From c36fc27be6e4c87f2f7b80960e560d677dcc9e94 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 1 May 2026 11:14:25 -0500 Subject: [PATCH 01/19] fix typo, bash->text --- docs/source_docs/user_guide/inputs/geometry.rst | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/geometry.rst b/docs/source_docs/user_guide/inputs/geometry.rst index b618656..8f260f4 100644 --- a/docs/source_docs/user_guide/inputs/geometry.rst +++ b/docs/source_docs/user_guide/inputs/geometry.rst @@ -85,8 +85,8 @@ overhang on the low and high *Z* domain faces. .. _inputs_box_geometry_ex: -.. code-block:: bash - :caption: Snippet of intpus for predefined EB ``box`` geometry example. This is not a complete input file. +.. code-block:: text + :caption: Snippet of inputs for predefined EB ``box`` geometry example. This is not a complete input file. # Define periodicity and domain extents # ------------------------------------------------------------- @@ -216,14 +216,15 @@ The cylinder is not assigned a length, therefore it runs past the low and high * .. _inputs_cylinder_geometry_ex: -.. code-block:: bash +.. code-block:: text :caption: Snippet of inputs for predefined EB ``cylinder`` geometry 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 # Select cylinder geometry and specify settings -- GitLab From 6ddd593558d6ce28c13b64c8a3bdd9bd5c3ea788 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 1 May 2026 11:15:23 -0500 Subject: [PATCH 02/19] fix example --- docs/source_docs/user_guide/inputs/geometry.rst | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/geometry.rst b/docs/source_docs/user_guide/inputs/geometry.rst index 8f260f4..ac70c49 100644 --- a/docs/source_docs/user_guide/inputs/geometry.rst +++ b/docs/source_docs/user_guide/inputs/geometry.rst @@ -223,8 +223,7 @@ The cylinder is not assigned a length, therefore it runs past the low and high * # ------------------------------------------------------------- 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 # Select cylinder geometry and specify settings -- GitLab From bad0e80aeb5c5aa6dc5e72a95f4adf4e93553ff7 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 1 May 2026 11:16:33 -0500 Subject: [PATCH 03/19] tidy up equations and units --- .../source_docs/user_guide/inputs/boundary_conditions.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/boundary_conditions.rst b/docs/source_docs/user_guide/inputs/boundary_conditions.rst index 0a899de..6359989 100644 --- a/docs/source_docs/user_guide/inputs/boundary_conditions.rst +++ b/docs/source_docs/user_guide/inputs/boundary_conditions.rst @@ -388,7 +388,7 @@ The model settings are defined using the prefix ``bc.[region_name].eb.temperatur .. |avg_T| replace:: :math:`T = \varepsilon_f T_f + (1-\varepsilon_f) \overline{T}_p` -.. |avg_Tp| replace:: :math:`\overline{T}_p = \left( {\sum_p^{N_p} T_p V_p} \right) / \left( {\sum_p^{N_p} V_p} \right)` +.. |avg_Tp| replace:: :math:`\displaystyle\overline{T}_p = \frac{\sum_{n=1}^{N_p} T_n V_n}{\sum_{n=1}^{N_p} V_n}` +----------------------------+------------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -397,14 +397,14 @@ The model settings are defined using the prefix ``bc.[region_name].eb.temperatur +----------------------------+------------------------------------------------------------------------+-------------+-----------+ | h_int | Heat Transfer Coefficient (fluid–wall, internal) | Real | None | | | | | | -| | Specifies the convective heat transfer coefficient [W/m² K] between | | | +| | Specifies the convective heat transfer coefficient [W/m²·K] between | | | | | the fluid and adjacent solid walls (EBs) located within the interior | | | | | of the computational domain. | | | | | | | | +----------------------------+------------------------------------------------------------------------+-------------+-----------+ | h_ext | Heat Transfer Coefficient (wall-environment, external) | Real | None | | | | | | -| | Specifies the convective heat transfer coefficient [W/m² K] between | | | +| | Specifies the convective heat transfer coefficient [W/m²·K] between | | | | | the wall and the external environment. | | | | | | | | +----------------------------+------------------------------------------------------------------------+-------------+-----------+ @@ -412,7 +412,7 @@ The model settings are defined using the prefix ``bc.[region_name].eb.temperatur +----------------------------+------------------------------------------------------------------------+-------------+-----------+ | wall.thickness | Wall thickness. | Real | None | +----------------------------+------------------------------------------------------------------------+-------------+-----------+ -| wall.heat_capacity | Lumped wall heat capacity per area [J/(m\ :sup:`2`\ K)] | Real | 0. | +| wall.heat_capacity | Lumped wall heat capacity per area [J/(m²·K)] | Real | 0. | +----------------------------+------------------------------------------------------------------------+-------------+-----------+ | phase_averaged_temperature | Use a phase averaged temperature for simulations containing particles. | Bool | false | | | The phase averaged temperature is computed as the volume fraction | | | -- GitLab From 25292d15d30e429f1a9e241e200aef2c0d92deec Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 4 May 2026 15:13:39 -0500 Subject: [PATCH 04/19] fix code-blocks --- .../references/Chemistry_Chapter.rst | 2 +- .../fluids/BuildingMacVelocities.rst | 20 ++--- docs/source_docs/references/fluids/Slopes.rst | 27 +++--- docs/source_docs/references/hpc/Bridges2.rst | 40 ++++----- docs/source_docs/references/hpc/Crusher.rst | 48 +++++------ docs/source_docs/references/hpc/Delta.rst | 50 +++++------ docs/source_docs/references/hpc/Frontier.rst | 36 ++++---- docs/source_docs/references/hpc/Joule3.rst | 54 ++++++------ .../source_docs/references/hpc/Perlmutter.rst | 56 ++++++------- docs/source_docs/references/hpc/Polaris.rst | 44 +++++----- docs/source_docs/references/hpc/Summit.rst | 50 +++++------ .../references/particles/ParticleBasics.rst | 6 +- .../qualitative_bencharks/mehrdadsbed.rst | 2 +- .../user_guide/inputs/output/reports.rst | 2 +- .../user_guide/quick_start/BuildingMFIX.rst | 84 +++++++++---------- 15 files changed, 258 insertions(+), 263 deletions(-) diff --git a/docs/source_docs/references/Chemistry_Chapter.rst b/docs/source_docs/references/Chemistry_Chapter.rst index c167a40..fbbdb5b 100644 --- a/docs/source_docs/references/Chemistry_Chapter.rst +++ b/docs/source_docs/references/Chemistry_Chapter.rst @@ -174,7 +174,7 @@ The molar concentrations for oxygen (``O2``) and methane (``CH4``) are accessed using the names provided in the inputs file. Similarly, the reaction rate is stored using the name given in the inputs file. -.. code-block:: bash +.. code-block:: text :caption: Snippet of inputs defining fluid species and adiabatic flame reaction # Fluid model settings diff --git a/docs/source_docs/references/fluids/BuildingMacVelocities.rst b/docs/source_docs/references/fluids/BuildingMacVelocities.rst index 5ed22ad..e65eb1f 100644 --- a/docs/source_docs/references/fluids/BuildingMacVelocities.rst +++ b/docs/source_docs/references/fluids/BuildingMacVelocities.rst @@ -1,12 +1,12 @@ -Creating the MAC velocities -~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Creating the MAC (Marker and Cell) velocities +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ To create the normal velocities on faces, we first extrapolate from the cell centers on each side using the -slopes as computed earlier, and upwind the face value to define :math:`U^{pred}` +slopes as computed earlier, and upwind the face value to define :math:`U^{pred}`. -. To compute the x-velocity on the x-faces of regular (ie not cut) cells, we call +To compute the x-velocity on the x-faces of regular (ie not cut) cells, we call - .. code:: shell + .. code-block:: cpp AMREX_CUDA_HOST_DEVICE_FOR_3D(ubx, i, j, k, { @@ -24,9 +24,9 @@ slopes as computed earlier, and upwind the face value to define :math:`U^{pred} } }); -For cut cells we test on whether the area fraction is non-zero: - - .. code:: shell +For cut cells we test on whether the area fraction is non-zero: + + .. code-block:: cpp AMREX_CUDA_HOST_DEVICE_FOR_3D(ubx, i, j, k, { @@ -49,11 +49,11 @@ For cut cells we test on whether the area fraction is non-zero: } }); -We then perform a MAC projection on the face-centered velocities to enforce that they satisfy +We then perform a MAC projection on the face-centered velocities to enforce that they satisfy .. math:: \nabla \cdot (\varepsilon_g U^{MAC}) = 0 -We do this by solving +We do this by solving .. math:: \nabla \cdot \frac{\varepsilon_g}{\rho_g} \nabla \phi^{MAC} = \nabla \cdot \left( \varepsilon_g U^{pred} \right) diff --git a/docs/source_docs/references/fluids/Slopes.rst b/docs/source_docs/references/fluids/Slopes.rst index ea366a0..4fab3ab 100644 --- a/docs/source_docs/references/fluids/Slopes.rst +++ b/docs/source_docs/references/fluids/Slopes.rst @@ -1,5 +1,5 @@ Computing slopes -~~~~~~~~~~~~~~~~~~~~~~~~~~~ +================ Slopes are computed one direction at a time for each scalar and each velocity component. @@ -8,38 +8,33 @@ We use the second order Monotonized Central (MC) limiter (van Leer, 1977). The scheme is described below for the u-velocity. The limiter computes the slope at cell "i" by combining the left, central -and right u-variation "du": - -.. code:: shell +and right u-variation "du":: du_l = u(i) - u(i-1) = left variation - du_c = 0.5 * ( u(i+1) - u(i-1) ) = central (umlimited) variation + du_c = 0.5 * ( u(i+1) - u(i-1) ) = central (unlimited) variation du_r = u(i+1) - u(i) = right variation -Finally, the u-variation at cell "i" is given by : - -.. code:: shell +Finally, the u-variation at cell "i" is given by:: du(i) = sign(du_c) * min(2|du_l|, |du_c|, 2|du_r|)) if du_l*du_r > 0 du(i) = 0 otherwise The above procedure is applied direction by direction. -BOUNDARY CONDITIONS -When periodic or Neumann's BCs are imposed, the scheme can be applied +Boundary conditions +------------------- +When periodic or Neumann BCs are imposed, the scheme can be applied without any change since the