From 039eadf9ea570e150a71af6d01fd5692ec4c6dca Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 16 Mar 2026 09:05:18 -0500 Subject: [PATCH 1/4] doc update --- docs/source_docs/references/hpc/Joule3.rst | 2 +- docs/source_docs/user_guide/inputs/domain.rst | 4 +- .../user_guide/quick_start/BuildingMFIX.rst | 136 +++++++++--------- 3 files changed, 71 insertions(+), 71 deletions(-) diff --git a/docs/source_docs/references/hpc/Joule3.rst b/docs/source_docs/references/hpc/Joule3.rst index 7f9dad2..609b066 100644 --- a/docs/source_docs/references/hpc/Joule3.rst +++ b/docs/source_docs/references/hpc/Joule3.rst @@ -315,7 +315,7 @@ prior to following any of the full build instructions above. .. code:: bash - git clone --branch v2.26.0 https://github.com/hypre-space/hypre.git + git clone https://github.com/hypre-space/hypre.git pushd hypre/src/ ./configure --prefix=$HYPRE_INSTALL_DIR --with-MPI make -j8 install diff --git a/docs/source_docs/user_guide/inputs/domain.rst b/docs/source_docs/user_guide/inputs/domain.rst index 5c5b148..33ba7d2 100644 --- a/docs/source_docs/user_guide/inputs/domain.rst +++ b/docs/source_docs/user_guide/inputs/domain.rst @@ -92,7 +92,9 @@ 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. ----- +Pressure drop +------------- + The following inputs are defined using the prefix ``mfix``: diff --git a/docs/source_docs/user_guide/quick_start/BuildingMFIX.rst b/docs/source_docs/user_guide/quick_start/BuildingMFIX.rst index 44d21d3..637006a 100644 --- a/docs/source_docs/user_guide/quick_start/BuildingMFIX.rst +++ b/docs/source_docs/user_guide/quick_start/BuildingMFIX.rst @@ -28,36 +28,39 @@ AMREX_HOME and AMREX_HYDRO_HOME are in the subprojects directory, which is where a cmake configuration may clone these repositories. Other options that you can set include -+-----------------+----------------------------------+------------------+-------------+ -| Option name | Description | Possible values | Default | -| | | | value | -+=================+==================================+==================+=============+ -| COMP | Compiler (gnu or intel) | gnu / intel | gnu | -+-----------------+----------------------------------+------------------+-------------+ -| USE_MPI | Enable MPI | TRUE / FALSE | FALSE | -+-----------------+----------------------------------+------------------+-------------+ -| USE_OMP | Enable OpenMP | TRUE / FALSE | FALSE | -+-----------------+----------------------------------+------------------+-------------+ -| USE_CSG | Enable CSG geometry file support | TRUE / FALSE | FALSE | -+-----------------+----------------------------------+------------------+-------------+ -| USE_CUDA | Enable CUDA GPU support | TRUE / FALSE | FALSE | -+-----------------+----------------------------------+------------------+-------------+ -| USE_HIP | Enable HIP GPU support | TRUE / FALSE | FALSE | -+-----------------+----------------------------------+------------------+-------------+ -| USE_SYCL | Enable dpc++ GPU support | TRUE / FALSE | FALSE | -+-----------------+----------------------------------+------------------+-------------+ -| USE_HYPRE | Enable HYPRE support | TRUE / FALSE | FALSE | -+-----------------+----------------------------------+------------------+-------------+ -| DEBUG | Create a DEBUG executable | TRUE / FALSE | FALSE | -+-----------------+----------------------------------+------------------+-------------+ -| PROFILE | Include profiling info | TRUE / FALSE | FALSE | -+-----------------+----------------------------------+------------------+-------------+ -| TRACE_PROFILE | Include trace profiling info | TRUE / FALSE | FALSE | -+-----------------+----------------------------------+------------------+-------------+ -| COMM_PROFILE | Include comm profiling info | TRUE / FALSE | FALSE | -+-----------------+----------------------------------+------------------+-------------+ -| TINY_PROFILE | Include tiny profiling info | TRUE / FALSE | FALSE | -+-----------------+----------------------------------+------------------+-------------+ ++-----------------+-----------------------------------+------------------+-------------+ +| Option name | Description | Possible values | Default | +| | | | value | ++=================+===================================+==================+=============+ +| COMP | Compiler (gnu or intel). | gnu / intel | gnu | ++-----------------+-----------------------------------+------------------+-------------+ +| USE\_MPI | Enable MPI. | TRUE / FALSE | FALSE | ++-----------------+-----------------------------------+------------------+-------------+ +| USE\_OMP | Enable OpenMP. | TRUE / FALSE | FALSE | ++-----------------+-----------------------------------+------------------+-------------+ +| USE\_CSG | Enable CSG geometry file support. | TRUE / FALSE | FALSE | ++-----------------+-----------------------------------+------------------+-------------+ +| USE\_CUDA | Enable CUDA GPU support. | TRUE / FALSE | FALSE | ++-----------------+-----------------------------------+------------------+-------------+ +| USE\_HIP | Enable HIP GPU support. | TRUE / FALSE | FALSE | ++-----------------+-----------------------------------+------------------+-------------+ +| USE\_SYCL | Enable dpc++ GPU support. | TRUE / FALSE | FALSE | ++-----------------+-----------------------------------+------------------+-------------+ +| USE\_HYPRE | Enable HYPRE support. | TRUE / FALSE | FALSE | ++-----------------+-----------------------------------+------------------+-------------+ +| USE\_RTE | Enable RTE (radation | TRUE / FALSE | FALSE | +| | model). Requires HYPRE. | | | ++-----------------+-----------------------------------+------------------+-------------+ +| DEBUG | Create a DEBUG executable. | TRUE / FALSE | FALSE | ++-----------------+-----------------------------------+------------------+-------------+ +| PROFILE | Include profiling info. | TRUE / FALSE | FALSE | ++-----------------+-----------------------------------+------------------+-------------+ +| TRACE\_PROFILE | Include trace profiling info. | TRUE / FALSE | FALSE | ++-----------------+-----------------------------------+------------------+-------------+ +| COMM\_PROFILE | Include comm profiling info. | TRUE / FALSE | FALSE | ++-----------------+-----------------------------------+------------------+-------------+ +| TINY\_PROFILE | Include tiny profiling info. | TRUE / FALSE | FALSE | ++-----------------+-----------------------------------+------------------+-------------+ .. note:: **Do not set both USE_OMP and USE_CUDA/HIP/SYCL to true.** @@ -72,7 +75,7 @@ An executable will appear; the executable name will reflect some of the build options above. -Building with cmake +Building with CMake -------------------- CMake build is a two-step process. First ``cmake`` is invoked to create @@ -247,9 +250,8 @@ Clone and build MFIX-Exa: Passing ``-DAMReX_ROOT=/absolute/path/to/amrex/installdir`` instructs CMake to search -``/absolute/path/to/amrex/installdir`` before searching system paths -for an available AMReX installation. -``AMReX_ROOT`` can also be set as an environmental variable instead of passing it as a command line option. +``/absolute/path/to/amrex/installdir`` before searching system paths for an available AMReX installation. +``AMReX_ROOT`` can also be set as an environment variable instead of passing it as a command line option. ``[mfix options]`` indicates any of the configuration option listed in the table below. @@ -257,39 +259,35 @@ for an available AMReX installation. .. table:: MFIX-Exa configuration options - +-----------------+------------------------------+------------------+-------------+ - | Option name | Description | Possible values | Default | - | | | | value | - +=================+==============================+==================+=============+ - | CMAKE\_CXX\ | User-defined C++ flags | valid C++ | None | - | _FLAGS | | compiler flags | | - +-----------------+------------------------------+------------------+-------------+ - | CMAKE\_CUDA\ | User-defined CUDA flags | valid CUDA | None | - | _FLAGS | | compiler flags | | - +-----------------+------------------------------+------------------+-------------+ - | MFIX\_MPI | Enable build with MPI | no/yes | yes | - | | | | | - +-----------------+------------------------------+------------------+-------------+ - | MFIX\_OMP | Enable build with OpenMP | no/yes | no | - | | | | | - +-----------------+------------------------------+------------------+-------------+ - | MFIX\_GPU\_ | On-node, accelerated GPU \ | NONE,SYSCL,\ | NONE | - | BACKEND | backend | CUDA,HIP | | - +-----------------+------------------------------+------------------+-------------+ - | MFIX\_HYPRE | Enable HYPRE support | no/yes | no | - | | | | | - +-----------------+------------------------------+------------------+-------------+ - | MFIX\_FPE | Build with Floating-Point | no/yes | no | - | | Exceptions checks | | | - +-----------------+------------------------------+------------------+-------------+ - | MFIX\_CSG | Build with CSG support | no/yes | no | - | | | | | - +-----------------+------------------------------+------------------+-------------+ - | MFIX\_MPI\_ | Concurrent MPI calls from | no/yes | no | - | THREAD\_MULTIPLE| multiple threads | | | - | | | | | - | | | | | - +-----------------+------------------------------+------------------+-------------+ + +--------------------+-----------------------------------+---------------------+-------------+ + | Option name | Description | Possible values | Default | + | | | | value | + +====================+===================================+=====================+=============+ + | CMAKE\_CXX\_FLAGS | User-defined C++ flags | valid C++ | None | + | | | compiler flags | | + +--------------------+-----------------------------------+---------------------+-------------+ + | CMAKE\_CUDA\_FLAGS | User-defined CUDA flags | valid CUDA | None | + | | | compiler flags | | + +--------------------+-----------------------------------+---------------------+-------------+ + | MFIX\_MPI | Enable build with MPI | no/yes | yes | + +--------------------+-----------------------------------+---------------------+-------------+ + | MFIX\_OMP | Enable build with OpenMP | no/yes | no | + +--------------------+-----------------------------------+---------------------+-------------+ + | MFIX\_GPU\_BACKEND | On-node, accelerated GPU backend. | NONE,SYSCL,CUDA,HIP | NONE | + +--------------------+-----------------------------------+---------------------+-------------+ + | MFIX\_HYPRE | Enable HYPRE support. | no/yes | no | + +--------------------+-----------------------------------+---------------------+-------------+ + | MFIX_RTE | Enable RTE (radiation transport | no/yes | no | + | | equation). Requires HYPRE. | | | + +--------------------+-----------------------------------+---------------------+-------------+ + | MFIX\_FPE | Build with Floating-Point | no/yes | no | + | | Exception checks. | | | + +--------------------+-----------------------------------+---------------------+-------------+ + | MFIX\_CSG | Build with CSG support. | no/yes | no | + +--------------------+-----------------------------------+---------------------+-------------+ + | MFIX\_MPI\_ | Concurrent MPI calls from | no/yes | no | + | THREAD\_MULTIPLE | multiple threads. | | | + +--------------------+-----------------------------------+---------------------+-------------+ @@ -311,10 +309,10 @@ the above command (with full path to the compiler) or the following: MFIX-Exa uses the same compiler flags used to build AMReX, unless ``CMAKE_CXX_FLAGS`` is explicitly provided, or -the environmental variable ``CXXFLAGS`` is set. +the environment variable ``CXXFLAGS`` is set. For GPU builds, MFIX-Exa relies on the `AMReX GPU build infrastructure `_ . The target architecture to build for can be specified via the AMReX configuration option ``-DAMReX_CUDA_ARCH=``, -or by defining the *environmental variable* ``AMREX_CUDA_ARCH`` (all caps). If no GPU architecture is specified, +or by defining the environment variable ``AMREX_CUDA_ARCH`` (all caps). If no GPU architecture is specified, CMake will try to determine which GPU is supported by the system. -- GitLab From 5e09f980c3c12c398410c2be293f5effd4ea6377 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Tue, 31 Mar 2026 19:11:58 -0500 Subject: [PATCH 2/4] update docs --- .../user_guide/inputs/boundary_conditions.rst | 21 ++++++++++--------- docs/source_docs/user_guide/inputs/domain.rst | 3 ++- .../user_guide/inputs/initial_conditions.rst | 20 +++++++++--------- .../user_guide/inputs/output/ascent.rst | 4 ++-- 4 files changed, 25 insertions(+), 23 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/boundary_conditions.rst b/docs/source_docs/user_guide/inputs/boundary_conditions.rst index 9bbda17..bd0a719 100644 --- a/docs/source_docs/user_guide/inputs/boundary_conditions.rst +++ b/docs/source_docs/user_guide/inputs/boundary_conditions.rst @@ -64,8 +64,8 @@ using the prefix ``bc.[region_name].[fluid_name]``: | 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 | None | -| | and bc type is ``mi`` or ``pi``] | | | +| species.[species_name] | Mass fraction of ``species_name`` [required if ``solve_species`` | Real | None | +| | is enabled and bc type is ``mi`` or ``pi``]. Must be a fluid species. | | | +------------------------+------------------------------------------------------------------------+-------------+-----------+ Note that for a ``mi`` only one of ``velocity`` or ``volflow`` or ``massflow`` should be specified. @@ -129,7 +129,7 @@ For each inflow boundary condition region, general solids inputs are defined usi | | Description | Type | Default | +======================+==================================================================+=============+===========+ | solids | Name of solid type in BC region. Only one solid is allowed in | String | None | -| | an BC region. | | | +| | a BC region. | | | +----------------------+------------------------------------------------------------------+-------------+-----------+ .. warning:: @@ -137,20 +137,22 @@ For each inflow boundary condition region, general solids inputs are defined usi Mass inflow boundary conditions, ``bc.