Add missing keys and move some for GUI workflow

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+2 −0
Changes for docs/source_docs/user_guide/inputs/output/plotting.rst: 2 added lines, 0 removed lines.
Original line number Diff line number Diff line
@@ -71,6 +71,8 @@ The following inputs must be preceded by the prefix ``mfix`` and control which v
+---------------------+-----------------------------------------------------------------------+-------------+-----------+
| plt_vort            | Plot fluid vorticity.                                                 |    Int      | 0         |
+---------------------+-----------------------------------------------------------------------+-------------+-----------+
| plt_X_g             | Plot fluid species mass fractions.                                    |    Int      | 0         |
+---------------------+-----------------------------------------------------------------------+-------------+-----------+

The following inputs must be preceded by the prefix ``mfix.solids`` and allow to write additional plotfiles which
contain only solids variables in specific regions at fixed timesteps or approximated simulation times.
+24 −36
Changes for docs/source_docs/user_guide/inputs/boundary_conditions.rst: 24 added lines, 36 removed lines.
Original line number Diff line number Diff line
@@ -17,18 +17,6 @@ The following inputs are defined using the prefix ``bc``:
|                     | and ``disk``. Embedded boundary (EB) regions support ``box``,            |             |           |
|                     | ``cylinder``, and ``sphere`` shapes.                                     |             |           |
+---------------------+--------------------------------------------------------------------------+-------------+-----------+
| delp_dir            | Direction for specified pressure drop. Note that this direction          |  Int        | 0         |
|                     | should also be periodic.                                                 |             |           |
|                     |                                                                          |             |           |
|                     | Options:                                                                 |             |           |
|                     |  * ``0``: X                                                              |             |           |
|                     |  * ``1``: Y                                                              |             |           |
|                     |  * ``2``: Z                                                              |             |           |
+---------------------+--------------------------------------------------------------------------+-------------+-----------+
| 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``:

@@ -59,24 +47,24 @@ using the prefix ``bc.[region_name].[fluid_name]``:
+------------------------+------------------------------------------------------------------------+-------------+-----------+
|                        | Description                                                            |   Type      | Default   |
+========================+========================================================================+=============+===========+
| volfrac                | Volume fraction [required if bc type is ``mi``]                        | Real        | 0         |
| volfrac                | Volume fraction [required if bc type is ``mi``]                        | Real        | None      |
+------------------------+------------------------------------------------------------------------+-------------+-----------+
| density                | Fluid density [required if bc type is ``mi`` or ``pi``]                | Real        | 0         |
| density                | Fluid density [required if bc type is ``mi`` or ``pi``]                | Real        | None      |
+------------------------+------------------------------------------------------------------------+-------------+-----------+
| pressure               | Fluid pressure [required if bc type is ``po' or ``pi``]                | Real        | 0         |
| pressure               | Fluid pressure [required if bc type is ``po' or ``pi``]                | Real        | None      |
+------------------------+------------------------------------------------------------------------+-------------+-----------+
| temperature            | Fluid temperature [required if bc type is ``mi`` or ``pi``]            | Real        | 0         |
| temperature            | Fluid temperature [required if bc type is ``mi`` or ``pi``]            | Real        | None      |
+------------------------+------------------------------------------------------------------------+-------------+-----------+
| velocity               | Velocity components [required if bc type is ``mi``                     | Reals<3>    | 0 0 0     |
| velocity               | Velocity components [required if bc type is ``mi``                     | Reals       | None      |
|                        | and ``volflow`` or ``massflow`` not specified]                         |             |           |
+------------------------+------------------------------------------------------------------------+-------------+-----------+
| volflow                | Volumetric flow rate [required if bc type is ``mi``                    | Real        | 0         |
| volflow                | Volumetric flow rate [required if bc type is ``mi``                    | Real        | None      |
|                        | and ``velocity`` or ``massflow`` not specified]                        |             |           |
+------------------------+------------------------------------------------------------------------+-------------+-----------+
| massflow               | Mass flow rate [required if bc type is ``mi``                          | Real        | 0         |
| massflow               | Mass flow rate [required if bc type is ``mi``                          | Real        | None      |
|                        | and ``velocity`` or ``volflow`` not specified]                         |             |           |
+------------------------+------------------------------------------------------------------------+-------------+-----------+
| species.[species_name] | Species `species_name` mass fraction [required if `solve_species`=1    | Real        | 0         |
| species.[species_name] | Species `species_name` mass fraction [required if `solve_species`=1    | Real        | None      |
|                        | and bc type is ``mi`` or ``pi``]                                       |             |           |
+------------------------+------------------------------------------------------------------------+-------------+-----------+