ghost cells at the boundary are filled by either periodicity or by extrapolation. -For Dirichlet's BCs in the transversal direction, the scheme can again +For Dirichlet BCs in the transversal direction, the scheme can again be applied as is since the velocity is known at the first ghost cell out of the domain. -However, for Dirichlet's BCs in the longitudinal direction, the velocity +However, for Dirichlet BCs in the longitudinal direction, the velocity is not known outside the domain since the BC is applied directly at the first valid node which lies on the boundary itself. Therefore, the scheme must be arranged as follows to use ONLY values from inside the domain. -For a left boundary (i=0), the u-variations are: - -.. code:: shell +For a left boundary (i=0), the u-variations are:: - du_l = 0 Dont use values on the left + du_l = 0 Don't use values on the left du_c = -1.5*u(0) + 2*u(1) -0.5*u(2) 2nd order right-biased du_r = u(1) - u(0) Right variation diff --git a/docs/source_docs/references/hpc/Bridges2.rst b/docs/source_docs/references/hpc/Bridges2.rst index 40f75b4..82908e1 100644 --- a/docs/source_docs/references/hpc/Bridges2.rst +++ b/docs/source_docs/references/hpc/Bridges2.rst @@ -15,7 +15,7 @@ review the general notes below and `Basics`_ section first. * For the dependencies, it is assumed that you have set the following environment variables: - .. code:: bash + .. code-block:: bash export HYPRE_INSTALL_DIR=$HOME/ export CSG_INSTALL_DIR=$HOME/ @@ -41,7 +41,7 @@ Modules There are (basically) no modules loaded by default on Bridges-2. -.. code:: bash +.. code-block:: bash module load gcc/10.2.0 # PrgEnv module load openmpi/4.0.5-gcc10.2.0 # MPI @@ -68,7 +68,7 @@ building MFIX-Exa is currently recommended. .. tab:: CPU - .. code:: bash + .. code-block:: bash cp -r exec exec.cpu make -C exec.cpu -j8 \ @@ -84,7 +84,7 @@ building MFIX-Exa is currently recommended. .. tab:: GPU - .. code:: bash + .. code-block:: bash cp -r exec exec.gpu make -C exec.gpu -j8 \ @@ -101,7 +101,7 @@ building MFIX-Exa is currently recommended. .. tab:: CPU-full - .. code:: bash + .. code-block:: bash export HYPRE_DIR=$HYPRE_INSTALL_DIR export HYPRE_HOME=$HYPRE_DIR @@ -127,7 +127,7 @@ building MFIX-Exa is currently recommended. .. tab:: GPU-full - .. code:: bash + .. code-block:: bash export HYPRE_DIR=$HYPRE_INSTALL_DIR export HYPRE_HOME=$HYPRE_DIR @@ -163,7 +163,7 @@ prior to following any of the full build instructions above. .. tab:: CPU - .. code:: bash + .. code-block:: bash git clone https://github.com/hypre-space/hypre.git pushd hypre/src/ @@ -174,7 +174,7 @@ prior to following any of the full build instructions above. .. tab:: GPU - .. code:: bash + .. code-block:: bash git clone https://github.com/hypre-space/hypre.git pushd hypre/src/ @@ -201,7 +201,7 @@ prior to following any of the full build instructions above. ``export CMAKE_INSTALL_DIR=$HOME/`` to a path that you have read/write access to. - .. code:: bash + .. code-block:: bash wget https://cmake.org/files/v3.23/cmake-3.23.2.tar.gz tar -zxvf cmake-3.23.2.tar.gz @@ -212,13 +212,13 @@ prior to following any of the full build instructions above. After installing cmake, you will need to prepend it to your path - .. code:: bash + .. code-block:: bash export PATH=$CMAKE_INSTALL_DIR/bin:$PATH #. Catch2 - .. code:: bash + .. code-block:: bash git clone --depth 1 --branch v3.11.0 https://github.com/catchorg/Catch2 pushd Catch2/ @@ -229,7 +229,7 @@ prior to following any of the full build instructions above. #. GMP - .. code:: bash + .. code-block:: bash wget --no-check-certificate https://ftp.gnu.org/gnu/gmp/gmp-6.2.1.tar.xz tar -xf gmp-6.2.1.tar.xz @@ -240,7 +240,7 @@ prior to following any of the full build instructions above. #. MPFR - .. code:: bash + .. code-block:: bash wget --no-check-certificate https://ftp.gnu.org/gnu/mpfr/mpfr-4.1.0.tar.xz tar -xf mpfr-4.1.0.tar.xz @@ -251,7 +251,7 @@ prior to following any of the full build instructions above. #. CGAL - .. code:: bash + .. code-block:: bash git clone --depth 1 --branch v6.1.1 https://github.com/CGAL/cgal pushd cgal/ @@ -263,7 +263,7 @@ prior to following any of the full build instructions above. #. PEGTL - .. code:: bash + .. code-block:: bash git clone --branch 3.2.8 https://github.com/taocpp/PEGTL pushd PEGTL/ @@ -277,7 +277,7 @@ prior to following any of the full build instructions above. Make sure you have boost loaded before building. (This is intended to be executed from inside the mfix repo.) - .. code:: bash + .. code-block:: bash make -C subprojects/csg-eb install DESTDIR=$CSG_LIB_DIR \ PEGTL_HOME=$CSG_INSTALL_DIR \ @@ -287,7 +287,7 @@ prior to following any of the full build instructions above. #. Conduit - .. code:: bash + .. code-block:: bash git clone --recursive https://github.com/LLNL/conduit.git pushd conduit/ @@ -303,7 +303,7 @@ prior to following any of the full build instructions above. #. Vtk-m - .. code:: bash + .. code-block:: bash git clone --branch master https://gitlab.kitware.com/vtk/vtk-m.git pushd vtk-m/ @@ -323,7 +323,7 @@ prior to following any of the full build instructions above. #. Ascent - .. code:: bash + .. code-block:: bash git clone --recursive https://github.com/Alpine-DAV/ascent.git pushd ascent @@ -361,7 +361,7 @@ Example run script for GPU is below. You can mirror the interactive commands above to convert this into a shared job script. CPU-only runs have not been tested on this machine. -.. code:: bash +.. code-block:: bash #!/bin/bash #!/bin/bash diff --git a/docs/source_docs/references/hpc/Crusher.rst b/docs/source_docs/references/hpc/Crusher.rst index 0cea165..571dbcd 100644 --- a/docs/source_docs/references/hpc/Crusher.rst +++ b/docs/source_docs/references/hpc/Crusher.rst @@ -17,7 +17,7 @@ review the general notes below and `Basics`_ section first. * For the dependencies, it is assumed that you have set the following environment variables: - .. code:: bash + .. code-block:: bash export HYPRE_INSTALL_DIR=$HOME/ export CSG_INSTALL_DIR=$HOME/ @@ -32,7 +32,7 @@ review the general notes below and `Basics`_ section first. build the PIC-to-DEM restarter app by executing the following command in the ``build`` directory - .. code:: bash + .. code-block:: bash cmake --build . --target pic2dem @@ -69,7 +69,7 @@ for the GPU with HIP-support. .. tab:: PrgEnv-cray - .. code:: bash + .. code-block:: bash module purge module reset @@ -90,7 +90,7 @@ for the GPU with HIP-support. Modules - .. code:: bash + .. code-block:: bash module purge module reset @@ -104,7 +104,7 @@ for the GPU with HIP-support. CPU compilers - .. code:: bash + .. code-block:: bash export CC=$(which cc) export CXX=$(which CC) @@ -112,7 +112,7 @@ for the GPU with HIP-support. GPU compilers - .. code:: bash + .. code-block:: bash export CC=$(which hipcc) export CXX=$(which hipcc) @@ -140,7 +140,7 @@ only provided for ``cmake``. .. tab:: CPU - .. code:: bash + .. code-block:: bash cmake -DMFIX_MPI=yes \ -DMFIX_OMP=no \ @@ -154,7 +154,7 @@ only provided for ``cmake``. .. tab:: GPU - .. code:: bash + .. code-block:: bash export AMREX_AMD_ARCH=gfx90a @@ -170,7 +170,7 @@ only provided for ``cmake``. .. tab:: CPU-full - .. code:: bash + .. code-block:: bash export HYPRE_DIR=$HYPRE_INSTALL_DIR export HYPRE_ROOT=$HYPRE_DIR @@ -202,7 +202,7 @@ only provided for ``cmake``. .. tab:: GPU-full - .. code:: bash + .. code-block:: bash export HYPRE_DIR=$HYPRE_INSTALL_DIR export HYPRE_ROOT=$HYPRE_DIR @@ -248,7 +248,7 @@ prior to following any of the full build instructions above. .. tab:: CPU - .. code:: bash + .. code-block:: bash git clone https://github.com/hypre-space/hypre.git pushd hypre/src/ @@ -259,7 +259,7 @@ prior to following any of the full build instructions above. .. tab:: GPU - .. code:: bash + .. code-block:: bash git clone https://github.com/hypre-space/hypre.git pushd hypre/src/ @@ -284,7 +284,7 @@ prior to following any of the full build instructions above. #. Catch2 - .. code:: bash + .. code-block:: bash git clone --depth 1 --branch v3.11.0 https://github.com/catchorg/Catch2 pushd Catch2/ @@ -296,7 +296,7 @@ prior to following any of the full build instructions above. #. GMP - .. code:: bash + .. code-block:: bash wget --no-check-certificate https://ftp.gnu.org/gnu/gmp/gmp-6.2.1.tar.xz tar -xf gmp-6.2.1.tar.xz @@ -308,7 +308,7 @@ prior to following any of the full build instructions above. #. MPFR - .. code:: bash + .. code-block:: bash wget https://www.mpfr.org/mpfr-current/mpfr-4.2.0.tar.gz tar -zxvf mpfr-4.2.0.tar.gz @@ -322,7 +322,7 @@ prior to following any of the full build instructions above. #. CGAL - .. code:: bash + .. code-block:: bash git clone --depth 1 --branch v6.1.1 https://github.com/CGAL/cgal pushd cgal/ @@ -334,7 +334,7 @@ prior to following any of the full build instructions above. #. PEGTL - .. code:: bash + .. code-block:: bash git clone --branch 3.2.8 https://github.com/taocpp/PEGTL pushd PEGTL/ @@ -352,7 +352,7 @@ prior to following any of the full build instructions above. Make sure that "experimental" precedes filesystem on or near lines 47 and 51 in ``CSG_INSTALL_DIR/include/tao/pegtl/internal/filesystem.hpp`` - .. code:: bash + .. code-block:: bash ... #include @@ -364,7 +364,7 @@ prior to following any of the full build instructions above. #. Boost - .. code:: bash + .. code-block:: bash wget https://boostorg.jfrog.io/artifactory/main/release/1.81.0/source/boost_1_81_0.tar.gz tar -zxvf boost_1_81_0.tar.gz @@ -381,7 +381,7 @@ prior to following any of the full build instructions above. #. Conduit - .. code:: bash + .. code-block:: bash git clone --recursive https://github.com/LLNL/conduit.git pushd conduit/ @@ -401,7 +401,7 @@ prior to following any of the full build instructions above. #. Vtk-m - .. code:: bash + .. code-block:: bash git clone --branch master https://gitlab.kitware.com/vtk/vtk-m.git pushd vtk-m/ @@ -423,7 +423,7 @@ prior to following any of the full build instructions above. #. Ascent - .. code:: bash + .. code-block:: bash git clone --recursive https://github.com/Alpine-DAV/ascent.git pushd ascent @@ -463,7 +463,7 @@ Example run scripts: .. tab:: PrgEnv-cray - .. code:: bash + .. code-block:: bash #!