defined using the prefix ``box``: +------------------------+-------------------------------------------------------------------+----------+---------------------+ | Hi | High corner of the embedded boundary box | Reals | ``prob_hi`` | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -| internal_flow | Flag to indicate that flow is *inside* the box. | Bool | true | +| internal_flow | Indicates that flow is *inside* the box. | Bool | true | +------------------------+-------------------------------------------------------------------+----------+---------------------+ | offset | Shift low side box walls by ``+offset`` and high side walls by | Real | 1.0e-15 | | | ``-offset``. An example use of this input would be to define a | | | @@ -158,7 +159,7 @@ The following inputs are defined using the prefix ``cylinder``: | | then the cylinder is made infinitely long to overhang the domain | | | | | extents. | | | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -| direction | Axis the cylinder runs along. | int | 0 | +| 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. | @@ -170,10 +171,10 @@ The following inputs are defined using the prefix ``cylinder``: | | long) can be rotated. | | | | | * Rotation is applied about the ``center`` of the cylinder. | | | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -| rotation_axe | Axis to rotate the cylinder about. | int | 0 | +| rotation_axe | Axis to rotate the cylinder about. | Int | 0 | | | (``0``: *X*, ``1``: *Y*, ``2``: *Z*) | | | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -| internal_flow | Flag to indicate that flow is *inside* the box. | Bool | true | +| internal_flow | Indicates that flow is *inside* the box. | Bool | true | +------------------------+-------------------------------------------------------------------+----------+---------------------+ The inputs for the predefined ``cylinder`` embedded boundary geometry are illustrated in :numref:`fig_cylinder_geometry_inputs`. @@ -211,7 +212,7 @@ The cylinder is not assigned a length, therefore it runs past the low and high * .. _inputs_cylinder_geometry_ex: .. code-block:: bash - :caption: Snippet of intpus for predefined EB ``cylinder`` geometry example. This is not a complete input file. + :caption: Snippet of inputs for predefined EB ``cylinder`` geometry example. This is not a complete input file. # Define periodicity and domain extents # ------------------------------------------------------------- @@ -346,11 +347,11 @@ The following inputs are defined using the prefix ``csg``: +========================+===================================================================+==========+=====================+ | geometry_filename | The CSG file that defines the EB geometry | String | '' | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -| internal_flow | Flag to indicate that flow is *inside* the box. | Bool | true | +| 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:: @@ -360,23 +361,23 @@ The following inputs are defined using the prefix ``csg``: .. _InputsGeometry_STL: -Standard triangle language (STL) +STL (Standard Triangle Language) -------------------------------- -* A standard triangle language (STL) geometry can be created using numerous CAD programs. +* An STL geometry can be created using numerous CAD programs. The following inputs are defined using the prefix ``stl``: +------------------------+-------------------------------------------------------------------+----------+---------------------+ | | Description | Type | Default | +========================+===================================================================+==========+=====================+ -| geometry_filename | The STL file that defines the EB geometry | String | '' | +| 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 | +| use_bvh | Use bounding volume optimization. | Bool | true | +------------------------+-------------------------------------------------------------------+----------+---------------------+ .. note:: diff --git a/docs/source_docs/user_guide/inputs/initial_conditions.rst b/docs/source_docs/user_guide/inputs/initial_conditions.rst index 2070877..8ce5183 100644 --- a/docs/source_docs/user_guide/inputs/initial_conditions.rst +++ b/docs/source_docs/user_guide/inputs/initial_conditions.rst @@ -1,4 +1,4 @@ -Initial Conditions +Initial conditions ================== The following inputs are defined using the prefix ``ic``: @@ -8,16 +8,17 @@ The following inputs are defined using the prefix ``ic``: +=======================+========================================================================+=============+===========+ | regions | Regions used to define initial conditions. | String | None | +-----------------------+------------------------------------------------------------------------+-------------+-----------+ -| allow_regions_overlap | Flag for allowing the user to decide whether particles will be | Bool | 1 (yes) | -| | generated/initialized more than once on the areas where the IC regions | | | -| | have an intersection | | | +| allow_regions_overlap | If enabled, particles will be generated/initialized more than once | Int | 1 | +| | on areas where the IC regions intersect | | | +-----------------------+------------------------------------------------------------------------+-------------+-----------+ -| ranking_type | IC regions are sorted during initialization. This input lets the user | String | Inputs | -| | decide the ranking criterion, which can be one of the following: | | | +| ranking_type | Specifies the order in which IC regions are sorted during | String | Inputs | +| | initialization. | | | | | | | | -| | * inputs -- the order in the inputs file | | | -| | * volume -- the volume of each IC region | | | -| | * priority -- the priority value provided by the user in the inputs | | | +| | Options: | | | +| | | | | +| | * ``Inputs`` - preserve order in inputs file | | | +| | * ``Volume`` - sort by volume of each IC region FIXME small to large? | | | +| | * ``Priority`` - sort by specified priority value | | | +-----------------------+------------------------------------------------------------------------+-------------+-----------+ @@ -53,22 +54,23 @@ using the compound prefix ``ic.[region]``: +----------------------+------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +======================+==================================================================+=============+===========+ -| solids | Name of solid type in IC region -- only one solid is allowed in | String | None | +| solids | Name of solid type in IC region -- only one solid is allowed in | String | None | | | an IC region. | | | +----------------------+------------------------------------------------------------------+-------------+-----------+ | packing | Specifies how auto-generated particles are placed in the IC | String | None | | | region: | | | | | | | | -| | * hcp -- hex-centered packing | | | -| | * pseudo_random -- random packing using a fixed random seed | | | -| | * random -- random packing (not repeatable) | | | -| | * oneper -- one particle per cell | | | -| | * eightper -- eight particles per cell | | | -| | * n-cube -- n^3 particles per cell where n is an integer | | | +| | * ``hcp`` - hex-centered packing | | | +| | * ``pseudo_random`` -- random packing using a fixed random seed | | | +| | * ``random`` -- random packing (not repeatable) | | | +| | * ``oneper`` -- one particle per cell | | | +| | * ``eightper`` -- eight particles per cell | | | +| | * ``n-cube`` -- n^3 particles per cell where n is an integer | | | | | | | | -| | (NOTE: oneper is equivalent to 1-cube and eightper to 2-cube) | | | +| | (NOTE: ``oneper`` is equivalent to ``1-cube`` and ``eightper`` | | | +| | to ``2-cube``) | | | +----------------------+------------------------------------------------------------------+-------------+-----------+ -| priority | Priority value for IC regions ranking as described above | Int | Max | +| priority | Priority value for IC regions ranking as described above | Int | Max FIXME | +----------------------+------------------------------------------------------------------+-------------+-----------+ For each initial condition region, the solid inputs are defined @@ -88,16 +90,21 @@ please refer to :ref:`ReferenceParticleDistributions ` by the @@ -85,7 +85,7 @@ mesh refinement algorithm and are only applicable when ``amr.max_level > 0``. | grid_eff | Threshold value to ensure grids do not contain too large a fraction | Real | 0.7 | | | of un-tagged cells. | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| n_error_buf | Controls the number of tagged cells before grids are defined. Used | int | 1 | +| n_error_buf | Controls the number of tagged cells before grids are defined. Used | Int | 1 | | | to ensure coarse/fine boundaries are not too close to tagged cells. | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ @@ -108,17 +108,17 @@ The following inputs are defined using the prefix ``amr``: +----------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +======================+=======================================================================+=============+===========+ -| max_grid_size_x | Maximum number of cells at level 0 in each grid in *X* | int | 32 | +| max_grid_size_x | Maximum number of cells at level 0 in each grid in *X* | Int | 32 | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| max_grid_size_y | Maximum number of cells at level 0 in each grid in *Y* | int | 32 | +| max_grid_size_y | Maximum number of cells at level 0 in each grid in *Y* | Int | 32 | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| max_grid_size_z | Maximum number of cells at level 0 in each grid in *Z* | int | 32 | +| max_grid_size_z | Maximum number of cells at level 0 in each grid in *Z* | Int | 32 | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| blocking_factor_x | Each grid in *X* must be divisible by ``blocking_factor_x`` | int | 8 | +| blocking_factor_x | Each grid in *X* must be divisible by ``blocking_factor_x`` | Int | 8 | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| blocking_factor_y | Each grid in *Y* must be divisible by ``blocking_factor_y`` | int | 8 | +| blocking_factor_y | Each grid in *Y* must be divisible by ``blocking_factor_y`` | Int | 8 | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| blocking_factor_z | Each grid in *Z* must be divisible by ``blocking_factor_z`` | int | 8 | +| blocking_factor_z | Each grid in *Z* must be divisible by ``blocking_factor_z`` | Int | 8 | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ The domain is decomposed into *grids* by dividing the number of cells by the max grid size diff --git a/docs/source_docs/user_guide/inputs/model_options.rst b/docs/source_docs/user_guide/inputs/model_options.rst index 3072d64..5a2193c 100644 --- a/docs/source_docs/user_guide/inputs/model_options.rst +++ b/docs/source_docs/user_guide/inputs/model_options.rst @@ -9,14 +9,13 @@ The following inputs are defined using the prefix ``mfix``: +========================+============================================================================+==========+=====================+ | gravity | Gravity vector [required] | Reals | 0 0 0 | +------------------------+----------------------------------------------------------------------------+----------+---------------------+ -| advect_density | Flag to enable time evolution of fluid density. | int | 0 | +| advect_density | Enable time evolution of fluid density. | Int | 0 | +------------------------+----------------------------------------------------------------------------+----------+---------------------+ -| advect_enthalpy | Flag to enable time evolution of fluid temperature and enthalpy. | int | 0 | +| advect_enthalpy | Enable time evolution of fluid temperature and enthalpy. | Int | 0 | +------------------------+----------------------------------------------------------------------------+----------+---------------------+ -| solve_species | Flag to enable the time evolution of fluid species mass | int | 0 | -| | fractions. | | | +| solve_species | Enable the time evolution of fluid species mass fractions. | Int | 0 | +------------------------+----------------------------------------------------------------------------+----------+---------------------+ -| constraint | Select low Mach number constraint. | string | IncompressibleFluid | +| constraint | Select low Mach number constraint. Options (case-insensitive): | String | IncompressibleFluid | | | | | | | | * ``IncompressibleFluid`` constraint is appropriate for cold flow systems | | | | | that do not have chemical reactions. Fluid temperature and species mass | | | @@ -47,46 +46,48 @@ The following inputs are defined using the prefix ``mfix``: +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | Key | Description | Type | Default | +=================================+=======================================================================+=============+==============+ -| advection_type | Advection scheme | string | Godunov | +| advection_type | Advection scheme. | String | Godunov | | | | | | -| | * ``mol`` Predictor-Corrector Method of Lines. MAC velocities and | | | +| | Options: | | | +| | | | | +| | * ``MOL``- Predictor-Corrector Method of Lines. MAC velocities and | | | | | edge states are extrapolated in space. | | | | | | | | -| | * ``godunov`` Godunov. MAC velocities and edge states are | | | +| | * ``Godunov`` - Godunov. MAC velocities and edge states are | | | | | extrapolated in space and time using a second-order Taylor series | | | | | expansion. | | | -| | | | | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | redistribution_type | Algorithms to address the '*small cell problem*' associated with | String | StateRedist | | | explicit cut-cell algorithms. | | | | | | | | +| | Options: | | | +| | | | | | | * ``StateRedist`` :cite:p:`berger21,giuliani22` | | | | | * ``FluxRedist`` :cite:p:`chern87,colella06` | | | -| | * ``NoRedist``: Do not redistribute fluxes. | | | -| | | | | +| | * ``NoRedist`` - Do not redistribute fluxes. | | | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| redistribute_before_nodal_proj | Redistribute the velocity field before the nodal projection | Bool | True | +| redistribute_before_nodal_proj | Redistribute the velocity field before the nodal projection. | Bool | true | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| redistribute_nodal_proj | Redistribute the velocity field after the nodal projection | Bool | False | +| redistribute_nodal_proj | Redistribute the velocity field after the nodal projection. | Bool | false | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| use_drag_coeff_in_proj_gp | Algebraically consistent p coeff in proj or (default) simplified form | Bool | False | +| use_drag_coeff_in_proj_gp | Algebraically consistent p coeff in proj or (default) simplified form.