@@ -154,15 +142,15 @@ For inflow boundary conditions , the solids inputs are defined using the prefix
+------------------------+-----------------------------------------------------------------------+-------------+-----------+
|                        | Description                                                           |   Type      | Default   |
+========================+=======================================================================+=============+===========+
| volfrac                | Volume fraction                                                       | Real        | 0         |
| volfrac                | Volume fraction                                                       | Real        | None      |
+------------------------+-----------------------------------------------------------------------+-------------+-----------+
| temperature            | Temperature                                                           | Real        | 0         |
| temperature            | Temperature                                                           | Real        | None      |
+------------------------+-----------------------------------------------------------------------+-------------+-----------+
| species.[species_name] | Mass fraction of ``species_name``                                     | Real        | 0         |
| species.[species_name] | Mass fraction of ``species_name``                                     | Real        | None      |
+------------------------+-----------------------------------------------------------------------+-------------+-----------+
| velocity               | Velocity components                                                   | Reals<3>    | 0 0 0     |
| velocity               | Velocity components                                                   | Reals       | None      |
+------------------------+-----------------------------------------------------------------------+-------------+-----------+
| volflow                | Volumetric flow rate.                                                 | Real        | 0         |
| volflow                | Volumetric flow rate.                                                 | Real        | None      |
+------------------------+-----------------------------------------------------------------------+-------------+-----------+


