diff --git a/docs/source_docs/tools/pic2dem.rst b/docs/source_docs/tools/pic2dem.rst index 494d291873f09f16bdf647379e5522a51690454b..ccdd9bf8cf5aab286e887cfd8af37623d95d1c89 100644 --- a/docs/source_docs/tools/pic2dem.rst +++ b/docs/source_docs/tools/pic2dem.rst @@ -50,10 +50,10 @@ The following inputs must be preceded by "pic2dem.": | | geometry for the DEM refined case will be read or | | | | | written | | | +------------------------+---------------------------------------------------+--------+---------+ -| geom_chk_write | Flag to turn on/off writing the EB geometry | bool | false | +| geom_chk_write | Enable writing the EB geometry | bool | false | | | checkpoint file for the DEM refined case | | | +------------------------+---------------------------------------------------+--------+---------+ -| geom_chk_read | Flag to turn on/off reading the EB geometry | bool | false | +| geom_chk_read | Enable reading the EB geometry | bool | false | | | checkpoint file for the DEM refined case | | | +------------------------+---------------------------------------------------+--------+---------+ | geometry_filename | CSG filename that will be used for generating the | string | "" | diff --git a/docs/source_docs/user_guide/inputs/advanced.rst b/docs/source_docs/user_guide/inputs/advanced.rst index ffe3b0ca3e2cbbba7f4f0bda5d5b5fa79f70edd2..12cb5d366c1f268ea24a532ae0ff4690245ea297 100644 --- a/docs/source_docs/user_guide/inputs/advanced.rst +++ b/docs/source_docs/user_guide/inputs/advanced.rst @@ -6,21 +6,21 @@ Advanced Testing / debugging ------------------- -The following inputs must be preceded by "mfix." +The following inputs must be preceded by the prefix ``mfix``: +------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +========================+=======================================================================+=============+==============+ | verbose | Verbosity in MFIX-Exa routines | Int | 0 | +------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| ooo_debug | If true then print the name of the routine we are in | Bool | False | +| ooo_debug | If true, print the name of the current routine. | Bool | false | +------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| only_print_grid_report | Do not time-march the simulation. Simply generate the grid report | Bool | False | +| only_print_grid_report | Do not time-march the simulation. Simply generate the grid report | Bool | false | | | and exit. | | | +------------------------+-----------------------------------------------------------------------+-------------+--------------+ -The following inputs must be preceded by "amrex." +The following inputs must be preceded by the prefix ``amrex``: +------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | @@ -63,23 +63,36 @@ The following inputs must be preceded by the prefix ``mfix`` and control load ba +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ | | Description | Type | Default | +==================================+=======================================================================+=============+===================+ -| regrid_int | How often to regrid (in number of steps at level 0) | int | 0 | -| | if regrid_int <= 0 then no regridding will occur | | | +| regrid_int | How often to regrid (in number of steps at level 0). | Int | 0 | +| | If regrid_int <= 0 then no regridding will occur. | | | +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ -| load_balance | * ``SingleGrid`` fluid and particles are co-located on the same grids | string | SingleGrid | +| | Grid type. | String | SingleGrid | +| | | | | +| | Options: | | | +| | | | | +| load_balance | * ``SingleGrid`` fluid and particles are co-located on the same grids | | | | | * ``DualGrid`` fluid and particles live on different grids | | | +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ -| load_balance.DualGrid.fluid | Regrid mesh (fluid) in addition to particles when using `DualGrid` | int | 0 | +| load_balance.DualGrid.fluid | Regrid mesh (fluid) in addition to particles when using `DualGrid` | Int | 0 | +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ -| load_balance.strategy | What strategy to use for load balancing | string | KnapSack | -| | Options are ``KnapSack`` and ``SFC`` | | | +| load_balance.strategy | Strategy to use for dynamic load balancing. | String | KnapSack | +| | | | | +| | Options (case-insensitive): | | | +| | | | | +| | * ``KnapSack`` | | | +| | * ``SFC`` | | | +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ -| load_balance.weighting | What weighting function to use if using Knapsack load balancing | string | ParticleRunTime | -| | Options are ``ParticleRunTime``, ``ParticleCount`` and ``CellCount`` | | | +| load_balance.weighting | Weighting function to use if using ``KnapSack`` load balancing | String | ParticleRunTime | +| | | | | +| | Options: | | | +| | | | | +| | * ``ParticleRunTime`` | | | +| | * ``ParticleCount`` | | | +| | * ``CellCount`` | | | +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ -| knapsack_nmax | Maximum number of grids per MPI process if using knapsack algorithm | int | 128 | +| knapsack_nmax | Maximum number of grids per MPI process if using knapsack algorithm | Int | 128 | +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ -| grid_pruning | Remove all covered grids from the base mesh; this may result in | bool | False | +| grid_pruning | Remove all covered grids from the base mesh; this may result in | Bool | false | | | disjoined grids | | | +----------------------------------+-----------------------------------------------------------------------+-------------+-------------------+ diff --git a/docs/source_docs/user_guide/inputs/boundary_conditions.rst b/docs/source_docs/user_guide/inputs/boundary_conditions.rst index 4a2fb3a18683471a67fbb48ae0221899a7914e17..4d5560396383b27e449644b4c06e30fdc73350e9 100644 --- a/docs/source_docs/user_guide/inputs/boundary_conditions.rst +++ b/docs/source_docs/user_guide/inputs/boundary_conditions.rst @@ -1,6 +1,6 @@ .. _InputsBoundaryConditions: -Boundary Conditions +Boundary conditions =================== @@ -9,29 +9,38 @@ General boundary conditions The following inputs are defined using the prefix ``bc``: -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| | Description | Type | Default | -+=====================+=======================================================================+=============+===========+ -| regions | Regions used to define boundary conditions. | String | None | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ - -The type of the boundary conditions in the BC region must be defined. ++---------------------+--------------------------------------------------------------------------+-------------+-----------+ +| | Description | Type | Default | ++=====================+==========================================================================+=============+===========+ +| regions | Regions used to define boundary conditions. | String | None | ++---------------------+--------------------------------------------------------------------------+-------------+-----------+ +| delp_dir | Direction for specified pressure drop. Note that this direction | Int | 0 | +| | should also be periodic. | | | ++---------------------+--------------------------------------------------------------------------+-------------+-----------+ +| delp | Pressure drop (Pa) | Real | 0 | ++---------------------+--------------------------------------------------------------------------+-------------+-----------+ +| po_no_par_out | Force particles to bounce back rather than exiting at pressure outflows. | Int | 0 | ++---------------------+--------------------------------------------------------------------------+-------------+-----------+ + +The type of the boundary conditions in the BC region must be defined with the prefix ``bc``: +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +=====================+=======================================================================+=============+===========+ -| [region] | Used to define boundary condition type. Available options include: | String | None | +| [region] | Specify boundary condition type. | String | None | | | | | | -| | * 'pi' for pressure inflow BC type | | | -| | * 'po' for pressure outflow BC type | | | -| | * 'mi' for mass inflow BC type | | | -| | * 'nsw' for no-slip wall BC type | | | -| | * 'eb' for inhomogeneous Dirichlet BCs of temperature or fluid | | | -| | velocity (mass inflow) on the contained EBs | | | -+---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| po_no_par_out | Let particles exit (default) or bounce-back at pressure outflows | Int | 0 | +| | Options: | | | +| | | | | +| | * ``pi`` - pressure inflow | | | +| | * ``po`` - pressure outflow | | | +| | * ``mi`` - mass inflow | | | +| | * ``nsw`` - no-slip wall | | | +| | * ``eb`` - embedded boundary - for inhomogeneous Dirichlet BCs | | | +| | of temperature or fluid velocity (mass inflow) on the | | | +| | contained EBs | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ + Fluid settings ~~~~~~~~~~~~~~ @@ -59,11 +68,6 @@ using the prefix ``bc.[region].[fluid]``: | massflow | Mass flow rate [required if bc_region_type='mi' | Real | 0 | | | and ``velocity`` or ``volflow`` not specified] | | | +------------------------+------------------------------------------------------------------------+-------------+-----------+ -| delp_dir | Direction for specified pressure drop. Note that this direction | Int | 0 | -| | should also be periodic. | | | -+------------------------+------------------------------------------------------------------------+-------------+-----------+ -| delp | Pressure drop (Pa) | Real | 0 | -+------------------------+------------------------------------------------------------------------+-------------+-----------+ | species.[species0] | Species 'species0' mass fraction [required if solve_species=1 | Real | 0 | | | and bc_region_type='mi' or 'pi']. | | | +------------------------+------------------------------------------------------------------------+-------------+-----------+ @@ -162,28 +166,28 @@ provided when appropriate. +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +=====================+=======================================================================+=============+===========+ -| fluid.velocity | (Required if not `volflow` or `massflow`) | | | +| fluid.velocity | [Required if not `volflow` or `massflow`] | | | | | Inflow fluid velocity on EB faces | Reals | 0 0 0 | | | contained in the (tridimensional) region. | | | | | Note that if only one value is specified, that is assumed to | | | | | be the magnitude in the direction of the EB face's normal. | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| fluid.volflow | (Required if not `velocity` or `massflow`) | | | +| fluid.volflow | [Required if not `velocity` or `massflow`] | | | | | Inflow BC for fluid volumetric flow | Real | 0 | | | rate in the (tridimensional) region. The flow is assumed to be | | | | | normal to the EB surface in the region. | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| fluid.massflow | (Required if not `velocity` or `volflow`) | | | +| fluid.massflow | [Required if not `velocity` or `volflow`] | | | | | Inflow BC for fluid mass flow rate in the (tridimensional) region. | Real | 0 | | | The flow is assumed to be normal to the EB surface in the region. | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| fluid.volfrac | (Required) Volume fraction. | Real | 0 | +| fluid.volfrac | [Required] Volume fraction. | Real | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| eb.normal | (Optional) When specified, only cells with EB face normal that is | Reals | 0 0 0 | +| eb.normal | [Optional] When specified, only cells with EB face normal that is | Reals | 0 0 0 | | | parallel and opposite in direction to the specified values | | | | | are imposed with the inflow velocity. | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| eb.normal_tol | (Optional) Used in conjunction with `eb.normal`. It determines the | Real | 0 | +| eb.normal_tol | [Optional] Used in conjunction with `eb.normal`. It determines the | Real | 0 | | | tolerance (in degrees) for choosing cells with a specific normal. | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ diff --git a/docs/source_docs/user_guide/inputs/chemical_reactions.rst b/docs/source_docs/user_guide/inputs/chemical_reactions.rst index 51e554ec9527fd478a2ebf3dfea17141333aa2db..5cdfdf6e95cf677133180f2cf55a167cade8db3d 100644 --- a/docs/source_docs/user_guide/inputs/chemical_reactions.rst +++ b/docs/source_docs/user_guide/inputs/chemical_reactions.rst @@ -1,48 +1,51 @@ -Chemical Reactions -================== +Defining chemical reactions +=========================== + +.. |tol_eq| replace:: :math:`\left|\sum\text{products - \sum\text{reactants}\right| < \text{tolerance}` The following inputs are defined using the prefix ``chemistry``: +--------------------------+---------------------------------------------------------+----------+----------------+ | | Description | Type | Default | +==========================+=========================================================+==========+================+ -| solve | Specify the name(s) of the chemical reactions or set | String | None | +| solve | Specify the name(s) of the chemical reactions or set | String | | | | to None to disable the chemistry solver. The name(s) | | | | | assigned to the chemistry solver are used to specify | | | | | the chemical reactions equations. | | | +--------------------------+---------------------------------------------------------+----------+----------------+ -| [reaction0].reaction | Chemical formula for the given reaction. The string | String | None | -| | given as input must not contain white spaces and | | | +| [reaction0].reaction | Chemical formula for the given reaction. The string | String | | +| | given as input must not contain white space and | | | | | the reaction direction has to be specified as '\-\->' | | | | | or '<\-\-'. Chemical species phases must be defined as | | | | | '(g)' for the fluid phase or '(s)' for the solid phase. | | | +--------------------------+---------------------------------------------------------+----------+----------------+ | mass_balance_tolerance | Tolerance used to test chemical formula conserves mass. | Real | 1e-12 | | | | | | -| | abs( sum(products) - sum(reactants)) < tolerance | | | +| | |tol_eq| | | | | | | | | +--------------------------+---------------------------------------------------------+----------+----------------+ -| solids.update_type | When updating the solids quantities in chemistry due to | String | ConstantVolume | -| | chemical reactions, choose the update type among: | | | +| solids.update_type | How to update solids quantities due to chemical | | ConstantVolume | +| | reactions. | | | | | | | | -| | * ``ConstantVolume`` keep particles' volume constant | | | -| | * ``ConstantDensity`` keep particles' density constant | | | +| | Options: | | | | | | | | +| | * ``ConstantVolume`` - keep particle volume constant | | | +| | * ``ConstantDensity`` - keep particle density constant | | | +--------------------------+---------------------------------------------------------+----------+----------------+ | solids.mass_threshold | Sets a threshold value for the particles' mass. When | Real | 0 | | | updating the solids quantities in chemistry, check | | | | | whether the solids mass is below the threshold, and in | | | -| | that case set the particle as invalid and remove it | | | +| | that case set the particle as invalid and remove it. | | | +--------------------------+---------------------------------------------------------+----------+----------------+ | solids.radius_threshold | Sets a threshold value for the particles' radius. When | Real | 0 | | | updating the solids quantities in chemistry, check | | | | | whether the solids radius is below the threshold, and | | | -| | in that case set the particle as invalid and remove it | | | +| | in that case set the particle as invalid and remove it. | | | +--------------------------+---------------------------------------------------------+----------+----------------+ | solids.density_threshold | Sets a threshold value for the particles' density. When | Real | 0 | | | updating the solids quantities in chemistry, check | | | | | whether the solids density is below the threshold, and | | | -| | in that case set the particle as invalid and remove it | | | +| | in that case set the particle as invalid and remove it. | | | +--------------------------+---------------------------------------------------------+----------+----------------+ Choosing the integrator type for the chemistry ODE integration operation that is @@ -54,8 +57,8 @@ class of integrators in AMReX-Astro/Microphysics +-------------------------+----------------------------------------------------------------------+----------+---------------+ | | Description | Type | Default | +=========================+======================================================================+==========+===============+ -| chemistry.integrator | Specified name of the chemistry ODE integrator type. Available types | String | ForwardEuler | -| | are (case insensitive): | | | +| chemistry.integrator | Specified name of the chemistry ODE integrator type. Options | String | ForwardEuler | +| | (case-insensitive): | | | | | | | | | | * ``ForwardEuler`` | | | | | * ``StiffSolver::ForwardEuler`` | | | @@ -73,52 +76,54 @@ prefix ``chemistry.integrator``: +-----------------------+---------------------------------------------------------------------+--------+-----------+ | | Description | Type | Default | +=======================+=====================================================================+========+===========+ -| burner_verbose | Enables the printing on screen of some integration statistics | int | 0 | +| burner_verbose | Enable printing of some integration statistics. | Int | 0 | +-----------------------+---------------------------------------------------------------------+--------+-----------+ -| ode_max_steps | The maximum number of substeps for the ODE integration | int | 150000 | +| ode_max_steps | The maximum number of substeps for the ODE integration. | Int | 150000 | +-----------------------+---------------------------------------------------------------------+--------+-----------+ -| jacobian_type | Select how to compute the jacobian for the ODE iterative solver. | string | Numerical | +| jacobian_type | Select how to compute the Jacobian for the ODE iterative solver. | String | Numerical | | | This option is available for ``StiffSolver::BackwardEuler`` and | | | -| | ``StiffSolver::VODE``. Available choices are: | | | +| | ``StiffSolver::VODE``. | | | +| | | | | +| | Options (case-insensitive): | | | | | | | | -| | * ``Numerical`` for a first-order numerical approximation | | | -| | * ``Broyden`` for Broyden's method (only for BackwardEuler) | | | +| | * ``Numerical`` - first-order numerical approximation | | | +| | * ``Broyden`` - Broyden's method (only for ``BackwardEuler``) | | | +-----------------------+---------------------------------------------------------------------+--------+-----------+ | atol | Absolute tolerance for the ODE integration error test between | Real | 1.e-6 | -| | the solution and the fine-step solution | | | +| | the solution and the fine-step solution. | | | +-----------------------+---------------------------------------------------------------------+--------+-----------+ | rtol | Relative tolerance for the ODE integration error test between | Real | 1.e-6 | -| | the solution and the fine-step solution | | | +| | the solution and the fine-step solution. | | | +-----------------------+---------------------------------------------------------------------+--------+-----------+ | retry_atol | Overwrites the absolute tolerance value atol in case the ODE | Real | -1 | -| | integration fails | | | +| | integration fails. | | | +-----------------------+---------------------------------------------------------------------+--------+-----------+ | retry_rtol | Overwrites the relative tolerance value rtol in case the ODE | Real | -1 | -| | integration fails | | | +| | integration fails. | | | +-----------------------+---------------------------------------------------------------------+--------+-----------+ -| retry_swap_jacobian | Swaps the type of jacobian (from 1 to 0 or vice versa) in | int | 1 | -| | case the ODE integration fails | | | +| retry_swap_jacobian | Swaps the type of Jacobian (from 1 to 0 or vice versa) in | Int | 1 | +| | case the ODE integration fails. | | | +-----------------------+---------------------------------------------------------------------+--------+-----------+ -| ode_max_dt | Maximum timestep size for the ODE integration substeps | Real | 1.e30 | +| ode_max_dt | Maximum timestep size for the ODE integration substeps. | Real | 1.e30 | +-----------------------+---------------------------------------------------------------------+--------+-----------+ | max_dt_change_factor | Only for StiffSolver::ForwardEuler, sets a maximum factor | Real | 1.001 | -| | for the change of the timestep for the internal substeps | | | +| | for the change of the timestep for the internal substeps. | | | +-----------------------+---------------------------------------------------------------------+--------+-----------+ -| max_iter | Maximum number of iterations for the internal Newton solver | int | 100 | +| max_iter | Maximum number of iterations for the internal Newton solver. | Int | 100 | +-----------------------+---------------------------------------------------------------------+--------+-----------+ -| linalg_do_pivoting | Only for StiffSolver::BackwardEuler and StiffSolver::VODE, | int | 1 | -| | switches on/off the pivoting when solving the linear algebra | | | -| | problem associated to the internal Newton solver | | | +| linalg_do_pivoting | Only for ``StiffSolver::BackwardEuler`` and ``StiffSolver::VODE``, | Int | 1 | +| | enables pivoting when solving the linear algebra | | | +| | problem associated to the internal Newton solver. | | | +-----------------------+---------------------------------------------------------------------+--------+-----------+ | rp_rtol | Relative tolerance for the convergence test of the internal | Real | 1.e-6 | -| | Newton solver. Valid only for StiffSolver::BackwardEuler | | | +| | Newton solver. Valid only for ``StiffSolver::BackwardEuler``. | | | +-----------------------+---------------------------------------------------------------------+--------+-----------+ -| use_jacobian_caching | Only for StiffSolver::VODE, enables caching the numerical | int | 1 | -| | jacobian | | | +| use_jacobian_caching | Only for ``StiffSolver::VODE``, enable caching the numerical | Int | 1 | +| | Jacobian. | | | +-----------------------+---------------------------------------------------------------------+--------+-----------+ -| X_reject_buffer | Only for StiffSolver::VODE, constrain species abundances | Real | 1.0 | +| X_reject_buffer | Only for ``StiffSolver::VODE``, constrain species abundances | Real | 1.0 | | | such that they don't change by more than a certain factor in | | | -| | a given step | | | +| | a given step. | | | +-----------------------+---------------------------------------------------------------------+--------+-----------+ diff --git a/docs/source_docs/user_guide/inputs/domain.rst b/docs/source_docs/user_guide/inputs/domain.rst index b62ac51f23def3d3144e5d878c5b67696e67dd25..f49b9c8298db6ca40ec73a23e1610819e075221d 100644 --- a/docs/source_docs/user_guide/inputs/domain.rst +++ b/docs/source_docs/user_guide/inputs/domain.rst @@ -16,7 +16,7 @@ The following inputs are defined using the prefix ``geometry``: | coord_sys | Coordinate system used in simulation. Only Cartesian coordinates | Int | 0 | | | (``coord_sys = 0``) are supported. | | | +-----------------+-----------------------------------------------------------------------+-------------+-----------+ -| is_periodic | 1 for true, 0 for false (one value for each coordinate direction) | Int | 0 0 0 | +| is_periodic | 1 for true, 0 for false (one value for each coordinate direction) | Ints | 0 0 0 | +-----------------+-----------------------------------------------------------------------+-------------+-----------+ | prob_lo | Low corner of physical domain (physical not index space) | Reals | 0 0 0 | +-----------------+-----------------------------------------------------------------------+-------------+-----------+ diff --git a/docs/source_docs/user_guide/inputs/fluid_model.rst b/docs/source_docs/user_guide/inputs/fluid_model.rst index 5d7e4cafc675a0b97e36aae9cdc809e81b5a80fb..98194eaefc304daf3341009b1d18dd3576b42557 100644 --- a/docs/source_docs/user_guide/inputs/fluid_model.rst +++ b/docs/source_docs/user_guide/inputs/fluid_model.rst @@ -11,7 +11,7 @@ The following inputs are defined using the prefix ``fluid``: | solve | Specify the name of the fluid or set to ``None`` to disable | String | ``None`` | | | the fluid solver. The name assigned to the fluid solver is | | | | | used to specify fluid properties and initial and boundary | | | -| | conditions. | | | +| | conditions. It is common to use the name ``fluid``. | | | +--------------------------------------------+-------------------------------------------------------------+--------+----------+ @@ -34,18 +34,19 @@ a single fluid; therefore, it is common to name the fluid ``fluid``. This is ill +============================================+============================================================+========+==========+ | viscosity.molecular | Specify which molecular viscosity model to use. | String | None | | | | | | -| | Available options include: | | | +| | Options: | | | | | | | | -| | * ``constant`` constant viscosity | | | -| | * ``Sutherland`` :cite:p:`suth1893` | | | +| | * ``None`` - no viscosity model. | | | +| | * ``constant`` - constant viscosity | | | +| | * ``Sutherland`` :cite:p:`suth1893` - | | | | | | | | | | |Sutherland_Eq| | | | | | | | | -| | * ``Reid`` :cite:p:`reid87` | | | +| | * ``Reid`` :cite:p:`reid87` - | | | | | | | | | | |Reid_4parm_Eq| | | | | | | | | -| | * ``mixture`` a mixture viscosity is computed from | | | +| | * ``mixture`` - a mixture viscosity is computed from | | | | | :ref:`species viscosities` | | | | | and local species mass fractions :cite:p:`bird06` | | | | | | | | @@ -58,31 +59,31 @@ a single fluid; therefore, it is common to name the fluid ``fluid``. This is ill | | | | | | | A value is required for ``constant`` viscosity model. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ -| viscosity.molecular.Sutherland.T_ref | Sutherland model reference temperature | Real | 0 | +| viscosity.molecular.Sutherland.T_ref | Sutherland model reference temperature. | Real | 0 | | | | | | | | A value is required for ``Sutherland`` viscosity model. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ -| viscosity.molecular.Sutherland.mu_ref | Sutherland model reference viscosity at T_ref | Real | 0 | +| viscosity.molecular.Sutherland.mu_ref | Sutherland model reference viscosity at T_ref. | Real | 0 | | | | | | | | A value is required for ``Sutherland`` viscosity model. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ -| viscosity.molecular.Sutherland.S | Sutherland model temperature | Real | 0 | +| viscosity.molecular.Sutherland.S | Sutherland model temperature. | Real | 0 | | | | | | | | A value is required for ``Sutherland`` viscosity model. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ -| viscosity.molecular.Reid.A | Reid model constants | Real | 0 | +| viscosity.molecular.Reid.A | Reid model constants. | Real | 0 | | viscosity.molecular.Reid.B | | | | | viscosity.molecular.Reid.C | Values are required for ``Reid`` viscosity model. | | | | viscosity.molecular.Reid.D | | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ -| viscosity.eddy | Specify eddy viscosity model. | String | None | +| viscosity.eddy | Specify eddy viscosity model. | | | | | | | | -| | Available options include: | | | -| | | | | -| | * ``None`` No eddy viscosity model | | | +| | Options: | | | +| | |String | None | +| | * ``None`` - No eddy viscosity model | | | | | * ``Smagorinsky-Lilly`` :cite:p:`Smag63,Lilly66` | | | | | * ``WALE`` :cite:p:`ducros98` | | | -| | | | | +| | * ``usr`` | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ | viscosity.eddy.Smagorinsky-Lilly.constant | Smagorinsky-Lilly constant which usually has values | Real | None | | | between 0.1 and 0.2. | | | @@ -94,29 +95,29 @@ a single fluid; therefore, it is common to name the fluid ``fluid``. This is ill +--------------------------------------------+------------------------------------------------------------+--------+----------+ | viscosity.suspension | Specify suspension viscosity model of the form | String | None | | | | | | -| | :math:`\mu_{susp}=\mu_{mol}(\mu^* - 1)` | | | +| | :math:`\mu_{susp} = \mu_{mol}(\mu^* - 1)` | | | | | | | | -| | Available options include: | | | +| | Options: | | | | | | | | -| | * ``None`` No eddy suspension model | | | +| | * ``None`` - No eddy suspension model | | | | | | | | -| | :math:`\mu^*=1` | | | +| | :math:`\mu^* = 1` | | | | | | | | | | * ``Einstein`` :cite:p:`einstein11` | | | | | | | | -| | :math:`\mu^*=1 + 2.5\varepsilon_s` | | | +| | :math:`\mu^* = 1 + 2.5\varepsilon_s` | | | | | | | | | | * ``Brinkman`` :cite:p:`brinkman52,gibilaro07` | | | | | | | | -| | :math:`\mu^*=(1-\varepsilon_s)^{-c}` | | | +| | :math:`\mu^* = (1-\varepsilon_s)^{-c}` | | | | | | | | | | * ``Roscoe`` :cite:p:`roscoe52,krieger59,maron56` | | | | | | | | -| | :math:`\mu^*=(1-\varepsilon_s/c_1)^{-c_2}` | | | +| | :math:`\mu^* = (1-\varepsilon_s/c_1)^{-c_2}` | | | | | | | | | | * ``ChengLaw`` :cite:p:`cheng03` | | | | | | | | -| | :math:`\mu^*=e^{2.5(1/(1-\varepsilon_s)^c-1)/c}` | | | +| | :math:`\mu^* = e^{2.5(1/(1-\varepsilon_s)^c-1)/c}` | | | | | | | | | | * ``Sato`` :cite:p:`sato81` | | | | | | | | @@ -129,19 +130,19 @@ a single fluid; therefore, it is common to name the fluid ``fluid``. This is ill +--------------------------------------------+------------------------------------------------------------+--------+----------+ | viscosity.suspension.Brinkman.constant | Constant for exponent in Brinkman suspension expression. | Real | None | | | | | | -| | A value is required when using the model ``Brinkman``. | | | +| | A value is required when using the ``Brinkman`` model. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ | viscosity.suspension.Roscoe.c1 | Constant for max packing in Roscoe suspension expression. | Real | None | | | | | | -| | A value is required when using the model ``Roscoe``. | | | +| | A value is required when using the ``Roscoe`` model. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ | viscosity.suspension.Roscoe.c2 | Constant for exponent in Roscoe suspension expression. | Real | None | | | | | | -| | A value is required when using the model ``Roscoe``. | | | +| | A value is required when using the ``Roscoe`` model. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ | viscosity.suspension.ChengLaw.constant | Constant for exponent in ChengLaw suspension expression. | Real | None | | | | | | -| | A value is required when using the model ``ChengLaw``. | | | +| | A value is required when using the ``ChengLaw`` model. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ | viscosity.suspension.Sato.constant | Constant for Sato suspension expression. | Real | 0.65 | | | | | | @@ -168,12 +169,12 @@ a single fluid; therefore, it is common to name the fluid ``fluid``. This is ill | | are not solved. | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ | specific_heat | Specify which specific heat model to use for the fluid. | String | None | -| | Available options include: | | | +| | Options: | | | | | | | | | | * ``constant`` - the fluid has a constant specific heat | | | | | | | | | | * ``NASA7-poly`` the fluid specific heat is defined by | | | -| | NASA-7 polynomails. | | | +| | NASA-7 polynomials. | | | | | | | | | | NASA7 polynomial format: | | | | | | | | @@ -206,7 +207,7 @@ a single fluid; therefore, it is common to name the fluid ``fluid``. This is ill | | | | | +--------------------------------------------+------------------------------------------------------------+--------+----------+ | thermal_conductivity | Specify which thermal conductivity model to use for | String | None | -| | fluid. Available options include: | | | +| | fluid. Options: | | | | | | | | | | * ``constant`` - the fluid has a constant thermal | | | | | conductivity model | | | @@ -422,5 +423,5 @@ of the damped Newton solver used to compute temperature from enthalpy and specif +------------------------------------------+----------------------------------------------------------+--------+----------+ | newton_solver.relative_tol | Define relative tolerance for the Newton solver | Real | 1.e-8 | +------------------------------------------+----------------------------------------------------------+--------+----------+ -| newton_solver.max_iterations | Define max number of iterations for the Newton solver | int | 500 | +| newton_solver.max_iterations | Define max number of iterations for the Newton solver | Int | 500 | +------------------------------------------+----------------------------------------------------------+--------+----------+ diff --git a/docs/source_docs/user_guide/inputs/geometry.rst b/docs/source_docs/user_guide/inputs/geometry.rst index d50d4d0196a88a7a85c8d3bbf04b9b8d75c42681..ac38cbf1417d6481c9d6255d67c145514a1b1ee9 100644 --- a/docs/source_docs/user_guide/inputs/geometry.rst +++ b/docs/source_docs/user_guide/inputs/geometry.rst @@ -9,12 +9,13 @@ The following inputs are defined using the prefix ``mfix``: | | Description | Type | Default | +========================+===============================================================================+==========+=====================+ | geometry | Specify the simulation geometry. | String | '' | +| | Options (case-insensitive): | | | | | | | | | | * ``box`` - predefined :ref:`box geometry` | | | | | * ``cylinder`` - predefined :ref:`cylinder geometry` | | | | | * ``generic`` - :ref:`user-defined geometry` | | | -| | * ``csg`` - use :ref:`Constructive Solid Geometry` file | | | -| | * ``stl`` - use :ref:`Standard Triangle Language` file | | | +| | * ``CSG`` - use :ref:`Constructive Solid Geometry` file | | | +| | * ``STL`` - use :ref:`Standard Triangle Language` file | | | | | | | | | | If left undefined, then the system should be fully periodic, or | | | | | :ref:`planar regions` should be used to | | | @@ -59,7 +60,7 @@ The following inputs are defined using the prefix ``box``: +------------------------+-------------------------------------------------------------------+----------+---------------------+ | Hi | High corner of the embedded boundary box | Reals | ``prob_hi`` | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -| internal_flow | Flag to indicate that flow is *inside* the box. | Bool | true | +| internal_flow | Indicates that flow is *inside* the box. | Bool | true | +------------------------+-------------------------------------------------------------------+----------+---------------------+ | offset | Shift low side box walls by ``+offset`` and high side walls by | Real | 1.0e-15 | | | ``-offset``. An example use of this input would be to define a | | | @@ -158,7 +159,7 @@ The following inputs are defined using the prefix ``cylinder``: | | then the cylinder is made infinitely long to overhang the domain | | | | | extents. | | | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -| direction | Axis the cylinder runs along. | int | 0 | +| direction | Axis the cylinder runs along. | Int | 0 | | | (``0``: *X*, ``1``: *Y*, ``2``: *Z*) | | | +------------------------+-------------------------------------------------------------------+----------+---------------------+ | center | Center of cylinder. For a cylinder with an undefined ``height``, | Reals | 0. 0. 0. | @@ -170,10 +171,10 @@ The following inputs are defined using the prefix ``cylinder``: | | long) can be rotated. | | | | | * Rotation is applied about the ``center`` of the cylinder. | | | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -| rotation_axe | Axis to rotate the cylinder about. | int | 0 | +| rotation_axe | Axis to rotate the cylinder about. | Int | 0 | | | (``0``: *X*, ``1``: *Y*, ``2``: *Z*) | | | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -| internal_flow | Flag to indicate that flow is *inside* the box. | Bool | true | +| internal_flow | Indicates that flow is *inside* the box. | Bool | true | +------------------------+-------------------------------------------------------------------+----------+---------------------+ The inputs for the predefined ``cylinder`` embedded boundary geometry are illustrated in :numref:`fig_cylinder_geometry_inputs`. @@ -211,7 +212,7 @@ The cylinder is not assigned a length, therefore it runs past the low and high * .. _inputs_cylinder_geometry_ex: .. code-block:: bash - :caption: Snippet of intpus for predefined EB ``cylinder`` geometry example. This is not a complete input file. + :caption: Snippet of inputs for predefined EB ``cylinder`` geometry example. This is not a complete input file. # Define periodicity and domain extents # ------------------------------------------------------------- @@ -344,13 +345,13 @@ The following inputs are defined using the prefix ``csg``: +------------------------+-------------------------------------------------------------------+----------+---------------------+ | | Description | Type | Default | +========================+===================================================================+==========+=====================+ -| geometry_filename | The CSG file that defines the EB geometry | String | '' | +| geometry_filename | The CSG file that defines the EB geometry. | String | '' | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -| internal_flow | Flag to indicate that flow is *inside* the box. | Bool | true | +| internal_flow | Indicates that flow is *inside* the box. | Bool | true | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -| scaling_factor | scale the geometry | Reals | 1. 1. 1. | +| scaling_factor | Scale the geometry. | Reals | 1. 1. 1. | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -| translation | translate the geometry | Reals | 0. 0. 0. | +| translation | Translate the geometry. | Reals | 0. 0. 0. | +------------------------+-------------------------------------------------------------------+----------+---------------------+ .. note:: @@ -360,23 +361,23 @@ The following inputs are defined using the prefix ``csg``: .. _InputsGeometry_STL: -Standard triangle language (STL) +STL (Standard Triangle Language) -------------------------------- -* A standard triangle language (STL) geometry can be created using numerous CAD programs. +* An STL geometry can be created using numerous CAD programs. The following inputs are defined using the prefix ``stl``: +------------------------+-------------------------------------------------------------------+----------+---------------------+ | | Description | Type | Default | +========================+===================================================================+==========+=====================+ -| geometry_filename | The STL file that defines the EB geometry | String | '' | +| geometry_filename | The STL file that defines the EB geometry. | String | '' | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -| scaling_factor | scale the geometry | Real | 1. | +| scaling_factor | Scale the geometry. | Real | 1. | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -| translation | translate the geometry | Reals | 0. 0. 0. | +| translation | Translate the geometry. | Reals | 0. 0. 0. | +------------------------+-------------------------------------------------------------------+----------+---------------------+ -| use_bvh | Use bounding volume optimization | Bool | True | +| use_bvh | Use bounding volume optimization. | Bool | true | +------------------------+-------------------------------------------------------------------+----------+---------------------+ .. note:: diff --git a/docs/source_docs/user_guide/inputs/initial_conditions.rst b/docs/source_docs/user_guide/inputs/initial_conditions.rst index 2070877f87dad6f1bd092f3ae0ffc41e8df7d7f4..a4cdd19e8dc7bdbbe28353558cbc70e8a3050e5f 100644 --- a/docs/source_docs/user_guide/inputs/initial_conditions.rst +++ b/docs/source_docs/user_guide/inputs/initial_conditions.rst @@ -1,4 +1,4 @@ -Initial Conditions +Initial conditions ================== The following inputs are defined using the prefix ``ic``: @@ -8,16 +8,17 @@ The following inputs are defined using the prefix ``ic``: +=======================+========================================================================+=============+===========+ | regions | Regions used to define initial conditions. | String | None | +-----------------------+------------------------------------------------------------------------+-------------+-----------+ -| allow_regions_overlap | Flag for allowing the user to decide whether particles will be | Bool | 1 (yes) | -| | generated/initialized more than once on the areas where the IC regions | | | -| | have an intersection | | | +| allow_regions_overlap | If enabled, particles will be generated/initialized more than once | Int | 1 | +| | on areas where the IC regions intersect. | | | +-----------------------+------------------------------------------------------------------------+-------------+-----------+ -| ranking_type | IC regions are sorted during initialization. This input lets the user | String | Inputs | -| | decide the ranking criterion, which can be one of the following: | | | +| ranking_type | Specifies the order in which IC regions are sorted during | String | Inputs | +| | initialization. | | | | | | | | -| | * inputs -- the order in the inputs file | | | -| | * volume -- the volume of each IC region | | | -| | * priority -- the priority value provided by the user in the inputs | | | +| | Options: | | | +| | | | | +| | * ``Inputs`` - preserve order in inputs file | | | +| | * ``Volume`` - sort by volume of each IC region | | | +| | * ``Priority`` - sort by specified priority value | | | +-----------------------+------------------------------------------------------------------------+-------------+-----------+ @@ -53,20 +54,21 @@ using the compound prefix ``ic.[region]``: +----------------------+------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +======================+==================================================================+=============+===========+ -| solids | Name of solid type in IC region -- only one solid is allowed in | String | None | +| solids | Name of solid type in IC region -- only one solid is allowed in | String | None | | | an IC region. | | | +----------------------+------------------------------------------------------------------+-------------+-----------+ | packing | Specifies how auto-generated particles are placed in the IC | String | None | | | region: | | | | | | | | -| | * hcp -- hex-centered packing | | | -| | * pseudo_random -- random packing using a fixed random seed | | | -| | * random -- random packing (not repeatable) | | | -| | * oneper -- one particle per cell | | | -| | * eightper -- eight particles per cell | | | -| | * n-cube -- n^3 particles per cell where n is an integer | | | +| | * ``hcp`` - hex-centered packing | | | +| | * ``pseudo_random`` -- random packing using a fixed random seed | | | +| | * ``random`` -- random packing (not repeatable) | | | +| | * ``oneper`` -- one particle per cell | | | +| | * ``eightper`` -- eight particles per cell | | | +| | * ``n-cube`` -- n^3 particles per cell where n is an integer | | | | | | | | -| | (NOTE: oneper is equivalent to 1-cube and eightper to 2-cube) | | | +| | (NOTE: ``oneper`` is equivalent to ``1-cube`` and ``eightper`` | | | +| | to ``2-cube``) | | | +----------------------+------------------------------------------------------------------+-------------+-----------+ | priority | Priority value for IC regions ranking as described above | Int | Max | +----------------------+------------------------------------------------------------------+-------------+-----------+ @@ -88,16 +90,23 @@ please refer to :ref:`ReferenceParticleDistributions ` by the @@ -85,7 +85,7 @@ mesh refinement algorithm and are only applicable when ``amr.max_level > 0``. | grid_eff | Threshold value to ensure grids do not contain too large a fraction | Real | 0.7 | | | of un-tagged cells. | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| n_error_buf | Controls the number of tagged cells before grids are defined. Used | int | 1 | +| n_error_buf | Controls the number of tagged cells before grids are defined. Used | Int | 1 | | | to ensure coarse/fine boundaries are not too close to tagged cells. | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ @@ -108,17 +108,17 @@ The following inputs are defined using the prefix ``amr``: +----------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +======================+=======================================================================+=============+===========+ -| max_grid_size_x | Maximum number of cells at level 0 in each grid in *X* | int | 32 | +| max_grid_size_x | Maximum number of cells at level 0 in each grid in *X* | Int | 32 | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| max_grid_size_y | Maximum number of cells at level 0 in each grid in *Y* | int | 32 | +| max_grid_size_y | Maximum number of cells at level 0 in each grid in *Y* | Int | 32 | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| max_grid_size_z | Maximum number of cells at level 0 in each grid in *Z* | int | 32 | +| max_grid_size_z | Maximum number of cells at level 0 in each grid in *Z* | Int | 32 | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| blocking_factor_x | Each grid in *X* must be divisible by ``blocking_factor_x`` | int | 8 | +| blocking_factor_x | Each grid in *X* must be divisible by ``blocking_factor_x`` | Int | 8 | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| blocking_factor_y | Each grid in *Y* must be divisible by ``blocking_factor_y`` | int | 8 | +| blocking_factor_y | Each grid in *Y* must be divisible by ``blocking_factor_y`` | Int | 8 | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| blocking_factor_z | Each grid in *Z* must be divisible by ``blocking_factor_z`` | int | 8 | +| blocking_factor_z | Each grid in *Z* must be divisible by ``blocking_factor_z`` | Int | 8 | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ The domain is decomposed into *grids* by dividing the number of cells by the max grid size diff --git a/docs/source_docs/user_guide/inputs/model_options.rst b/docs/source_docs/user_guide/inputs/model_options.rst index 3072d6409a4cf12d3315e135549d4c0642e34a8c..6679ff9d55459199e00141b79fa2dfcd6c8bfb1b 100644 --- a/docs/source_docs/user_guide/inputs/model_options.rst +++ b/docs/source_docs/user_guide/inputs/model_options.rst @@ -9,14 +9,15 @@ The following inputs are defined using the prefix ``mfix``: +========================+============================================================================+==========+=====================+ | gravity | Gravity vector [required] | Reals | 0 0 0 | +------------------------+----------------------------------------------------------------------------+----------+---------------------+ -| advect_density | Flag to enable time evolution of fluid density. | int | 0 | +| advect_density | Enable time evolution of fluid density. | Int | 0 | +------------------------+----------------------------------------------------------------------------+----------+---------------------+ -| advect_enthalpy | Flag to enable time evolution of fluid temperature and enthalpy. | int | 0 | +| advect_enthalpy | Enable time evolution of fluid temperature and enthalpy. | Int | 0 | +------------------------+----------------------------------------------------------------------------+----------+---------------------+ -| solve_species | Flag to enable the time evolution of fluid species mass | int | 0 | -| | fractions. | | | +| solve_species | Enable the time evolution of fluid species mass fractions. | Int | 0 | +------------------------+----------------------------------------------------------------------------+----------+---------------------+ -| constraint | Select low Mach number constraint. | string | IncompressibleFluid | +| constraint | Select low Mach number constraint. | String | IncompressibleFluid | +| | | | | +| | Options (case-insensitive): | | | | | | | | | | * ``IncompressibleFluid`` constraint is appropriate for cold flow systems | | | | | that do not have chemical reactions. Fluid temperature and species mass | | | @@ -47,46 +48,48 @@ The following inputs are defined using the prefix ``mfix``: +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | Key | Description | Type | Default | +=================================+=======================================================================+=============+==============+ -| advection_type | Advection scheme | string | Godunov | +| advection_type | Advection scheme. | String | Godunov | +| | | | | +| | Options: | | | | | | | | -| | * ``mol`` Predictor-Corrector Method of Lines. MAC velocities and | | | +| | * ``MOL``- Predictor-Corrector Method of Lines. MAC velocities and | | | | | edge states are extrapolated in space. | | | | | | | | -| | * ``godunov`` Godunov. MAC velocities and edge states are | | | +| | * ``Godunov`` - Godunov. MAC velocities and edge states are | | | | | extrapolated in space and time using a second-order Taylor series | | | | | expansion. | | | -| | | | | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | redistribution_type | Algorithms to address the '*small cell problem*' associated with | String | StateRedist | | | explicit cut-cell algorithms. | | | | | | | | +| | Options: | | | +| | | | | | | * ``StateRedist`` :cite:p:`berger21,giuliani22` | | | | | * ``FluxRedist`` :cite:p:`chern87,colella06` | | | -| | * ``NoRedist``: Do not redistribute fluxes. | | | -| | | | | +| | * ``NoRedist`` - Do not redistribute fluxes. | | | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| redistribute_before_nodal_proj | Redistribute the velocity field before the nodal projection | Bool | True | +| redistribute_before_nodal_proj | Redistribute the velocity field before the nodal projection. | Bool | true | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| redistribute_nodal_proj | Redistribute the velocity field after the nodal projection | Bool | False | +| redistribute_nodal_proj | Redistribute the velocity field after the nodal projection. | Bool | false | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| use_drag_coeff_in_proj_gp | Algebraically consistent p coeff in proj or (default) simplified form | Bool | False | +| use_drag_coeff_in_proj_gp | Algebraically consistent p coeff in proj or (default) simplified form.| Bool | false | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| use_drag_in_godunov | Include a drag term in the Godunov flux or (default) not | Bool | False | +| use_drag_in_godunov | Include a drag term in the Godunov flux. | Bool | false | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| godunov_ppm | When using Godunov, use piecewise parabolic (PPM) instead of | Bool | False | -| | piecewise linear (PLM) reconstruction | | | +| godunov_ppm | When using Godunov, use piecewise parabolic (PPM) instead of | Bool | false | +| | piecewise linear (PLM) reconstruction. | | | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| godunov_include_diff_in_forcing | When using Godunov, include viscous/diffusive terms in forcing terms | Bool | True | +| godunov_include_diff_in_forcing | When using Godunov, include viscous/diffusive terms in forcing terms. | Bool | true | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| godunov_use_forces_in_trans | When using Godunov, add forcing terms in the construction of `trans` | Bool | False | -| | velocities | | | +| godunov_use_forces_in_trans | When using Godunov, add forcing terms in the construction of | Bool | false | +| | transverse velocities. | | | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| use_mac_phi_in_godunov | When using Godunov, don't include the pressure gradient in the | Bool | False | -| | forcing term passed into the godunov routine; instead use gradient of | | | -| | mac phi which contains the full pressure | | | +| use_mac_phi_in_godunov | When using Godunov, don't include the pressure gradient in the | Bool | false | +| | forcing term passed into the Godunov routine; instead use gradient of | | | +| | mac phi which contains the full pressure. | | | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | correction_small_volfrac | Threshold volume fraction for correcting small cell velocity | | | -| | at the end of the predictor and corrector | Real | 1.e-4 | +| | at the end of the predictor and corrector. | Real | 1.e-4 | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ @@ -102,9 +105,11 @@ The following inputs are defined using the prefix ``particles``: +---------------------+---------------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +=====================+===========================================================================+=============+===========+ -| constraint | Constraint type. Available options include: | String | None | +| constraint | Constraint type. | String | None | +| | | | | +| | Options: | | | | | | | | -| | * 'mean_velocity' | | | +| | * ``mean_velocity`` | | | | | | | | +---------------------+---------------------------------------------------------------------------+-------------+-----------+ @@ -147,6 +152,8 @@ The following inputs are defined using the prefix ``mfix``: | | grid. An overview of the schemes is provided | | | | | :ref:`below`. | | | | | | | | +| | Options: | | | +| | | | | | | * ``centroid`` | | | | | * ``trilinear`` | | | | | * ``true-dpvm`` | | | @@ -154,8 +161,8 @@ The following inputs are defined using the prefix ``mfix``: +----------------------------+--------------------------------------------------------------------+-----------+---------------+ | deposition_scale_factor | The deposition scale factor. | Real | 1.0 | | | | | | -| | Applicable only with `true-dpvm` and `trilinear-dpvm-square` | | | -| | deposition schemes. The value must be in the intervarl | | | +| | Applicable only with ``true-dpvm`` and ``trilinear-dpvm-square`` | | | +| | deposition schemes. The value must be in the interval | | | | | :math:`[0,\Delta x/2]` where :math:`\Delta x` is the mesh spacing. | | | +----------------------------+--------------------------------------------------------------------+-----------+---------------+ | deposition_diffusion_coeff | If a positive value is set, a diffusion equation | Real | -1.0 | @@ -265,13 +272,15 @@ The following inputs are defined using the prefix ``mfix``: | deposition_redist_type | Algorithm used to redistribute excess solids to adjacent cells. This | String | MaxPack | | | typically applies only to small cut-cells along the geometry. | | | | | | | | -| | * ``MaxPack`` If the solids volume fraction exceeds the prescribed | | | +| | Options: | | | +| | | | | +| | * ``MaxPack`` - If the solids volume fraction exceeds the prescribed | | | | | ``max_solids_volume_fraction``, then the local average solids | | | | | volume is computed and solids volume exceeding the average is | | | | | reallocated to adjacent cells. The fraction of redistributed solids | | | | | is applied to all transferred properties. | | | | | | | | -| | * ``StateRedist`` Use the state redistribution algorithm of | | | +| | * ``StateRedist`` - Use the state redistribution algorithm of | | | | | :cite:p:`berger21,giuliani22` to reallocate | | | | | transferred quantities in small cells. | | | | | | | | @@ -303,7 +312,7 @@ The following input is defined using the prefix ``mfix.drag``: +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +==========================+=======================================================================+=============+===========+ -| model | Fluid-particle drag model. | String | None | +| model | Fluid-particle drag model. Options: | String | None | | | | | | | | * ``WenYu`` :cite:p:`Wen66` | | | | | * ``Gidaspow`` :cite:p:`ding90,Lat00` | | | @@ -315,7 +324,7 @@ The following input is defined using the prefix ``mfix.drag``: | model.SyamOBrien.c1 | Fitting parameters for ``SyamOBrien`` drag model | Real | None | | model.SyamOBrien.d1 | | | | +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ -| include_divtau | Interpolate the fluid shear stress to particles and include in the | int | 0 | +| include_divtau | Interpolate the fluid shear stress to particles and include in the | Int | 0 | | | fluid-particle drag force. The force is applied to the fluid by | | | | | multiplying the shear stress by fluid volume fraction. | | | +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ @@ -324,13 +333,13 @@ The following input is defined using the prefix ``mfix.drag``: | | | | | | | |VirtualMass_Eq| | | | | | | | | -| | * ``Null`` zero virtual mass coefficient, :math:`C_p^{vm}=0` | | | -| | * ``Constant`` - user-specified constant coefficient | | | -| | * ``Zuber`` :cite:p:`zuber64` | | | +| | * ``Null`` - zero virtual mass coefficient, :math:`C_p^{vm}=0` | | | +| | * ``Constant`` - specified constant coefficient | | | +| | * ``Zuber`` - :cite:p:`zuber64` | | | | | | | | | | |VM_Zuber_Eq| | | | | | | | | -| | * ``Nijssen`` :cite:p:`nijssen20` | | | +| | * ``Nijssen`` - :cite:p:`nijssen20` | | | | | | | | | | |VM_Nijssen_Eq| | | | | | | | | @@ -341,7 +350,7 @@ The following input is defined using the prefix ``mfix.drag``: .. note:: - The ``UserDrag`` keyword is used to invoke a user defined drag model. This is accomplished + The ``UserDrag`` keyword is used to invoke a user-defined drag model. This is accomplished by copying ``src/usr/usr_drag.cpp`` file into the build directory, implementing the desired drag model, and recompiling the code. An example can be found in ``tests/DEM06-x``. diff --git a/docs/source_docs/user_guide/inputs/multigrid-solvers.rst b/docs/source_docs/user_guide/inputs/multigrid_solvers.rst similarity index 55% rename from docs/source_docs/user_guide/inputs/multigrid-solvers.rst rename to docs/source_docs/user_guide/inputs/multigrid_solvers.rst index 6330643f7597e97c6d91219db574b605c8d98edc..c3d2fc43d211d54ced04931d9ff63fe5b33740fb 100644 --- a/docs/source_docs/user_guide/inputs/multigrid-solvers.rst +++ b/docs/source_docs/user_guide/inputs/multigrid_solvers.rst @@ -11,32 +11,45 @@ The following inputs are defined using the prefix ``nodal_proj``: +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +=========================+=======================================================================+=============+==============+ -| verbose | Verbosity of multigrid solver in nodal projection | Int | 0 | +| verbose | Verbosity of multigrid solver in nodal projection. | Int | 0 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_verbose | Verbosity of BiCGStab solver in nodal projection | Int | 0 | +| bottom_verbose | Verbosity of BiCGStab solver in nodal projection. | Int | 0 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_rtol | Relative tolerance in nodal projection | Real | 1.e-11 | +| mg_rtol | Relative tolerance in nodal projection. | Real | 1.e-11 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_atol | Absolute tolerance in nodal projection | Real | 1.e-14 | +| mg_atol | Absolute tolerance in nodal projection. | Real | 1.e-14 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| maxiter | Maximum number of iterations in the nodal projection | Int | 100 | +| maxiter | Maximum number of iterations in the nodal projection. | Int | 100 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_maxiter | Maximum number of iterations in the nodal projection | Int | 100 | -| | bottom solver if using bicg, cg, bicgcg or cgbicg | | | +| bottom_maxiter | Maximum number of iterations in the nodal projection | Int | 100 | +| | bottom solver if using bicg, cg, bicgcg or cgbicg. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_max_coarsening_level | Maximum number of coarser levels to allow in the nodal projection | Int | 100 | -| | If set to 0, the bottom solver will be called at the current level | | | +| mg_max_coarsening_level | Maximum number of coarser levels to allow in the nodal projection. | Int | 100 | +| | If set to 0, the bottom solver will be called at the current level. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_solver | Which bottom solver to use in the nodal projection | String | bicgcg | +| bottom_solver | Which bottom solver to use in the nodal projection. | String | bicgcg | +| | | | | +| | Options: | | | +| | | | | +| | * ``bicgcg`` | | | +| | * ``bicgstab`` | | | +| | * ``cg`` | | | +| | * ``cgbicg`` | | | +| | * ``hypre`` | | | +| | * ``smoother`` | | | | | | | | -| | Options are bicgcg, bicgstab, cg, cgbicg, smoother or hypre | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | hypre_namespace | Namespace to use in the nodal projection when using hypre | String | hypre | | | to control hypre specific settings. It can be any string. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| hypre_interface | Which interface to use in the nodal projection when using hypre | String | ij | +| hypre_interface | Which interface to use in the nodal projection when using ``hypre``. | String | ij | +| | | | | | | | | | -| | Options are ij, semi_structured or structured | | | +| | Options: | | | +| | | | | +| | * ``ij`` | | | +| | * ``semi-structured`` | | | +| | * ``structured`` | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ @@ -48,32 +61,43 @@ The following inputs are defined using the prefix ``mac_proj``: +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +=========================+=======================================================================+=============+==============+ -| verbose | Verbosity of multigrid solver in MAC projection | Int | 0 | +| verbose | Verbosity of multigrid solver in MAC projection. | Int | 0 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_verbose | Verbosity of BiCGStab solver in MAC projection | Int | 0 | +| bottom_verbose | Verbosity of BiCGStab solver in MAC projection. | Int | 0 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_rtol | Relative tolerance in MAC projection | Real | 1.e-11 | +| mg_rtol | Relative tolerance in MAC projection. | Real | 1.e-11 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_atol | Absolute tolerance in MAC projection | Real | 1.e-14 | +| mg_atol | Absolute tolerance in MAC projection. | Real | 1.e-14 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| maxiter | Maximum number of iterations in the MAC projection | Int | 200 | +| maxiter | Maximum number of iterations in the MAC projection. | Int | 200 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bottom_maxiter | Maximum number of iterations in the MAC projection | Int | 200 | -| | bottom solver if using bicg, cg, bicgcg or cgbicg | | | +| | bottom solver if using bicg, cg, bicgcg or cgbicg. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | mg_max_coarsening_level | Maximum number of coarser levels to allow in the MAC projection | Int | 100 | | | If set to 0, the bottom solver will be called at the current level | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_solver | Which bottom solver to use in the MAC projection | String | bicgcg | +| bottom_solver | Which bottom solver to use in the MAC projection. | String | bicgcg | +| | | | | +| | Options: | | | | | | | | -| | Options are bicgcg, bicgstab, cg, cgbicg, smoother or hypre | | | +| | * ``bicgcg`` | | | +| | * ``bicgstab`` | | | +| | * ``cg`` | | | +| | * ``cgbicg`` | | | +| | * ``hypre`` | | | +| | * ``smoother`` | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| hypre_namespace | Namespace to use in the MAC projection when using hypre | String | hypre | +| hypre_namespace | Namespace to use in the MAC projection when using ``hypre`` | String | hypre | | | to control hypre specific settings. It can be any string. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| hypre_interface | Which interface to use in the MAC projection when using hypre | String | ij | +| hypre_interface | Which interface to use in the MAC projection when using ``hypre``. | String | ij | +| | | | | +| | Options: | | | | | | | | -| | Options are ij, semi_structured or structured | | | +| | * ``ij`` | | | +| | * ``semi-structured`` | | | +| | * ``structured`` | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ @@ -86,25 +110,30 @@ The following inputs are defined using the prefix ``diffusion``: +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +=========================+=======================================================================+=============+==============+ -| verbose | Verbosity of linear solver for diffusion solve | int | 0 | +| verbose | Verbosity of linear solver for diffusion. | Int | 0 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_verbose | Verbosity of BiCGStab solver in diffusion solve | int | 0 | +| bottom_verbose | Verbosity of BiCGStab solver in diffusion. | Int | 0 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_rtol | Relative tolerance in diffusion solve | Real | 1.e-11 | +| mg_rtol | Relative tolerance in diffusion solver. | Real | 1.e-11 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_atol | Absolute tolerance in diffusion solve | Real | 1.e-14 | +| mg_atol | Absolute tolerance in diffusion solver. | Real | 1.e-14 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| maxiter | Maximum number of iterations in diffusion solve | int | 100 | +| maxiter | Maximum number of iterations in diffusion solver. | Int | 100 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_maxiter | Maximum number of iterations in diffusion solve | int | 100 | -| | bottom solver if using bicg, cg, bicgcg or cgbicg | | | +| bottom_maxiter | Maximum number of iterations in diffusion solver | Int | 100 | +| | bottom solver if using ``bicg``, ``cg``, ``bicgcg``, or ``cgbicg``. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_max_coarsening_level | Maximum number of coarser levels to allow in diffusion solve | int | 100 | -| | If set to 0, the bottom solver will be called at the current level | | | +| mg_max_coarsening_level | Maximum number of coarser levels to allow in diffusion solve | Int | 100 | +| | If set to 0, the bottom solver will be called at the current level. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_solver | Which bottom solver to use in the diffusion solve | string | bicgcg | +| bottom_solver | Which bottom solver to use for diffusion. | String | bicgcg | +| | | | | +| | Options: | | | | | | | | -| | Options are bicgcg, bicgstab, cg, cgbicg, or smoother | | | +| | * ``bicgcg`` | | | +| | * ``cg`` - | | | +| | * ``cgbicg`` - | | | +| | * ``smoother`` - | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ @@ -112,36 +141,50 @@ Hypre Settings -------------- `hypre` settings are specified using the following inputs which are read directly by AMReX when `hypre` is used as -the bottom solve for the MAC and/or nodal projections. By default, these inputs are defined using the +the bottom solver for the MAC and/or nodal projections. By default, these inputs are defined using the prefix ``hypre``, however different settings for the nodal and MAC projections can be used by specifying a ``hpyre_namespace`` for each solver. .. warning:: - * MFIX-Exa must be built with `hypre` enabled to use `hypre` as the bottom solve. + * MFIX-Exa must be built with `hypre` enabled to use `hypre` as the bottom solver. * If `hypre` is used for the nodal and MAC projections, then either the ``hypre_namespace`` must be left as the default (``hypre``) or unique name spaces must be provided for both. + * These inputs are all case-sensitive. + These inputs follow the typical approach for using `hypre` in MFIX-Exa where `BoomerAMG` is employed as a preconditioner and `GMRES` for the linear solver. +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +===================================+=======================================================================+=============+==============+ -| hypre_preconditioner | Type of preconditioner | string | none | +| hypre_preconditioner | Type of preconditioner when using ``hypre``. | String | none | | | | | | -| | Options are BoomerAMG or euclid | | | +| | Options: | | | +| | | | | +| | * ``none`` - no preconditioner | | | +| | * ``BoomerAMG`` | | | +| | * ``euclid`` | | | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| recompute_preconditioner | Recompute preconditioner during runs | Bool | true | +| recompute_preconditioner | Recompute preconditioner during runs. | Bool | true | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| hypre_solver | Type of hypre solver | string | BoomerAMG | +| hypre_solver | Type of hypre solver. | String | BoomerAMG | +| | | | | +| | Options: | | | | | | | | -| | Options are BoomerAMG, GMRES, COGMRES, LGMRES, FlexGMRES, BiCGSTAB, | | | -| | PCG or Hybrid | | | +| | * ``BoomerAMG`` | | | +| | * ``GMRES`` | | | +| | * ``COGMRES`` | | | +| | * ``LGMRES`` | | | +| | * ``FlexGMRES`` | | | +| | * ``BiCGSTAB`` | | | +| | * ``PCG`` | | | +| | * ``Hybrid`` | | | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| verbose | Verbosity of hypre | int | 0 | +| verbose | Verbosity of hypre. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| num_krylov | Number of iterations | int | 50 | +| num_krylov | Number of iterations. | Int | 50 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ @@ -150,61 +193,61 @@ The following inputs are valid when using ``BoomerAMG`` as a preconditioner or s +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +===================================+=======================================================================+=============+==============+ -| bamg_verbose | Set BoomerAMG verbosity | int | 0 | +| bamg_agg_interp_type | See ``HYPRE_BoomerAMGSetAggInterpType``. | Int | 4 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_logging | See HYPRE_BoomerAMGSetLogging | int | 0 | +| bamg_agg_num_levels | See ``HYPRE_BoomerAMGSetAggNumLevels``. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_max_iterations | See HYPRE_BoomerAMGSetMaxIter | int | 1 | +| bamg_agg_pmax_elmts | See ``HYPRE_BoomerAMGSetAggPMaxElmts``. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_precond_tolerance | See HYPRE_BoomerAMGSetTol | Real | 0.0 | +| bamg_coarse_relax_type | See ``HYPRE_BoomerAMGSetCycleRelaxType``. | Int | 11 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_coarsen_type | See HYPRE_BoomerAMGSetCoarsenType | int | 6 | +| bamg_coarsen_type | See ``HYPRE_BoomerAMGSetCoarsenType``. | Int | 6 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_cycle_type | See HYPRE_BoomerAMGSetCycleType | int | 1 | +| bamg_cycle_type | See ``HYPRE_BoomerAMGSetCycleType``. | Int | 1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_relax_order | See HYPRE_BoomerAMGSetRelaxOrder | int | 1 | +| bamg_down_relax_type | See ``HYPRE_BoomerAMGSetCycleRelaxType``. | Int | 11 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_relax_type | See HYPRE_BoomerAMGSetRelaxType | int | 6 | +| bamg_interp_type | See ``HYPRE_BoomerAMGSetInterpType``. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_down_relax_type | See HYPRE_BoomerAMGSetCycleRelaxType | int | 11 | +| bamg_keep_transpose | See ``HYPRE_BoomerAMGSetKeepTranspose``. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_up_relax_type | See HYPRE_BoomerAMGSetCycleRelaxType | int | 11 | +| bamg_logging | See ``HYPRE_BoomerAMGSetLogging``. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_coarse_relax_type | See HYPRE_BoomerAMGSetCycleRelaxType | int | 11 | +| bamg_max_coarse_size | See ``HYPRE_BoomerAMGSetMaxCoarseSize``. | Int | 9 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_num_sweeps | See HYPRE_BoomerAMGSetNumSweeps | int | 2 | +| bamg_max_iterations | See ``HYPRE_BoomerAMGSetMaxIter``. | Int | 1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_num_down_sweeps | See HYPRE_BoomerAMGSetCycleNumSweeps | int | 2 | +| bamg_max_levels | See ``HYPRE_BoomerAMGSetMaxLevels``. | Int | 20 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_num_up_sweeps | See HYPRE_BoomerAMGSetCycleNumSweeps | int | 2 | +| bamg_min_coarse_size | See ``HYPRE_BoomerAMGSetMinCoarseSize``. | Int | 1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_num_coarse_sweeps | See HYPRE_BoomerAMGSetCycleNumSweeps | int | 1 | +| bamg_num_coarse_sweeps | See ``HYPRE_BoomerAMGSetCycleNumSweeps``. | Int | 1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_max_levels | See HYPRE_BoomerAMGSetMaxLevels | int | 20 | +| bamg_num_down_sweeps | See ``HYPRE_BoomerAMGSetCycleNumSweeps``. | Int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_strong_threshold | See HYPRE_BoomerAMGSetStrongThreshold | Real | 0.57 | +| bamg_num_sweeps | See ``HYPRE_BoomerAMGSetNumSweeps``. | int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_interp_type | See HYPRE_BoomerAMGSetInterpType | int | 0 | +| bamg_num_up_sweeps | See ``HYPRE_BoomerAMGSetCycleNumSweeps``. | Int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_variant | See HYPRE_BoomerAMGSetVariant | int | 0 | +| bamg_pmax_elmts | See ``HYPRE_BoomerAMGSetPMaxElmts``. | Int | 4 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_keep_transpose | See HYPRE_BoomerAMGSetKeepTranspose | int | 0 | +| bamg_precond_tolerance | See ``HYPRE_BoomerAMGSetTol``. | Real | 0.0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_min_coarse_size | See HYPRE_BoomerAMGSetMinCoarseSize | int | 1 | +| bamg_relax_order | See ``HYPRE_BoomerAMGSetRelaxOrder``. | Int | 1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_max_coarse_size | See HYPRE_BoomerAMGSetMaxCoarseSize | int | 9 | +| bamg_relax_type | See ``HYPRE_BoomerAMGSetRelaxType``. | Int | 6 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_pmax_elmts | See HYPRE_BoomerAMGSetPMaxElmts | int | 4 | +| bamg_set_restriction | See ``HYPRE_BoomerAMGSetRestriction``. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_agg_num_levels | See HYPRE_BoomerAMGSetAggNumLevels | int | 0 | +| bamg_strong_threshold | See ``HYPRE_BoomerAMGSetStrongThreshold``. | Real | 0.57 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_agg_interp_type | See HYPRE_BoomerAMGSetAggInterpType | int | 4 | +| bamg_trunc_factor | See ``HYPRE_BoomerAMGSetTruncFactor``. | Real | 0.1 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_agg_pmax_elmts | See HYPRE_BoomerAMGSetAggPMaxElmts | int | 0 | +| bamg_up_relax_type | See ``HYPRE_BoomerAMGSetCycleRelaxType``. | Int | 11 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_trunc_factor | See HYPRE_BoomerAMGSetTruncFactor | Real | 0.1 | +| bamg_variant | See ``HYPRE_BoomerAMGSetVariant``. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_set_restriction | See HYPRE_BoomerAMGSetRestriction | int | 0 | +| bamg_verbose | Set ``BoomerAMG`` verbosity. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ @@ -212,15 +255,14 @@ The following inputs are valid when using ``BoomerAMG`` as a preconditioner or s - +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +===================================+=======================================================================+=============+==============+ -| adjust_singular_matrix | Should be true if the problem to be solved has singular matrix | Bool | false | +| adjust_singular_matrix | Enable if the problem to be solved has a singular matrix. | Bool | false | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| overwrite_existing_matrix_files | Over-write existing matrix files | Bool | false | +| overwrite_existing_matrix_files | Overwrite existing matrix files. | Bool | false | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| write_matrix_files | Write out matrix into text files | Bool | false | +| write_matrix_files | Write matrix into text files. | Bool | false | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ diff --git a/docs/source_docs/user_guide/inputs/output.rst b/docs/source_docs/user_guide/inputs/output.rst index 897e6681629432dbf4f3bb4bfb4de183fe8e3dc4..27398949e3e1611ca56cc1fd51d6d516e90dc20d 100644 --- a/docs/source_docs/user_guide/inputs/output.rst +++ b/docs/source_docs/user_guide/inputs/output.rst @@ -7,7 +7,7 @@ Various options for outputting simulation data from MFIX-Exa. :maxdepth: 0 output/checkpointing - output/plotfiles + output/plotting output/monitors output/reports output/ascent diff --git a/docs/source_docs/user_guide/inputs/output/ascent.rst b/docs/source_docs/user_guide/inputs/output/ascent.rst index d30ae2a98ac82464ce0671ee90befabb8ebcbf59..118111d8d8606b4b38a230efbd712e48cf20126e 100644 --- a/docs/source_docs/user_guide/inputs/output/ascent.rst +++ b/docs/source_docs/user_guide/inputs/output/ascent.rst @@ -1,5 +1,5 @@ Ascent ------- +====== The following inputs must be preceded by the prefix ``mfix`` and control frequency and naming of plotfile generation as well as whether the EB geometry or level set should be written out, and if the particles should be written out in Ascii diff --git a/docs/source_docs/user_guide/inputs/output/checkpointing.rst b/docs/source_docs/user_guide/inputs/output/checkpointing.rst index 2f363ca12eaa5cd6e492116a5ca2f7d4ae190b8f..e5714589e1ea04d91ec35ea99f6fa88b46f42c1e 100644 --- a/docs/source_docs/user_guide/inputs/output/checkpointing.rst +++ b/docs/source_docs/user_guide/inputs/output/checkpointing.rst @@ -8,23 +8,23 @@ The following inputs must be preceded by the prefix ``mfix`` and control checkpo +-------------------------+-----------------------------------------------------------------------+-------------+------------+ | | Description | Type | Default | +=========================+=======================================================================+=============+============+ -| restart | If present, then the name of file to restart from | String | None | +| restart | If present, then the name of file to restart from | String | None | +-------------------------+-----------------------------------------------------------------------+-------------+------------+ -| check_int | Frequency of checkpoint output in timesteps number; | Int | -1 | +| check_int | Frequency of checkpoint output in number of timesteps; | Int | -1 | | | if -1 then no checkpoints will be written | | | +-------------------------+-----------------------------------------------------------------------+-------------+------------+ -| check_per_approx | Frequency of checkpoint output in simulation time; | Real | 0 | +| check_per_approx | Frequency of checkpoint output in simulation time; | Real | 0 | | | if 0 then no checkpoints will be written | | | +-------------------------+-----------------------------------------------------------------------+-------------+------------+ -| check_walltime_interval | Frequency of checkpoint output in runtime (HH:MM:SS) | String | "" | +| check_walltime_interval | Frequency of checkpoint output in runtime (HH:MM:SS) | String | None | +-------------------------+-----------------------------------------------------------------------+-------------+------------+ | check_file | Prefix to use for checkpoint output | String | chk | +-------------------------+-----------------------------------------------------------------------+-------------+------------+ -| geom_chk_write | When True, writes the EB geometry data into geom_chk_file | bool | False | +| geom_chk_write | When enabled, write the EB geometry data into geom_chk_file | Bool | false | | | and additionally, geom_levelset_chk_file, if levelset | | | | | refinement is enabled. | | | +-------------------------+-----------------------------------------------------------------------+-------------+------------+ -| geom_chk_read | When True, reads the EB geometry data from geom_chk_file | bool | False | +| geom_chk_read | When true, read the EB geometry data from geom_chk_file | Bool | false | | | and additionally, geom_levelset_chk_file, if levelset | | | | | refinement is enabled. | | | +-------------------------+-----------------------------------------------------------------------+-------------+------------+ diff --git a/docs/source_docs/user_guide/inputs/output/monitors.rst b/docs/source_docs/user_guide/inputs/output/monitors.rst index 5c8e680e3aa7d9e89aabd1914d14fc08c3c29d67..835437d2418b7012f8d1b4bf0b24f86df3ca8fe5 100644 --- a/docs/source_docs/user_guide/inputs/output/monitors.rst +++ b/docs/source_docs/user_guide/inputs/output/monitors.rst @@ -1,11 +1,11 @@ Monitors ======== -A Monitor is a tool for capturing data from the solver about the model. +A monitor is a tool for capturing data from the solver about the model. Data (such as volume fraction, pressure, velocity, etc.) for a given monitor region is written to a CSV file while the solver is running. -To define monitors, the following inputs must be preceded by "mfix.": +To define monitors, the following inputs must be preceded by the prefix ``mfix``: +--------------------+------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -23,13 +23,13 @@ To define monitors, the following inputs must be preceded by "mfix.": mfix.monitors.my_monitor1 = Lagrangian::Average::VolumeWeightedAverage -Region Selection +Region selection ---------------- To define a monitor, there must be a region already defined in the regions inputs. A Monitor region is a single point, plane, or volume. Multiple regions cannot be combined for a monitor. The following inputs must be preceded by -"mfix.monitors.": +the prefix ``mfix.monitors``: +------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -44,14 +44,14 @@ cannot be combined for a monitor. The following inputs must be preceded by mfix.monitors.my_monitor1.region = regionB -Monitor Output +Monitor output -------------- The monitor data will be output to a file with name given by the input "plot_file", and the extension ``.csv`` is automatically added. The monitor output file is in Comma Separated Value (CSV) format. The first line of the file provides header information. The following inputs must be preceded by -"mfix.monitors.": +the prefix ``mfix.monitors``: +-------------------------------+----------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -65,11 +65,12 @@ provides header information. The following inputs must be preceded by | [monitor].plot_per_approx | Define the approximated simulation time at which saving | Real | 0 | | | monitored data | | | +-------------------------------+----------------------------------------------------------+-------------+-----------+ -| [monitor].output.openmode | Sets the open mode for the monitor output file. | String | "app" | -| | Admissible values are: | | | +| [monitor].output.openmode | Sets the open mode for the monitor output file. | String | app | | | | | | -| | * "app" for appending to the file if it already exists | | | -| | * "trunc" for overwriting the output file if it exists | | | +| | Options: | | | +| | | | | +| | * ``app`` - append to the file if it already exists | | | +| | * ``trunc`` - overwrite the output file if it exists | | | +-------------------------------+----------------------------------------------------------+-------------+-----------+ | [monitor].output.setw | Sets the field width to be used on output file | Int | 0 | +-------------------------------+----------------------------------------------------------+-------------+-----------+ @@ -94,11 +95,11 @@ provides header information. The following inputs must be preceded by mfix.monitors.my_monitor1.plot_per_approx = 0.01 -Monitor Variables +Monitor variables ----------------- The variables to be monitored can be specified in the inputs by including the -following input preceded by the "mfix.monitors.": +following input preceded by the prefix ``mfix.monitors``: +---------------------+--------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -113,7 +114,7 @@ following input preceded by the "mfix.monitors.": mfix.monitors.my_monitor1.variables = density drag_y T_s txfr_vel_x -Eulerian Monitors +Eulerian monitors ----------------- There are different types of monitors available. A monitor type applies an @@ -151,13 +152,11 @@ The following table lists all the fluid phase variables that can be monitored: +--------------------------+-----------------------------------------------------------------------------------------+ | trac | tracer | +--------------------------+-----------------------------------------------------------------------------------------+ -| vel_g | fluid velocity | -| | (all the three components of the velocity) | +| vel_g | fluid velocity (all three components) | +--------------------------+-----------------------------------------------------------------------------------------+ | vel_g_[x/y/z] | x, y, or z component of the fluid velocity | +--------------------------+-----------------------------------------------------------------------------------------+ -| gp | fluid pressure gradient | -| | (all the three components of the gradient) | +| gp | fluid pressure gradient (all three components) | +--------------------------+-----------------------------------------------------------------------------------------+ | gp_[x/y/z] | x, y, or z component of the fluid pressure gradient | +--------------------------+-----------------------------------------------------------------------------------------+ @@ -169,13 +168,11 @@ The following table lists all the fluid phase variables that can be monitored: +--------------------------+-----------------------------------------------------------------------------------------+ | X_gk_[species] | fluid "species" mass fraction (only species "species" is monitored) | +--------------------------+-----------------------------------------------------------------------------------------+ -| vort | fluid vorticity | -| | (all the three components of the vorticity) | +| vort | fluid vorticity (all three components) | +--------------------------+-----------------------------------------------------------------------------------------+ | vort[x/y/z] | x, y, or z component of the fluid vorticity | +--------------------------+-----------------------------------------------------------------------------------------+ -| txfr_velocity | interphase velocity transferred to the fluid | -| | (all the three components of the velocity) | +| txfr_velocity | interphase velocity transferred to the fluid (all three components) | +--------------------------+-----------------------------------------------------------------------------------------+ | txfr_vel_[x/y/z] | x, y, or z component of the interphase velocity transferred to the fluid | +--------------------------+-----------------------------------------------------------------------------------------+ @@ -192,20 +189,19 @@ The following table lists all the fluid phase variables that can be monitored: | | (only species "species" is monitored) | +--------------------------+-----------------------------------------------------------------------------------------+ | chem_txfr_velocity | rate of velocity transferred to the fluid phase due to heterogeneous chemical reactions | -| | (all the three components of the velocity) | +| | (all three components) | +--------------------------+-----------------------------------------------------------------------------------------+ | chem_txfr_vel_[x/y/z] | x, y, or z component of the rate of velocity transferred due to heterogeneous reactions | +--------------------------+-----------------------------------------------------------------------------------------+ | chem_txfr_h | rate of enthalpy transferred to the fluid phase due to heterogeneous chemical reactions | +--------------------------+-----------------------------------------------------------------------------------------+ -| divtau | divergence of the viscous stress tensor | -| | (all the three components) | +| divtau | divergence of the viscous stress tensor (all three components) | +--------------------------+-----------------------------------------------------------------------------------------+ | divtau_[x/y/z] | x, y, or z component of the divergence of the viscous stress tensor | +--------------------------+-----------------------------------------------------------------------------------------+ -Uniform Scalar Field +Uniform scalar field ~~~~~~~~~~~~~~~~~~~~ The following table lists all the fluid phase space-uniform variables that can @@ -230,7 +226,7 @@ Value .. math:: \phi_{ijk} -Point Region +Point region ~~~~~~~~~~~~ For a point region, the monitor data value is simply the value of the variable @@ -246,7 +242,7 @@ Value .. math:: \phi_{ijk} -Area or Volume Region +Area or volume region ~~~~~~~~~~~~~~~~~~~~~ The following monitor types are valid for area and volume regions: @@ -297,7 +293,7 @@ Average .. math:: \phi_0 = \frac{\sum_{ijk} \phi_{ijk}}{N} -Standard Deviation +Standard deviation +-------------------------------------------+ | Eulerian::AreaRegion::StandardDeviation | +-------------------------------------------+ @@ -310,7 +306,7 @@ Standard Deviation .. math:: \sigma_{\phi} = \sqrt{\frac{ \sum_{ijk} (\phi_{ijk}-\phi_{0})^2 }{N}} -Surface Integrals +Surface integrals ~~~~~~~~~~~~~~~~~ The following types are only valid for area regions: @@ -325,7 +321,7 @@ Area .. math:: \int dA = \sum_{ijk} \lvert A_{ijk} \rvert -Area-Weighted Average +Area-weighted average +------------------------------------------------+ | Eulerian::SurfaceIntegral::AreaWeightedAverage | +------------------------------------------------+ @@ -336,7 +332,7 @@ Area-Weighted Average .. math:: \frac{\int\phi dA}{A} = \frac{\sum_{ijk}{\phi_{ijk} \lvert A_{ijk} \rvert}}{\sum_{ijk}{\lvert A_{ijk} \rvert}} -Flow Rate +Flow rate +-------------------------------------+ | Eulerian::SurfaceIntegral::FlowRate | +-------------------------------------+ @@ -347,7 +343,7 @@ Flow Rate .. math:: \int\varepsilon\rho\phi{v_n}dA = \sum_{ijk}\varepsilon_{ijk}\rho_{ijk}\phi_{ijk} {v}_{n,ijk} \lvert A_{ijk} \rvert -Mass Flow Rate +Mass flow rate +-----------------------------------------+ | Eulerian::SurfaceIntegral::MassFlowRate | +-----------------------------------------+ @@ -358,7 +354,7 @@ Mass Flow Rate .. math:: \int\varepsilon\rho{v_n} dA = \sum_{ijk}\varepsilon_{ijk}\rho_{ijk}{v}_{n,ijk} \lvert A_{ijk} \rvert -Mass-Weighted Average +Mass-weighted average +------------------------------------------------+ | Eulerian::SurfaceIntegral::MassWeightedAverage | +------------------------------------------------+ @@ -369,7 +365,7 @@ Mass-Weighted Average .. math:: \frac{\int\varepsilon\rho\phi{v_n}dA}{\int\varepsilon\rho{v_n}dA} = \frac{\sum_{ijk}\varepsilon_{ijk}\rho_{ijk}\phi_{ijk} {v}_{n,ijk} \lvert A_{ijk} \rvert}{\sum_{ijk}\varepsilon_{ijk}\rho_{ijk} {v}_{n,ijk} \lvert A_{ijk} \rvert} -Volume Flow Rate +Volume flow rate +-------------------------------------------+ | Eulerian::SurfaceIntegral::VolumeFlowRate | +-------------------------------------------+ @@ -381,7 +377,7 @@ Volume Flow Rate .. math:: \int\varepsilon{v_n}dA = \sum_{ijk}\varepsilon_{ijk}{v}_{n,ijk} \lvert A_{ijk} \rvert -Volume Integrals +Volume integrals ~~~~~~~~~~~~~~~~ The following types are only valid for volume regions: @@ -396,7 +392,7 @@ Volume .. math:: \int dV = \sum_{ijk}{ \lvert V_{ijk}} \rvert -Volume Integral +Volume integral +------------------------------------------+ | Eulerian::VolumeIntegral::VolumeIntegral | +------------------------------------------+ @@ -406,7 +402,7 @@ Volume Integral .. math:: \int \phi dV = \sum_{ijk}{\phi_{ijk} \lvert V_{ijk}} \rvert -Volume-Weighted Average +Volume-weighted average +-------------------------------------------------+ | Eulerian::VolumeIntegral::VolumeWeightedAverage | +-------------------------------------------------+ @@ -417,7 +413,7 @@ Volume-Weighted Average .. math:: \frac{\int\phi dV}{V} = \frac{\sum_{ijk}{\phi_{ijk} \lvert V_{ijk} \rvert}}{\sum_{ijk}{\lvert V_{ijk} \rvert}} -Mass-Weighted Integral +Mass-weighted integral +------------------------------------------------+ | Eulerian::VolumeIntegral::MassWeightedIntegral | +------------------------------------------------+ @@ -427,7 +423,7 @@ Mass-Weighted Integral .. math:: \int \varepsilon\rho\phi dV = \sum_{ijk}\varepsilon_{ijk}\rho_{ijk}\phi_{ijk} \lvert V_{ijk}\rvert -Mass-Weighted Average +Mass-weighted Average +-----------------------------------------------+ | Eulerian::VolumeIntegral::MassWeightedAverage | +-----------------------------------------------+ @@ -441,7 +437,7 @@ Mass-Weighted Average -Lagrangian Monitors +Lagrangian monitors ------------------- There are different types of monitors available. A monitor type applies an @@ -480,7 +476,7 @@ The following table lists all the solids phase variables that can be monitored: +--------------------------+-----------------------------------------------------------------------------------------+ | id | particles id | +--------------------------+-----------------------------------------------------------------------------------------+ -| cpu | particles cpu | +| cpu | particles CPU | +--------------------------+-----------------------------------------------------------------------------------------+ | radius | particles radius | +--------------------------+-----------------------------------------------------------------------------------------+ @@ -521,7 +517,7 @@ The following table lists all the solids phase variables that can be monitored: | X_sn_[species] | solids "species" mass fraction (only species "species" is monitored) | +--------------------------+-----------------------------------------------------------------------------------------+ | txfr_velocity | rate of