| Bool | false | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| use_drag_in_godunov | Include a drag term in the Godunov flux or (default) not | Bool | False | +| use_drag_in_godunov | Include a drag term in the Godunov flux. | Bool | false | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| godunov_ppm | When using Godunov, use piecewise parabolic (PPM) instead of | Bool | False | -| | piecewise linear (PLM) reconstruction | | | +| godunov_ppm | When using Godunov, use piecewise parabolic (PPM) instead of | Bool | false | +| | piecewise linear (PLM) reconstruction. | | | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| godunov_include_diff_in_forcing | When using Godunov, include viscous/diffusive terms in forcing terms | Bool | True | +| godunov_include_diff_in_forcing | When using Godunov, include viscous/diffusive terms in forcing terms. | Bool | true | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| godunov_use_forces_in_trans | When using Godunov, add forcing terms in the construction of `trans` | Bool | False | -| | velocities | | | +| godunov_use_forces_in_trans | When using Godunov, add forcing terms in the construction of | Bool | false | +| | transverse velocities. | | | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| use_mac_phi_in_godunov | When using Godunov, don't include the pressure gradient in the | Bool | False | -| | forcing term passed into the godunov routine; instead use gradient of | | | -| | mac phi which contains the full pressure | | | +| use_mac_phi_in_godunov | When using Godunov, don't include the pressure gradient in the | Bool | false | +| | forcing term passed into the Godunov routine; instead use gradient of | | | +| | mac phi which contains the full pressure. | | | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | correction_small_volfrac | Threshold volume fraction for correcting small cell velocity | | | -| | at the end of the predictor and corrector | Real | 1.e-4 | +| | at the end of the predictor and corrector. | Real | 1.e-4 | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ @@ -102,9 +103,9 @@ The following inputs are defined using the prefix ``particles``: +---------------------+---------------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +=====================+===========================================================================+=============+===========+ -| constraint | Constraint type. Available options include: | String | None | +| constraint | Constraint type. Options: | String | None | | | | | | -| | * 'mean_velocity' | | | +| | * ``mean_velocity`` | | | | | | | | +---------------------+---------------------------------------------------------------------------+-------------+-----------+ @@ -145,7 +146,7 @@ The following inputs are defined using the prefix ``mfix``: +============================+====================================================================+===========+===============+ | deposition_scheme | The algorithm used to transfer particle properties to the Eulerian | String | trilinear | | | grid. An overview of the schemes is provided | | | -| | :ref:`below`. | | | +| | :ref:`below`. Options: | | | | | | | | | | * ``centroid`` | | | | | * ``trilinear`` | | | @@ -154,8 +155,8 @@ The following inputs are defined using the prefix ``mfix``: +----------------------------+--------------------------------------------------------------------+-----------+---------------+ | deposition_scale_factor | The deposition scale factor. | Real | 1.0 | | | | | | -| | Applicable only with `true-dpvm` and `trilinear-dpvm-square` | | | -| | deposition schemes. The value must be in the intervarl | | | +| | Applicable only with ``true-dpvm`` and ``trilinear-dpvm-square`` | | | +| | deposition schemes. The value must be in the interval | | | | | :math:`[0,\Delta x/2]` where :math:`\Delta x` is the mesh spacing. | | | +----------------------------+--------------------------------------------------------------------+-----------+---------------+ | deposition_diffusion_coeff | If a positive value is set, a diffusion equation | Real | -1.0 | @@ -265,13 +266,15 @@ The following inputs are defined using the prefix ``mfix``: | deposition_redist_type | Algorithm used to redistribute excess solids to adjacent cells. This | String | MaxPack | | | typically applies only to small cut-cells along the geometry. | | | | | | | | -| | * ``MaxPack`` If the solids volume fraction exceeds the prescribed | | | +| | Options: | | | +| | | | | +| | * ``MaxPack`` - If the solids volume fraction exceeds the prescribed | | | | | ``max_solids_volume_fraction``, then the local average solids | | | | | volume is computed and solids volume exceeding the average is | | | | | reallocated to adjacent cells. The fraction of redistributed solids | | | | | is applied to all transferred properties. | | | | | | | | -| | * ``StateRedist`` Use the state redistribution algorithm of | | | +| | * ``StateRedist`` - Use the state redistribution algorithm of | | | | | :cite:p:`berger21,giuliani22` to reallocate | | | | | transferred quantities in small cells. | | | | | | | | @@ -303,7 +306,7 @@ The following input is defined using the prefix ``mfix.drag``: +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +==========================+=======================================================================+=============+===========+ -| model | Fluid-particle drag model. | String | None | +| model | Fluid-particle drag model. Options: | String | None | | | | | | | | * ``WenYu`` :cite:p:`Wen66` | | | | | * ``Gidaspow`` :cite:p:`ding90,Lat00` | | | @@ -315,7 +318,7 @@ The following input is defined using the prefix ``mfix.drag``: | model.SyamOBrien.c1 | Fitting parameters for ``SyamOBrien`` drag model | Real | None | | model.SyamOBrien.d1 | | | | +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ -| include_divtau | Interpolate the fluid shear stress to particles and include in the | int | 0 | +| include_divtau | Interpolate the fluid shear stress to particles and include in the | Int | 0 | | | fluid-particle drag force. The force is applied to the fluid by | | | | | multiplying the shear stress by fluid volume fraction. | | | +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ @@ -324,13 +327,13 @@ The following input is defined using the prefix ``mfix.drag``: | | | | | | | |VirtualMass_Eq| | | | | | | | | -| | * ``Null`` zero virtual mass coefficient, :math:`C_p^{vm}=0` | | | -| | * ``Constant`` - user-specified constant coefficient | | | -| | * ``Zuber`` :cite:p:`zuber64` | | | +| | * ``Null`` - zero virtual mass coefficient, :math:`C_p^{vm}=0` | | | +| | * ``Constant`` - specified constant coefficient | | | +| | * ``Zuber`` - :cite:p:`zuber64` | | | | | | | | | | |VM_Zuber_Eq| | | | | | | | | -| | * ``Nijssen`` :cite:p:`nijssen20` | | | +| | * ``Nijssen`` - :cite:p:`nijssen20` | | | | | | | | | | |VM_Nijssen_Eq| | | | | | | | | @@ -341,7 +344,7 @@ The following input is defined using the prefix ``mfix.drag``: .. note:: - The ``UserDrag`` keyword is used to invoke a user defined drag model. This is accomplished + The ``UserDrag`` keyword is used to invoke a user-defined drag model. This is accomplished by copying ``src/usr/usr_drag.cpp`` file into the build directory, implementing the desired drag model, and recompiling the code. An example can be found in ``tests/DEM06-x``. diff --git a/docs/source_docs/user_guide/inputs/multigrid_solvers.rst b/docs/source_docs/user_guide/inputs/multigrid_solvers.rst index 6330643..bc94cbd 100644 --- a/docs/source_docs/user_guide/inputs/multigrid_solvers.rst +++ b/docs/source_docs/user_guide/inputs/multigrid_solvers.rst @@ -11,32 +11,45 @@ The following inputs are defined using the prefix ``nodal_proj``: +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +=========================+=======================================================================+=============+==============+ -| verbose | Verbosity of multigrid solver in nodal projection | Int | 0 | +| verbose | Verbosity of multigrid solver in nodal projection | Int | 0 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_verbose | Verbosity of BiCGStab solver in nodal projection | Int | 0 | +| bottom_verbose | Verbosity of BiCGStab solver in nodal projection | Int | 0 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_rtol | Relative tolerance in nodal projection | Real | 1.e-11 | +| mg_rtol | Relative tolerance in nodal projection | Real | 1.e-11 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_atol | Absolute tolerance in nodal projection | Real | 1.e-14 | +| mg_atol | Absolute tolerance in nodal projection | Real | 1.e-14 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| maxiter | Maximum number of iterations in the nodal projection | Int | 100 | +| maxiter | Maximum number of iterations in the nodal projection | Int | 100 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_maxiter | Maximum number of iterations in the nodal projection | Int | 100 | +| bottom_maxiter | Maximum number of iterations in the nodal projection | Int | 100 | | | bottom solver if using bicg, cg, bicgcg or cgbicg | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_max_coarsening_level | Maximum number of coarser levels to allow in the nodal projection | Int | 100 | +| mg_max_coarsening_level | Maximum number of coarser levels to allow in the nodal projection. | Int | 100 | | | If set to 0, the bottom solver will be called at the current level | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_solver | Which bottom solver to use in the nodal projection | String | bicgcg | +| bottom_solver | Which bottom solver to use in the nodal projection. | String | bicgcg | +| | | | | +| | Options: | | | +| | | | | +| | * ``bicgcg`` - FIXME | | | +| | * ``bicgstab`` - FIXME | | | +| | * ``cg`` - FIXME | | | +| | * ``cgbicg`` - FIXME | | | +| | * ``hypre`` - FIXME | | | +| | * ``smoother`` - FIXME | | | | | | | | -| | Options are bicgcg, bicgstab, cg, cgbicg, smoother or hypre | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | hypre_namespace | Namespace to use in the nodal projection when using hypre | String | hypre | | | to control hypre specific settings. It can be any string. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| hypre_interface | Which interface to use in the nodal projection when using hypre | String | ij | +| hypre_interface | Which interface to use in the nodal projection when using ``hypre``. | String | ij | +| | | | | | | | | | -| | Options are ij, semi_structured or structured | | | +| | Options: | | | +| | | | | +| | * ``ij`` - FIXME | | | +| | * ``semi-structured`` - FIXME | | | +| | * ``structured`` - FIXME | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ @@ -64,16 +77,27 @@ The following inputs are defined using the prefix ``mac_proj``: | mg_max_coarsening_level | Maximum number of coarser levels to allow in the MAC projection | Int | 100 | | | If set to 0, the bottom solver will be called at the current level | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_solver | Which bottom solver to use in the MAC projection | String | bicgcg | +| bottom_solver | Which bottom solver to use in the MAC projection. | String | bicgcg | +| | | | | +| | Options: | | | | | | | | -| | Options are bicgcg, bicgstab, cg, cgbicg, smoother or hypre | | | +| | * ``bicgcg`` - FIXME | | | +| | * ``bicgstab`` - FIXME | | | +| | * ``cg`` - FIXME | | | +| | * ``cgbicg`` - FIXME | | | +| | * ``hypre`` - FIXME | | | +| | * ``smoother`` - FIXME | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| hypre_namespace | Namespace to use in the MAC projection when using hypre | String | hypre | +| hypre_namespace | Namespace to use in the MAC projection when using ``hypre`` | String | hypre | | | to control hypre specific settings. It can be any string. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| hypre_interface | Which interface to use in the MAC projection when using hypre | String | ij | +| hypre_interface | Which interface to use in the MAC projection when using ``hypre``. | String | ij | +| | | | | +| | Options: | | | | | | | | -| | Options are ij, semi_structured or structured | | | +| | * ``ij`` - FIXME | | | +| | * ``semi-structured`` - FIXME | | | +| | * ``structured`` - FIXME | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ @@ -86,25 +110,30 @@ The following inputs are defined using the prefix ``diffusion``: +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +=========================+=======================================================================+=============+==============+ -| verbose | Verbosity of linear solver for diffusion solve | int | 0 | +| verbose | Verbosity of linear solver for diffusion. | Int | 0 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_verbose | Verbosity of BiCGStab solver in diffusion solve | int | 0 | +| bottom_verbose | Verbosity of BiCGStab solver in diffusion. | Int | 0 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_rtol | Relative tolerance in diffusion solve | Real | 1.e-11 | +| mg_rtol | Relative tolerance in diffusion solver. | Real | 1.e-11 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_atol | Absolute tolerance in diffusion solve | Real | 1.e-14 | +| mg_atol | Absolute tolerance in diffusion solver. | Real | 1.e-14 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| maxiter | Maximum number of iterations in diffusion solve | int | 100 | +| maxiter | Maximum number of iterations in diffusion solver. | Int | 100 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_maxiter | Maximum number of iterations in diffusion solve | int | 100 | -| | bottom solver if using bicg, cg, bicgcg or cgbicg | | | +| bottom_maxiter | Maximum number of iterations in diffusion solver | Int | 100 | +| | bottom solver if using ``bicg``, ``cg``, ``bicgcg``, or ``cgbicg``. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_max_coarsening_level | Maximum number of coarser levels to allow in diffusion solve | int | 100 | +| mg_max_coarsening_level | Maximum number of coarser levels to allow in diffusion solve | Int | 100 | | | If set to 0, the bottom solver will be called at the current level | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_solver | Which bottom solver to use in the diffusion solve | string | bicgcg | +| bottom_solver | Which bottom solver to use for diffusion. | String | bicgcg | +| | | | | +| | Options: | | | | | | | | -| | Options are bicgcg, bicgstab, cg, cgbicg, or smoother | | | +| | * ``bicgcg`` - FIXME | | | +| | * ``cg`` - | | | +| | * ``cgbicg`` - | | | +| | * ``smoother`` - | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ @@ -112,36 +141,50 @@ Hypre Settings -------------- `hypre` settings are specified using the following inputs which are read directly by AMReX when `hypre` is used as -the bottom solve for the MAC and/or nodal projections. By default, these inputs are defined using the +the bottom solver for the MAC and/or nodal projections. By default, these inputs are defined using the prefix ``hypre``, however different settings for the nodal and MAC projections can be used by specifying a ``hpyre_namespace`` for each solver. .. warning:: - * MFIX-Exa must be built with `hypre` enabled to use `hypre` as the bottom solve. + * MFIX-Exa must be built with `hypre` enabled to use `hypre` as the bottom solver. * If `hypre` is used for the nodal and MAC projections, then either the ``hypre_namespace`` must be left as the default (``hypre``) or unique name spaces must be provided for both. + * These inputs are all case-sensitive. + These inputs follow the typical approach for using `hypre` in MFIX-Exa where `BoomerAMG` is employed as a preconditioner -and `GMRES` for the linear solver. +and `GMRES` for the linear solver. FIXME UNCLEAR +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +===================================+=======================================================================+=============+==============+ -| hypre_preconditioner | Type of preconditioner | string | none | +| hypre_preconditioner | Type of preconditioner when using ``hypre`` | String | none | | | | | | -| | Options are BoomerAMG or euclid | | | +| | Options: | | | +| | | | | +| | * ``none`` - no preconditioner | | | +| | * ``BoomerAMG`` - FIXME | | | +| | * ``euclid`` - FIXME | | | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| recompute_preconditioner | Recompute preconditioner during runs | Bool | true | +| recompute_preconditioner | Recompute preconditioner during runs | Bool | true | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| hypre_solver | Type of hypre solver | string | BoomerAMG | +| hypre_solver | Type of hypre solver. | String | BoomerAMG | +| | | | | +| | Options: | | | | | | | | -| | Options are BoomerAMG, GMRES, COGMRES, LGMRES, FlexGMRES, BiCGSTAB, | | | -| | PCG or Hybrid | | | +| | * ``BoomerAMG`` - FIXME DESC | | | +| | * ``GMRES`` | | | +| | * ``COGMRES`` | | | +| | * ``LGMRES`` | | | +| | * ``FlexGMRES`` | | | +| | * ``BiCGSTAB`` | | | +| | * ``PCG`` | | | +| | * ``Hybrid`` | | | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| verbose | Verbosity of hypre | int | 0 | +| verbose | Verbosity of hypre. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| num_krylov | Number of iterations | int | 50 | +| num_krylov | Number of iterations. | Int | 50 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ @@ -150,61 +193,61 @@ The following inputs are valid when using ``BoomerAMG`` as a preconditioner or s +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +===================================+=======================================================================+=============+==============+ -| bamg_verbose | Set BoomerAMG verbosity | int | 0 | +| bamg_verbose | Set BoomerAMG verbosity | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_logging | See HYPRE_BoomerAMGSetLogging | int | 0 | +| bamg_logging | See HYPRE_BoomerAMGSetLogging | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_max_iterations | See HYPRE_BoomerAMGSetMaxIter | int | 1 | +| bamg_max_iterations | See HYPRE_BoomerAMGSetMaxIter | Int | 1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_precond_tolerance | See HYPRE_BoomerAMGSetTol | Real | 0.0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_coarsen_type | See HYPRE_BoomerAMGSetCoarsenType | int | 6 | +| bamg_coarsen_type | See HYPRE_BoomerAMGSetCoarsenType | Int | 6 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_cycle_type | See HYPRE_BoomerAMGSetCycleType | int | 1 | +| bamg_cycle_type | See HYPRE_BoomerAMGSetCycleType | Int | 1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_relax_order | See HYPRE_BoomerAMGSetRelaxOrder | int | 1 | +| bamg_relax_order | See HYPRE_BoomerAMGSetRelaxOrder | Int | 1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_relax_type | See HYPRE_BoomerAMGSetRelaxType | int | 6 | +| bamg_relax_type | See HYPRE_BoomerAMGSetRelaxType | Int | 6 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_down_relax_type | See HYPRE_BoomerAMGSetCycleRelaxType | int | 11 | +| bamg_down_relax_type | See HYPRE_BoomerAMGSetCycleRelaxType | Int | 11 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_up_relax_type | See HYPRE_BoomerAMGSetCycleRelaxType | int | 11 | +| bamg_up_relax_type | See HYPRE_BoomerAMGSetCycleRelaxType | Int | 11 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_coarse_relax_type | See HYPRE_BoomerAMGSetCycleRelaxType | int | 11 | +| bamg_coarse_relax_type | See HYPRE_BoomerAMGSetCycleRelaxType | Int | 11 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_num_sweeps | See HYPRE_BoomerAMGSetNumSweeps | int | 2 | +| bamg_num_sweeps | See HYPRE_BoomerAMGSetNumSweeps | Int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_num_down_sweeps | See HYPRE_BoomerAMGSetCycleNumSweeps | int | 2 | +| bamg_num_down_sweeps | See HYPRE_BoomerAMGSetCycleNumSweeps | Int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_num_up_sweeps | See HYPRE_BoomerAMGSetCycleNumSweeps | int | 2 | +| bamg_num_up_sweeps | See HYPRE_BoomerAMGSetCycleNumSweeps | Int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_num_coarse_sweeps | See HYPRE_BoomerAMGSetCycleNumSweeps | int | 1 | +| bamg_num_coarse_sweeps | See HYPRE_BoomerAMGSetCycleNumSweeps | Int | 1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_max_levels | See HYPRE_BoomerAMGSetMaxLevels | int | 20 | +| bamg_mdax_levels | See HYPRE_BoomerAMGSetMaxLevels | Int | 20 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_strong_threshold | See HYPRE_BoomerAMGSetStrongThreshold | Real | 0.57 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_interp_type | See HYPRE_BoomerAMGSetInterpType | int | 0 | +| bamg_interp_type | See HYPRE_BoomerAMGSetInterpType | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_variant | See HYPRE_BoomerAMGSetVariant | int | 0 | +| bamg_variant | See HYPRE_BoomerAMGSetVariant | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_keep_transpose | See HYPRE_BoomerAMGSetKeepTranspose | int | 0 | +| bamg_keep_transpose | See HYPRE_BoomerAMGSetKeepTranspose | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_min_coarse_size | See HYPRE_BoomerAMGSetMinCoarseSize | int | 1 | +| bamg_min_coarse_size | See HYPRE_BoomerAMGSetMinCoarseSize | Int | 1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_max_coarse_size | See HYPRE_BoomerAMGSetMaxCoarseSize | int | 9 | +| bamg_max_coarse_size | See HYPRE_BoomerAMGSetMaxCoarseSize | Int | 9 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_pmax_elmts | See HYPRE_BoomerAMGSetPMaxElmts | int | 4 | +| bamg_pmax_elmts | See HYPRE_BoomerAMGSetPMaxElmts | Int | 4 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_agg_num_levels | See HYPRE_BoomerAMGSetAggNumLevels | int | 0 | +| bamg_agg_num_levels | See HYPRE_BoomerAMGSetAggNumLevels | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_agg_interp_type | See HYPRE_BoomerAMGSetAggInterpType | int | 4 | +| bamg_agg_interp_type | See HYPRE_BoomerAMGSetAggInterpType | Int | 4 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_agg_pmax_elmts | See HYPRE_BoomerAMGSetAggPMaxElmts | int | 0 | +| bamg_agg_pmax_elmts | See HYPRE_BoomerAMGSetAggPMaxElmts | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_trunc_factor | See HYPRE_BoomerAMGSetTruncFactor | Real | 0.1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_set_restriction | See HYPRE_BoomerAMGSetRestriction | int | 0 | +| bamg_set_restriction | See HYPRE_BoomerAMGSetRestriction | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ @@ -216,11 +259,11 @@ The following inputs are valid when using ``BoomerAMG`` as a preconditioner or s +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +===================================+=======================================================================+=============+==============+ -| adjust_singular_matrix | Should be true if the problem to be solved has singular matrix | Bool | false | +| adjust_singular_matrix | Enable if the problem to be solved has a singular matrix | Bool | false | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| overwrite_existing_matrix_files | Over-write existing matrix files | Bool | false | +| overwrite_existing_matrix_files | Overwrite existing matrix files | Bool | false | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| write_matrix_files | Write out matrix into text files | Bool | false | +| write_matrix_files | Write matrix into text files | Bool | false | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ diff --git a/docs/source_docs/user_guide/inputs/output.rst b/docs/source_docs/user_guide/inputs/output.rst index 2043e27..d081483 100644 --- a/docs/source_docs/user_guide/inputs/output.rst +++ b/docs/source_docs/user_guide/inputs/output.rst @@ -7,6 +7,6 @@ Stuff here? :maxdepth: 0 output/checkpointing - output/plotfiles + output/plotting output/monitors output/ascent diff --git a/docs/source_docs/user_guide/inputs/output/ascent.rst b/docs/source_docs/user_guide/inputs/output/ascent.rst index d30ae2a..118111d 100644 --- a/docs/source_docs/user_guide/inputs/output/ascent.rst +++ b/docs/source_docs/user_guide/inputs/output/ascent.rst @@ -1,5 +1,5 @@ Ascent ------- +====== The following inputs must be preceded by the prefix ``mfix`` and control frequency and naming of plotfile generation as well as whether the EB geometry or level set should be written out, and if the particles should be written out in Ascii diff --git a/docs/source_docs/user_guide/inputs/output/checkpointing.rst b/docs/source_docs/user_guide/inputs/output/checkpointing.rst index 2f363ca..e571458 100644 --- a/docs/source_docs/user_guide/inputs/output/checkpointing.rst +++ b/docs/source_docs/user_guide/inputs/output/checkpointing.rst @@ -8,23 +8,23 @@ The following inputs must be preceded by the prefix ``mfix`` and control checkpo +-------------------------+-----------------------------------------------------------------------+-------------+------------+ | | Description | Type | Default | +=========================+=======================================================================+=============+============+ -| restart | If present, then the name of file to restart from | String | None | +| restart | If present, then the name of file to restart from | String | None | +-------------------------+-----------------------------------------------------------------------+-------------+------------+ -| check_int | Frequency of checkpoint output in timesteps number; | Int | -1 | +| check_int | Frequency of checkpoint output in number of timesteps; | Int | -1 | | | if -1 then no checkpoints will be written | | | +-------------------------+-----------------------------------------------------------------------+-------------+------------+ -| check_per_approx | Frequency of checkpoint output in simulation time; | Real | 0 | +| check_per_approx | Frequency of checkpoint output in simulation time; | Real | 0 | | | if 0 then no checkpoints will be written | | | +-------------------------+-----------------------------------------------------------------------+-------------+------------+ -| check_walltime_interval | Frequency of checkpoint output in runtime (HH:MM:SS) | String | "" | +| check_walltime_interval | Frequency of checkpoint output in runtime (HH:MM:SS) | String | None | +-------------------------+-----------------------------------------------------------------------+-------------+------------+ | check_file | Prefix to use for checkpoint output | String | chk | +-------------------------+-----------------------------------------------------------------------+-------------+------------+ -| geom_chk_write | When True, writes the EB geometry data into geom_chk_file | bool | False | +| 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, reads the EB geometry data from geom_chk_file | bool | False | +| 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. | | | +-------------------------+-----------------------------------------------------------------------+-------------+------------+ diff --git a/docs/source_docs/user_guide/inputs/output/monitors.rst b/docs/source_docs/user_guide/inputs/output/monitors.rst index 66ee112..5bf5501 100644 --- a/docs/source_docs/user_guide/inputs/output/monitors.rst +++ b/docs/source_docs/user_guide/inputs/output/monitors.rst @@ -5,7 +5,7 @@ A Monitor is a tool for capturing data from the solver about the model. Data (such as volume fraction, pressure, velocity, etc.) for a given monitor region is written to a CSV file while the solver is running. -To define monitors, the following inputs must be preceded by "mfix.": +To define monitors, the following inputs must be preceded by the prefix ``mfix``: +--------------------+------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -23,13 +23,13 @@ To define monitors, the following inputs must be preceded by "mfix.": mfix.monitors.my_monitor1 = Lagrangian::Average::VolumeWeightedAverage -Region Selection +Region selection ---------------- To define a monitor, there must be a region already defined in the regions inputs. A Monitor region is a single point, plane, or volume. Multiple regions cannot be combined for a monitor. The following inputs must be preceded by -"mfix.monitors.": +the prefix ``mfix.monitors``: +------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -44,14 +44,14 @@ cannot be combined for a monitor. The following inputs must be preceded by mfix.monitors.my_monitor1.region = regionB -Monitor Output +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 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 -"mfix.monitors.": +the prefix ``mfix.monitors``: +-------------------------------+----------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -65,11 +65,12 @@ provides header information. The following inputs must be preceded by | [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" | -| | Admissible values are: | | | +| [monitor].output.openmode | Sets the open mode for the monitor output file. | String | app | | | | | | -| | * "app" for appending to the file if it already exists | | | -| | * "trunc" for overwriting the output file if it exists | | | +| | 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 | +-------------------------------+----------------------------------------------------------+-------------+-----------+ @@ -94,11 +95,11 @@ provides header information. The following inputs must be preceded by mfix.monitors.my_monitor1.plot_per_approx = 0.01 -Monitor Variables +Monitor variables ----------------- The variables to be monitored can be specified in the inputs by including the -following input preceded by the "mfix.monitors.": +following input preceded by the prefix ``mfix.monitors``: +---------------------+--------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -113,7 +114,7 @@ following input preceded by the "mfix.monitors.": mfix.monitors.my_monitor1.variables = density drag_y T_s txfr_vel_x -Eulerian Monitors +Eulerian monitors ----------------- There are different types of monitors available. A monitor type applies an @@ -205,7 +206,7 @@ The following table lists all the fluid phase variables that can be monitored: +--------------------------+-----------------------------------------------------------------------------------------+ -Uniform Scalar Field +Uniform scalar field ~~~~~~~~~~~~~~~~~~~~ The following table lists all the fluid phase space-uniform variables that can @@ -230,7 +231,7 @@ Value .. math:: \phi_{ijk} -Point Region +Point region ~~~~~~~~~~~~ For a point region, the monitor data value is simply the value of the variable @@ -246,7 +247,7 @@ Value .. math:: \phi_{ijk} -Area or Volume Region +Area or volume region ~~~~~~~~~~~~~~~~~~~~~ The following monitor types are valid for area and volume regions: @@ -297,7 +298,7 @@ Average .. math:: \phi_0 = \frac{\sum_{ijk} \phi_{ijk}}{N} -Standard Deviation +Standard deviation +-------------------------------------------+ | Eulerian::AreaRegion::StandardDeviation | +-------------------------------------------+ @@ -310,7 +311,7 @@ Standard Deviation .. math:: \sigma_{\phi} = \sqrt{\frac{ \sum_{ijk} (\phi_{ijk}-\phi_{0})^2 }{N}} -Surface Integrals +Surface integrals ~~~~~~~~~~~~~~~~~ The following types are only valid for area regions: @@ -325,7 +326,7 @@ Area .. math:: \int dA = \sum_{ijk} \lvert A_{ijk} \rvert -Area-Weighted Average +Area-weighted average +------------------------------------------------+ | Eulerian::SurfaceIntegral::AreaWeightedAverage | +------------------------------------------------+ @@ -336,7 +337,7 @@ Area-Weighted Average .. math:: \frac{\int\phi dA}{A} = \frac{\sum_{ijk}{\phi_{ijk} \lvert A_{ijk} \rvert}}{\sum_{ijk}{\lvert A_{ijk} \rvert}} -Flow Rate +Flow rate +-------------------------------------+ | Eulerian::SurfaceIntegral::FlowRate | +-------------------------------------+ @@ -347,7 +348,7 @@ Flow Rate .. math:: \int\varepsilon\rho\phi{v_n}dA = \sum_{ijk}\varepsilon_{ijk}\rho_{ijk}\phi_{ijk} {v}_{n,ijk} \lvert A_{ijk} \rvert -Mass Flow Rate +Mass flow rate +-----------------------------------------+ | Eulerian::SurfaceIntegral::MassFlowRate | +-----------------------------------------+ @@ -358,7 +359,7 @@ Mass Flow Rate .. math:: \int\varepsilon\rho{v_n} dA = \sum_{ijk}\varepsilon_{ijk}\rho_{ijk}{v}_{n,ijk} \lvert A_{ijk} \rvert -Mass-Weighted Average +Mass-weighted average +------------------------------------------------+ | Eulerian::SurfaceIntegral::MassWeightedAverage | +------------------------------------------------+ @@ -369,7 +370,7 @@ Mass-Weighted Average .. math:: \frac{\int\varepsilon\rho\phi{v_n}dA}{\int\varepsilon\rho{v_n}dA} = \frac{\sum_{ijk}\varepsilon_{ijk}\rho_{ijk}\phi_{ijk} {v}_{n,ijk} \lvert A_{ijk} \rvert}{\sum_{ijk}\varepsilon_{ijk}\rho_{ijk} {v}_{n,ijk} \lvert A_{ijk} \rvert} -Volume Flow Rate +Volume flow rate +-------------------------------------------+ | Eulerian::SurfaceIntegral::VolumeFlowRate | +-------------------------------------------+ @@ -381,7 +382,7 @@ Volume Flow Rate .. math:: \int\varepsilon{v_n}dA = \sum_{ijk}\varepsilon_{ijk}{v}_{n,ijk} \lvert A_{ijk} \rvert -Volume