@@ -199,20 +187,20 @@ please refer to :ref:`ReferenceParticleDistributions <ReferenceParticleDistribut
|                        | approximate the number of particles within a boundary condition       |             |           |
|                        | region.                                                               |             |           |
+------------------------+-----------------------------------------------------------------------+-------------+-----------+
| constant               | Monodisperse (single valued) particle diameter.                       | Real        | 0         |
| constant               | Monodisperse (single valued) particle diameter.                       | Real        | None      |
|                        | Required for ``constant`` distributions.                              |             |           |
+------------------------+-----------------------------------------------------------------------+-------------+-----------+
| mean                   | Distribution mean.                                                    | Real        | 0         |
| mean                   | Distribution mean.                                                    | Real        | None      |
|                        | Required for ``normal`` and ``log-normal`` distributions.             |             |           |
+------------------------+-----------------------------------------------------------------------+-------------+-----------+
| std                    | Distribution standard deviation.                                      | Real        | 0         |
| std                    | Distribution standard deviation.                                      | Real        | None      |
|                        | Required for ``normal`` and ``log-normal`` distributions.             |             |           |
+------------------------+-----------------------------------------------------------------------+-------------+-----------+
| min                    | Minimum diameter to clip distribution.                                | Real        | 0         |
| min                    | Minimum diameter to clip distribution.                                | Real        | None      |
|                        | Required for ``normal``, ``log-normal``, and ``uniform``              |             |           |
|                        | distributions.                                                        |             |           |
+------------------------+-----------------------------------------------------------------------+-------------+-----------+
| max                    | Maximum diameter to clip distribution.                                | Real        | 0         |
| max                    | Maximum diameter to clip distribution.                                | Real        | None      |
|                        | Required for ``normal``, ``log-normal``, and ``uniform``              |             |           |
|                        | distributions.                                                        |             |           |
+------------------------+-----------------------------------------------------------------------+-------------+-----------+
@@ -243,20 +231,20 @@ the prefix ``bc.[region_name].[solid_name].density``:
|                        | * ``log-normal`` - log-noremal distribution                           |             |           |
|                        | * ``custom`` - user-defined distribution                              |             |           |
+------------------------+-----------------------------------------------------------------------+-------------+-----------+
| constant               | Monodisperse (single valued) particle diameter.                       | Real        | 0         |
| constant               | Monodisperse (single valued) particle diameter.                       | Real        | None      |
|                        | Required for ``constant`` distributions.                              |             |           |
+------------------------+-----------------------------------------------------------------------+-------------+-----------+
| mean                   | Distribution mean.                                                    | Real        | 0         |
| mean                   | Distribution mean.                                                    | Real        | None      |
|                        | Required for ``normal`` and ``log-normal`` distributions.             |             |           |
+------------------------+-----------------------------------------------------------------------+-------------+-----------+
| std                    | Distribution standard deviation.                                      | Real        | 0         |
| std                    | Distribution standard deviation.                                      | Real        | None      |
|                        | Required for ``normal`` and ``log-normal`` distributions.             |             |           |
+------------------------+-----------------------------------------------------------------------+-------------+-----------+
| min                    | Minimum density to clip distribution.                                 | Real        | 0         |
| min                    | Minimum density to clip distribution.                                 | Real        | None      |
|                        | Required for ``normal``, ``log-normal``, and ``uniform``              |             |           |
|                        | distributions.                                                        |             |           |
+------------------------+-----------------------------------------------------------------------+-------------+-----------+
| max                    | Maximum density to clip distribution.                                 | Real        | 0         |
| max                    | Maximum density to clip distribution.                                 | Real        | None      |
|                        | Required for ``normal``, ``log-normal``, and ``uniform``              |             |           |
|                        | distributions.                                                        |             |           |
+------------------------+-----------------------------------------------------------------------+-------------+-----------+
@@ -310,7 +298,7 @@ angular tolerance. The following inputs are defined using the prefix ``bc.[regio
+--------------------+-----------------------------------------------------------------------+-------------+-----------+
|                    | Description                                                           |   Type      | Default   |
+====================+=======================================================================+=============+===========+
| normal             | [Optional] Specifies the target face normal direction. Only EB faces  | Reals<3>    | 0 0 0     |
| normal             | [Optional] Specifies the target face normal direction. Only EB faces  | Reals<3>    | None      |
|                    | whose normals are parallel (within the specified tolerance) will have |             |           |
|                    | the boundary condition applied.                                       |             |           |
+--------------------+-----------------------------------------------------------------------+-------------+-----------+
+22 −3
Changes for docs/source_docs/user_guide/inputs/domain.rst: 22 added lines, 3 removed lines.
Original line number Diff line number Diff line
@@ -18,9 +18,9 @@ The following inputs are defined using the prefix ``geometry``:
+-----------------+-----------------------------------------------------------------------+-------------+-----------+
| is_periodic     | 1 for true, 0 for false (one value for each coordinate direction)     |   Ints<3>   | 0 0 0     |
+-----------------+-----------------------------------------------------------------------+-------------+-----------+
| prob_lo         | Low corner of physical domain (physical not index space)              |   Reals<3>  | 0 0 0     |
| prob_lo         | Low corner of physical domain (physical not index space)              |   Reals<3>  | None      |
+-----------------+-----------------------------------------------------------------------+-------------+-----------+
| prob_hi         | High corner of physical domain (physical not index space)             |   Reals<3>  | 0 0 0     |
| prob_hi         | High corner of physical domain (physical not index space)             |   Reals<3>  | None      |
+-----------------+-----------------------------------------------------------------------+-------------+-----------+

.. attention::
@@ -30,6 +30,7 @@ The following inputs are defined using the prefix ``geometry``:
   * There is **no support** for 1D or 2D simulation domains.
   * Cartesian is the **only supported** coordinate system.

----

Mesh
----
@@ -42,7 +43,7 @@ The following inputs are defined using the prefix ``amr``:
|                      | Description                                                           |   Type      | Default   |
|                      |                                                                       |             |           |
+======================+=======================================================================+=============+===========+
| n_cell               | Number of cells at level 0 in each coordinate direction.              |    Ints<3>  | 0 0 0     |
| n_cell               | Number of cells at level 0 in each coordinate direction.              |    Ints<3>  | None      |
+----------------------+-----------------------------------------------------------------------+-------------+-----------+

The base mesh spacing is computed for each direction by dividing the :ref:`domain length<InputsTable_domain>` by the
@@ -90,3 +91,21 @@ The result is a uniform mesh spacing of :math:`0.125` *m* in all three direction
.. warning::

   MFIX-Exa simulations with a non-uniform mesh will not run.

