From 123abdde8a2d63735b802ca9a082c4f37a18416c Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Thu, 16 Apr 2026 15:32:09 -0500 Subject: [PATCH 1/7] minor edit --- docs/source_docs/user_guide/inputs/regions.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/regions.rst b/docs/source_docs/user_guide/inputs/regions.rst index 4fbb0aa..ac134b3 100644 --- a/docs/source_docs/user_guide/inputs/regions.rst +++ b/docs/source_docs/user_guide/inputs/regions.rst @@ -61,9 +61,9 @@ For each region, the inputs are defined using the compound prefix ``regions.[reg +==========================+=======================================================================+=============+===========+ | radius | cylinder radius | Real | None | +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ -| start | Coordinates of the cylinder's bottom cap | Reals<3> | | +| start | Coordinates of the center of the cylinder's bottom cap | Reals<3> | | +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ -| end | Coordinates of the cylinder's top cap | Reals<3> | | +| end | Coordinates of the center of the cylinder's top cap | Reals<3> | | +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ -- GitLab From 91a08a2ce3b8888d1411d4417571fccc159795c0 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 27 Apr 2026 12:07:23 -0500 Subject: [PATCH 2/7] move regions --- docs/source_docs/user_guide/run-time_inputs.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/run-time_inputs.rst b/docs/source_docs/user_guide/run-time_inputs.rst index 955d4e5..96209b7 100644 --- a/docs/source_docs/user_guide/run-time_inputs.rst +++ b/docs/source_docs/user_guide/run-time_inputs.rst @@ -41,11 +41,11 @@ keywords such as ``mfix``, ``amr``, ``geometry``, ``nodal_proj`` etc. inputs/domain inputs/geometry + inputs/regions inputs/model_options inputs/species inputs/fluid_model inputs/solids_model - inputs/regions inputs/initial_conditions inputs/boundary_conditions inputs/chemical_reactions -- GitLab From 7c58d9d377ad3e2d11da27a03d1d99a4c3c5dee2 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 27 Apr 2026 12:11:12 -0500 Subject: [PATCH 3/7] move "periodic" --- docs/source_docs/user_guide/inputs/domain.rst | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/domain.rst b/docs/source_docs/user_guide/inputs/domain.rst index 800d634..808a583 100644 --- a/docs/source_docs/user_guide/inputs/domain.rst +++ b/docs/source_docs/user_guide/inputs/domain.rst @@ -16,8 +16,6 @@ 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) | Ints<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> | None | -- GitLab From ac77ef36bc443c051224f72ebe5974cc0752336e Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 27 Apr 2026 12:11:23 -0500 Subject: [PATCH 4/7] fix equation TeX --- docs/source_docs/user_guide/inputs/domain.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/domain.rst b/docs/source_docs/user_guide/inputs/domain.rst index 808a583..1fbc80e 100644 --- a/docs/source_docs/user_guide/inputs/domain.rst +++ b/docs/source_docs/user_guide/inputs/domain.rst @@ -50,13 +50,13 @@ number of cells. The mesh spacing is required to be the same in all directions: .. math:: - \frac{\text{prob\_hi[0] - prob\_lo[0]}}{\text{n\_cell[0]}} - = \frac{\text{prob\_hi[1] - prob\_lo[1]}}{\text{n\_cell[1]}} - = \frac{\text{prob\_hi[2] - prob\_lo[2]}}{\text{n\_cell[2]}} + \frac{\mathtt{prob\_hi[0]} - \mathtt{prob\_lo[0]}}{\mathtt{n\_cell[0]}} + = \frac{\mathtt{prob\_hi[1]} - \mathtt{prob\_lo[1]}}{\mathtt{n\_cell[1]}} + = \frac{\mathtt{prob\_hi[2]} - \mathtt{prob\_lo[2]}}{\mathtt{n\_cell[2]}} The inputs for defining the mesh for a single-level simulation are demonstrated in the -:ref:`following example` and illustrated in :numref:`fig_basic_mesh_ex`. +:ref:`following example` and illustrated in :numref:`fig_basic_mesh_ex`. In this example, the domain is a :math:`4 \times 1 \times 1` cuboid, and there are :math:`32 \times 8 \times 8` cells in the *X*, *Y*, and *Z* directions, respectively. The result is a uniform mesh spacing of :math:`0.125` *m* in all three directions. -- GitLab From 102d74360011c5e013082511cd19fff2ab99a938 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 27 Apr 2026 12:11:44 -0500 Subject: [PATCH 5/7] spelling --- docs/source_docs/user_guide/inputs/domain.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/domain.rst b/docs/source_docs/user_guide/inputs/domain.rst index 1fbc80e..0f528db 100644 --- a/docs/source_docs/user_guide/inputs/domain.rst +++ b/docs/source_docs/user_guide/inputs/domain.rst @@ -64,13 +64,13 @@ The result is a uniform mesh spacing of :math:`0.125` *m* in all three direction .. _inputs_mesh_ex: .. code-block:: bash - :caption: Snippet of inptus for mesh example. This is not a complete input file. + :caption: Snippet of inputs for mesh example. This is not a complete input file. # Define periodicity and domain extents # ------------------------------------------------------------- geometry.coord_sys = 0 # Cartesian coordinates geometry.is_periodic = 0 0 0 # periodicity for each direction - geometry.prob_lo = 0. 0. 0 # lo corner of physical domain. + geometry.prob_lo = 0. 0. 