/bin/bash -l @@ -503,7 +503,7 @@ Example run scripts: .. tab:: PrgEnv-gnu - .. code:: bash + .. code-block:: bash #!/bin/bash -l diff --git a/docs/source_docs/references/hpc/Delta.rst b/docs/source_docs/references/hpc/Delta.rst index 56fcef4..81d27ce 100644 --- a/docs/source_docs/references/hpc/Delta.rst +++ b/docs/source_docs/references/hpc/Delta.rst @@ -22,7 +22,7 @@ review the general notes below and `Basics`_ section first. * For the dependencies, it is assumed that you have set the following environment variables: - .. code:: bash + .. code-block:: bash export HYPRE_INSTALL_DIR=$HOME/ export CSG_INSTALL_DIR=$HOME/ @@ -36,7 +36,7 @@ review the general notes below and `Basics`_ section first. build the PIC-to-DEM restarter app by executing the following command in the ``build`` directory - .. code:: bash + .. code-block:: bash cmake --build . --target pic2dem @@ -58,21 +58,21 @@ The default modules on Delta are *almost* all that you need to build and compile all dependencies. If you are using ``cmake`` to build, you need to load a newer version, such as -.. code:: bash +.. code-block:: bash module load cmake/3.23.1 If you are building the CSG library or building MFIX-Exa with CSG support, you need to load boost, such as -.. code:: bash +.. code-block:: bash module load boost/1.80.0 There is a known incompatibility with AMReX and the pre-loaded cuda version 11.6.1. To build with GPU support you will need to downgrade or upgrade versions, such as -.. code:: bash +.. code-block:: bash module swap cuda/11.6.1 cuda/11.7.0 @@ -99,7 +99,7 @@ cmake .. tab:: CPU - .. code:: bash + .. code-block:: bash cmake -DMFIX_MPI=yes \ -DMFIX_OMP=no \ @@ -113,7 +113,7 @@ cmake .. tab:: GPU - .. code:: bash + .. code-block:: bash cmake -DMFIX_MPI=yes \ -DMFIX_OMP=no \ @@ -130,7 +130,7 @@ cmake .. tab:: CPU-full - .. code:: bash + .. code-block:: bash export HYPRE_DIR=$HYPRE_INSTALL_DIR export HYPRE_ROOT=$HYPRE_DIR @@ -159,7 +159,7 @@ cmake .. tab:: GPU-full - .. code:: bash + .. code-block:: bash export HYPRE_DIR=$HYPRE_INSTALL_DIR export HYPRE_ROOT=$HYPRE_DIR @@ -199,7 +199,7 @@ gmake .. tab:: CPU - .. code:: bash + .. code-block:: bash make -C exec -j8 \ COMP=gnu \ @@ -214,7 +214,7 @@ gmake .. tab:: GPU - .. code:: bash + .. code-block:: bash make -C exec -j8 COMP=gnu \ @@ -230,7 +230,7 @@ gmake .. tab:: CPU-full - .. code:: bash + .. code-block:: bash export HYPRE_DIR=$HYPRE_INSTALL_DIR export HYPRE_HOME=$HYPRE_DIR @@ -256,7 +256,7 @@ gmake .. tab:: GPU-full - .. code:: bash + .. code-block:: bash export HYPRE_DIR=$HYPRE_INSTALL_DIR export HYPRE_HOME=$HYPRE_DIR @@ -294,7 +294,7 @@ prior to following any of the full build instructions above. .. tab:: CPU - .. code:: bash + .. code-block:: bash git clone https://github.com/hypre-space/hypre.git pushd hypre/src/ @@ -305,7 +305,7 @@ prior to following any of the full build instructions above. .. tab:: GPU - .. code:: bash + .. code-block:: bash git clone https://github.com/hypre-space/hypre.git pushd hypre/src/ @@ -325,7 +325,7 @@ prior to following any of the full build instructions above. #. Catch2 - .. code:: bash + .. code-block:: bash git clone --depth 1 --branch v3.11.0 https://github.com/catchorg/Catch2 pushd Catch2/ @@ -336,7 +336,7 @@ prior to following any of the full build instructions above. #. GMP - .. code:: bash + .. code-block:: bash wget --no-check-certificate https://ftp.gnu.org/gnu/gmp/gmp-6.2.1.tar.xz tar -xf gmp-6.2.1.tar.xz @@ -347,7 +347,7 @@ prior to following any of the full build instructions above. #. MPFR - .. code:: bash + .. code-block:: bash wget --no-check-certificate https://ftp.gnu.org/gnu/mpfr/mpfr-4.1.0.tar.xz tar -xf mpfr-4.1.0.tar.xz @@ -358,7 +358,7 @@ prior to following any of the full build instructions above. #. CGAL - .. code:: bash + .. code-block:: bash git clone --depth 1 --branch v6.1.1 https://github.com/CGAL/cgal pushd cgal/ @@ -370,7 +370,7 @@ prior to following any of the full build instructions above. #. PEGTL - .. code:: bash + .. code-block:: bash git clone --branch 3.2.8 https://github.com/taocpp/PEGTL pushd PEGTL/ @@ -388,7 +388,7 @@ prior to following any of the full build instructions above. Make sure you have boost loaded before building. (This is intended to be executed from inside the mfix repo.) - .. code:: bash + .. code-block:: bash make -C subprojects/csg-eb install DESTDIR=$CSG_LIB_DIR \ PEGTL_HOME=$CSG_INSTALL_DIR \ @@ -398,7 +398,7 @@ prior to following any of the full build instructions above. #. Conduit - .. code:: bash + .. code-block:: bash git clone --recursive https://github.com/LLNL/conduit.git pushd conduit/ @@ -414,7 +414,7 @@ prior to following any of the full build instructions above. #. Vtk-m - .. code:: bash + .. code-block:: bash git clone --branch master https://gitlab.kitware.com/vtk/vtk-m.git pushd vtk-m/ @@ -434,7 +434,7 @@ prior to following any of the full build instructions above. #. Ascent - .. code:: bash + .. code-block:: bash git clone --recursive https://github.com/Alpine-DAV/ascent.git pushd ascent @@ -470,7 +470,7 @@ Common Slurm commands: Example run script for GPU is below, CPU-only runs have not been tested on this machine. -.. code:: bash +.. code-block:: bash #!/bin/bash #SBATCH --nodes=3 diff --git a/docs/source_docs/references/hpc/Frontier.rst b/docs/source_docs/references/hpc/Frontier.rst index f4c3b6d..58a17e2 100644 --- a/docs/source_docs/references/hpc/Frontier.rst +++ b/docs/source_docs/references/hpc/Frontier.rst @@ -17,7 +17,7 @@ review the general notes below and `Basics`_ section first. * For the dependencies, it is assumed that you have set the following environment variables: - .. code:: bash + .. code-block:: bash export HYPRE_INSTALL_DIR=$HOME/ export CSG_INSTALL_DIR=$HOME/ @@ -30,7 +30,7 @@ review the general notes below and `Basics`_ section first. build the PIC-to-DEM restarter app by executing the following command in the ``build`` directory - .. code:: bash + .. code-block:: bash cmake --build . --target pic2dem * These instructions have targeded the Cray Programming Environment. @@ -65,7 +65,7 @@ programming environment and the ``cmake`` build method. .. tab:: CPU - .. code:: bash + .. code-block:: bash module purge module reset @@ -78,7 +78,7 @@ programming environment and the ``cmake`` build method. .. tab:: GPU - .. code:: bash + .. code-block:: bash module purge module reset @@ -112,7 +112,7 @@ only provided for ``cmake``. .. tab:: CPU - .. code:: bash + .. code-block:: bash cmake -DCMAKE_BUILD_TYPE=Release \ -DAMReX_TINY_PROFILE=no \ @@ -126,7 +126,7 @@ only provided for ``cmake``. .. tab:: GPU - .. code:: bash + .. code-block:: bash export AMREX_AMD_ARCH=gfx90a @@ -142,7 +142,7 @@ only provided for ``cmake``. .. tab:: CPU-full - .. code:: bash + .. code-block:: bash export HYPRE_DIR=$HYPRE_INSTALL_DIR export HYPRE_ROOT=$HYPRE_DIR @@ -173,7 +173,7 @@ only provided for ``cmake``. .. tab:: GPU-full - .. code:: bash + .. code-block:: bash export HYPRE_DIR=$HYPRE_INSTALL_DIR export HYPRE_ROOT=$HYPRE_DIR @@ -218,7 +218,7 @@ prior to following any of the full build instructions above. .. tab:: CPU - .. code:: bash + .. code-block:: bash git clone https://github.com/hypre-space/hypre.git pushd hypre/src/ @@ -229,7 +229,7 @@ prior to following any of the full build instructions above. .. tab:: GPU - .. code:: bash + .. code-block:: bash git clone https://github.com/hypre-space/hypre.git pushd hypre/src/ @@ -254,7 +254,7 @@ prior to following any of the full build instructions above. #. Catch2 - .. code:: bash + .. code-block:: bash git clone --depth 1 --branch v3.11.0 https://github.com/catchorg/Catch2 pushd Catch2/ @@ -266,7 +266,7 @@ prior to following any of the full build instructions above. #. MPFR - .. code:: bash + .. code-block:: bash wget https://www.mpfr.org/mpfr-current/mpfr-4.2.0.tar.gz tar -zxvf mpfr-4.2.0.tar.gz @@ -280,7 +280,7 @@ prior to following any of the full build instructions above. #. CGAL - .. code:: bash + .. code-block:: bash git clone --depth 1 --branch v6.1.1 https://github.com/CGAL/cgal pushd cgal/ @@ -292,7 +292,7 @@ prior to following any of the full build instructions above. #. PEGTL - .. code:: bash + .. code-block:: bash git clone --branch 3.2.8 https://github.com/taocpp/PEGTL pushd PEGTL/ @@ -304,7 +304,7 @@ prior to following any of the full build instructions above. #. Conduit - .. code:: bash + .. code-block:: bash git clone --recursive https://github.com/LLNL/conduit.git pushd conduit/ @@ -324,7 +324,7 @@ prior to following any of the full build instructions above. #. Vtk-m - .. code:: bash + .. code-block:: bash git clone --branch master https://gitlab.kitware.com/vtk/vtk-m.git pushd vtk-m/ @@ -346,7 +346,7 @@ prior to following any of the full build instructions above. #. Ascent - .. code:: bash + .. code-block:: bash git clone --recursive https://github.com/Alpine-DAV/ascent.git pushd ascent @@ -389,7 +389,7 @@ Example run scripts: error. The ``FI_*`` flags seem to be unnecessary for CPU-only runs, but this has not been extensively tested yet. -.. code:: bash +.. code-block:: bash #!