----

The following inputs are defined using the prefix ``mfix``:

+--------------------------+----------------------------------------------------------------------------+----------+---------+
|                          | Description                                                                |   Type   | Default |
+==========================+============================================================================+==========+=========+
| delp_dir                 | Direction for specified pressure drop. The domain must be periodic in the  |  Int     | None    |
|                          | the specified direction.                                                   |          |         |
|                          |                                                                            |          |         |
|                          | Options:                                                                   |          |         |
|                          |  * ``0``: X                                                                |          |         |
|                          |  * ``1``: Y                                                                |          |         |
|                          |  * ``2``: Z                                                                |          |         |
+--------------------------+----------------------------------------------------------------------------+----------+---------+
| delp                     | Pressure drop (Pa)                                                         |  Real    | 0       |
+--------------------------+----------------------------------------------------------------------------+----------+---------+
+6 −7
Changes for docs/source_docs/user_guide/inputs/fluid_model.rst: 6 added lines, 7 removed lines.
Original line number Diff line number Diff line
@@ -50,11 +50,10 @@ The following inputs are defined using the prefix ``[fluid_name].viscosity.molec
+------------------------+----------------------------------------------------------------+--------+----------+
|                        | Description                                                    |  Type  | Default  |
+========================+================================================================+========+==========+
| model                  | Specify which molecular viscosity model to use.                | String |  None    |
| model                  | Specify which molecular viscosity model to use.                | String | constant |
|                        |                                                                |        |          |
|                        | Options:                                                       |        |          |
|                        |                                                                |        |          |
|                        | * ``None`` - no viscosity model.                               |        |          |
|                        | * ``constant`` - constant viscosity                            |        |          |
|                        | * ``Sutherland`` :cite:p:`suth1893` -                          |        |          |
|                        |                                                                |        |          |
@@ -73,23 +72,23 @@ The following inputs are defined using the prefix ``[fluid_name].viscosity.molec
|                        | A viscosity model is required if the fluid solver is           |        |          |
|                        | enabled.                                                       |        |          |
+------------------------+----------------------------------------------------------------+--------+----------+
| constant               | Constant fluid viscosity.                                      |  Real  |  0       |
| constant               | Constant fluid viscosity.                                      |  Real  |  None    |
|                        |                                                                |        |          |
|                        | A value is required for ``constant`` viscosity model.          |        |          |
+------------------------+----------------------------------------------------------------+--------+----------+
| Sutherland.T_ref       | Sutherland model reference temperature.                        |  Real  |  0       |
| Sutherland.T_ref       | Sutherland model reference temperature.                        |  Real  |  None    |
|                        |                                                                |        |          |
|                        | A value is required for ``Sutherland`` viscosity model.        |        |          |
+------------------------+----------------------------------------------------------------+--------+----------+
| Sutherland.mu_ref      | Sutherland model reference viscosity at T_ref.                 |  Real  |  0       |
| Sutherland.mu_ref      | Sutherland model reference viscosity at T_ref.                 |  Real  |  None    |
|                        |                                                                |        |          |
|                        | A value is required for ``Sutherland`` viscosity model.        |        |          |
+------------------------+----------------------------------------------------------------+--------+----------+
| Sutherland.S           | Sutherland model temperature.                                  |  Real  |  0       |
| Sutherland.S           | Sutherland model temperature.                                  |  Real  |  None    |
|                        |                                                                |        |          |
|                        | A value is required for ``Sutherland`` viscosity model.        |        |          |
+------------------------+----------------------------------------------------------------+--------+----------+
| Reid.A                 | Reid model constants.                                          |  Real  |  0       |
| Reid.A                 | Reid model constants.                                          |  Real  |  None    |
| Reid.B                 |                                                                |        |          |
| Reid.C                 | Values are required for ``Reid`` viscosity model.              |        |          |
| Reid.D                 |                                                                |        |          |
+25 −16
Changes for docs/source_docs/user_guide/inputs/geometry.rst: 25 added lines, 16 removed lines.
Original line number Diff line number Diff line
@@ -13,6 +13,7 @@ The following inputs are defined using the prefix ``mfix``:
|                        |                                                                               |          |                     |
|                        | * ``box`` - predefined :ref:`box geometry<InputsGeometry_box>`                |          |                     |
|                        | * ``cylinder`` - predefined :ref:`cylinder geometry<InputsGeometry_cylinder>` |          |                     |
|                        | * ``sphere`` - predefined :ref:`sphere geometry<InputsGeometry_sphere>`       |          |                     |
|                        | * ``generic`` - :ref:`user-defined geometry<InputsGeometry_generic>`          |          |                     |
|                        | * ``CSG`` - use :ref:`Constructive Solid Geometry<InputsGeometry_CSG>` file   |          |                     |
|                        | * ``STL`` - use :ref:`Standard Triangle Language<InputsGeometry_STL>` file    |          |                     |
@@ -265,6 +266,26 @@ the EB ``cylinder`` are *covered* and thereby excluded from calculations.
  on the low *X* face and a pressure outflow on the *X* high face.