0. # lo corner of physical domain. geometry.prob_hi = 4. 1. 1. # hi corner of physical domain # Define the maximum level of refinement and number of cells -- GitLab From fa1b3b605739f1f5f999d1c011fcd7f9da7bdd54 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 27 Apr 2026 12:12:20 -0500 Subject: [PATCH 6/7] move max_grid_size and blocking_factor --- docs/source_docs/user_guide/inputs/domain.rst | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/docs/source_docs/user_guide/inputs/domain.rst b/docs/source_docs/user_guide/inputs/domain.rst index 0f528db..fc4da1f 100644 --- a/docs/source_docs/user_guide/inputs/domain.rst +++ b/docs/source_docs/user_guide/inputs/domain.rst @@ -91,6 +91,46 @@ The result is a uniform mesh spacing of :math:`0.125` *m* in all three direction MFIX-Exa simulations with a non-uniform mesh will not run. + +Grid settings +------------- + +The following inputs are defined using the prefix ``amr``: + ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| | Description | Type | Default | ++======================+=======================================================================+=============+===========+ +| max_grid_size_x | Maximum number of cells in each grid in *X*. Can be specified | Ints | 32 | +| | per-level. | | | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| max_grid_size_y | Maximum number of cells in each grid in *Y*. Can be specified | Ints | 32 | +| | per-level. | | | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| max_grid_size_z | Maximum number of cells in each grid in *Z*. Can be specified | Ints | 32 | +| | per-level. | | | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| blocking_factor_x | Each grid in *X* must be divisible by ``blocking_factor_x``. Can be | Ints | 8 | +| | specified per-level. | | | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| blocking_factor_y | Each grid in *Y* must be divisible by ``blocking_factor_y``. Can be | Ints | 8 | +| | specified per-level. | | | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| blocking_factor_z | Each grid in *Z* must be divisible by ``blocking_factor_z``. Can be | Ints | 8 | +| | specified per-level. | | | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ + +Periodic domains +---------------- + +The following inputs are defined using the prefix ``geometry``: + ++-----------------+-----------------------------------------------------------------------+-------------+-----------+ +| | Description | Type | Default | ++=================+=======================================================================+=============+===========+ +| is_periodic | 1 for true, 0 for false (one value for each coordinate direction) | Ints<3> | 0 0 0 | ++-----------------+-----------------------------------------------------------------------+-------------+-----------+ + + Pressure drop ------------- -- GitLab From 4a153adabaa454959f708373f4aad97e07edfccc Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 27 Apr 2026 12:12:37 -0500 Subject: [PATCH 7/7] move max_grid_size and blocking_factor --- .../user_guide/inputs/gridding.rst | 30 +++---------------- 1 file changed, 4 insertions(+), 26 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/gridding.rst b/docs/source_docs/user_guide/inputs/gridding.rst index 4f7d462..5edb4ed 100644 --- a/docs/source_docs/user_guide/inputs/gridding.rst +++ b/docs/source_docs/user_guide/inputs/gridding.rst @@ -1,34 +1,12 @@ .. sec:InputsMeshAndGridding: -Grids and tiles -=============== - +Grids, tiles, and tagging +========================= -Grids ------ -The following inputs are defined using the prefix ``amr``: +Grid layout +----------- -+----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| | Description | Type | Default | -+======================+=======================================================================+=============+===========+ -| max_grid_size_x | Maximum number of cells in each grid in *X*. Can be specified | Ints | 32 | -| | per-level. | | | -+----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| max_grid_size_y | Maximum number of cells in each grid in *Y*. Can be specified | Ints | 32 | -| | per-level. | | | -+----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| max_grid_size_z | Maximum number of cells in each grid in *Z*. Can be specified | Ints | 32 | -| | per-level. | | | -+----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| blocking_factor_x | Each grid in *X* must be divisible by ``blocking_factor_x``. Can be | Ints | 8 | -| | specified per-level. | | | -+----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| blocking_factor_y | Each grid in *Y* must be divisible by ``blocking_factor_y``. Can be | Ints | 8 | -| | specified per-level. | | | -+----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| blocking_factor_z | Each grid in *Z* must be divisible by ``blocking_factor_z``.Can be | Ints | 8 | -| | specified per-level. | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ | refine_grid_layout_x | If set, AMReX will attempt to chop new grids into smaller chunks along| Bool | true | | | the x axis, ensuring at least one grid per MPI process, provided this | | | -- GitLab