/bin/bash -l diff --git a/docs/source_docs/references/hpc/Joule3.rst b/docs/source_docs/references/hpc/Joule3.rst index 609b066..7f4761e 100644 --- a/docs/source_docs/references/hpc/Joule3.rst +++ b/docs/source_docs/references/hpc/Joule3.rst @@ -16,7 +16,7 @@ review the general notes below and `Basics`_ section first. * For the dependencies, it is assumed that you have set the following environment variables: - .. code:: bash + .. code-block:: bash export HYPRE_INSTALL_DIR=$HOME/ export CSG_INSTALL_DIR=$HOME/ @@ -30,7 +30,7 @@ review the general notes below and `Basics`_ section first. build the PIC-to-DEM restarter app by executing the following command in the ``build`` directory - .. code:: bash + .. code-block:: bash cmake --build . --target pic2dem @@ -51,7 +51,7 @@ Modules All of the build instructions below have been tested with the following modules -.. code:: bash +.. code-block:: bash module purge module load cmake @@ -60,7 +60,7 @@ following modules The GPU-enabled builds additionally require -.. code:: bash +.. code-block:: bash module load cuda @@ -87,7 +87,7 @@ cmake .. tab:: CPU - .. code:: bash + .. code-block:: bash mkdir build; cd build @@ -105,7 +105,7 @@ cmake .. tab:: GPU - .. code:: bash + .. code-block:: bash mkdir build; cd build @@ -127,7 +127,7 @@ cmake .. tab:: CPU-full - .. code:: bash + .. code-block:: bash export HYPRE_DIR=$HYPRE_INSTALL_DIR export HYPRE_ROOT=$HYPRE_DIR @@ -162,7 +162,7 @@ cmake .. tab:: GPU-full - .. code:: bash + .. code-block:: bash mkdir build; cd build @@ -207,7 +207,7 @@ gmake .. tab:: CPU - .. code:: bash + .. code-block:: bash make -C exec -j8 \ COMP=gnu \ @@ -222,7 +222,7 @@ gmake .. tab:: GPU - .. code:: bash + .. code-block:: bash make -C exec -j8 COMP=gnu \ @@ -238,7 +238,7 @@ gmake .. tab:: CPU-full - .. code:: bash + .. code-block:: bash export HYPRE_DIR=$HYPRE_INSTALL_DIR export HYPRE_HOME=$HYPRE_DIR @@ -264,7 +264,7 @@ gmake .. tab:: GPU-full - .. code:: bash + .. code-block:: bash export HYPRE_DIR=$HYPRE_INSTALL_DIR export HYPRE_HOME=$HYPRE_DIR @@ -298,7 +298,7 @@ prior to following any of the full build instructions above. #. Set environment helpers - .. code:: bash + .. code-block:: bash export CC=$(which mpicc) export CXX=$(which mpic++) @@ -313,7 +313,7 @@ prior to following any of the full build instructions above. .. tab:: CPU - .. code:: bash + .. code-block:: bash git clone https://github.com/hypre-space/hypre.git pushd hypre/src/ @@ -323,7 +323,7 @@ prior to following any of the full build instructions above. .. tab:: GPU - .. code:: bash + .. code-block:: bash git clone https://github.com/hypre-space/hypre.git pushd hypre/src/ @@ -343,7 +343,7 @@ prior to following any of the full build instructions above. #. Catch2 - .. code:: bash + .. code-block:: bash git clone --depth 1 --branch v3.11.0 https://github.com/catchorg/Catch2 pushd Catch2/ @@ -354,7 +354,7 @@ prior to following any of the full build instructions above. #. GMP - .. code:: bash + .. code-block:: bash wget --no-check-certificate https://ftp.gnu.org/gnu/gmp/gmp-6.2.1.tar.xz tar -xf gmp-6.2.1.tar.xz @@ -365,7 +365,7 @@ prior to following any of the full build instructions above. #. MPFR - .. code:: bash + .. code-block:: bash wget --no-check-certificate https://ftp.gnu.org/gnu/mpfr/mpfr-4.1.0.tar.xz tar -xf mpfr-4.1.0.tar.xz @@ -376,7 +376,7 @@ prior to following any of the full build instructions above. #. CGAL - .. code:: bash + .. code-block:: bash git clone --depth 1 --branch v6.4 https://github.com/CGAL/cgal pushd cgal/ @@ -388,7 +388,7 @@ prior to following any of the full build instructions above. #. PEGTL - .. code:: bash + .. code-block:: bash git clone --branch 3.2.8 https://github.com/taocpp/PEGTL pushd PEGTL/ @@ -406,7 +406,7 @@ prior to following any of the full build instructions above. .. tab:: cmake - .. code:: bash + .. code-block:: bash cd subprojects/csg-eb @@ -424,7 +424,7 @@ prior to following any of the full build instructions above. .. tab:: gmake - .. code:: bash + .. code-block:: bash make -C subprojects/csg-eb install DESTDIR=$CSG_LIB_DIR \ BOOST_HOME=/nfs/apps/Libraries/Boost/1.83.0/gnu/13.2.0/openmpi/4.1.4 \ @@ -435,7 +435,7 @@ prior to following any of the full build instructions above. #. Conduit - .. code:: bash + .. code-block:: bash git clone --recursive https://github.com/LLNL/conduit.git pushd conduit/ @@ -451,7 +451,7 @@ prior to following any of the full build instructions above. #. Vtk-m - .. code:: bash + .. code-block:: bash git clone --branch master https://gitlab.kitware.com/vtk/vtk-m.git pushd vtk-m/ @@ -471,7 +471,7 @@ prior to following any of the full build instructions above. #. Ascent - .. code:: bash + .. code-block:: bash git clone --recursive https://github.com/Alpine-DAV/ascent.git pushd ascent @@ -511,7 +511,7 @@ Example run scripts: .. tab:: CPU - .. code:: bash + .. code-block:: bash #!/bin/bash -l @@ -537,7 +537,7 @@ Example run scripts: .. tab:: GPU - .. code:: bash + .. code-block:: bash #!/bin/bash -l diff --git a/docs/source_docs/references/hpc/Perlmutter.rst b/docs/source_docs/references/hpc/Perlmutter.rst index 7c49b7a..69dd363 100644 --- a/docs/source_docs/references/hpc/Perlmutter.rst +++ b/docs/source_docs/references/hpc/Perlmutter.rst @@ -7,7 +7,7 @@ review the general notes below and `Basics`_ section first. * The documentation for this system can be found `here. `_ * Perlmutter can be accessed from a system with ssh client installed. These connections also work from NETL's SciLAN and Joule: - .. code:: bash + .. code-block:: bash ssh @perlmutter-p1.nersc.gov ssh @saul-p1.nersc.gov @@ -23,7 +23,7 @@ review the general notes below and `Basics`_ section first. * For the dependencies, it is assumed that you have set the following environment variables: - .. code:: bash + .. code-block:: bash export HYPRE_INSTALL_DIR=$HOME/ export CSG_INSTALL_DIR=$HOME/ @@ -38,7 +38,7 @@ review the general notes below and `Basics`_ section first. build the PIC-to-DEM restarter app by executing the following command in the `build` directory - .. code:: bash + .. code-block:: bash cmake --build . --target pic2dem @@ -63,7 +63,7 @@ Modules All of the build instructions below have been tested with the following modules and environment helpers -.. code:: bash +.. code-block:: bash module load PrgEnv-gnu/8.5.0 module load cmake/3.22.0 @@ -74,7 +74,7 @@ following modules and environment helpers The GPU-enabled builds additionally require -.. code:: bash +.. code-block:: bash module load cudatoolkit/12.4 @@ -107,7 +107,7 @@ cmake .. tab:: CPU - .. code:: bash + .. code-block:: bash cmake -DMFIX_MPI=yes \ -DMFIX_OMP=no \ @@ -121,7 +121,7 @@ cmake .. tab:: GPU - .. code:: bash + .. code-block:: bash cmake -DMFIX_MPI=yes \ -DMFIX_OMP=no \ @@ -138,7 +138,7 @@ cmake .. tab:: CPU-full - .. code:: bash + .. code-block:: bash export HYPRE_DIR=$HYPRE_INSTALL_DIR export HYPRE_ROOT=$HYPRE_DIR @@ -166,7 +166,7 @@ cmake .. tab:: GPU-full - .. code:: bash + .. code-block:: bash export HYPRE_DIR=$HYPRE_INSTALL_DIR export HYPRE_ROOT=$HYPRE_DIR @@ -203,7 +203,7 @@ gmake .. tab:: CPU - .. code:: bash + .. code-block:: bash make -C exec -j8 \ COMP=gnu \ @@ -218,7 +218,7 @@ gmake .. tab:: GPU - .. code:: bash + .. code-block:: bash make -C exec -j8 COMP=gnu \ @@ -234,7 +234,7 @@ gmake .. tab:: CPU-full - .. code:: bash + .. code-block:: bash export HYPRE_DIR=$HYPRE_INSTALL_DIR export HYPRE_HOME=$HYPRE_DIR @@ -260,7 +260,7 @@ gmake .. tab:: GPU-full - .. code:: bash + .. code-block:: bash export HYPRE_DIR=$HYPRE_INSTALL_DIR export HYPRE_HOME=$HYPRE_DIR @@ -298,7 +298,7 @@ prior to following any of the full build instructions above. .. tab:: CPU - .. code:: bash + .. code-block:: bash git clone https://github.com/hypre-space/hypre.git pushd hypre/src/ @@ -309,7 +309,7 @@ prior to following any of the full build instructions above. .. tab:: GPU - .. code:: bash + .. code-block:: bash git clone https://github.com/hypre-space/hypre.git pushd hypre/src/ @@ -331,7 +331,7 @@ prior to following any of the full build instructions above. #. Catch2 - .. code:: bash + .. code-block:: bash git clone --depth 1 --branch v3.11.0 https://github.com/catchorg/Catch2 pushd Catch2/ @@ -342,7 +342,7 @@ prior to following any of the full build instructions above. #. GMP - .. code:: bash + .. code-block:: bash wget --no-check-certificate https://ftp.gnu.org/gnu/gmp/gmp-6.2.1.tar.xz tar -xf gmp-6.2.1.tar.xz @@ -353,7 +353,7 @@ prior to following any of the full build instructions above. #. MPFR - .. code:: bash + .. code-block:: bash wget --no-check-certificate https://ftp.gnu.org/gnu/mpfr/mpfr-4.1.0.tar.xz tar -xf mpfr-4.1.0.tar.xz @@ -364,7 +364,7 @@ prior to following any of the full build instructions above. #. Boost - .. code:: bash + .. code-block:: bash wget https://boostorg.jfrog.io/artifactory/main/release/1.81.0/source/boost_1_81_0.tar.gz tar -zxvf boost_1_81_0.tar.gz @@ -375,7 +375,7 @@ prior to following any of the full build instructions above. #. CGAL - .. code:: bash + .. code-block:: bash git clone --depth 1 --branch v6.1.1 https://github.com/CGAL/cgal pushd cgal/ @@ -388,7 +388,7 @@ prior to following any of the full build instructions above. #. PEGTL - .. code:: bash + .. code-block:: bash git clone --branch 3.2.8 https://github.com/taocpp/PEGTL pushd PEGTL/ @@ -406,7 +406,7 @@ prior to following any of the full build instructions above. .. tab:: cmake - .. code:: bash + .. code-block:: bash cd subprojects/csg-eb @@ -420,7 +420,7 @@ prior to following any of the full build instructions above. .. tab:: gmake - .. code:: bash + .. code-block:: bash make -C subprojects/csg-eb install DESTDIR=$CSG_LIB_DIR \ PEGTL_HOME=$CSG_INSTALL_DIR \ @@ -430,7 +430,7 @@ prior to following any of the full build instructions above. #. Conduit - .. code:: bash + .. code-block:: bash git clone --recursive https://github.com/LLNL/conduit.git pushd conduit/ @@ -446,7 +446,7 @@ prior to following any of the full build instructions above. #. Vtk-m - .. code:: bash + .. code-block:: bash git clone --branch master https://gitlab.kitware.com/vtk/vtk-m.git pushd vtk-m/ @@ -466,7 +466,7 @@ prior to following any of the full build instructions above. #. Ascent - .. code:: bash + .. code-block:: bash git clone --recursive https://github.com/Alpine-DAV/ascent.git pushd ascent @@ -505,7 +505,7 @@ Example run scripts: .. tab:: CPU - .. code:: bash + .. code-block:: bash #!/bin/bash #SBATCH --job-name run-mfix-exa @@ -526,7 +526,7 @@ Example run scripts: .. tab:: GPU - .. code:: bash + .. code-block:: bash #!