From 46458c16ad0ed8aa72369a539cd9c04af8e9102c Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 22 Aug 2025 14:25:07 -0500 Subject: [PATCH 01/31] 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 02/31] 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 03/31] 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 04/31] 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 05/31] 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 06/31] 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 07/31] 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 08/31] 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 09/31] 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 10/31] 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 11/31] 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 12/31] 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 13/31] 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 14/31] 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 15/31] 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 16/31] 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 17/31] 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 18/31] 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 19/31] 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 20/31] 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 21/31] 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 22/31] 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 23/31] 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 24/31] 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 25/31] 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 26/31] 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 27/31] 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 28/31] 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 29/31] 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 30/31] 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 31/31] 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