velocity transferred to the fluid phase due to heterogeneous chemical reactions | -| | (all the three components) | +| | (all three components) | +--------------------------+-----------------------------------------------------------------------------------------+ | txfr_vel_[x/y/z] | x, y, or z components of the transferred velocity due to heterogeneous reactions | +--------------------------+-----------------------------------------------------------------------------------------+ @@ -551,7 +547,7 @@ Sum .. math:: \sum_p w_p \phi_p -Mass-Weighted Sum +Mass-weighted sum +----------------------------------------------+ | Lagrangian::GeneralProperty::MassWeightedSum | @@ -604,7 +600,7 @@ Average .. math:: \bar{\phi} = \frac{\sum_p w_p \phi_p}{\sum_p w_p} -Standard Deviation +Standard deviation +-------------------------------------------------+ | Lagrangian::AveragedProperty::StandardDeviation | +-------------------------------------------------+ @@ -647,7 +643,7 @@ used, preceded by the prefix ``mfix.monitors``: +------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +==================+=======================================================================+=============+===========+ -| [monitor].plane | defines the plane through which the flow rate of the particles in the | String | None | +| [monitor].plane | Defines the plane through which the flow rate of the particles in the | String | None | | | monitoring region [region] will be computed | | | +------------------+-----------------------------------------------------------------------+-------------+-----------+ diff --git a/docs/source_docs/user_guide/inputs/output/plotfiles.rst b/docs/source_docs/user_guide/inputs/output/plotting.rst similarity index 73% rename from docs/source_docs/user_guide/inputs/output/plotfiles.rst rename to docs/source_docs/user_guide/inputs/output/plotting.rst index 0cc9ae5e7d50dad48ae1b6357ce66b5295654761..2da4b06a6a4ccc6da7bb7b8844d285d8971c6e64 100644 --- a/docs/source_docs/user_guide/inputs/output/plotfiles.rst +++ b/docs/source_docs/user_guide/inputs/output/plotting.rst @@ -1,10 +1,10 @@ .. _Chap:InputsPlotfiles: -Plotfiles and Other Output +Plotfiles and other output ========================== The following inputs must be preceded by the prefix ``mfix`` and control frequency and naming of plotfile generation as well -as whether the EB geometry or level set should be written out, and if the particles should be written out in Ascii +as whether the EB geometry or level set should be written, and if the particles should be written out in Ascii format (for debugging). +----------------------+-----------------------------------------------------------------------+-------------+-----------+ @@ -16,7 +16,7 @@ format (for debugging). | plot_per_approx | Time period of plotfile output (approximate); does not modify dt | Real | -1 | | | if -1 then no plotfiles will be written at this frequency | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plotfile_on_restart | Should we write a plotfile when we restart (only used if plot_int>0) | Bool | False | +| plotfile_on_restart | Write a plotfile when we restart (only used if plot_int>0) | Bool | false | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ | plot_file | Prefix to use for plotfile output | String | plt | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ @@ -39,63 +39,63 @@ format (for debugging). +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -The following inputs must be preceded by "mfix." and control what variables will be written in plotfiles. +The following inputs must be preceded by the prefix ``mfix`` and control which variables will be written in plotfiles. +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +=====================+=======================================================================+=============+===========+ -| plt_regtest | Save all variables to plot file (overrides all other IO flags) | Int | 0 | +| plt_regtest | Plot all variables (overrides all other plot flags) | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_vel_g | Save fluid velocity data to plot file | Int | 1 | +| plt_drag_p | Plot particle drag force | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_ep_g | Save fluid volume fraction to plot file | Int | 1 | +| plt_ep_g | Plot fluid volume fraction | Int | 1 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_p_g | Save fluid pressure to plot file | Int | 0 | +| plt_gradp_g | Plot gradient of fluid pressure | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_ro_g | Save fluid density to plot file | Int | 0 | +| plt_mu_g | Plot fluid molecular viscosity | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_mu_g | Save fluid molecular viscosity to plot file | Int | 0 | +| plt_omega_p | Plot particle angular velocity | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_T_g | Save fluid temperature plot file | Int | 0 | +| plt_p_g | Plot fluid pressure | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_volfrac | Save Eulerian grid volume fraction (from cut cells) to plot file | Int | 0 | +| plt_phase | Plot particle type | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_gradp_g | Save gradient of pressure filed to plot file | Int | 0 | +| plt_radius | Plot particle radius | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_vort | Save vorticity to plot file | Int | 0 | +| plt_ro_g | Plot fluid density | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_vel_p | Save particle velocity to plot file | Int | 1 | +| plt_ro_p | Plot particle density | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_radius | Save particle radius to plot file | Int | 0 | +| plt_statwt | Plot particle (parcel) statistical weight | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_ro_p | Save particle density to plot file | Int | 0 | +| plt_T_g | Plot fluid temperature | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_T_p | Save particle temperature to plot file | Int | 0 | +| plt_T_p | Plot particle temperature | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_omega_p | Save particle angular velocity to plot file | Int | 0 | +| plt_vel_g | Plot fluid velocity data | Int | 1 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_drag_p | Save particle drag force to plot file | Int | 0 | +| plt_vel_p | Plot particle velocity | Int | 1 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_phase | Save particle type to plot file | Int | 0 | +| plt_volfrac | Plot Eulerian grid volume fraction (from cut cells) | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_statwt | Save particle (parcel) statistical weight to plot file | Int | 0 | +| plt_vort | Plot vorticity | Int | 0 | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -The following inputs must be preceded by the prefix ``mfix`` and control whether the EB geometry or level set should be written out: +The following inputs must be preceded by the prefix ``mfix`` and control whether the EB geometry or level set should be written: -+----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| | Description | Type | Default | -+======================+=======================================================================+=============+===========+ -| write_ls | Should we write a plotfile holding the level set and volfrac? | Bool | False | -| | If true, it will only be written once,after initialization or restart | | | -+----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| write_eb_surface | Should we write out the EB geometry in vtp format | Bool | False | -| | If true, it will only be written once,after initialization or restart | | | -+----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| plt_geom | Should we write a plotfile holding the EB geometry data? | Bool | False | -| | If true, it will only be written once,after initialization or restart | | | -+----------------------+-----------------------------------------------------------------------+-------------+-----------+ ++----------------------+--------------------------------------------------------------------------+-------------+-----------+ +| | Description | Type | Default | ++======================+==========================================================================+=============+===========+ +| write_ls | Write a plotfile holding the level set and volfrac. | Bool | false | +| | If enabled, it will only be written once, after initialization or restart| | | ++----------------------+--------------------------------------------------------------------------+-------------+-----------+ +| write_eb_surface | Write out the EB geometry in vtp format. | Bool | false | +| | If enabled, it will only be written once, after initialization or restart| | | ++----------------------+--------------------------------------------------------------------------+-------------+-----------+ +| plt_geom | Write a plotfile holding the EB geometry data. | Bool | false | +| | If true, it will only be written once,after initialization or restart | | | ++----------------------+--------------------------------------------------------------------------+-------------+-----------+ `Ascent `_ has been integrated into MFIX-Exa for *in situ* visualization. @@ -129,41 +129,41 @@ All these parameters are user-defined. +---------------------------+-----------------------------------------------------------------+-------------+-----------+ | [region].plot_per_approx | Specify time interval frequency for plotting the file | Real | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_regtest | Save all variables to plot file (overrides all other IO flags) | Int | 0 | +| [region].plt_regtest | Plot all variables (overrides all other plot flags) | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_radius | Save particle radius to plot file | Int | 0 | +| [region].plt_cp_s | Plot particle specific heat coefficient | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_volume | Save particle volume to plot file | Int | 0 | +| [region].plt_drag_p | Plot particle drag force | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_mass | Save particle mass to plot file | Int | 0 | +| [region].plt_h_s_txfr | Plot particle interphase enthalpy transfer | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_ro_p | Save particle density to plot file | Int | 0 | +| [region].plt_mass | Plot particle mass | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_omoi | Save inverse of particle momentum of inertia to plot file | Int | 0 | +| [region].plt_mass_sn_txfr | Plot particle interphase mass transfer | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_vel_p | Save particle velocity to plot file | Int | 0 | +| [region].plt_omega_p | Plot particle angular velocity | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_omega_p | Save particle angular velocity to plot file | Int | 0 | +| [region].plt_omoi | Plot inverse of particle momentum of inertia | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_statwt | Save particle statistical weight to plot file | Int | 0 | +| [region].plt_phase | Plot particle phase | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_drag_p | Save particle drag force to plot file | Int | 0 | +| [region].plt_radius | Plot particle radius | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_cp_s | Save particle specific heat coefficient to plot file | Int | 0 | +| [region].plt_ro_p | Plot particle density | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_T_p | Save particle temperature to plot file | Int | 0 | +| [region].plt_state | Plot particle state | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_X_s | Save particle species mass fractions to plot file | Int | 0 | +| [region].plt_statwt | Plot particle statistical weight | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_vel_s_txfr | Save particle interphase velocity transfer to plot file | Int | 0 | +| [region].plt_T_p | Plot particle temperature | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_h_s_txfr | Save particle interphase enthalpy transfer to plot file | Int | 0 | +| [region].plt_vel_p | Plot particle velocity | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_mass_sn_txfr | Save particle interphase mass transfer to plot file | Int | 0 | +| [region].plt_vel_s_txfr | Plot particle interphase velocity transfer | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_phase | Save particle phase to plot file | Int | 0 | +| [region].plt_volume | Plot particle volume | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region].plt_state | Save particle state to plot file | Int | 0 | +| [region].plt_X_s | Plot particle species mass fractions | Int | 0 | +---------------------------+-----------------------------------------------------------------+-------------+-----------+ For each region with name [region] specified in the inputs, it will be saved a plotfile with name "partsXXXXX_[region]", where XXXXX stands for the timestep number. diff --git a/docs/source_docs/user_guide/inputs/porous_media_defs.rst b/docs/source_docs/user_guide/inputs/porous_media.rst similarity index 95% rename from docs/source_docs/user_guide/inputs/porous_media_defs.rst rename to docs/source_docs/user_guide/inputs/porous_media.rst index 6d4b01152c85be4716dbac5bd4f6aebc97d40ab0..bed06fa9e44df6cacef6684bf9f4b3f985292755 100644 --- a/docs/source_docs/user_guide/inputs/porous_media_defs.rst +++ b/docs/source_docs/user_guide/inputs/porous_media.rst @@ -1,7 +1,7 @@ .. _InputsPorousMediaDefs: -Porous media -============ +Porous media definitions +======================== Homogeneous porous media are modeled by the addition of a momentum source term, :math:`\boldsymbol{S}_{pm}`, to the fluid momentum equation. @@ -11,7 +11,7 @@ source term, :math:`\boldsymbol{S}_{pm}`, to the fluid momentum equation. \boldsymbol{S}_{pm} =-\frac{\mu_f}{C_1} \boldsymbol{u}_f - C_2\frac{1}{2}\rho_f\lvert \boldsymbol{u}_f \rvert \boldsymbol{u}_f :math:`\mu_f`, :math:`\rho_f`, and :math:`\boldsymbol{u}_f` are the fluid viscosity, density, and velocity and -:math:`C_1` and :math:`C_2` are user defined constants. +:math:`C_1` and :math:`C_2` are user-defined constants. The following inputs are defined using the prefix ``pm``: diff --git a/docs/source_docs/user_guide/inputs/regions_defs.rst b/docs/source_docs/user_guide/inputs/regions.rst similarity index 100% rename from docs/source_docs/user_guide/inputs/regions_defs.rst rename to docs/source_docs/user_guide/inputs/regions.rst diff --git a/docs/source_docs/user_guide/inputs/solids_model.rst b/docs/source_docs/user_guide/inputs/solids_model.rst index 034f19e82ea5725995b3874da83c1f64488a0f31..1c096821a397fcdb24272250765a6ef493c1e765 100644 --- a/docs/source_docs/user_guide/inputs/solids_model.rst +++ b/docs/source_docs/user_guide/inputs/solids_model.rst @@ -11,25 +11,22 @@ models. The following inputs are defined with the prefix ``solids``: | | Description | Type | Default | +==========================================+=============================================================+==========+==========+ | types | Specified name(s) of the SOLIDS types or None to disable | String | None | -| | the SOLIDS solver. The user defined names are used to | | | +| | the SOLIDS solver. The user-defined names are used to | | | | | specify DEM and/or PIC model inputs. | | | +------------------------------------------+-------------------------------------------------------------+----------+----------+ -| molecular_weight | Value of constant solid molecular | Real | 0 | -| | weight | | | +| molecular_weight | Value of constant solid molecular weight. | Real | 0 | +------------------------------------------+-------------------------------------------------------------+----------+----------+ -| specific_heat | Specify which specific heat model to | String | None | -| | use for solid. Available options | | | -| | include: | | | +| specific_heat | Specify which specific heat model to use for solids. | String | constant | +| | use for solid. | | | | | | | | -| | * 'constant' for constant specific heat | | | -| | model | | | +| | Options: | | | +| | | | | +| | * ``constant`` - constant specific heat | | | +------------------------------------------+-------------------------------------------------------------+----------+----------+ -| specific_heat.constant | Value of species molecular weight. | Real | 0 | -| | [required if fluid.specific_heat = | | | -| | 'constant']. | | | +| specific_heat.constant | Constant solids specific heat value. | Real | 0 | +| | A value is required for ``constant`` specific heat model. | | | +------------------------------------------+-------------------------------------------------------------+----------+----------+ -| reference_temperature | Value of the reference temperature used | Real | 0 | -| | for specific enthalpy | | | +| reference_temperature | Reference temperature used for specific enthalpy. | Real | 0 | +------------------------------------------+-------------------------------------------------------------+----------+----------+ | species | Specify which species can constitute | String | None | | | the fluid phase [defined species must | | | @@ -40,7 +37,7 @@ models. The following inputs are defined with the prefix ``solids``: +------------------------------------------+-------------------------------------------------------------+----------+----------+ | newton_solver.relative_tol | Define relative tolerance for damped Newton solver | Real | 1.e-6 | +------------------------------------------+-------------------------------------------------------------+----------+----------+ -| newton_solver.max_iterations | Define max number of iterations for damped Newton solver | int | 100 | +| newton_solver.max_iterations | Define max number of iterations for damped Newton solver | Int | 100 | +------------------------------------------+-------------------------------------------------------------+----------+----------+ Below is an example for specifying the solids solver model options. @@ -70,7 +67,7 @@ Enabling the DEM solver and specifying model options. The following keys must b | | Description | Type | Default | +===============================+=========================================================================+==========+===========+ | solve | Specified name(s) of the DEM types or None to disable the DEM solver. | String | None | -| | The user defined names are used to specify DEM model inputs. | | | +| | The user-defined names are used to specify DEM model inputs. | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ | friction_coeff.pp | Friction coefficient :: particle to particle collisions [required] | Real | 0 | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ @@ -92,10 +89,10 @@ Enabling the DEM solver and specifying model options. The following keys must b | damping_tang_fac.pw | Factor relating the tangential damping coefficient to the normal | Real | 0.5 | | | damping coefficient :: particle to wall collisions | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| implicit_drag | Apply fluid-particle drag force by | int | 0 | +| implicit_drag | Apply fluid-particle drag force by | Int | 0 | | | :ref:`implicit velocity update`. | | | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ -| tan_history | Include tangential history force in the collision model. | Bool | False | +| tan_history | Include tangential history force in the collision model. | Bool | false | +-------------------------------+-------------------------------------------------------------------------+----------+-----------+ | tan_history.max_contacts | When tangential history is enabled, the maximum number of contacts | Int | 10 | | | per particle that are tracked at any point | | | @@ -119,7 +116,7 @@ Enabling the DEM solver and specifying model options. The following keys must b The following inputs use the DEM type names specified using the `dem.solve` input to define restitution coefficients and -are proceeded with `dem.restitution_coeff`. These must be defined for all solid-solid and solid-wall combinations. +are proceeded with the prefix ``dem.restitution_coeff``. These must be defined for all solid-solid and solid-wall combinations. +-------------------------+-------------------------------------------------------------------------+----------+-----------+ | | Description | Type | Default | diff --git a/docs/source_docs/user_guide/inputs/species_defs.rst b/docs/source_docs/user_guide/inputs/species.rst similarity index 89% rename from docs/source_docs/user_guide/inputs/species_defs.rst rename to docs/source_docs/user_guide/inputs/species.rst index 44959f978fadb4d610f535404f6858dc15c41b7c..dd04b4c5ae838a90a4a839382158043e695ecb38 100644 --- a/docs/source_docs/user_guide/inputs/species_defs.rst +++ b/docs/source_docs/user_guide/inputs/species.rst @@ -8,29 +8,33 @@ The following inputs are defined using the prefix ``species``: +--------------------------+------------------------------------------------------------------------+----------+-----------+ | | Description | Type | Default | +==========================+========================================================================+==========+===========+ -| solve | Specified name of the species or None to disable the | String | None | +| solve | Specified name(s) of the species or None to disable the | String | None | | | species solver. The name assigned to the species | | | | | solver is used to specify species inputs. | | | +--------------------------+------------------------------------------------------------------------+----------+-----------+ | diffusivity | Fluid species diffusivity model. | String | None | | | | | | -| | * ``constant`` a constant diffusion coefficient is used for | | | +| | Options: | | | +| | | | | +| | * ``constant`` - a constant diffusion coefficient is used for | | | | | all fluid species. | | | | | | | | +--------------------------+------------------------------------------------------------------------+----------+-----------+ -| diffusivity.constant | Constant species diffusivity -- required for | Real | 0 | +| diffusivity.constant | Constant species diffusivity - required for | Real | 0 | | | ``constant`` diffusivity model | | | | | | | | +--------------------------+------------------------------------------------------------------------+----------+-----------+ -| specific_heat | Species specific heat model. This setting only applies if either | String | None | +| specific_heat | Species specific heat model. This setting only applies if either | String | | | | ``fluid.specific_heat = mixture`` or | | | | | ``solids.specific_heat = mixture`` | | | | | | | | -| | * ``constant`` a constant specific heat is defined for each species | | | +| | Options (case-insensitive): | | | +| | | | | +| | * ``constant`` - a constant specific heat is defined for each species | | | | | and a *mixture* specific heat is computed based on the fluid or | | | | | particle composition. | | | | | | | | -| | * ``NASA7-poly`` the specific heat of each species is defined by one | | | +| | * ``NASA7-poly`` - the specific heat of each species is defined by one | | | | | or more polynomials that are a function of temperature, then the | | | | | *mixture* specific heat is computed based on the fluid or particle | | | | | composition. | | | @@ -40,7 +44,7 @@ The following inputs are defined using the prefix ``species``: | | :math:`c_p(T)/R = \sum_{i=0}^4 a_{i}T^{i}` | | | | | | | | +--------------------------+------------------------------------------------------------------------+----------+-----------+ -| ignore_discontinuities | MFIX-Exa asserts that the low and high NASA-7 polynomials are | int | 0 | +| ignore_discontinuities | MFIX-Exa asserts that the low and high NASA-7 polynomials are | Int | 0 | | | continuous at the 1000K temperature split. However, some polynomials | | | | | do not have valid high temperature coefficients, for example, liquid | | | | | water. By setting this keyword to 1, the simulation will only warn | | | @@ -50,15 +54,21 @@ The following inputs are defined using the prefix ``species``: | | Therefore, this option should only be used when the simulation is not | | | | | expected to cross over the transition temperature. | | | +--------------------------+------------------------------------------------------------------------+----------+-----------+ -| viscosity.molecular | Molecular viscosity model of species. This setting only applies when | String | 0 | +| viscosity.molecular | Molecular viscosity model of species. This setting only applies when | String | | | | ``fluid.viscosity.molecular = mixture``. | | | | | | | | -| | Options are ``constant`` or ``Sutherland`` or ``Reid``. | | | -| | See :ref:`viscosity model descriptions `. | | | +| | Options: | | | +| | | | | +| | * ``constant`` - constant viscosity | | | +| | * ``Sutherland`` :cite:p:`suth1893` | | | +| | * ``Reid`` :cite:p:`reid87` | | | +| | | | | +| | See :ref:`viscosity model descriptions ` | | | +| | in fluid section. | | | +--------------------------+------------------------------------------------------------------------+----------+-----------+ -The following inputs are defined for each species using the prefix ``species.[species name]``: +The following inputs are defined for each species using the prefix ``species.[species_name]``: +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ | | Description | Type | Default | @@ -102,7 +112,7 @@ The following inputs are defined for each species using the prefix ``species.[sp | | polynomials are used to define the specific heat and enthalpy. | | | | | | | | +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ -| enthalpy_of_formation | Enthalpy of formation of species. This input is required only when | Real | 0 | +| enthalpy_of_formation | Enthalpy of formation of species. Required only when | Real | 0 | | | the specific heat model is ``constant`` and chemical reactions | | | | | are defined. | | | +---------------------------------------+------------------------------------------------------------------------+----------+-----------+ diff --git a/docs/source_docs/user_guide/inputs/time-stepping.rst b/docs/source_docs/user_guide/inputs/time_stepping.rst similarity index 87% rename from docs/source_docs/user_guide/inputs/time-stepping.rst rename to docs/source_docs/user_guide/inputs/time_stepping.rst index e2cff95331c62d5bc8d4834a60998e61ad06cad1..4ae0a4754b804c9719b24924cfb1362ac593cccc 100644 --- a/docs/source_docs/user_guide/inputs/time-stepping.rst +++ b/docs/source_docs/user_guide/inputs/time_stepping.rst @@ -57,7 +57,7 @@ the result by the number of steps per collision, ``tcoll_ratio``: ``mfix.fixed_dt`` must be defined for particle-only DEM simulations, however it is only used to determine the frequency of outputs and has no effect on the particle advance. If - a positive value is not specified for ``mfix.fixed_dt``, then the code aborts with the + a positive value is not specified for ``mfix.fixed_dt``, then the solver aborts with the following message: .. highlight:: c++ @@ -99,7 +99,7 @@ The following inputs are defined using the prefix ``mfix``: +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | stop_time | Maximum time to reach (s) | Real | -1.0 | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ -| fixed_dt | Flag to use a fixed time step | Int | 0 | +| fixed_dt | Use a fixed time step | Int | 0 | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | cfl | CFL constraint (dt < cfl * dx / u) | Real | See note | | | | | | @@ -109,17 +109,17 @@ The following inputs are defined using the prefix ``mfix``: +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | dt_min | Abort if ``dt`` gets smaller than this value | Real | 1.e-6 | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ -| dt_max | Maximum value of ``dt`` if ``fixed_dt`` is not 1 | Real | 1.e14 | +| dt_max | Maximum value of ``dt`` if ``fixed_dt`` is not set | Real | 1.e14 | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | tcoll_ratio | DEM time step equals the min collision time divided by this value | Real | 50.0 | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | walltime_limit | Runtime limit specified with format HH:MM:SS. When the runtime has | String | "" | | | almost reached the limit (approaching is computed by considering the | | | -| | average runtime needed for each step) then the simulation ends and | | | +| | average runtime needed for each step), then the simulation ends and | | | | | a clean exit is performed | | | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ -| clean_exit | This input represents the name of a file that, if found in the run | String | "" | -| | folder, makes the code stop and perform a clean exit | | | +| clean_exit | The name of a file that, if found in the run | String | "" | +| | folder, makes the solver stop and perform a clean exit. | | | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ In the case of unsteady flow, the simulation will stop when either the number of steps @@ -131,14 +131,10 @@ The following inputs are defined using the prefix ``mfix`` and are only relevant +-----------------------+-----------------------------------------------------------------------+-------------+------------+ | Key | Description | Type | Default | +=======================+=======================================================================+=============+============+ -| steady_state | Are we running a steady-state calculation? | Int | 0 | +| steady_state | Run a steady-state calculation. | Int | 0 | +-----------------------+-----------------------------------------------------------------------+-------------+------------+ -| steady_state_tol | Tolerance for checking if we have reached steady state | Real | None | -| | | | | -| | (Must be set if steady_state = 1) | | | +| steady_state_tol | Tolerance for checking if steady state has been reached. | Real | None | +| | (Must be set if steady_state is enabled) | | | +-----------------------+-----------------------------------------------------------------------+-------------+------------+ | steady_state_maxiter | Maximum number of allowed iterations to converge to steady state | Int | 100000000 | +-----------------------+-----------------------------------------------------------------------+-------------+------------+ - - - diff --git a/docs/source_docs/user_guide/run-time_inputs.rst b/docs/source_docs/user_guide/run-time_inputs.rst index 17e22db82ac8eca64db4dd898623b25d84193e13..f3550781c26a4bb37cdee3ea57563aeb1564f8a5 100644 --- a/docs/source_docs/user_guide/run-time_inputs.rst +++ b/docs/source_docs/user_guide/run-time_inputs.rst @@ -36,26 +36,24 @@ values for setting up a problem. Pay special attention to any prefixes for the keywords such as ``mfix``, ``amr``, ``geometry``, ``nodal_proj`` etc. .. toctree:: - :maxdepth: 0 - :hidden: + :maxdepth: 1 :titlesonly: inputs/initialization - inputs/time-stepping + inputs/time_stepping inputs/domain inputs/geometry inputs/mesh_and_gridding - inputs/multigrid-solvers + inputs/multigrid_solvers inputs/model_options inputs/fluid_model inputs/solids_model - inputs/species_defs - inputs/porous_media_defs + inputs/species inputs/chemical_reactions - inputs/regions_defs + inputs/regions inputs/initial_conditions inputs/boundary_conditions + inputs/porous_media inputs/output inputs/advanced inputs/mpmd -