/bin/bash #SBATCH --job-name run-mfix-exa diff --git a/docs/source_docs/references/hpc/Polaris.rst b/docs/source_docs/references/hpc/Polaris.rst index fa0a622..f2e8549 100644 --- a/docs/source_docs/references/hpc/Polaris.rst +++ b/docs/source_docs/references/hpc/Polaris.rst @@ -7,7 +7,7 @@ review the general notes below and `Basics`_ section first. * The documentation for this system can be found `here. `_ * Polaris can be accessed from a system with ssh client installed. These connections also work from NETL's SciLAN and Joule: - .. code:: bash + .. code-block:: bash ssh @polaris.alcf.anl.gov @@ -22,7 +22,7 @@ review the general notes below and `Basics`_ section first. * For the dependencies, it is assumed that you have set the following environment variables: - .. code:: bash + .. code-block:: bash export HYPRE_INSTALL_DIR=$HOME/ export CSG_INSTALL_DIR=$HOME/ @@ -37,7 +37,7 @@ review the general notes below and `Basics`_ section first. build the PIC-to-DEM restarter app by executing the following command in the `build` directory - .. code:: bash + .. code-block:: bash cmake --build . --target pic2dem @@ -57,7 +57,7 @@ Modules All of the build instructions below have been tested with the following modules and environment helpers -.. code:: bash +.. code-block:: bash module swap PrgEnv-nvhpc PrgEnv-gnu module load cmake/3.23.2 @@ -65,7 +65,7 @@ following modules and environment helpers The GPU-enabled builds additionally require -.. code:: bash +.. code-block:: bash module load nvhpc-mixed @@ -94,7 +94,7 @@ cmake .. tab:: CPU - .. code:: bash + .. code-block:: bash cmake -DCMAKE_C_COMPILER=gcc \ -DCMAKE_CXX_COMPILER=g++ \ @@ -111,7 +111,7 @@ cmake .. tab:: GPU - .. code:: bash + .. code-block:: bash cmake -DCMAKE_C_COMPILER=gcc \ -DCMAKE_CXX_COMPILER=g++ \ @@ -129,7 +129,7 @@ cmake .. tab:: CPU-full - .. code:: bash + .. code-block:: bash export HYPRE_DIR=$HYPRE_INSTALL_DIR export HYPRE_ROOT=$HYPRE_DIR @@ -160,7 +160,7 @@ cmake .. tab:: GPU-full - .. code:: bash + .. code-block:: bash export HYPRE_DIR=$HYPRE_INSTALL_DIR export HYPRE_ROOT=$HYPRE_DIR @@ -199,7 +199,7 @@ prior to following any of the full build instructions above. #. Set environment helpers - .. code:: bash + .. code-block:: bash export CC=$(which cc) export CXX=$(which CC) @@ -214,7 +214,7 @@ prior to following any of the full build instructions above. .. tab:: CPU - .. code:: bash + .. code-block:: bash git clone https://github.com/hypre-space/hypre.git pushd hypre/src/ @@ -225,7 +225,7 @@ prior to following any of the full build instructions above. .. tab:: GPU - .. code:: bash + .. code-block:: bash git clone https://github.com/hypre-space/hypre.git pushd hypre/src/ @@ -252,7 +252,7 @@ prior to following any of the full build instructions above. #. Catch2 - .. code:: bash + .. code-block:: bash git clone --depth 1 --branch v3.11.0 https://github.com/catchorg/Catch2 pushd Catch2/ @@ -263,7 +263,7 @@ prior to following any of the full build instructions above. #. GMP - .. code:: bash + .. code-block:: bash wget --no-check-certificate https://ftp.gnu.org/gnu/gmp/gmp-6.2.1.tar.xz tar -xf gmp-6.2.1.tar.xz @@ -274,7 +274,7 @@ prior to following any of the full build instructions above. #. MPFR - .. code:: bash + .. code-block:: bash wget --no-check-certificate https://ftp.gnu.org/gnu/mpfr/mpfr-4.1.0.tar.xz tar -xf mpfr-4.1.0.tar.xz @@ -285,7 +285,7 @@ prior to following any of the full build instructions above. #. Boost - .. code:: bash + .. code-block:: bash wget https://boostorg.jfrog.io/artifactory/main/release/1.81.0/source/boost_1_81_0.tar.gz tar -zxvf boost_1_81_0.tar.gz @@ -296,7 +296,7 @@ prior to following any of the full build instructions above. #. CGAL - .. code:: bash + .. code-block:: bash git clone --depth 1 --branch v6.1.1 https://github.com/CGAL/cgal pushd cgal/ @@ -307,7 +307,7 @@ prior to following any of the full build instructions above. #. PEGTL - .. code:: bash + .. code-block:: bash git clone --branch 3.2.8 https://github.com/taocpp/PEGTL pushd PEGTL/ @@ -318,7 +318,7 @@ prior to following any of the full build instructions above. #. Conduit - .. code:: bash + .. code-block:: bash git clone --recursive https://github.com/LLNL/conduit.git pushd conduit/ @@ -334,7 +334,7 @@ prior to following any of the full build instructions above. #. Vtk-m - .. code:: bash + .. code-block:: bash git clone --branch master https://gitlab.kitware.com/vtk/vtk-m.git pushd vtk-m/ @@ -354,7 +354,7 @@ prior to following any of the full build instructions above. #. Ascent - .. code:: bash + .. code-block:: bash git clone --recursive https://github.com/Alpine-DAV/ascent.git pushd ascent @@ -391,7 +391,7 @@ Example run script for GPU is below. For CPU-only, remove ``module load nvhpc-mixed`` and ``export MPICH_GPU_SUPPORT_ENABLED=1``, and the options ``ppn`` and ``--cpu-bind core`` from the run line. -.. code:: bash +.. code-block:: bash #!/bin/bash #PBS -A diff --git a/docs/source_docs/references/hpc/Summit.rst b/docs/source_docs/references/hpc/Summit.rst index c5b0bc8..5be4125 100644 --- a/docs/source_docs/references/hpc/Summit.rst +++ b/docs/source_docs/references/hpc/Summit.rst @@ -17,7 +17,7 @@ review the general notes below and `Basics`_ section first. * For the dependencies, it is assumed that you have set the following environment variables: - .. code:: bash + .. code-block:: bash export HYPRE_INSTALL_DIR=$HOME/ export CSG_INSTALL_DIR=$HOME/ @@ -31,7 +31,7 @@ review the general notes below and `Basics`_ section first. build the PIC-to-DEM restarter app by executing the following command in the ``build`` directory - .. code:: bash + .. code-block:: bash cmake --build . --target pic2dem @@ -52,7 +52,7 @@ Modules All of the build instructions below have been tested with the following modules -.. code:: bash +.. code-block:: bash module load cmake/3.23.2 module load gcc/9.3.0 @@ -61,7 +61,7 @@ Do **NOT** purge your default modules. You do not need to load an MPI module, this is handled by the preloaded ``spectrum-mpi`` module. The GPU-enabled builds additionally require -.. code:: bash +.. code-block:: bash module load cuda/11.5.2 @@ -88,7 +88,7 @@ cmake .. tab:: CPU - .. code:: bash + .. code-block:: bash cmake -DCMAKE_C_COMPILER=gcc \ -DCMAKE_CXX_COMPILER=g++ \ @@ -104,7 +104,7 @@ cmake .. tab:: GPU - .. code:: bash + .. code-block:: bash cmake -DCMAKE_C_COMPILER=gcc \ -DCMAKE_CXX_COMPILER=g++ \ @@ -124,7 +124,7 @@ cmake .. tab:: CPU-full - .. code:: bash + .. code-block:: bash module load mpfr/4.0.2 module load boost/1.77.0 @@ -160,7 +160,7 @@ cmake .. tab:: GPU-full - .. code:: bash + .. code-block:: bash module load mpfr/4.0.2 module load boost/1.77.0 @@ -207,7 +207,7 @@ gmake .. tab:: CPU - .. code:: bash + .. code-block:: bash make -C exec -j8 \ COMP=gnu \ @@ -222,7 +222,7 @@ gmake .. tab:: GPU - .. code:: bash + .. code-block:: bash make -C exec -j8 COMP=gnu \ @@ -238,7 +238,7 @@ gmake .. tab:: CPU-full - .. code:: bash + .. code-block:: bash module load mpfr/4.0.2 module load boost/1.77.0 @@ -267,7 +267,7 @@ gmake .. tab:: GPU-full - .. code:: bash + .. code-block:: bash module load mpfr/4.0.2 module load boost/1.77.0 @@ -304,7 +304,7 @@ prior to following any of the full build instructions above. #. Set environment helpers - .. code:: bash + .. code-block:: bash export CC=$(which gcc) export CXX=$(which g++) @@ -324,7 +324,7 @@ prior to following any of the full build instructions above. .. tab:: CPU - .. code:: bash + .. code-block:: bash git clone https://github.com/hypre-space/hypre.git pushd hypre/src/ @@ -335,7 +335,7 @@ prior to following any of the full build instructions above. .. tab:: GPU - .. code:: bash + .. code-block:: bash git clone https://github.com/hypre-space/hypre.git pushd hypre/src/ @@ -356,7 +356,7 @@ prior to following any of the full build instructions above. #. Catch2 - .. code:: bash + .. code-block:: bash git clone --depth 1 --branch v3.11.0 https://github.com/catchorg/Catch2 pushd Catch2/ @@ -367,7 +367,7 @@ prior to following any of the full build instructions above. #. GMP - .. code:: bash + .. code-block:: bash wget --no-check-certificate https://ftp.gnu.org/gnu/gmp/gmp-6.2.1.tar.xz tar -xf gmp-6.2.1.tar.xz @@ -378,7 +378,7 @@ prior to following any of the full build instructions above. #. CGAL - .. code:: bash + .. code-block:: bash git clone --depth 1 --branch v6.1.1 https://github.com/CGAL/cgal pushd cgal/ @@ -390,7 +390,7 @@ prior to following any of the full build instructions above. #. PEGTL - .. code:: bash + .. code-block:: bash git clone --branch 3.2.8 https://github.com/taocpp/PEGTL pushd PEGTL/ @@ -408,7 +408,7 @@ prior to following any of the full build instructions above. .. tab:: cmake - .. code:: bash + .. code-block:: bash cd subprojects/csg-eb @@ -425,7 +425,7 @@ prior to following any of the full build instructions above. .. tab:: gmake - .. code:: bash + .. code-block:: bash export CSG_DIR=$CSG_INSTALL_DIR @@ -438,7 +438,7 @@ prior to following any of the full build instructions above. #. Conduit - .. code:: bash + .. code-block:: bash git clone --recursive https://github.com/LLNL/conduit.git pushd conduit/ @@ -456,7 +456,7 @@ prior to following any of the full build instructions above. #. Vtk-m - .. code:: bash + .. code-block:: bash git clone --branch master https://gitlab.kitware.com/vtk/vtk-m.git pushd vtk-m/ @@ -476,7 +476,7 @@ prior to following any of the full build instructions above. #. Ascent - .. code:: bash + .. code-block:: bash git clone --recursive https://github.com/Alpine-DAV/ascent.git pushd ascent @@ -509,7 +509,7 @@ Example run scripts for GPU is below. For CPU-only, you remove ``module load cuda``, set ``--gpu_per_rs 0`` and remove ``--bind packed:1`` from the run line. -.. code:: bash +.. code-block:: bash #!