[region_name] = mi``, only support PIC parcels. EB inflow boundary conditions, ``bc.[region_name] = eb``, support DEM particles and PIC parcels. -For inflow boundary conditions , the solids inputs are defined using the prefix ``bc.[region_name].[solid_name]``: +For mass inflow boundary conditions, the solids inputs are defined using the prefix ``bc.[region_name].[solid_name]``: +------------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +========================+=======================================================================+=============+===========+ -| volfrac | Volume fraction | Real | None | +| volfrac | Volume fraction. | Real | None | +------------------------+-----------------------------------------------------------------------+-------------+-----------+ -| temperature | Temperature | Real | None | +| temperature | Temperature. | Real | None | +------------------------+-----------------------------------------------------------------------+-------------+-----------+ -| species.[species_name] | Mass fraction of ``species_name`` | Real | None | +| species.[species_name] | Mass fraction of ``species_name``. Must be a solid species. | Real | None | +------------------------+-----------------------------------------------------------------------+-------------+-----------+ -| velocity | Velocity components | Reals | None | +| velocity | Velocity components. ``velocity`` and ``volflow`` cannot both be | Reals | None | +| | specified. | | | +------------------------+-----------------------------------------------------------------------+-------------+-----------+ -| volflow | Volumetric flow rate. | Real | None | +| volflow | Volumetric flow rate. ``velocity`` and ``volflow`` cannot both be | Real | None | +| | specified. | | | +------------------------+-----------------------------------------------------------------------+-------------+-----------+ @@ -321,7 +323,6 @@ inputs defined using the prefix ``bc.[region_name].eb``. | | * ``constant`` - impose a constant temperature along the EB. | | | | | * ``CHT-1D`` - compute a temperature for the wall using the 1D | | | | | conjugate heat transfer model. | | | -| | | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ | temperature.constant | Constant wall temperature. | Real | None | | | A valid is required for ``constant`` EB temperature model. | | | diff --git a/docs/source_docs/user_guide/inputs/domain.rst b/docs/source_docs/user_guide/inputs/domain.rst index 33ba7d2..800d634 100644 --- a/docs/source_docs/user_guide/inputs/domain.rst +++ b/docs/source_docs/user_guide/inputs/domain.rst @@ -43,7 +43,8 @@ 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> | None | +| n_cell | Number of cells at level 0 in each coordinate direction. Must be | Ints<3> | None | +| | divisible by ``amr.blocking_factor`` in each dimension. | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ The base mesh spacing is computed for each direction by dividing the :ref:`domain length` by the diff --git a/docs/source_docs/user_guide/inputs/initial_conditions.rst b/docs/source_docs/user_guide/inputs/initial_conditions.rst index 7220f9c..f996a7f 100644 --- a/docs/source_docs/user_guide/inputs/initial_conditions.rst +++ b/docs/source_docs/user_guide/inputs/initial_conditions.rst @@ -26,17 +26,17 @@ using the compound prefix ``ic.[region_name].[fluid_name]``: +------------------------+------------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +========================+========================================================================+=============+===========+ -| volfrac | Volume fraction [required] | Real | None | +| volfrac | Volume fraction [required]. | Real | None | +------------------------+------------------------------------------------------------------------+-------------+-----------+ -| density | Fluid density | Real | None | +| density | Fluid density. | Real | None | +------------------------+------------------------------------------------------------------------+-------------+-----------+ -| velocity | Velocity components | Reals<3> | None | +| velocity | Velocity components. | Reals<3> | None | +------------------------+------------------------------------------------------------------------+-------------+-----------+ -| pressure | Fluid pressure | Real | None | +| pressure | Fluid pressure. | Real | None | +------------------------+------------------------------------------------------------------------+-------------+-----------+ -| temperature | Fluid temperature | Real | None | +| temperature | Fluid temperature. | Real | None | +------------------------+------------------------------------------------------------------------+-------------+-----------+ -| species.