Integrals +Volume integrals ~~~~~~~~~~~~~~~~ The following types are only valid for volume regions: @@ -396,7 +397,7 @@ Volume .. math:: \int dV = \sum_{ijk}{ \lvert V_{ijk}} \rvert -Volume Integral +Volume integral +------------------------------------------+ | Eulerian::VolumeIntegral::VolumeIntegral | +------------------------------------------+ @@ -406,7 +407,7 @@ Volume Integral .. math:: \int \phi dV = \sum_{ijk}{\phi_{ijk} \lvert V_{ijk}} \rvert -Volume-Weighted Average +Volume-weighted average +-------------------------------------------------+ | Eulerian::VolumeIntegral::VolumeWeightedAverage | +-------------------------------------------------+ @@ -417,7 +418,7 @@ Volume-Weighted Average .. math:: \frac{\int\phi dV}{V} = \frac{\sum_{ijk}{\phi_{ijk} \lvert V_{ijk} \rvert}}{\sum_{ijk}{\lvert V_{ijk} \rvert}} -Mass-Weighted Integral +Mass-weighted integral +------------------------------------------------+ | Eulerian::VolumeIntegral::MassWeightedIntegral | +------------------------------------------------+ @@ -427,7 +428,7 @@ Mass-Weighted Integral .. math:: \int \varepsilon\rho\phi dV = \sum_{ijk}\varepsilon_{ijk}\rho_{ijk}\phi_{ijk} \lvert V_{ijk}\rvert -Mass-Weighted Average +Mass-weighted Average +-----------------------------------------------+ | Eulerian::VolumeIntegral::MassWeightedAverage | +-----------------------------------------------+ @@ -441,7 +442,7 @@ Mass-Weighted Average -Lagrangian Monitors +Lagrangian monitors ------------------- There are different types of monitors available. A monitor type applies an @@ -553,7 +554,7 @@ Sum .. math:: \sum_p w_p \phi_p -Mass-Weighted Sum +Mass-weighted sum +----------------------------------------------+ | Lagrangian::GeneralProperty::MassWeightedSum | @@ -606,7 +607,7 @@ Average .. math:: \bar{\phi} = \frac{\sum_p w_p \phi_p}{\sum_p w_p} -Standard Deviation +Standard deviation +-------------------------------------------------+ | Lagrangian::AveragedProperty::StandardDeviation | +-------------------------------------------------+ @@ -649,7 +650,7 @@ used, preceded by the prefix ``mfix.monitors``: +------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +==================+=======================================================================+=============+===========+ -| [monitor].plane | defines the plane through which the flow rate of the particles in the | String | None | +| [monitor].plane | Defines the plane through which the flow rate of the particles in the | String | None | | | monitoring region [region] will be computed | | | +------------------+-----------------------------------------------------------------------+-------------+-----------+ diff --git a/docs/source_docs/user_guide/inputs/output/plotfiles.rst b/docs/source_docs/user_guide/inputs/output/plotting.rst similarity index 73% rename from docs/source_docs/user_guide/inputs/output/plotfiles.rst rename to docs/source_docs/user_guide/inputs/output/plotting.rst index 175ba49..273356f 100644 --- a/docs/source_docs/user_guide/inputs/output/plotfiles.rst +++ b/docs/source_docs/user_guide/inputs/output/plotting.rst @@ -1,10 +1,10 @@ .. _Chap:InputsPlotfiles: -Plotfiles and Other Output +Plotfiles and other output ========================== The following inputs must be preceded by the prefix ``mfix`` and control frequency and naming of plotfile generation as well -as whether the EB geometry or level set should be written out, and if the particles should be written out in Ascii +as whether the EB geometry or level set should be written, and if the particles should be written out in Ascii format (for debugging). +----------------------+-----------------------------------------------------------------------+-------------+-----------+ @@ -16,7 +16,7 @@ format (for debugging). | plot_per_approx | Time period of plotfile output (approximate); does not modify dt | Real | -1 | | | if -1 then no plotfiles will be written at this frequency | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plotfile_on_restart | Should we write a plotfile when we restart (only used if plot_int>0) | Bool | False | +| plotfile_on_restart | Write a plotfile when we restart (only used if plot_int>0) | Bool | false | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ | plot_file | Prefix to use for plotfile output | String | plt | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ @@ -39,67 +39,67 @@ format (for debugging). +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -The following inputs must be preceded by "mfix." and control what variables will be written in plotfiles. +The following inputs must be preceded by the prefix ``mfix`` and control which variables will be written in plotfiles. +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +=====================+=======================================================================+=============+===========+ -| plt_regtest | Save all variables to plot file (overrides all other IO flags) | Int | 0 | +| plt_regtest | Plot all variables (overrides all other plot flags) | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_vel_g | Save fluid velocity data to plot file | Int | 1 | +| plt_vel_g | Plot fluid velocity data | Int | 1 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_ep_g | Save fluid volume fraction to plot file | Int | 1 | +| plt_ep_g | Plot fluid volume fraction | Int | 1 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_p_g | Save fluid pressure to plot file | Int | 0 | +| plt_p_g | Plot fluid pressure | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_ro_g | Save fluid density to plot file | Int | 0 | +| plt_ro_g | Plot fluid density | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_mu_g | Save fluid molecular viscosity to plot file | Int | 0 | +| plt_mu_g | Plot fluid molecular viscosity | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_volfrac | Save Eulerian grid volume fraction (from cut cells) to plot file | Int | 0 | +| plt_volfrac | Plot Eulerian grid volume fraction (from cut cells) | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_gradp_g | Save gradient of pressure filed to plot file | Int | 0 | +| plt_gradp_g | Plot gradient of pressure | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_vort | Save vorticity to plot file | Int | 0 | +| plt_vort | Plot vorticity | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_vel_p | Save particle velocity to plot file | Int | 1 | +| plt_vel_p | Plot particle velocity | Int | 1 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_radius | Save particle radius to plot file | Int | 0 | +| plt_radius | Plot particle radius | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_volume | Save particle volume to plot file | Int | 0 | +| plt_volume | Plot particle volume | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_volume | Save particle volume to plot file | Int | 0 | +| plt_volume | Plot particle volume | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_mass | Save particle mass to plot file | Int | 0 | +| plt_mass | Plot particle mass | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_ro_p | Save particle density to plot file | Int | 0 | +| plt_ro_p | Plot particle density | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_omoi | Save (one divided by the) particle momentum of inertia to plot file | Int | 0 | +| plt_omoi | Plot (one divided by the) particle momentum of inertia | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_mass | Save particle mass to plot file | Int | 0 | +| plt_mass | Plot particle mass | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_omega_p | Save particle angular velocity to plot file | Int | 0 | +| plt_omega_p | Plot particle angular velocity | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_drag_p | Save particle drag force to plot file | Int | 0 | +| plt_drag_p | Plot particle drag force | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_phase | Save particle type to plot file | Int | 0 | +| plt_phase | Plot particle type | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ The following inputs must be preceded by the prefix ``mfix`` and control whether the EB geometry or level set should be written out: -+----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| | Description | Type | Default | -+======================+=======================================================================+=============+===========+ -| write_ls | Should we write a plotfile holding the level set and volfrac? | Bool | False | -| | If true, it will only be written once,after initialization or restart | | | -+----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| write_eb_surface | Should we write out the EB geometry in vtp format | Bool | False | -| | If true, it will only be written once,after initialization or restart | | | -+----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_geom | Should we write a plotfile holding the EB geometry data? | Bool | False | -| | If true, it will only be written once,after initialization or restart | | | -+----------------------+-----------------------------------------------------------------------+-------------+-----------+ ++----------------------+--------------------------------------------------------------------------+-------------+-----------+ +| | Description | Type | Default | ++======================+==========================================================================+=============+===========+ +| write_ls | Write a plotfile holding the level set and volfrac. | Bool | false | +| | If enabled, it will only be written once, after initialization or restart| | | ++----------------------+--------------------------------------------------------------------------+-------------+-----------+ +| write_eb_surface | Write out the EB geometry in vtp format. | Bool | false | +| | If enabled, it will only be written once, after initialization or restart| | | ++----------------------+--------------------------------------------------------------------------+-------------+-----------+ +| plt_geom | Write a plotfile holding the EB geometry data. | Bool | false | +| | If true, it will only be written once,after initialization or restart | | | ++----------------------+--------------------------------------------------------------------------+-------------+-----------+ `Ascent `_ has been integrated into MFIX-Exa for *in situ* visualization. @@ -133,43 +133,43 @@ All these parameters are user-defined. +---------------------------+-----------------------------------------------------------------+-------------+-----------+ | [region].plot_per_approx | Specify time interval frequency for plotting the file | Real | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_regtest | Save all variables to plot file (overrides all other IO flags) | Int | 0 | +| [region].plt_regtest | Plot all variables (overrides all other plot flags) | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_radius | Save particle radius to plot file | Int | 0 | +| [region].plt_radius | Plot particle radius | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_volume | Save particle volume to plot file | Int | 0 | +| [region].plt_volume | Plot particle volume | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_mass | Save particle mass to plot file | Int | 0 | +| [region].plt_mass | Plot particle mass | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_ro_p | Save particle density to plot file | Int | 0 | +| [region].plt_ro_p | Plot particle density | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_omoi | Save inverse of particle momentum of inertia to plot file | Int | 0 | +| [region].plt_omoi | Plot inverse of particle momentum of inertia | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_vel_p | Save particle velocity to plot file | Int | 0 | +| [region].plt_vel_p | Plot particle velocity | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_omega_p | Save particle angular velocity to plot file | Int | 0 | +| [region].plt_omega_p | Plot particle angular velocity | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_statwt | Save particle statistical weight to plot file | Int | 0 | +| [region].plt_statwt | Plot particle statistical weight | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_drag_p | Save particle drag force to plot file | Int | 0 | +| [region].plt_drag_p | Plot particle drag force | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_cp_s | Save particle specific heat coefficient to plot file | Int | 0 | +| [region].plt_cp_s | Plot particle specific heat coefficient | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_T_p | Save particle temperature to plot file | Int | 0 | +| [region].plt_T_p | Plot particle temperature | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_convection | Save particle convection coefficient to plot file | Int | 0 | +| [region].plt_convection | Plot particle convection coefficient | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_X_s | Save particle species mass fractions to plot file | Int | 0 | +| [region].plt_X_s | Plot particle species mass fractions | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_vel_s_txfr | Save particle interphase velocity transfer to plot file | Int | 0 | +| [region].plt_vel_s_txfr | Plot particle interphase velocity transfer | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_h_s_txfr | Save particle interphase enthalpy transfer to plot file | Int | 0 | +| [region].plt_h_s_txfr | Plot particle interphase enthalpy transfer | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_mass_sn_txfr | Save particle interphase mass transfer to plot file | Int | 0 | +| [region].plt_mass_sn_txfr | Plot particle interphase mass transfer | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_phase | Save particle phase to plot file | Int | 0 | +| [region].plt_phase | Plot particle phase | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_state | Save particle state to plot file | Int | 0 | +| [region].plt_state | Plot particle state | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ For each region with name [region] specified in the inputs, it will be saved a plotfile with name "partsXXXXX_[region]", where XXXXX stands for the timestep number. diff --git a/docs/source_docs/user_guide/inputs/porous_media_defs.rst b/docs/source_docs/user_guide/inputs/porous_media.rst similarity index 95% rename from docs/source_docs/user_guide/inputs/porous_media_defs.rst rename to docs/source_docs/user_guide/inputs/porous_media.rst index 6d4b011..bed06fa 100644 --- a/docs/source_docs/user_guide/inputs/porous_media_defs.rst +++ b/docs/source_docs/user_guide/inputs/porous_media.rst @@ -1,7 +1,7 @@ .. _InputsPorousMediaDefs: -Porous media -============ +Porous media definitions +======================== Homogeneous porous media are modeled by the addition of a momentum source term, :math:`\boldsymbol{S}_{pm}`, to the fluid momentum equation. @@ -11,7 +11,7 @@ source term, :math:`\boldsymbol{S}_{pm}`, to the fluid momentum equation. \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. +:math:`C_1` and :math:`C_2` are user-defined constants. The following inputs are defined using the prefix ``pm``: diff --git a/docs/source_docs/user_guide/inputs/regions_defs.rst b/docs/source_docs/user_guide/inputs/regions.rst similarity index 100% rename from docs/source_docs/user_guide/inputs/regions_defs.rst rename to docs/source_docs/user_guide/inputs/regions.rst diff --git a/docs/source_docs/user_guide/inputs/solids_model.rst b/docs/source_docs/user_guide/inputs/solids_model.rst index 034f19e..1c09682 100644 --- a/docs/source_docs/user_guide/inputs/solids_model.rst +++ b/docs/source_docs/user_guide/inputs/solids_model.rst @@ -11,25 +11,22 @@ 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 | | | +| | the SOLIDS solver. The user-defined names are used to | | | | | specify DEM and/or PIC model inputs. | | | +------------------------------------------+-------------------------------------------------------------+----------+----------+ -| molecular_weight | Value of constant solid molecular | Real | 0 | -| | weight | | | +| molecular_weight | Value of constant solid molecular weight. | Real | 0 | +------------------------------------------+-------------------------------------------------------------+----------+----------+ -| specific_heat | Specify which specific heat model to | String | None | -| | use for solid. Available options | | | -| | include: | | | +| specific_heat | Specify which specific heat model to use for solids. | String | constant | +| | use for solid. | | | | | | | | -| | * 'constant' for constant specific heat | | | -| | model | | | +| | Options: | | | +| | | | | +| | * ``constant`` - constant specific heat | | | +------------------------------------------+-------------------------------------------------------------+----------+----------+ -| specific_heat.constant | Value of species molecular weight. | Real | 0 | -| | [required if fluid.specific_heat = | | | -| | 'constant']. | | | +| specific_heat.constant | Constant solids specific heat value. | Real | 0 | +| | A value is required for ``constant`` specific heat model. | | | +------------------------------------------+-------------------------------------------------------------+----------+----------+ -| reference_temperature | Value of the reference temperature used | Real | 0 | -| | for specific enthalpy | | | +| reference_temperature | Reference temperature used for specific enthalpy. | Real | 0 | +------------------------------------------+-------------------------------------------------------------+----------+----------+ | species | Specify which species can constitute | String | None | | | the fluid phase [defined species must | | | @@ -40,7 +37,7 @@ models. The following inputs are defined with the prefix ``solids``: +------------------------------------------+-------------------------------------------------------------+----------+----------+ | newton_solver.relative_tol | Define relative tolerance for damped Newton solver | Real | 1.e-6 | +------------------------------------------+-------------------------------------------------------------+----------+----------+ -| newton_solver.max_iterations | Define max number of iterations for damped Newton solver | int | 100 | +| newton_solver.max_iterations | Define max number of iterations for damped Newton solver | Int | 100 | +------------------------------------------+-------------------------------------------------------------+----------+----------+ Below is an example for specifying the solids solver model options. @@ -70,7 +67,7 @@ Enabling the DEM solver and specifying model options. The following keys must b | | Description | Type | Default | +===============================+=========================================================================+==========+===========+ | solve | Specified name(s) of the DEM types or None to disable the DEM solver. | String | None | -| | The user defined names are used to specify DEM model inputs. | | | +| | The user-defined names are used to specify DEM model inputs. | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ | friction_coeff.pp | Friction coefficient :: particle to particle collisions [required] | Real | 0 | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ @@ -92,10 +89,10 @@ Enabling the DEM solver and specifying model options. The following keys must b | damping_tang_fac.pw | Factor relating the tangential damping coefficient to the normal | Real | 0.5 | | | damping coefficient :: particle to wall collisions | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| implicit_drag | Apply fluid-particle drag force by | int | 0 | +| implicit_drag | Apply fluid-particle drag force by | Int | 0 | | | :ref:`implicit velocity update`. | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| tan_history | Include tangential history force in the collision model. | Bool | False | +| 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 | | | @@ -119,7 +116,7 @@ Enabling the DEM solver and specifying model options. The following keys must b The following inputs use the DEM type names specified using the `dem.solve` input to define restitution coefficients and -are proceeded with `dem.restitution_coeff`. These must be defined for all solid-solid and solid-wall combinations. +are proceeded with the prefix ``dem.restitution_coeff``. These must be defined for all solid-solid and solid-wall combinations. +-------------------------+-------------------------------------------------------------------------+----------+-----------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/species_defs.rst b/docs/source_docs/user_guide/inputs/species.rst similarity index 89% rename from docs/source_docs/user_guide/inputs/species_defs.rst rename to docs/source_docs/user_guide/inputs/species.rst index 44959f9..3bc75d8 100644 --- a/docs/source_docs/user_guide/inputs/species_defs.rst +++ b/docs/source_docs/user_guide/inputs/species.rst @@ -8,29 +8,33 @@ The following inputs are defined using the prefix ``species``: +--------------------------+------------------------------------------------------------------------+----------+-----------+ | | Description | Type | Default | +==========================+========================================================================+==========+===========+ -| solve | Specified name of the species or None to disable the | String | None | +| solve | Specified name(s) of the species or None to disable the | String | None | | | species solver. The name assigned to the species | | | | | solver is used to specify species inputs. | | | +--------------------------+------------------------------------------------------------------------+----------+-----------+ | diffusivity | Fluid species diffusivity model. | String | None | | | | | | -| | * ``constant`` a constant diffusion coefficient is used for | | | +| | Options: | | | +| | | | | +| | * ``constant`` - a constant diffusion coefficient is used for | | | | | all fluid species. | | | | | | | | +--------------------------+------------------------------------------------------------------------+----------+-----------+ -| diffusivity.constant | Constant species diffusivity -- required for | Real | 0 | +| diffusivity.constant | Constant species diffusivity - required for | Real | 0 | | | ``constant`` diffusivity model | | | | | | | | +--------------------------+------------------------------------------------------------------------+----------+-----------+ -| specific_heat | Species specific heat model. This setting only applies if either | String | None | +| specific_heat | Species specific heat model. This setting only applies if either | String | FIXME | | | ``fluid.specific_heat = mixture`` or | | | | | ``solids.specific_heat = mixture`` | | | | | | | | -| | * ``constant`` a constant specific heat is defined for each species | | | +| | Options (case-insensitive): | | | +| | | | | +| | * ``constant`` - a constant specific heat is defined for each species | | | | | and a *mixture* specific heat is computed based on the fluid or | | | | | particle composition. | | | | | | | | -| | * ``NASA7-poly`` the specific heat of each species is defined by one | | | +| | * ``NASA7-poly`` - the specific heat of each species is defined by one | | | | | or more polynomials that are a function of temperature, then the | | | | | *mixture* specific heat is computed based on the fluid or particle | | | | | composition. | | | @@ -40,7 +44,7 @@ The following inputs are defined using the prefix ``species``: | | :math:`c_p(T)/R = \sum_{i=0}^4 a_{i}T^{i}` | | | | | | | | +--------------------------+------------------------------------------------------------------------+----------+-----------+ -| ignore_discontinuities | MFIX-Exa asserts that the low and high NASA-7 polynomials are | int | 0 | +| ignore_discontinuities | MFIX-Exa asserts that the low and high NASA-7 polynomials are | Int | 0 | | | continuous at the 1000K temperature split. However, some polynomials | | | | | do not have valid high temperature coefficients, for example, liquid | | | | | water. By setting this keyword to 1, the simulation will only warn | | | @@ -50,15 +54,21 @@ The following inputs are defined using the prefix ``species``: | | Therefore, this option should only be used when the simulation is not | | | | | expected to cross over the transition temperature. | | | +--------------------------+------------------------------------------------------------------------+----------+-----------+ -| viscosity.molecular | Molecular viscosity model of species. This setting only applies when | String | 0 | +| viscosity.molecular | Molecular viscosity model of species. This setting only applies when | String | FIXME | | | ``fluid.viscosity.molecular = mixture``. | | | | | | | | -| | Options are ``constant`` or ``Sutherland`` or ``Reid``. | | | -| | See :ref:`viscosity model descriptions `. | | | +| | Options: | | | +| | | | | +| | * ``constant`` - constant viscosity | | | +| | * ``Sutherland`` :cite:p:`suth1893` | | | +| | * ``Reid`` :cite:p:`reid87` | | | +| | | | | +| | See :ref:`viscosity model descriptions ` | | | +| | in fluid section. | | | +--------------------------+------------------------------------------------------------------------+----------+-----------+ -The following inputs are defined for each species using the prefix ``species.[species name]``: +The following inputs are defined for each species using the prefix ``species.[species_name]``: +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ | | Description | Type | Default | @@ -102,7 +112,7 @@ The following inputs are defined for each species using the prefix ``species.[sp | | polynomials are used to define the specific heat and enthalpy. | | | | | | | | +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ -| enthalpy_of_formation | Enthalpy of formation of species. This input is required only when | Real | 0 | +| enthalpy_of_formation | Enthalpy of formation of species. Required only when | Real | 0 | | | the specific heat model is ``constant`` and chemical reactions | | | | | are defined. | | | +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ diff --git a/docs/source_docs/user_guide/inputs/time_stepping.rst b/docs/source_docs/user_guide/inputs/time_stepping.rst index e2cff95..4ae0a47 100644 --- a/docs/source_docs/user_guide/inputs/time_stepping.rst +++ b/docs/source_docs/user_guide/inputs/time_stepping.rst @@ -57,7 +57,7 @@ the result by the number of steps per collision, ``tcoll_ratio``: ``mfix.fixed_dt`` must be defined for particle-only DEM simulations, however it is only used to determine the frequency of outputs and has no effect on the particle advance. If - a positive value is not specified for ``mfix.fixed_dt``, then the code aborts with the + a positive value is not specified for ``mfix.fixed_dt``, then the solver aborts with the following message: .. highlight:: c++ @@ -99,7 +99,7 @@ The following inputs are defined using the prefix ``mfix``: +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | stop_time | Maximum time to reach (s) | Real | -1.0 | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ -| fixed_dt | Flag to use a fixed time step | Int | 0 | +| fixed_dt | Use a fixed time step | Int | 0 | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | cfl | CFL constraint (dt < cfl * dx / u) | Real | See note | | | | | | @@ -109,17 +109,17 @@ The following inputs are defined using the prefix ``mfix``: +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | dt_min | Abort if ``dt`` gets smaller than this value | Real | 1.e-6 | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ -| dt_max | Maximum value of ``dt`` if ``fixed_dt`` is not 1 | Real | 1.e14 | +| dt_max | Maximum value of ``dt`` if ``fixed_dt`` is not set | Real | 1.e14 | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | tcoll_ratio | DEM time step equals the min collision time divided by this value | Real | 50.0 | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | walltime_limit | Runtime limit specified with format HH:MM:SS. When the runtime has | String | "" | | | almost reached the limit (approaching is computed by considering the | | | -| | average runtime needed for each step) then the simulation ends and | | | +| | average runtime needed for each step), then the simulation ends and | | | | | a clean exit is performed | | | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ -| clean_exit | This input represents the name of a file that, if found in the run | String | "" | -| | folder, makes the code stop and perform a clean exit | | | +| clean_exit | The name of a file that, if found in the run | String | "" | +| | folder, makes the solver stop and perform a clean exit. | | | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ In the case of unsteady flow, the simulation will stop when either the number of steps @@ -131,14 +131,10 @@ The following inputs are defined using the prefix ``mfix`` and are only relevant +-----------------------+-----------------------------------------------------------------------+-------------+------------+ | Key | Description | Type | Default | +=======================+=======================================================================+=============+============+ -| steady_state | Are we running a steady-state calculation? | Int | 0 | +| steady_state | Run a steady-state calculation. | Int | 0 | +-----------------------+-----------------------------------------------------------------------+-------------+------------+ -| steady_state_tol | Tolerance for checking if we have reached steady state | Real | None | -| | | | | -| | (Must be set if steady_state = 1) | | | +| steady_state_tol | Tolerance for checking if steady state has been reached. | Real | None | +| | (Must be set if steady_state is enabled) | | | +-----------------------+-----------------------------------------------------------------------+-------------+------------+ | steady_state_maxiter | Maximum number of allowed iterations to converge to steady state | Int | 100000000 | +-----------------------+-----------------------------------------------------------------------+-------------+------------+ - - - diff --git a/docs/source_docs/user_guide/run-time_inputs.rst b/docs/source_docs/user_guide/run-time_inputs.rst index 2448226..f355078 100644 --- a/docs/source_docs/user_guide/run-time_inputs.rst +++ b/docs/source_docs/user_guide/run-time_inputs.rst @@ -48,12 +48,12 @@ keywords such as ``mfix``, ``amr``, ``geometry``, ``nodal_proj`` etc. inputs/model_options inputs/fluid_model inputs/solids_model - inputs/species_defs - inputs/porous_media_defs + inputs/species inputs/chemical_reactions - inputs/regions_defs + inputs/regions inputs/initial_conditions inputs/boundary_conditions + inputs/porous_media inputs/output inputs/advanced inputs/mpmd -- GitLab From 0267b2978b73b1d106f00d64059d11359b0de2f4 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Tue, 9 Sep 2025 14:11:06 -0500 Subject: [PATCH 34/47] remove FIXME --- .../user_guide/inputs/advanced.rst | 6 +-- .../user_guide/inputs/boundary_conditions.rst | 3 +- .../user_guide/inputs/fluid_model.rst | 4 +- .../user_guide/inputs/initial_conditions.rst | 4 +- .../user_guide/inputs/multigrid_solvers.rst | 46 +++++++++---------- .../source_docs/user_guide/inputs/species.rst | 6 +-- 6 files changed, 34 insertions(+), 35 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/advanced.rst b/docs/source_docs/user_guide/inputs/advanced.rst index 9e94245..12cb5d3 100644 --- a/docs/source_docs/user_guide/inputs/advanced.rst +++ b/docs/source_docs/user_guide/inputs/advanced.rst @@ -79,14 +79,14 @@ The following inputs must be preceded by the prefix ``mfix`` and control load ba | | | | | | | Options (case-insensitive): | | | | | | | | -| | * ``KnapSack`` - FIXME | | | -| | * ``SFC`` - FIXME | | | +| | * ``KnapSack`` | | | +| | * ``SFC`` | | | +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ | load_balance.weighting | Weighting function to use if using ``KnapSack`` load balancing | String | ParticleRunTime | | | | | | | | Options: | | | | | | | | -| | * ``ParticleRunTime`` - FIXME | | | +| | * ``ParticleRunTime`` | | | | | * ``ParticleCount`` | | | | | * ``CellCount`` | | | +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ diff --git a/docs/source_docs/user_guide/inputs/boundary_conditions.rst b/docs/source_docs/user_guide/inputs/boundary_conditions.rst index 1c950c4..4d55603 100644 --- a/docs/source_docs/user_guide/inputs/boundary_conditions.rst +++ b/docs/source_docs/user_guide/inputs/boundary_conditions.rst @@ -185,8 +185,7 @@ provided when appropriate. +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | eb.normal | [Optional] When specified, only cells with EB face normal that is | Reals | 0 0 0 | | | parallel and opposite in direction to the specified values | | | -| | are imposed with the inflow velocity. FIXME what does OPTIONAL mean | | | -| | with a default value of 0? | | | +| | are imposed with the inflow velocity. | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | eb.normal_tol | [Optional] Used in conjunction with `eb.normal`. It determines the | Real | 0 | | | tolerance (in degrees) for choosing cells with a specific normal. | | | diff --git a/docs/source_docs/user_guide/inputs/fluid_model.rst b/docs/source_docs/user_guide/inputs/fluid_model.rst index 9c7d51d..6410ff6 100644 --- a/docs/source_docs/user_guide/inputs/fluid_model.rst +++ b/docs/source_docs/user_guide/inputs/fluid_model.rst @@ -53,7 +53,7 @@ a single fluid; therefore, it is common to name the fluid ``fluid``. This is ill | | |mix_Eq| | | | | | | | | | | A viscosity model is required if the fluid solver is | | | -| | enabled. FIXME NEED A DEFAULT | | | +| | enabled. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ | viscosity.molecular.constant | Constant fluid viscosity. | Real | 0 | | | | | | @@ -83,7 +83,7 @@ a single fluid; therefore, it is common to name the fluid ``fluid``. This is ill | | * ``None`` - No eddy viscosity model | | | | | * ``Smagorinsky-Lilly`` :cite:p:`Smag63,Lilly66` | | | | | * ``WALE`` :cite:p:`ducros98` | | | -| | * ``usr`` -- FIXME | | | +| | * ``usr`` | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ | viscosity.eddy.Smagorinsky-Lilly.constant | Smagorinsky-Lilly constant which usually has values | Real | None | | | between 0.1 and 0.2. | | | diff --git a/docs/source_docs/user_guide/inputs/initial_conditions.rst b/docs/source_docs/user_guide/inputs/initial_conditions.rst index 8ce5183..9866715 100644 --- a/docs/source_docs/user_guide/inputs/initial_conditions.rst +++ b/docs/source_docs/user_guide/inputs/initial_conditions.rst @@ -17,7 +17,7 @@ The following inputs are defined using the prefix ``ic``: | | Options: | | | | | | | | | | * ``Inputs`` - preserve order in inputs file | | | -| | * ``Volume`` - sort by volume of each IC region FIXME small to large? | | | +| | * ``Volume`` - sort by volume of each IC region | | | | | * ``Priority`` - sort by specified priority value | | | +-----------------------+------------------------------------------------------------------------+-------------+-----------+ @@ -70,7 +70,7 @@ using the compound prefix ``ic.[region]``: | | (NOTE: ``oneper`` is equivalent to ``1-cube`` and ``eightper`` | | | | | to ``2-cube``) | | | +----------------------+------------------------------------------------------------------+-------------+-----------+ -| priority | Priority value for IC regions ranking as described above | Int | Max FIXME | +| priority | Priority value for IC regions ranking as described above | Int | Max | +----------------------+------------------------------------------------------------------+-------------+-----------+ For each initial condition region, the solid inputs are defined diff --git a/docs/source_docs/user_guide/inputs/multigrid_solvers.rst b/docs/source_docs/user_guide/inputs/multigrid_solvers.rst index 9ee3018..d513a5e 100644 --- a/docs/source_docs/user_guide/inputs/multigrid_solvers.rst +++ b/docs/source_docs/user_guide/inputs/multigrid_solvers.rst @@ -31,12 +31,12 @@ The following inputs are defined using the prefix ``nodal_proj``: | | | | | | | Options: | | | | | | | | -| | * ``bicgcg`` - FIXME | | | -| | * ``bicgstab`` - FIXME | | | -| | * ``cg`` - FIXME | | | -| | * ``cgbicg`` - FIXME | | | -| | * ``hypre`` - FIXME | | | -| | * ``smoother`` - FIXME | | | +| | * ``bicgcg`` | | | +| | * ``bicgstab`` | | | +| | * ``cg`` | | | +| | * ``cgbicg`` | | | +| | * ``hypre`` | | | +| | * ``smoother`` | | | | | | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | hypre_namespace | Namespace to use in the nodal projection when using hypre | String | hypre | @@ -47,9 +47,9 @@ The following inputs are defined using the prefix ``nodal_proj``: | | | | | | | Options: | | | | | | | | -| | * ``ij`` - FIXME | | | -| | * ``semi-structured`` - FIXME | | | -| | * ``structured`` - FIXME | | | +| | * ``ij`` | | | +| | * ``semi-structured`` | | | +| | * ``structured`` | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ @@ -81,12 +81,12 @@ The following inputs are defined using the prefix ``mac_proj``: | | | | | | | Options: | | | | | | | | -| | * ``bicgcg`` - FIXME | | | -| | * ``bicgstab`` - FIXME | | | -| | * ``cg`` - FIXME | | | -| | * ``cgbicg`` - FIXME | | | -| | * ``hypre`` - FIXME | | | -| | * ``smoother`` - FIXME | | | +| | * ``bicgcg`` | | | +| | * ``bicgstab`` | | | +| | * ``cg`` | | | +| | * ``cgbicg`` | | | +| | * ``hypre`` | | | +| | * ``smoother`` | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | hypre_namespace | Namespace to use in the MAC projection when using ``hypre`` | String | hypre | | | to control hypre specific settings. It can be any string. | | | @@ -95,9 +95,9 @@ The following inputs are defined using the prefix ``mac_proj``: | | | | | | | Options: | | | | | | | | -| | * ``ij`` - FIXME | | | -| | * ``semi-structured`` - FIXME | | | -| | * ``structured`` - FIXME | | | +| | * ``ij`` | | | +| | * ``semi-structured`` | | | +| | * ``structured`` | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ @@ -130,7 +130,7 @@ The following inputs are defined using the prefix ``diffusion``: | | | | | | | Options: | | | | | | | | -| | * ``bicgcg`` - FIXME | | | +| | * ``bicgcg`` | | | | | * ``cg`` - | | | | | * ``cgbicg`` - | | | | | * ``smoother`` - | | | @@ -154,7 +154,7 @@ a ``hpyre_namespace`` for each solver. * These inputs are all case-sensitive. These inputs follow the typical approach for using `hypre` in MFIX-Exa where `BoomerAMG` is employed as a preconditioner -and `GMRES` for the linear solver. FIXME UNCLEAR +and `GMRES` for the linear solver. +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | @@ -164,8 +164,8 @@ and `GMRES` for the linear solver. FIXME UNCLEAR | | Options: | | | | | | | | | | * ``none`` - no preconditioner | | | -| | * ``BoomerAMG`` - FIXME | | | -| | * ``euclid`` - FIXME | | | +| | * ``BoomerAMG`` | | | +| | * ``euclid`` | | | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | recompute_preconditioner | Recompute preconditioner during runs | Bool | true | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ @@ -173,7 +173,7 @@ and `GMRES` for the linear solver. FIXME UNCLEAR | | | | | | | Options: | | | | | | | | -| | * ``BoomerAMG`` - FIXME DESC | | | +| | * ``BoomerAMG`` | | | | | * ``GMRES`` | | | | | * ``COGMRES`` | | | | | * ``LGMRES`` | | | diff --git a/docs/source_docs/user_guide/inputs/species.rst b/docs/source_docs/user_guide/inputs/species.rst index 3bc75d8..dd04b4c 100644 --- a/docs/source_docs/user_guide/inputs/species.rst +++ b/docs/source_docs/user_guide/inputs/species.rst @@ -24,11 +24,11 @@ The following inputs are defined using the prefix ``species``: | | ``constant`` diffusivity model | | | | | | | | +--------------------------+------------------------------------------------------------------------+----------+-----------+ -| specific_heat | Species specific heat model. This setting only applies if either | String | FIXME | +| specific_heat | Species specific heat model. This setting only applies if either | String | | | | ``fluid.specific_heat = mixture`` or | | | | | ``solids.specific_heat = mixture`` | | | | | | | | -| | Options (case-insensitive): | | | +| | Options (case-insensitive): | | | | | | | | | | * ``constant`` - a constant specific heat is defined for each species | | | | | and a *mixture* specific heat is computed based on the fluid or | | | @@ -54,7 +54,7 @@ The following inputs are defined using the prefix ``species``: | | Therefore, this option should only be used when the simulation is not | | | | | expected to cross over the transition temperature. | | | +--------------------------+------------------------------------------------------------------------+----------+-----------+ -| viscosity.molecular | Molecular viscosity model of species. This setting only applies when | String | FIXME | +| viscosity.molecular | Molecular viscosity model of species. This setting only applies when | String | | | | ``fluid.viscosity.molecular = mixture``. | | | | | | | | | | Options: | | | -- GitLab From 1daaaf01792d0421129daad939a94fed9e7bb8f3 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Tue, 9 Sep 2025 14:19:39 -0500 Subject: [PATCH 35/47] remove convection --- .../user_guide/inputs/output/monitors.rst | 23 ++++++++----------- .../user_guide/inputs/output/plotting.rst | 2 -- 2 files changed, 9 insertions(+), 16 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/output/monitors.rst b/docs/source_docs/user_guide/inputs/output/monitors.rst index 951cdbf..835437d 100644 --- a/docs/source_docs/user_guide/inputs/output/monitors.rst +++ b/docs/source_docs/user_guide/inputs/output/monitors.rst @@ -1,7 +1,7 @@ Monitors ======== -A Monitor is a tool for capturing data from the solver about the model. +A monitor is a tool for capturing data from the solver about the model. Data (such as volume fraction, pressure, velocity, etc.) for a given monitor region is written to a CSV file while the solver is running. @@ -152,13 +152,11 @@ The following table lists all the fluid phase variables that can be monitored: +--------------------------+-----------------------------------------------------------------------------------------+ | trac | tracer | +--------------------------+-----------------------------------------------------------------------------------------+ -| vel_g | fluid velocity | -| | (all the three components of the velocity) | +| vel_g | fluid velocity (all three components) | +--------------------------+-----------------------------------------------------------------------------------------+ | vel_g_[x/y/z] | x, y, or z component of the fluid velocity | +--------------------------+-----------------------------------------------------------------------------------------+ -| gp | fluid pressure gradient | -| | (all the three components of the gradient) | +| gp | fluid pressure gradient (all three components) | +--------------------------+-----------------------------------------------------------------------------------------+ | gp_[x/y/z] | x, y, or z component of the fluid pressure gradient | +--------------------------+-----------------------------------------------------------------------------------------+ @@ -170,13 +168,11 @@ The following table lists all the fluid phase variables that can be monitored: +--------------------------+-----------------------------------------------------------------------------------------+ | X_gk_[species] | fluid "species" mass fraction (only species "species" is monitored) | +--------------------------+-----------------------------------------------------------------------------------------+ -| vort | fluid vorticity | -| | (all the three components of the vorticity) | +| vort | fluid vorticity (all three components) | +--------------------------+-----------------------------------------------------------------------------------------+ | vort[x/y/z] | x, y, or z component of the fluid vorticity | +--------------------------+-----------------------------------------------------------------------------------------+ -| txfr_velocity | interphase velocity transferred to the fluid | -| | (all the three components of the velocity) | +| txfr_velocity | interphase velocity transferred to the fluid (all three components) | +--------------------------+-----------------------------------------------------------------------------------------+ | txfr_vel_[x/y/z] | x, y, or z component of the interphase velocity transferred to the fluid | +--------------------------+-----------------------------------------------------------------------------------------+ @@ -193,14 +189,13 @@ The following table lists all the fluid phase variables that can be monitored: | | (only species "species" is monitored) | +--------------------------+-----------------------------------------------------------------------------------------+ | chem_txfr_velocity | rate of velocity transferred to the fluid phase due to heterogeneous chemical reactions | -| | (all the three components of the velocity) | +| | (all three components) | +--------------------------+-----------------------------------------------------------------------------------------+ | chem_txfr_vel_[x/y/z] | x, y, or z component of the rate of velocity transferred due to heterogeneous reactions | +--------------------------+-----------------------------------------------------------------------------------------+ | chem_txfr_h | rate of enthalpy transferred to the fluid phase due to heterogeneous chemical reactions | +--------------------------+-----------------------------------------------------------------------------------------+ -| divtau | divergence of the viscous stress tensor | -| | (all the three components) | +| divtau | divergence of the viscous stress tensor (all three components) | +--------------------------+-----------------------------------------------------------------------------------------+ | divtau_[x/y/z] | x, y, or z component of the divergence of the viscous stress tensor | +--------------------------+-----------------------------------------------------------------------------------------+ @@ -481,7 +476,7 @@ The following table lists all the solids phase variables that can be monitored: +--------------------------+-----------------------------------------------------------------------------------------+ | id | particles id | +--------------------------+-----------------------------------------------------------------------------------------+ -| cpu | particles cpu | +| cpu | particles CPU | +--------------------------+-----------------------------------------------------------------------------------------+ | radius | particles radius | +--------------------------+-----------------------------------------------------------------------------------------+ @@ -522,7 +517,7 @@ The following table lists all the solids phase variables that can be monitored: | X_sn_[species] | solids "species" mass fraction (only species "species" is monitored) | +--------------------------+-----------------------------------------------------------------------------------------+ | txfr_velocity | rate of velocity transferred to the fluid phase due to heterogeneous chemical reactions | -| | (all the three components) | +| | (all three components) | +--------------------------+-----------------------------------------------------------------------------------------+ | txfr_vel_[x/y/z] | x, y, or z components of the transferred velocity due to heterogeneous reactions | +--------------------------+-----------------------------------------------------------------------------------------+ diff --git a/docs/source_docs/user_guide/inputs/output/plotting.rst b/docs/source_docs/user_guide/inputs/output/plotting.rst index fa6e1f9..5994515 100644 --- a/docs/source_docs/user_guide/inputs/output/plotting.rst +++ b/docs/source_docs/user_guide/inputs/output/plotting.rst @@ -145,8 +145,6 @@ All these parameters are user-defined. +---------------------------+-----------------------------------------------------------------+-------------+-----------+ | [region].plt_regtest | Plot all variables (overrides all other plot flags) | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_convection | Plot particle convection coefficient | Int | 0 | -+---------------------------+-----------------------------------------------------------------+-------------+-----------+ | [region].plt_cp_s | Plot particle specific heat coefficient | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ | [region].plt_drag_p | Plot particle drag force | Int | 0 | -- GitLab From 431140dcbf677a53c2dbb3ead014a8518d05dcc5 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Tue, 9 Sep 2025 14:31:21 -0500 Subject: [PATCH 36/47] correct variable list --- .../user_guide/inputs/output/plotting.rst | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/output/plotting.rst b/docs/source_docs/user_guide/inputs/output/plotting.rst index 5994515..696f908 100644 --- a/docs/source_docs/user_guide/inputs/output/plotting.rst +++ b/docs/source_docs/user_guide/inputs/output/plotting.rst @@ -45,10 +45,6 @@ The following inputs must be preceded by the prefix ``mfix`` and control which v | | Description | Type | Default | +=====================+=======================================================================+=============+===========+ | plt_regtest | Plot all variables (overrides all other plot flags) | Int | 0 | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ - -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ - +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | plt_drag_p | Plot particle drag force | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ @@ -56,16 +52,10 @@ The following inputs must be preceded by the prefix ``mfix`` and control which v +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | plt_gradp_g | Plot gradient of pressure | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_mass | Plot particle mass | Int | 0 | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_mass | Plot particle mass | Int | 0 | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ | plt_mu_g | Plot fluid molecular viscosity | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | plt_omega_p | Plot particle angular velocity | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_omoi | Plot (one divided by the) particle momentum of inertia | Int | 0 | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ | plt_p_g | Plot fluid pressure | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | plt_phase | Plot particle type | Int | 0 | @@ -76,8 +66,6 @@ The following inputs must be preceded by the prefix ``mfix`` and control which v +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | plt_ro_p | Plot particle density | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_ro_p | Plot particle density | Int | 0 | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ | plt_statwt | Plot particle (parcel) statistical weight | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | plt_T_g | Plot fluid temperature | Int | 0 | @@ -90,8 +78,6 @@ The following inputs must be preceded by the prefix ``mfix`` and control which v +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | plt_volfrac | Plot Eulerian grid volume fraction (from cut cells) | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_volume | Plot particle volume | Int | 0 | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ | plt_vort | Plot vorticity | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -- GitLab From c47e42514840f72a0ea86bdc971e11fcfb336247 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Tue, 9 Sep 2025 14:34:14 -0500 Subject: [PATCH 37/47] correct variable list --- docs/source_docs/user_guide/inputs/output/plotting.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/output/plotting.rst b/docs/source_docs/user_guide/inputs/output/plotting.rst index 696f908..06d090c 100644 --- a/docs/source_docs/user_guide/inputs/output/plotting.rst +++ b/docs/source_docs/user_guide/inputs/output/plotting.rst @@ -50,7 +50,7 @@ The following inputs must be preceded by the prefix ``mfix`` and control which v +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | plt_ep_g | Plot fluid volume fraction | Int | 1 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_gradp_g | Plot gradient of pressure | Int | 0 | +| plt_gradp_g | Plot gradient of fluid pressure | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | plt_mu_g | Plot fluid molecular viscosity | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -- GitLab From c56d0404c66223f0e8e8d53a60e1e99babaf4983 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Tue, 9 Sep 2025 14:34:30 -0500 Subject: [PATCH 38/47] correct variable list --- docs/source_docs/user_guide/inputs/output/plotting.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/output/plotting.rst b/docs/source_docs/user_guide/inputs/output/plotting.rst index 06d090c..2da4b06 100644 --- a/docs/source_docs/user_guide/inputs/output/plotting.rst +++ b/docs/source_docs/user_guide/inputs/output/plotting.rst @@ -82,7 +82,7 @@ The following inputs must be preceded by the prefix ``mfix`` and control which v +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -The following inputs must be preceded by the prefix ``mfix`` and control whether the EB geometry or level set should be written out: +The following inputs must be preceded by the prefix ``mfix`` and control whether the EB geometry or level set should be written: +----------------------+--------------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | -- GitLab From aa1804f4f227e017f402a3f64fd733aef32e91cb Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Tue, 9 Sep 2025 14:39:55 -0500 Subject: [PATCH 39/47] update docs for doc_scanner --- docs/source_docs/user_guide/inputs/fluid_model.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/fluid_model.rst b/docs/source_docs/user_guide/inputs/fluid_model.rst index 6410ff6..3e4d7ee 100644 --- a/docs/source_docs/user_guide/inputs/fluid_model.rst +++ b/docs/source_docs/user_guide/inputs/fluid_model.rst @@ -207,7 +207,7 @@ a single fluid; therefore, it is common to name the fluid ``fluid``. This is ill | | | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ | thermal_conductivity | Specify which thermal conductivity model to use for | String | None | -| | fluid. Options: : | | | +| | fluid. Options: | | | | | | | | | | * ``constant`` - the fluid has a constant thermal | | | | | conductivity model | | | -- GitLab From f5dc3171c587670f8ce8e5ae782544eef823ec00 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Tue, 9 Sep 2025 14:41:41 -0500 Subject: [PATCH 40/47] update docs for doc_scanner --- docs/source_docs/user_guide/inputs/geometry.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/geometry.rst b/docs/source_docs/user_guide/inputs/geometry.rst index 90a7b5a..ac38cbf 100644 --- a/docs/source_docs/user_guide/inputs/geometry.rst +++ b/docs/source_docs/user_guide/inputs/geometry.rst @@ -345,7 +345,7 @@ The following inputs are defined using the prefix ``csg``: +------------------------+-------------------------------------------------------------------+----------+---------------------+ | | Description | Type | Default | +========================+===================================================================+==========+=====================+ -| geometry_filename | The CSG file that defines the EB geometry | String | '' | +| geometry_filename | The CSG file that defines the EB geometry. | String | '' | +------------------------+-------------------------------------------------------------------+----------+---------------------+ | internal_flow | Indicates that flow is *inside* the box. | Bool | true | +------------------------+-------------------------------------------------------------------+----------+---------------------+ @@ -371,7 +371,7 @@ The following inputs are defined using the prefix ``stl``: +------------------------+-------------------------------------------------------------------+----------+---------------------+ | | Description | Type | Default | +========================+===================================================================+==========+=====================+ -| geometry_filename | The STL file that defines the EB geometry . | String | '' | +| geometry_filename | The STL file that defines the EB geometry. | String | '' | +------------------------+-------------------------------------------------------------------+----------+---------------------+ | scaling_factor | Scale the geometry. | Real | 1. | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -- GitLab From 094f9e7671b5ea592b888ac3aa69ef58f98be8d2 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Tue, 9 Sep 2025 14:42:29 -0500 Subject: [PATCH 41/47] update docs for doc_scanner --- docs/source_docs/user_guide/inputs/initial_conditions.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/initial_conditions.rst b/docs/source_docs/user_guide/inputs/initial_conditions.rst index 9866715..905efb6 100644 --- a/docs/source_docs/user_guide/inputs/initial_conditions.rst +++ b/docs/source_docs/user_guide/inputs/initial_conditions.rst @@ -9,7 +9,7 @@ The following inputs are defined using the prefix ``ic``: | regions | Regions used to define initial conditions. | String | None | +-----------------------+------------------------------------------------------------------------+-------------+-----------+ | allow_regions_overlap | If enabled, particles will be generated/initialized more than once | Int | 1 | -| | on areas where the IC regions intersect | | | +| | on areas where the IC regions intersect. | | | +-----------------------+------------------------------------------------------------------------+-------------+-----------+ | ranking_type | Specifies the order in which IC regions are sorted during | String | Inputs | | | initialization. | | | -- GitLab From e0af2254cda186c5290eb0899ec05ecca3535fd5 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Tue, 9 Sep 2025 14:43:57 -0500 Subject: [PATCH 42/47] update docs for doc_scanner --- docs/source_docs/user_guide/inputs/initial_conditions.rst | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/initial_conditions.rst b/docs/source_docs/user_guide/inputs/initial_conditions.rst index 905efb6..39e7ca6 100644 --- a/docs/source_docs/user_guide/inputs/initial_conditions.rst +++ b/docs/source_docs/user_guide/inputs/initial_conditions.rst @@ -90,7 +90,9 @@ please refer to :ref:`ReferenceParticleDistributions Date: Tue, 9 Sep 2025 14:44:44 -0500 Subject: [PATCH 43/47] update docs for doc_scanner --- docs/source_docs/user_guide/inputs/initial_conditions.rst | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/initial_conditions.rst b/docs/source_docs/user_guide/inputs/initial_conditions.rst index 39e7ca6..bd85252 100644 --- a/docs/source_docs/user_guide/inputs/initial_conditions.rst +++ b/docs/source_docs/user_guide/inputs/initial_conditions.rst @@ -128,7 +128,9 @@ please refer to :ref:`ReferenceParticleDistributions Date: Tue, 9 Sep 2025 14:45:39 -0500 Subject: [PATCH 44/47] update docs for doc_scanner --- .../source_docs/user_guide/inputs/initialization.rst | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/initialization.rst b/docs/source_docs/user_guide/inputs/initialization.rst index a5c95f0..a4bb68e 100644 --- a/docs/source_docs/user_guide/inputs/initialization.rst +++ b/docs/source_docs/user_guide/inputs/initialization.rst @@ -10,18 +10,18 @@ They must be defined with the prefix ``mfix``: +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +======================+=======================================================================+=============+==============+ -| do_initial_proj | Perform an initial projection | Bool | true | +| do_initial_proj | Perform an initial projection. | Bool | true | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ -| initial_iterations | Number of pressure iterations to execute before time-marching | Int | 3 | +| initial_iterations | Number of pressure iterations to execute before time-marching. | Int | 3 | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | scale_init_dt | Factor by which ``dt`` is scaled in the initial iterations and step. | Real | 1.0 | | | Must be a value <= 1.0 | | | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ -| restart | If set, then restart from this file rather than from scratch | String | None | +| restart | If set, then restart from this file rather than from scratch. | String | None | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ -| repl_x | Replicate initial data by this factor in the x-direction | Int | 1 | +| repl_x | Replicate initial data by this factor in the x-direction. | Int | 1 | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ -| repl_y | Replicate initial data by this factor in the y-direction | Int | 1 | +| repl_y | Replicate initial data by this factor in the y-direction. | Int | 1 | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ -| repl_z | Replicate initial data by this factor in the z-direction | Int | 1 | +| repl_z | Replicate initial data by this factor in the z-direction. | Int | 1 | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ -- GitLab From 8e7795aa89b76c323a68168522dd0d6a6e1af332 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Tue, 9 Sep 2025 14:55:13 -0500 Subject: [PATCH 45/47] update docs for doc_scanner --- .../user_guide/inputs/model_options.rst | 12 ++- .../user_guide/inputs/multigrid_solvers.rst | 100 +++++++++--------- 2 files changed, 59 insertions(+), 53 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/model_options.rst b/docs/source_docs/user_guide/inputs/model_options.rst index 5a2193c..6679ff9 100644 --- a/docs/source_docs/user_guide/inputs/model_options.rst +++ b/docs/source_docs/user_guide/inputs/model_options.rst @@ -15,7 +15,9 @@ The following inputs are defined using the prefix ``mfix``: +------------------------+----------------------------------------------------------------------------+----------+---------------------+ | solve_species | Enable the time evolution of fluid species mass fractions. | Int | 0 | +------------------------+----------------------------------------------------------------------------+----------+---------------------+ -| constraint | Select low Mach number constraint. Options (case-insensitive): | String | IncompressibleFluid | +| constraint | Select low Mach number constraint. | String | IncompressibleFluid | +| | | | | +| | Options (case-insensitive): | | | | | | | | | | * ``IncompressibleFluid`` constraint is appropriate for cold flow systems | | | | | that do not have chemical reactions. Fluid temperature and species mass | | | @@ -103,7 +105,9 @@ The following inputs are defined using the prefix ``particles``: +---------------------+---------------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +=====================+===========================================================================+=============+===========+ -| constraint | Constraint type. Options: | String | None | +| constraint | Constraint type. | String | None | +| | | | | +| | Options: | | | | | | | | | | * ``mean_velocity`` | | | | | | | | @@ -146,7 +150,9 @@ The following inputs are defined using the prefix ``mfix``: +============================+====================================================================+===========+===============+ | deposition_scheme | The algorithm used to transfer particle properties to the Eulerian | String | trilinear | | | grid. An overview of the schemes is provided | | | -| | :ref:`below`. Options: | | | +| | :ref:`below`. | | | +| | | | | +| | Options: | | | | | | | | | | * ``centroid`` | | | | | * ``trilinear`` | | | diff --git a/docs/source_docs/user_guide/inputs/multigrid_solvers.rst b/docs/source_docs/user_guide/inputs/multigrid_solvers.rst index d513a5e..94487ed 100644 --- a/docs/source_docs/user_guide/inputs/multigrid_solvers.rst +++ b/docs/source_docs/user_guide/inputs/multigrid_solvers.rst @@ -11,21 +11,21 @@ The following inputs are defined using the prefix ``nodal_proj``: +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +=========================+=======================================================================+=============+==============+ -| verbose | Verbosity of multigrid solver in nodal projection | Int | 0 | +| verbose | Verbosity of multigrid solver in nodal projection. | Int | 0 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_verbose | Verbosity of BiCGStab solver in nodal projection | Int | 0 | +| bottom_verbose | Verbosity of BiCGStab solver in nodal projection. | Int | 0 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_rtol | Relative tolerance in nodal projection | Real | 1.e-11 | +| mg_rtol | Relative tolerance in nodal projection. | Real | 1.e-11 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_atol | Absolute tolerance in nodal projection | Real | 1.e-14 | +| mg_atol | Absolute tolerance in nodal projection. | Real | 1.e-14 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| maxiter | Maximum number of iterations in the nodal projection | Int | 100 | +| maxiter | Maximum number of iterations in the nodal projection. | Int | 100 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bottom_maxiter | Maximum number of iterations in the nodal projection | Int | 100 | -| | bottom solver if using bicg, cg, bicgcg or cgbicg | | | +| | bottom solver if using bicg, cg, bicgcg or cgbicg. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | mg_max_coarsening_level | Maximum number of coarser levels to allow in the nodal projection. | Int | 100 | -| | If set to 0, the bottom solver will be called at the current level | | | +| | If set to 0, the bottom solver will be called at the current level. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bottom_solver | Which bottom solver to use in the nodal projection. | String | bicgcg | | | | | | @@ -61,18 +61,18 @@ The following inputs are defined using the prefix ``mac_proj``: +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +=========================+=======================================================================+=============+==============+ -| verbose | Verbosity of multigrid solver in MAC projection | Int | 0 | +| verbose | Verbosity of multigrid solver in MAC projection. | Int | 0 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_verbose | Verbosity of BiCGStab solver in MAC projection | Int | 0 | +| bottom_verbose | Verbosity of BiCGStab solver in MAC projection. | Int | 0 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_rtol | Relative tolerance in MAC projection | Real | 1.e-11 | +| mg_rtol | Relative tolerance in MAC projection. | Real | 1.e-11 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_atol | Absolute tolerance in MAC projection | Real | 1.e-14 | +| mg_atol | Absolute tolerance in MAC projection. | Real | 1.e-14 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| maxiter | Maximum number of iterations in the MAC projection | Int | 200 | +| maxiter | Maximum number of iterations in the MAC projection. | Int | 200 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bottom_maxiter | Maximum number of iterations in the MAC projection | Int | 200 | -| | bottom solver if using bicg, cg, bicgcg or cgbicg | | | +| | bottom solver if using bicg, cg, bicgcg or cgbicg. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | mg_max_coarsening_level | Maximum number of coarser levels to allow in the MAC projection | Int | 100 | | | If set to 0, the bottom solver will be called at the current level | | | @@ -124,7 +124,7 @@ The following inputs are defined using the prefix ``diffusion``: | | bottom solver if using ``bicg``, ``cg``, ``bicgcg``, or ``cgbicg``. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | mg_max_coarsening_level | Maximum number of coarser levels to allow in diffusion solve | Int | 100 | -| | If set to 0, the bottom solver will be called at the current level | | | +| | If set to 0, the bottom solver will be called at the current level. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bottom_solver | Which bottom solver to use for diffusion. | String | bicgcg | | | | | | @@ -159,7 +159,7 @@ and `GMRES` for the linear solver. +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +===================================+=======================================================================+=============+==============+ -| hypre_preconditioner | Type of preconditioner when using ``hypre`` | String | none | +| hypre_preconditioner | Type of preconditioner when using ``hypre``. | String | none | | | | | | | | Options: | | | | | | | | @@ -167,7 +167,7 @@ and `GMRES` for the linear solver. | | * ``BoomerAMG`` | | | | | * ``euclid`` | | | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| recompute_preconditioner | Recompute preconditioner during runs | Bool | true | +| recompute_preconditioner | Recompute preconditioner during runs. | Bool | true | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | hypre_solver | Type of hypre solver. | String | BoomerAMG | | | | | | @@ -193,65 +193,65 @@ The following inputs are valid when using ``BoomerAMG`` as a preconditioner or s +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +===================================+=======================================================================+=============+==============+ -| bamg_agg_interp_type | See HYPRE_BoomerAMGSetAggInterpType | Int | 4 | -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_agg_num_levels | See HYPRE_BoomerAMGSetAggNumLevels | Int | 0 | +| bamg_agg_interp_type | See ``HYPRE_BoomerAMGSetAggInterpType``. | Int | 4 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_agg_pmax_elmts | See HYPRE_BoomerAMGSetAggPMaxElmts | Int | 0 | +| bamg_agg_num_levels | See ``HYPRE_BoomerAMGSetAggNumLevels``. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_coarse_relax_type | See HYPRE_BoomerAMGSetCycleRelaxType | Int | 11 | +| bamg_agg_pmax_elmts | See ``HYPRE_BoomerAMGSetAggPMaxElmts``. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_coarsen_type | See HYPRE_BoomerAMGSetCoarsenType | Int | 6 | +| bamg_coarse_relax_type | See ``HYPRE_BoomerAMGSetCycleRelaxType``. | Int | 11 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_cycle_type | See HYPRE_BoomerAMGSetCycleType | Int | 1 | +| bamg_coarsen_type | See ``HYPRE_BoomerAMGSetCoarsenType``. | Int | 6 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_down_relax_type | See HYPRE_BoomerAMGSetCycleRelaxType | Int | 11 | +| bamg_cycle_type | See ``HYPRE_BoomerAMGSetCycleType``. | Int | 1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_interp_type | See HYPRE_BoomerAMGSetInterpType | Int | 0 | +| bamg_down_relax_type | See ``HYPRE_BoomerAMGSetCycleRelaxType``. | Int | 11 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_keep_transpose | See HYPRE_BoomerAMGSetKeepTranspose | Int | 0 | +| bamg_interp_type | See ``HYPRE_BoomerAMGSetInterpType``. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_logging | See HYPRE_BoomerAMGSetLogging | Int | 0 | +| bamg_keep_transpose | See ``HYPRE_BoomerAMGSetKeepTranspose``. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_max_coarse_size | See HYPRE_BoomerAMGSetMaxCoarseSize | Int | 9 | +| bamg_logging | See ``HYPRE_BoomerAMGSetLogging``. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_max_iterations | See HYPRE_BoomerAMGSetMaxIter | Int | 1 | +| bamg_max_coarse_size | See ``HYPRE_BoomerAMGSetMaxCoarseSize``. | Int | 9 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_max_levels | See HYPRE_BoomerAMGSetMaxLevels | Int | 20 | +| bamg_max_iterations | See ``HYPRE_BoomerAMGSetMaxIter``. | Int | 1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_min_coarse_size | See HYPRE_BoomerAMGSetMinCoarseSize | Int | 1 | +| bamg_max_levels | See ``HYPRE_BoomerAMGSetMaxLevels``. | Int | 20 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_num_coarse_sweeps | See HYPRE_BoomerAMGSetCycleNumSweeps | Int | 1 | +| bamg_min_coarse_size | See ``HYPRE_BoomerAMGSetMinCoarseSize``. | Int | 1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_num_down_sweeps | See HYPRE_BoomerAMGSetCycleNumSweeps | Int | 2 | +| bamg_num_coarse_sweeps | See ``HYPRE_BoomerAMGSetCycleNumSweeps``. | Int | 1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_num_down_sweeps | See HYPRE_BoomerAMGSetCycleNumSweeps | Int | 2 | +| bamg_num_down_sweeps | See ``HYPRE_BoomerAMGSetCycleNumSweeps``. | Int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_num_sweeps | See HYPRE_BoomerAMGSetNumSweeps | Int | 2 | +| bamg_num_down_sweeps | See ``HYPRE_BoomerAMGSetCycleNumSweeps``. | 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 | +| bamg_num_sweeps | See ``HYPRE_BoomerAMGSetNumSweeps``. | int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_pmax_elmts | See HYPRE_BoomerAMGSetPMaxElmts | Int | 4 | +| bamg_num_up_sweeps | See ``HYPRE_BoomerAMGSetCycleNumSweeps``. | Int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_precond_tolerance | See HYPRE_BoomerAMGSetTol | Real | 0.0 | +| bamg_pmax_elmts | See ``HYPRE_BoomerAMGSetPMaxElmts``. | Int | 4 | ++-----------------------------------+------------------------------ ----------------------------------------+-------------+--------------+ +| bamg_precond_tolerance | See ``HYPRE_BoomerAMGSetTol``. | Real | 0.0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_relax_order | See HYPRE_BoomerAMGSetRelaxOrder | Int | 1 | +| bamg_relax_order | See ``HYPRE_BoomerAMGSetRelaxOrder``. | Int | 1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_relax_type | See HYPRE_BoomerAMGSetRelaxType | Int | 6 | +| bamg_relax_type | See ``HYPRE_BoomerAMGSetRelaxType``. | Int | 6 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_set_restriction | See HYPRE_BoomerAMGSetRestriction | Int | 0 | +| bamg_set_restriction | See ``HYPRE_BoomerAMGSetRestriction``. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_strong_threshold | See HYPRE_BoomerAMGSetStrongThreshold | Real | 0.57 | +| bamg_strong_threshold | See ``HYPRE_BoomerAMGSetStrongThreshold``. | Real | 0.57 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_trunc_factor | See HYPRE_BoomerAMGSetTruncFactor | Real | 0.1 | +| bamg_trunc_factor | See ``HYPRE_BoomerAMGSetTruncFactor``. | Real | 0.1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_up_relax_type | See HYPRE_BoomerAMGSetCycleRelaxType | Int | 11 | +| bamg_up_relax_type | See ``HYPRE_BoomerAMGSetCycleRelaxType``. | Int | 11 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_variant | See HYPRE_BoomerAMGSetVariant | Int | 0 | +| bamg_variant | See ``HYPRE_BoomerAMGSetVariant``. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_verbose | Set BoomerAMG verbosity | Int | 0 | +| bamg_verbose | Set ``BoomerAMG` verbosity. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ @@ -262,11 +262,11 @@ The following inputs are valid when using ``BoomerAMG`` as a preconditioner or s +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +===================================+=======================================================================+=============+==============+ -| adjust_singular_matrix | Enable if the problem to be solved has a singular matrix | Bool | false | +| adjust_singular_matrix | Enable if the problem to be solved has a singular matrix. | Bool | false | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| overwrite_existing_matrix_files | Overwrite existing matrix files | Bool | false | +| overwrite_existing_matrix_files | Overwrite existing matrix files. | Bool | false | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| write_matrix_files | Write matrix into text files | Bool | false | +| write_matrix_files | Write matrix into text files. | Bool | false | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -- GitLab From 39ef7e899c10124f8e326169402105fd21dd61f6 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Tue, 9 Sep 2025 15:03:55 -0500 Subject: [PATCH 46/47] update docs --- docs/source_docs/user_guide/inputs/multigrid_solvers.rst | 4 ---- 1 file changed, 4 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/multigrid_solvers.rst b/docs/source_docs/user_guide/inputs/multigrid_solvers.rst index 94487ed..b628574 100644 --- a/docs/source_docs/user_guide/inputs/multigrid_solvers.rst +++ b/docs/source_docs/user_guide/inputs/multigrid_solvers.rst @@ -225,10 +225,6 @@ The following inputs are valid when using ``BoomerAMG`` as a preconditioner or s +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_num_down_sweeps | See ``HYPRE_BoomerAMGSetCycleNumSweeps``. | Int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_num_down_sweeps | See ``HYPRE_BoomerAMGSetCycleNumSweeps``. | 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 | -- GitLab From c4359b479c1d6ec98fc536e8561461e5a3b17297 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Tue, 9 Sep 2025 15:47:03 -0500 Subject: [PATCH 47/47] documentation fixes --- docs/source_docs/user_guide/inputs/fluid_model.rst | 2 +- docs/source_docs/user_guide/inputs/initial_conditions.rst | 2 +- docs/source_docs/user_guide/inputs/multigrid_solvers.rst | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/fluid_model.rst b/docs/source_docs/user_guide/inputs/fluid_model.rst index 3e4d7ee..98194ea 100644 --- a/docs/source_docs/user_guide/inputs/fluid_model.rst +++ b/docs/source_docs/user_guide/inputs/fluid_model.rst @@ -1,4 +1,4 @@ -. _InputsFluidModel: +.. _InputsFluidModel: Fluid model =========== diff --git a/docs/source_docs/user_guide/inputs/initial_conditions.rst b/docs/source_docs/user_guide/inputs/initial_conditions.rst index bd85252..a4cdd19 100644 --- a/docs/source_docs/user_guide/inputs/initial_conditions.rst +++ b/docs/source_docs/user_guide/inputs/initial_conditions.rst @@ -177,7 +177,7 @@ The following input must be preceded by the prefix ``particles``: | | Description | Type | Default | +====================+===========================================================================+=============+===========+ | removeOutOfRange | Remove particles at initialization that are touching a wall. | Int | 1 | ---------------------+---------------------------------------------------------------------------+-------------+-----------+ ++--------------------+---------------------------------------------------------------------------+-------------+-----------+ Below is an example for specifying an initial condition for a fluid (``fluid``) and one solid (``solid0``). diff --git a/docs/source_docs/user_guide/inputs/multigrid_solvers.rst b/docs/source_docs/user_guide/inputs/multigrid_solvers.rst index b628574..c3d2fc4 100644 --- a/docs/source_docs/user_guide/inputs/multigrid_solvers.rst +++ b/docs/source_docs/user_guide/inputs/multigrid_solvers.rst @@ -230,7 +230,7 @@ The following inputs are valid when using ``BoomerAMG`` as a preconditioner or s | bamg_num_up_sweeps | See ``HYPRE_BoomerAMGSetCycleNumSweeps``. | Int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_pmax_elmts | See ``HYPRE_BoomerAMGSetPMaxElmts``. | Int | 4 | -+-----------------------------------+------------------------------ ----------------------------------------+-------------+--------------+ ++-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_precond_tolerance | See ``HYPRE_BoomerAMGSetTol``. | Real | 0.0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_relax_order | See ``HYPRE_BoomerAMGSetRelaxOrder``. | Int | 1 | @@ -247,7 +247,7 @@ The following inputs are valid when using ``BoomerAMG`` as a preconditioner or s +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_variant | See ``HYPRE_BoomerAMGSetVariant``. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_verbose | Set ``BoomerAMG` verbosity. | Int | 0 | +| bamg_verbose | Set ``BoomerAMG`` verbosity. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -- GitLab