/bin/bash #BSUB -P CFD122 diff --git a/docs/source_docs/references/particles/ParticleBasics.rst b/docs/source_docs/references/particles/ParticleBasics.rst index 3725539..eb896c3 100644 --- a/docs/source_docs/references/particles/ParticleBasics.rst +++ b/docs/source_docs/references/particles/ParticleBasics.rst @@ -10,7 +10,7 @@ Particle Basics In MFIX-Exa, particles are managed by the `MFIXParticleContainer `_ class. This class is derived from AMReX's :cpp:`NeighborParticleContainer` -and handles all of the particle data. +and handles all of the particle data. :cpp:`MFIXParticleContainer` provides the functions for solving the particle dynamics (based on particle-particle, particle-fluid, and particle-wall forces) @@ -22,9 +22,9 @@ Particle Dynamics During the DES steps, particle positions are updated using the `MFIXParticleContainer::EvolveParticles `_ -method. It's structure is: +method. Its structure is: -.. code-block:: c++ +.. code-block:: cpp :linenos: :emphasize-lines: 29-39, 42-45 diff --git a/docs/source_docs/test_benchmarks/qualitative_bencharks/mehrdadsbed.rst b/docs/source_docs/test_benchmarks/qualitative_bencharks/mehrdadsbed.rst index 90ad6d8..80528f6 100644 --- a/docs/source_docs/test_benchmarks/qualitative_bencharks/mehrdadsbed.rst +++ b/docs/source_docs/test_benchmarks/qualitative_bencharks/mehrdadsbed.rst @@ -24,7 +24,7 @@ are applied on the vertical domain extents with a mass inflow at the bottom and a pressure outflow at the top of the domain. The mass inflow is defined in `usr1.f90` as: -.. code:: fortran +.. code-block:: fortran real(rt), intent(in ) :: time real(rt) :: usr_pi, usr_umf diff --git a/docs/source_docs/user_guide/inputs/output/reports.rst b/docs/source_docs/user_guide/inputs/output/reports.rst index f13f869..8cf8500 100644 --- a/docs/source_docs/user_guide/inputs/output/reports.rst +++ b/docs/source_docs/user_guide/inputs/output/reports.rst @@ -48,7 +48,7 @@ that is output every 50 time steps. The ``right-side`` report is a PSD consistin .. _inputs_psd_report_ex: -.. code-block:: bash +.. code-block:: text :caption: Snippet of inputs for particle size distribution reports. # Define two regions for collecting report data diff --git a/docs/source_docs/user_guide/quick_start/BuildingMFIX.rst b/docs/source_docs/user_guide/quick_start/BuildingMFIX.rst index c87bda8..2dceb3c 100644 --- a/docs/source_docs/user_guide/quick_start/BuildingMFIX.rst +++ b/docs/source_docs/user_guide/quick_start/BuildingMFIX.rst @@ -14,11 +14,11 @@ Building with gmake If you want to use gmake to build MFIX_Exa, you will need to clone amrex and AMReX-Hydro into a local directories: -.. code:: shell +.. code-block:: console - > git clone https://github.com/AMReX-Codes/amrex.git - > git clone https://github.com/AMReX-Codes/AMReX-Hydro.git - > cd mfix/exec + $ git clone https://github.com/AMReX-Codes/amrex.git + $ git clone https://github.com/AMReX-Codes/AMReX-Hydro.git + $ cd mfix/exec Then, edit the GNUmakefile (or set an environment variable) to define AMREX_HOME and AMREX_HYDRO_HOME @@ -67,7 +67,7 @@ Other options that you can set include Then type -.. code:: shell +.. code-block:: console > make -j @@ -128,13 +128,13 @@ In this mode, MFIX-Exa CMake inherits AMReX CMake targets and configuration opti Assuming no valid AMReX installation is present on the target system, and ``AMReX_ROOT`` is not set (see :ref:`sec:build:standalone`), the following code will build MFIX-Exa in **SUPERBUILD** mode: -.. code:: shell +.. code-block:: console - > cd mfix/ - > mkdir build - > cd build - > cmake [mfix options] [amrex options] -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] .. - > make -j + $ cd mfix/ + $ mkdir build + $ cd build + $ cmake [mfix options] [amrex options] -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] .. + $ make -j ``[amrex options]`` in the snippet above is a list of any of the AMReX configuration options listed in the `AMReX user guide `_, @@ -143,9 +143,9 @@ while ``[mfix options]`` is any of the configuration options listed :ref:`here < For example, to enable AMReX profiling capabilities in MFIX_Exa, configure as follows: -.. code:: shell +.. code-block:: console - > cmake [mfix options] -DAMReX_TINY_PROFILE=yes -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] .. + $ cmake [mfix options] -DAMReX_TINY_PROFILE=yes -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] .. @@ -164,11 +164,11 @@ commands. Either ``cd subprojects/amrex`` to run Git commands in the ``amrex`` directory, or use ``git -C subprojects/amrex`` in the MFIX-Exa repo. For instance, to build with the ``my-amrex-branch`` branch of the AMReX repo: -.. code:: shell +.. code-block:: console - > cd /path/to/mfix - > git -C subprojects/amrex checkout my-amrex-branch - > git status + $ cd /path/to/mfix + $ git -C subprojects/amrex checkout my-amrex-branch + $ git status ... modified: subprojects/amrex (new commits) @@ -177,10 +177,10 @@ The branch ``my-amrex-branch`` will then be used when building MFIX-Exa. To revert to the default version of the AMReX submodule, run ``git submodule update``: -.. code:: shell +.. code-block:: console - > cd /path/to/mfix - > git submodule update + $ cd /path/to/mfix + $ git submodule update You can edit, commit, pull, and push AMReX changes from ``subprojects/amrex``. AMReX development is outside the scope of this document. Run ``git status`` in @@ -189,11 +189,11 @@ modified files, or untracked files. To update the AMReX submodule referenced by MFIX-Exa: -.. code:: shell +.. code-block:: console - > git -C subprojects/amrex checkout UPDATED_AMREX_COMMIT_SHA1 - > git add subprojects/amrex - > git commit -m 'Updating AMReX version' + $ git -C subprojects/amrex checkout UPDATED_AMREX_COMMIT_SHA1 + $ git add subprojects/amrex + $ git commit -m 'Updating AMReX version' This will only update the AMReX SHA-1 referenced by MFIX-Exa. Uncommitted AMReX changes and untracked AMReX files under ``subprojects/amrex`` are not added by @@ -218,19 +218,19 @@ Building AMReX Clone AMReX from the official Git repository. Note that the only branch available is *development*: -.. code:: shell +.. code-block:: console - > git clone https://github.com/AMReX-Codes/amrex.git + $ git clone https://github.com/AMReX-Codes/amrex.git Next, configure, build and install AMReX as follows: -.. code:: shell +.. code-block:: console - > cd amrex - > mkdir build - > cd build - > cmake -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] -DAMReX_PARTICLES=yes -DAMReX_EB=yes -DAMReX_PLOTFILE_TOOLS=yes [other amrex options] -DCMAKE_INSTALL_PREFIX:PATH=/absolute_path_to_amrex_installdir .. - > make install + $ cd amrex + $ mkdir build + $ cd build + $ cmake -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] -DAMReX_PARTICLES=yes -DAMReX_EB=yes -DAMReX_PLOTFILE_TOOLS=yes [other amrex options] -DCMAKE_INSTALL_PREFIX:PATH=/absolute_path_to_amrex_installdir .. + $ make install The options **AMReX\_PARTICLES=yes**, **AMReX\_EB=yes** and **AMReX\_PLOTFILE\_TOOLS=yes** are required by MFIX-Exa. ``[other amrex options]`` in the snippet above refers to any other AMReX configuration option in addition to the required ones. Please refer to the `AMReX user guide `_ for more details on building AMReX with CMake. @@ -240,13 +240,13 @@ Building MFIX-Exa Clone and build MFIX-Exa: -.. code:: shell +.. code-block:: console - > cd mfix/ - > mkdir build - > cd build - > cmake -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] [mfix options] -DAMReX_ROOT=/absolute/path/to/amrex/installdir .. - > make -j + $ cd mfix/ + $ mkdir build + $ cd build + $ cmake -DCMAKE_BUILD_TYPE=[Debug|Release|RelWithDebInfo|MinSizeRel] [mfix options] -DAMReX_ROOT=/absolute/path/to/amrex/installdir .. + $ make -j Passing ``-DAMReX_ROOT=/absolute/path/to/amrex/installdir`` instructs CMake to search @@ -296,16 +296,16 @@ A few more notes on building MFIX-Exa with CMake The system default compilers can be overridden as follows: -.. code:: shell +.. code-block:: console - > cmake -DCMAKE_CXX_COMPILER= [options] .. + $ cmake -DCMAKE_CXX_COMPILER= [options] .. When building on a platform that uses the ``module`` utility, use either the above command (with full path to the compiler) or the following: -.. code:: shell +.. code-block:: console - > cmake -DCMAKE_CXX_COMPILER=$CXX [options] .. + $ cmake -DCMAKE_CXX_COMPILER=$CXX [options] .. MFIX-Exa uses the same compiler flags used to build AMReX, unless ``CMAKE_CXX_FLAGS`` is explicitly provided, or -- GitLab From b6e4093f65e906185d5e2ab9e493475546299992 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 4 May 2026 15:14:36 -0500 Subject: [PATCH 05/19] fix template path, change to furo theme --- docs/picvva/conf.py | 2 +- docs/source_docs/conf.py | 95 +++++++++++++++------------------------- 2 files changed, 37 insertions(+), 60 deletions(-) diff --git a/docs/picvva/conf.py b/docs/picvva/conf.py index ff404dc..42725e6 100644 --- a/docs/picvva/conf.py +++ b/docs/picvva/conf.py @@ -36,7 +36,7 @@ extensions = ['sphinx.ext.mathjax', 'sphinx.ext.viewcode'] # Add any paths that contain templates here, relative to this directory. -templates_path = ['ytemplates'] +templates_path = ['_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: diff --git a/docs/source_docs/conf.py b/docs/source_docs/conf.py index d0173ca..c6b0495 100644 --- a/docs/source_docs/conf.py +++ b/docs/source_docs/conf.py @@ -1,27 +1,6 @@ -# -*- coding: utf-8 -*- +# Configuration for MFIX-Exa docs. +# Updated 2026-04-30, Charles G Waldman # -# amrex documentation build configuration file, created by -# sphinx-quickstart on Thu Oct 19 14:30:08 2017. -# -# This file is execfile()d with the current directory set to its -# containing dir. -# -# Note that not all possible configuration values are present in this -# autogenerated file. -# -# All configuration values have a default; values that are commented out -# serve to show the default. - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -# -# import os -# import sys -# sys.path.insert(0, os.path.abspath('.')) - -import sphinx_rtd_theme - # -- General configuration ------------------------------------------------ # If your documentation needs a minimal Sphinx version, state it here. @@ -39,7 +18,10 @@ extensions = ['sphinx.ext.mathjax', 'sphinxcontrib.bibtex' ] # Add any paths that contain templates here, relative to this directory. -templates_path = ['ytemplates'] +templates_path = ['_templates'] + +# No highligting unless specified + highlight_language = 'none' # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: @@ -52,7 +34,7 @@ master_doc = 'index' # General information about the project. project = u'MFIX-Exa' -copyright = u'2017-2018, MFIX-Exa Team' +copyright = u'2017-2026, MFIX-Exa Team' author = u'MFIX-Exa Team' # The version info for the project you're documenting, acts as replacement for @@ -97,25 +79,9 @@ bibtex_bibfiles = ['refs.bib'] # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # -html_theme = 'sphinx_rtd_theme' - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -# -html_theme_options = { - 'logo_only': False, - 'prev_next_buttons_location': 'bottom', - 'style_external_links': False, - 'vcs_pageview_mode': '', - # Toc options - 'collapse_navigation': True, - 'sticky_navigation': True, - 'navigation_depth': 4, - 'includehidden': True, - 'titles_only': False -} - +#html_theme = 