----

.. _InputsGeometry_sphere:

``sphere`` geometry
^^^^^^^^^^^^^^^^^^^

The following inputs are defined using the prefix ``sphere``:

+------------------------+-------------------------------------------------------------------+----------+---------------------+
|                        | Description                                                       |   Type   | Default             |
+========================+===================================================================+==========+=====================+
| radius                 | Sphere radius.                                                    | Real     | None                |
+------------------------+-------------------------------------------------------------------+----------+---------------------+
| center                 | Center of sphere.                                                 | Reals<3> |  0  0  0            |
+------------------------+-------------------------------------------------------------------+----------+---------------------+
| internal_flow          | Indicates that flow is *inside* the sphere.                       | Bool     | false               |
+------------------------+-------------------------------------------------------------------+----------+---------------------+


----

.. _InputsGeometry_generic:
@@ -300,12 +321,12 @@ The following inputs are defined using the prefix ``csg``:
+========================+===================================================================+==========+=====================+
| geometry_filename      | The CSG file that defines the EB geometry.                        | String   | ''                  |
+------------------------+-------------------------------------------------------------------+----------+---------------------+
| internal_flow          | Indicates that flow is *inside* the box.                          | Bool     | true                |
+------------------------+-------------------------------------------------------------------+----------+---------------------+
| scaling_factor         | Scale the geometry.                                               | Reals<3> | 1  1  1             |
+------------------------+-------------------------------------------------------------------+----------+---------------------+
| translation            | Translate the geometry.                                           | Reals<3> | 0  0  0             |
+------------------------+-------------------------------------------------------------------+----------+---------------------+
| internal_flow          | Indicates that flow is *inside* the the CSG geometry.             | Bool     | true                |
+------------------------+-------------------------------------------------------------------+----------+---------------------+

.. note::
   A full description of this feature is beyond the scope of this section. A future update to
@@ -330,6 +351,8 @@ The following inputs are defined using the prefix ``stl``:
+------------------------+-------------------------------------------------------------------+----------+---------------------+
| translation            | Translate the geometry.                                           | Reals<3> | 0  0  0             |
+------------------------+-------------------------------------------------------------------+----------+---------------------+
| internal_flow          | Indicates that flow is *inside* the STL geometry.                 | Bool     | true                |
+------------------------+-------------------------------------------------------------------+----------+---------------------+
| use_bvh                | Use bounding volume optimization.                                 | Bool     | true                |
+------------------------+-------------------------------------------------------------------+----------+---------------------+

@@ -338,20 +361,6 @@ The following inputs are defined using the prefix ``stl``:
   the documentation may include a tutorial to better demonstrate this feature.


Checkpoint geometry
-------------------

Read EB geometry data from a checkpoint file.

The following inputs are defined using the prefix ``mfix``.

+----------------------+-----------------------------------------------------------------------+-------------+--------------+
|                      | Description                                                           |   Type      | Default      |
+======================+=======================================================================+=============+==============+
| geom_chk_read        | Flag to read the EB geometry data from the ``geom_chk_file``          |  Bool       |  false       |
|                      | :ref:`checkpoint file<Chap:InputsCheckpoint>`. If levelset refinement |             |              |
|                      | is enabled, levelset data is read from ``geom_levelset_chk_file``.    |             |              |
+----------------------+-----------------------------------------------------------------------+-------------+--------------+

Levelset refinement
-------------------
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