diff --git a/docs/source_docs/user_guide/inputs/advanced.rst b/docs/source_docs/user_guide/inputs/advanced.rst index a1d2f7fda81022d0618f54d849f880d2cdf310e7..ffe3b0ca3e2cbbba7f4f0bda5d5b5fa79f70edd2 100644 --- a/docs/source_docs/user_guide/inputs/advanced.rst +++ b/docs/source_docs/user_guide/inputs/advanced.rst @@ -35,15 +35,15 @@ 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 | +============================+=======================================================================+=============+===============+ | 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. | | | @@ -58,12 +58,12 @@ 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 | +==================================+=======================================================================+=============+===================+ -| 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 | @@ -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 bf097d4e2d4c848eb2d345d2cc03195a75e583d2..4a2fb3a18683471a67fbb48ae0221899a7914e17 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]``: +------------------------+------------------------------------------------------------------------+-------------+-----------+ @@ -51,13 +51,13 @@ using the ``bc.[region].[fluid]`` prefix. | 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. | | | diff --git a/docs/source_docs/user_guide/inputs/chemical_reactions.rst b/docs/source_docs/user_guide/inputs/chemical_reactions.rst index b72dd3d92015d5dd5c836d50341182ce37d07440..51e554ec9527fd478a2ebf3dfea17141333aa2db 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 | @@ -47,7 +47,7 @@ The following inputs are defined using the ``chemistry`` prefix. 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) @@ -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 fe18fc18467de6f64f67cab8eafe61c76ac8d945..b62ac51f23def3d3144e5d878c5b67696e67dd25 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 1aef1bad2c4d00e3429c1bcf643de0e70aabcdd5..5d7e4cafc675a0b97e36aae9cdc809e81b5a80fb 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 | @@ -15,7 +15,7 @@ The following inputs are defined using the ``fluid`` prefix. +--------------------------------------------+-------------------------------------------------------------+--------+----------+ -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. @@ -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 | @@ -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 c1aa586f5e5dcffd3eae100b82147c6400734f83..d50d4d0196a88a7a85c8d3bbf04b9b8d75c42681 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 12195a9a5a5f7ea157e8bdccf6d4c9d13eb934e4..2070877f87dad6f1bd092f3ae0ffc41e8df7d7f4 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 82fbc73354c3301b2c1a83c50834cd20075757dd..ecc812719d41b7c4f5068826f7cad99d667e63f1 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 6eaf50496e11e491c2aa7913f75b432df1f1fb36..3072d6409a4cf12d3315e135549d4c0642e34a8c 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 89546541e8b79637875924630d00bb6553df6d1f..dd845ac8ddd3d8a466730be6a88194accb8c7038 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 4eea8047cc39818671bfde35aba231db33bd5971..6330643f7597e97c6d91219db574b605c8d98edc 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:: @@ -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 | | | @@ -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 | @@ -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 | diff --git a/docs/source_docs/user_guide/inputs/output/ascent.rst b/docs/source_docs/user_guide/inputs/output/ascent.rst index a2272c947c0104341ed5f786f30c8c7b879a54e1..d30ae2a98ac82464ce0671ee90befabb8ebcbf59 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 8e4c718e987e2d87b1a0062f1d3d5ac0e8bd3118..2f363ca12eaa5cd6e492116a5ca2f7d4ae190b8f 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 5ff9dd7519d6f6f8173ce7804b1a7b59267ff9d3..66ee112b8d784288915eeacbd6efaeaae78918d4 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 1f524b1f610e8fdb1f85ed8f4ea47a98d02a10be..175ba495785cb08ee40a411addceadd149e57409 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 47d9e4686ed81b3797ccb8ddfbbd90757689d0cd..6d4b01152c85be4716dbac5bd4f6aebc97d40ab0 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 1fc5741a3efcbd5173590e1aa0d0b415ff57a0d0..034f19e82ea5725995b3874da83c1f64488a0f31 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 | @@ -36,11 +36,11 @@ models. The following inputs must be preceded by the "solids." root | | 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. @@ -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`` | | | @@ -114,7 +114,7 @@ Enabling the DEM solver and specifying model options. | | |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 | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ diff --git a/docs/source_docs/user_guide/inputs/species_defs.rst b/docs/source_docs/user_guide/inputs/species_defs.rst index ad83fcf0ac6efddc535624d77439920cc5be3d2f..44959f978fadb4d610f535404f6858dc15c41b7c 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 defined for each species using the prefix ``species.[species name]``: +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ | | Description | Type | Default | @@ -83,11 +83,11 @@ The following inputs are for each species defined using the ``species.[species n | | | | | | | * 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. | | | @@ -122,9 +122,9 @@ The following inputs are for each species defined using the ``species.[species n | | | | | | | 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 | Values are required for ``Reid`` species viscosity model. | | | | viscosity.molecular.Reid.D | | | | +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ diff --git a/docs/source_docs/user_guide/inputs/time-stepping.rst b/docs/source_docs/user_guide/inputs/time-stepping.rst index 97dc7ea13724701df7643d1774ea49ec24943125..e2cff95331c62d5bc8d4834a60998e61ad06cad1 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 |