'sphinx_rtd_theme' +html_theme = 'furo' +html_show_sourcelink = False # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, @@ -128,21 +94,15 @@ html_css_files = ['theme_overrides.css'] # # This is required for the alabaster theme # refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars -html_sidebars = { - '**': [ - 'about.html', - 'navigation.html', - 'relations.html', # needs 'show_related': True theme option to display - 'searchbox.html', - 'donate.html', - ] -} - - -# -- Options for HTMLHelp output ------------------------------------------ - -# Output file base name for HTML help builder. -htmlhelp_basename = 'amrexdoc' +# html_sidebars = { +# '**': [ +# 'about.html', +# 'navigation.html', +# 'relations.html', # needs 'show_related': True theme option to display +# 'searchbox.html', +# 'donate.html', +# ] +# } # -- Options for LaTeX output --------------------------------------------- @@ -216,3 +176,20 @@ latex_elements = { } # Use longtable for better page breaks and wrapping latex_table_style = ['longtable', 'colorrows'] + +# Force SVG for mathjax equations, avoids line height issues +# with CHTML + +mathjax_path = 'https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-svg.js' + +# Keep users from selecting CHTML via menu +mathjax3_config = { + 'options': { + 'enableMenu': False, + 'menuOptions': { + 'settings': { + 'renderer': 'svg', + } + } + } +} -- GitLab From 2bdc2e94e13bab67b84a44a02671a3f1418408a6 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 4 May 2026 15:14:49 -0500 Subject: [PATCH 06/19] code-block --- docs/source_docs/references/size_distributions.rst | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/source_docs/references/size_distributions.rst b/docs/source_docs/references/size_distributions.rst index 517a0e1..19c16b7 100644 --- a/docs/source_docs/references/size_distributions.rst +++ b/docs/source_docs/references/size_distributions.rst @@ -310,7 +310,7 @@ are found by setting the derivative of :eq:`eq_normal_dist_FV_to_FN_initial_expr MFIX-Exa samples the normal distribution with mean ``m_mean`` and standard deviation ``m_stddev`` to return an distribution observation. -.. code:: +.. code-block:: amrex::Real observation; @@ -474,7 +474,7 @@ while the parameter :math:`\mu` is computed directly from the other distribution Rather than sample the log-normal distribution, MFIX-Exa samples the normal distribution with mean ``m_mean`` and standard deviation ``m_stddev``. -.. code:: +.. code-block:: amrex::Real observation; @@ -602,7 +602,7 @@ PIC simulations where a volume-weighted distribution is specified compute a unif distributed variable :math:`rand \in \left( 0, 1 \right)`, then scale and translate the result such that :math:`x \in \left[ x_\mathrm{min}, x_\mathrm{max} \right)`. -.. code:: +.. code-block:: amrex::Real rand = amrex::Random(a_engine); @@ -650,7 +650,7 @@ and where :math:`a = x_{\mathrm{min}}` and :math:`b = x_{\mathrm{max}}`. To sample :math:`f_X^V(x)`, a uniformly distributed variable :math:`u \in \mathcal{U}(0,1)` is generated and substituted into the inverse cumulative distribution function. -.. code:: +.. code-block:: amrex::Real rand = amrex::Random(a_engine); @@ -687,7 +687,7 @@ and where :math:`a = x_{\mathrm{min}}` and :math:`b = x_{\mathrm{max}}`. To sample :math:`f_X^V(x)`, a uniformly distributed variable :math:`u \in \mathcal{U}(0,1)` is generated and substituted into the inverse cumulative distribution function. -.. code:: +.. code-block:: amrex::Real rand = amrex::Random(a_engine); -- GitLab From 46aff5236421582a3dac94c7fd50769fe0107f92 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 4 May 2026 15:15:03 -0500 Subject: [PATCH 07/19] code-block --- docs/source_docs/tools/pic2dem.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source_docs/tools/pic2dem.rst b/docs/source_docs/tools/pic2dem.rst index 66e3cf0..aa707f7 100644 --- a/docs/source_docs/tools/pic2dem.rst +++ b/docs/source_docs/tools/pic2dem.rst @@ -5,15 +5,15 @@ PIC to DEM conversion The PIC to DEM tool allows to convert a checkpoint file obtained from a PIC run into a new checkpoint file on a custom-refined mesh with DEM particles. The DEM -particles positions are initialized such that the original PIC parcels +particles positions are initialized such that the original PIC parcel distribution (aka the solids volume fraction) is preserved in each cell up to a negligible error. Building the PIC to DEM tool using CMake (from inside the build directory): -:: +.. code-block:: bash - cmake --build ./ --target pic2dem + cmake --build . --target pic2dem The following inputs must be preceded by "pic2dem.": -- GitLab From e3e9331215eb5b491cfdbccbbcde498bc1b4e0b6 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 4 May 2026 15:15:16 -0500 Subject: [PATCH 08/19] clean up units and equations --- .../user_guide/inputs/boundary_conditions.rst | 21 ++++++++++--------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/boundary_conditions.rst b/docs/source_docs/user_guide/inputs/boundary_conditions.rst index 6359989..68d1c66 100644 --- a/docs/source_docs/user_guide/inputs/boundary_conditions.rst +++ b/docs/source_docs/user_guide/inputs/boundary_conditions.rst @@ -373,7 +373,7 @@ where :math:`h_{int}` is the internal convective heat transfer coefficient. Posi denotes radiative heat loss from the wall. By default, the CHT-1D wall has no thermal storage, so the wall temperature responds instantaneously to changes in the local heat balance. -If a wall heat capacity :math:`C_A` [J/(m\ :sup:`2`\ K)] is specified, the wall is modeled as a lumped thermal +If a wall heat capacity :math:`C_A` [J/(m²·K)] is specified, the wall is modeled as a lumped thermal mass with a single spatially uniform temperature. In that case, the wall temperature evolves according to .. math:: @@ -395,16 +395,16 @@ The model settings are defined using the prefix ``bc.[region_name].eb.temperatur +============================+========================================================================+=============+===========+ | T_env | Environment temperature | Real | None | +----------------------------+------------------------------------------------------------------------+-------------+-----------+ -| h_int | Heat Transfer Coefficient (fluid–wall, internal) | Real | None | +| h_int | Heat Transfer Coefficient (fluid–wall, internal). | Real | None | | | | | | -| | Specifies the convective heat transfer coefficient [W/m²·K] between | | | +| | Specifies the convective heat transfer coefficient [W/(m²·K)] between | | | | | the fluid and adjacent solid walls (EBs) located within the interior | | | | | of the computational domain. | | | | | | | | +----------------------------+------------------------------------------------------------------------+-------------+-----------+ -| h_ext | Heat Transfer Coefficient (wall-environment, external) | Real | None | +| h_ext | Heat Transfer Coefficient (wall-environment, external). | Real | None | | | | | | -| | Specifies the convective heat transfer coefficient [W/m²·K] between | | | +| | Specifies the convective heat transfer coefficient [W/(m²·K)] between | | | | | the wall and the external environment. | | | | | | | | +----------------------------+------------------------------------------------------------------------+-------------+-----------+ @@ -414,16 +414,17 @@ The model settings are defined using the prefix ``bc.[region_name].eb.temperatur +----------------------------+------------------------------------------------------------------------+-------------+-----------+ | wall.heat_capacity | Lumped wall heat capacity per area [J/(m²·K)] | Real | 0. | +----------------------------+------------------------------------------------------------------------+-------------+-----------+ -| phase_averaged_temperature | Use a phase averaged temperature for simulations containing particles. | Bool | false | -| | The phase averaged temperature is computed as the volume fraction | | | -| | weighted sum of the fluid and averaged particle temperatures. | | | +| phase_averaged_temperature | Use a phase-averaged temperature for simulations containing particles. | Bool | false | +| | The phase-averaged temperature is computed per-cell as the | | | +| | volume-fraction-weighted sum of the fluid and averaged particle | | | +| | temperatures: | | | | | | | | | | |avg_T| | | | | | | | | -| | The averaged particle temperature is computed by depositing the | | | -| | volume-averaged particle temperature to the grid. | | | +| | where the averaged particle temperature is computed per-cell as: | | | | | | | | | | |avg_Tp| | | | +| | | | | +----------------------------+------------------------------------------------------------------------+-------------+-----------+ -- GitLab From 307b38d8d75227163bc46a4962d2442666ea7167 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 4 May 2026 15:15:32 -0500 Subject: [PATCH 09/19] clean up units and equations --- docs/source_docs/user_guide/inputs/fluid_model.rst | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/fluid_model.rst b/docs/source_docs/user_guide/inputs/fluid_model.rst index 58ceadc..1a83a6d 100644 --- a/docs/source_docs/user_guide/inputs/fluid_model.rst +++ b/docs/source_docs/user_guide/inputs/fluid_model.rst @@ -32,14 +32,14 @@ Viscosity --------- -.. |Sutherland_Eq| replace:: :math:`\mu(T) = \mu_{ref}\left(\frac{T}{T_{ref}}\right)^{3/2}\times\frac{(T_{ref} + S)}{(T+S)}` +.. |Sutherland_Eq| replace:: :math:`\displaystyle\mu(T) = \mu_{ref}\left(\frac{T}{T_{ref}}\right)^{3/2}\times\frac{(T_{ref}+S)}{(T+S)}` -.. |Reid_4param_Eq| replace:: :math:`\mu(T) = Ae^{\left(\frac{B}{T} + CT + DT^2 \right)}` +.. |Reid_4param_Eq| replace:: :math:`\displaystyle\mu(T) = Ae^{\left(\frac{B}{T} + CT + DT^2 \right)}` -.. |Sato_Eq| replace:: :math:`\mu_{pit} = C d_s \rho \left|\boldsymbol{u} - \boldsymbol{u_s}\right|` +.. |Sato_Eq| replace:: :math:`\displaystyle\mu_{pit} = C d_s \rho \left|\boldsymbol{u} - \boldsymbol{u_s}\right|` -.. |eff_visc| replace:: :math:`\mu_{eff} = \mu_{mol} + \mu_{eddy} + \mu_{susp} + \mu_{pit}` -.. |mix_Eq| replace:: :math:`\mu_{mix} = \sum_{\alpha=1}^{N} \frac{X_{\alpha} \mu_{\alpha}}{\sum_{\beta} X_{\beta} \phi_{\alpha \beta}}` +.. |eff_visc| replace:: :math:`\displaystyle\mu_{eff} = \mu_{mol} + \mu_{eddy} + \mu_{susp} + \mu_{pit}` +.. |mix_Eq| replace:: :math:`\displaystyle\mu_{mix} = \sum_{\alpha=1}^{N} \frac{X_{\alpha} \mu_{\alpha}}{\sum_{\beta} X_{\beta} \phi_{\alpha \beta}}` Molecular viscosity @@ -304,9 +304,9 @@ The following inputs are defined using the prefix ``[fluid_name]``. Thermal conductivity -------------------- -.. |Sutherland_k_Eq| replace:: :math:`\kappa(T) = \kappa_{ref}\left(\frac{T}{T_{ref}}\right)^{3/2}\frac{T_{ref} + S}{T+S}` +.. |Sutherland_k_Eq| replace:: :math:`\displaystyle\kappa(T) = \kappa_{ref}\left(\frac{T}{T_{ref}}\right)^{3/2}\times\frac{(T_{ref}+S)}{(T+S)}` -.. |PowerLaw_k_Eq| replace:: :math:`\kappa(T) = \left( \frac{T}{T_{ref}} \right)^n` +.. |PowerLaw_k_Eq| replace:: :math:`\displaystyle\kappa(T) = \left(\frac{T}{T_{ref}}\right)^n` The following inputs are defined using the prefix ``[fluid_name].thermal_conductivity``. -- GitLab From 0a917982beec95058999c0fc08704ee1dc54c884 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 4 May 2026 15:15:37 -0500 Subject: [PATCH 10/19] code-block --- docs/source_docs/user_guide/inputs/fluid_model.