[species_name] | Mass fraction of ``species_name``. Species must be a fluid species. | Real | None | +| species.[species_name] | Mass fraction of ``species_name``. Must be a fluid species. | Real | None | +------------------------+------------------------------------------------------------------------+-------------+-----------+ @@ -80,13 +80,13 @@ using the compound prefix ``ic.[region_name].[solid_name]``: +------------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +========================+=======================================================================+=============+===========+ -| volfrac | Volume fraction | Real | None | +| volfrac | Volume fraction. | Real | None | +------------------------+-----------------------------------------------------------------------+-------------+-----------+ -| temperature | Temperature | Real | None | +| temperature | Temperature. | Real | None | +------------------------+-----------------------------------------------------------------------+-------------+-----------+ -| species.[species_name] | Mass fraction of `species_name`. Must be a solid species. | Real | None | +| species.[species_name] | Mass fraction of ``species_name``. Must be a solid species. | Real | None | +------------------------+-----------------------------------------------------------------------+-------------+-----------+ -| velocity | Velocity components | Reals<3> | None | +| velocity | Velocity components. | Reals<3> | None | +------------------------+-----------------------------------------------------------------------+-------------+-----------+ For automatically generated particles, diameter and density distributions can be specified. diff --git a/docs/source_docs/user_guide/inputs/output/ascent.rst b/docs/source_docs/user_guide/inputs/output/ascent.rst index 6147796..64de114 100644 --- a/docs/source_docs/user_guide/inputs/output/ascent.rst +++ b/docs/source_docs/user_guide/inputs/output/ascent.rst @@ -31,6 +31,6 @@ is being included in a GPU build/run, then you must enable managed memory,i.e., +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +=====================+=======================================================================+=============+===========+ -| actions | yaml file of the ascent actions (ex. ascent_actions.yaml). If no file | String | | -| | name is provided, then calls to Ascent are skipped. | | | +| actions | Name of yaml file of the ascent actions (ex. ascent_actions.yaml). If | String | | +| | no file name is provided, then calls to Ascent are skipped. | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -- GitLab From 2d3fb1f093a4209094fa7621f605b93bb971f15e Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Tue, 31 Mar 2026 19:14:25 -0500 Subject: [PATCH 3/4] update docs --- docs/source_docs/user_guide/quick_start/BuildingMFIX.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source_docs/user_guide/quick_start/BuildingMFIX.rst b/docs/source_docs/user_guide/quick_start/BuildingMFIX.rst index 637006a..c87bda8 100644 --- a/docs/source_docs/user_guide/quick_start/BuildingMFIX.rst +++ b/docs/source_docs/user_guide/quick_start/BuildingMFIX.rst @@ -48,8 +48,8 @@ Other options that you can set include +-----------------+-----------------------------------+------------------+-------------+ | USE\_HYPRE | Enable HYPRE support. | TRUE / FALSE | FALSE | +-----------------+-----------------------------------+------------------+-------------+ -| USE\_RTE | Enable RTE (radation | TRUE / FALSE | FALSE | -| | model). Requires HYPRE. | | | +| USE\_RTE | Enable RTE (radiative transfer | TRUE / FALSE | FALSE | +| | equation). Requires HYPRE. | | | +-----------------+-----------------------------------+------------------+-------------+ | DEBUG | Create a DEBUG executable. | TRUE / FALSE | FALSE | +-----------------+-----------------------------------+------------------+-------------+ -- GitLab From 61e006cc1818f43114b3d1940c06d6dd9e00db0f Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Tue, 31 Mar 2026 19:18:05 -0500 Subject: [PATCH 4/4] update docs --- nonexistent-keys.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/nonexistent-keys.txt b/nonexistent-keys.txt index 1f3d3bc..18a87fb 100644 --- a/nonexistent-keys.txt +++ b/nonexistent-keys.txt @@ -1,4 +1,3 @@ -bc.[region_name].[solid_name].massflow mfix.solids.[region_name].plt_cp_s mfix.solids.[region_name].plt_h_s_txfr mfix.solids.[region_name].plt_mass -- GitLab