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/fluid_model.rst b/docs/source_docs/user_guide/inputs/fluid_model.rst index 1a83a6d..76294f7 100644 --- a/docs/source_docs/user_guide/inputs/fluid_model.rst +++ b/docs/source_docs/user_guide/inputs/fluid_model.rst @@ -372,7 +372,7 @@ constraint; therefore, the *constant* fluid density is defined by the initial and boundary conditions. The fluid energy and species equations are not solved. -.. code-block:: bash +.. code-block:: text :caption: Snippet of inputs defining a simple incompressible fluid. This is not a complete input file. mfix.constraint = IncompressibleFluid @@ -426,7 +426,7 @@ of state. Lastly, the outflow boundary pressure is taken as the thermodynamic pressure when evaluating the equation of state. -.. code-block:: bash +.. code-block:: text :caption: Snippet of inputs defining a simple ideal gas. This is not a complete input file. mfix.constraint = IdealGasOpenSystem @@ -484,7 +484,7 @@ boundary conditions, and the outflow boundary pressure is taken as the thermodynamic pressure for the system. -.. code-block:: bash +.. code-block:: text :caption: Snippet of inputs defining an idea gas with energy. This is not a complete input file. mfix.constraint = IdealGasOpenSystem -- GitLab From 476162c69c913fdf98349205566358900395b4de Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 4 May 2026 15:15:42 -0500 Subject: [PATCH 11/19] formatting --- docs/source_docs/user_guide/inputs/geometry.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/geometry.rst b/docs/source_docs/user_guide/inputs/geometry.rst index ac70c49..5d6a699 100644 --- a/docs/source_docs/user_guide/inputs/geometry.rst +++ b/docs/source_docs/user_guide/inputs/geometry.rst @@ -8,7 +8,7 @@ The following inputs are defined using the prefix ``mfix``: +------------------------+-------------------------------------------------------------------------------+----------+---------------------+ | | Description | Type | Default | +========================+===============================================================================+==========+=====================+ -| geometry | Simulation geometry type. | String | | +| geometry | Simulation geometry type. | String | | | | Options (case-insensitive): | | | | | | | | | | * ``box`` - predefined :ref:`box geometry` | | | -- GitLab From 9886fa793f3b7d15092f506ff1c8edac7ee39697 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 4 May 2026 15:15:47 -0500 Subject: [PATCH 12/19] clean up equations --- docs/source_docs/user_guide/inputs/model_options.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/model_options.rst b/docs/source_docs/user_guide/inputs/model_options.rst index 4801e51..03210a0 100644 --- a/docs/source_docs/user_guide/inputs/model_options.rst +++ b/docs/source_docs/user_guide/inputs/model_options.rst @@ -189,11 +189,11 @@ Drag coefficient The following input is defined using the prefix ``mfix.drag``: -.. |VirtualMass_Eq| replace:: :math:`\mathbf{F}_p,vm = -C_{p,vm} \rho_f \left( \frac{D\mathbf{u}_f}{Dt} - \frac{d\mathbf{u}_p}{dt}\right)\mathcal{V}_p` +.. |VirtualMass_Eq| replace:: :math:`\mathbf{F}_p,vm = -C_{p,vm} \rho_f \left(\frac{D\mathbf{u}_f}{Dt} - \frac{d\mathbf{u}_p}{dt}\right)\mathcal{V}_p` .. |VM_Zuber_Eq| replace:: :math:`C_{p,vm} = (\frac{1}{2})\frac{(1+2\varepsilon_p)}{(1-\varepsilon_p)}` -.. |VM_Nijssen_Eq| replace:: :math:`C_{p,vm} = C_{0,vm} + \sum_{k=1}^3 \left\{ \left[ a_{k,0} + a_{k,1} \ln \left( \frac{\rho_p}{\rho_f} \right) \right] \varepsilon_p^k \right\}` +.. |VM_Nijssen_Eq| replace:: :math:`C_{p,vm} = C_{0,vm} + \sum_{k=1}^3 \left\{ \left[a_{k,0} + a_{k,1} \ln\left(\frac{\rho_p}{\rho_f}\right)\right] \varepsilon_p^k \right\}` +--------------------------+-------------------------------------------------------------------------------------------+-----------+-----------+ -- GitLab From 55eb4e84145f1c80145e6e6af72e80cb6f5099bf Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 4 May 2026 15:15:56 -0500 Subject: [PATCH 13/19] remove dup --- docs/source_docs/user_guide/inputs/multigrid_solvers.rst | 4 ---- 1 file changed, 4 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/multigrid_solvers.rst b/docs/source_docs/user_guide/inputs/multigrid_solvers.rst index c52c7ab..fbaa953 100644 --- a/docs/source_docs/user_guide/inputs/multigrid_solvers.rst +++ b/docs/source_docs/user_guide/inputs/multigrid_solvers.rst @@ -265,10 +265,6 @@ prefix ``hypre``: +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_num_down_sweeps | See ``HYPRE_BoomerAMGSetCycleNumSweeps``. | Int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_num_down_sweeps | See ``HYPRE_BoomerAMGSetCycleNumSweeps``. | Int | 2 | -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bamg_num_sweeps | See ``HYPRE_BoomerAMGSetNumSweeps``. | Int | 2 | -+-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_num_sweeps | See ``HYPRE_BoomerAMGSetNumSweeps``. | Int | 2 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | bamg_num_up_sweeps | See ``HYPRE_BoomerAMGSetCycleNumSweeps``. | Int | 2 | -- GitLab From 4c40349288eb72e2d0775cc35d4f62ebe42fb7b7 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 4 May 2026 15:16:11 -0500 Subject: [PATCH 14/19] clean up equations and description --- .../user_guide/inputs/output/monitors.rst | 28 ++++++++++--------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/output/monitors.rst b/docs/source_docs/user_guide/inputs/output/monitors.rst index 3ebec56..7545b35 100644 --- a/docs/source_docs/user_guide/inputs/output/monitors.rst +++ b/docs/source_docs/user_guide/inputs/output/monitors.rst @@ -284,7 +284,7 @@ Average Average value of the field quantity in the selected region where :math:`N` is the total number of observations (cells) in the selected region. - .. math:: \phi_0 = \frac{\sum_{ijk} \phi_{ijk}}{N} + .. math:: \bar{\phi} = \frac{\sum_{ijk} \phi_{ijk}}{N} Standard deviation +-------------------------------------------+ @@ -294,9 +294,9 @@ Standard deviation +-------------------------------------------+ Standard deviation of the field quantity in the selected region where - :math:`\phi_0` is the average of the variable in the selected region. + :math:`\bar{\phi}` is the average of the variable in the selected region. - .. math:: \sigma_{\phi} = \sqrt{\frac{ \sum_{ijk} (\phi_{ijk}-\phi_{0})^2 }{N}} + .. math:: \sigma_{\phi} = \sqrt{\frac{ \sum_{ijk} (\phi_{ijk}-\bar{\phi})^{2}}{N}} Surface integrals @@ -319,7 +319,7 @@ Area-weighted average | Eulerian::SurfaceIntegral::AreaWeightedAverage | +------------------------------------------------+ - Area-weighted average is computed by dividing the summation of the + Area-weighted average is computed by dividing the sum of the product of the selected variable and facet area by the total area of the region. @@ -352,9 +352,11 @@ Mass-weighted average | Eulerian::SurfaceIntegral::MassWeightedAverage | +------------------------------------------------+ - Mass flow rate through a surface is computed by summing the product of - the phase volume fraction, density, phase velocity normal to the facet, and - the facet area. + Mass-weighted average through a surface is computed by dividing the sum + of the product of the phase volume fraction, density, phase velocity + normal to the facet :math:`v_n`, the facet area, and the selected field + variable by the sum of the product of phase volume fraction, density, + normal phase velocity, and facet area. .. 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} A_{ijk}}{\sum_{ijk}\varepsilon_{ijk}\rho_{ijk} {v}_{n,ijk} A_{ijk}} @@ -400,7 +402,7 @@ Volume-weighted average | Eulerian::VolumeIntegral::VolumeWeightedAverage | +-------------------------------------------------+ - Volume-weighted average is computed by dividing the summation of the + Volume-weighted average is computed by dividing the sum of the product of the selected field variable and cell volume by the sum of the cell volumes. @@ -423,7 +425,7 @@ Mass-weighted average Mass-weighted average is computed by dividing the sum of the product of phase volume fraction, density, selected field variable, and cell volume by - the summation of the product of the phase volume fraction, density, and cell + the sum of the product of the phase volume fraction, density, and cell volume. .. math:: \frac{\int\phi\rho\varepsilon dV}{\int\rho\varepsilon dV} = \frac{\sum_{ijk}\varepsilon_{ijk}\rho_{ijk}\phi_{ijk} V_{ijk}}{\sum_{ijk}\varepsilon_{ijk}\rho_{ijk} V_{ijk}} @@ -596,11 +598,11 @@ Standard deviation | Lagrangian::AveragedProperty::StandardDeviation | +-------------------------------------------------+ - Standard deviation of particle property :math:`phi_p` in the selected - region is calculated using the following expression. :math:`\bar{\phi}` is - the averaged variable in the selected region. + Standard deviation of particle property :math:`\phi_p` in the selected + region is calculated using the following expression, where :math:`\bar{\phi}` is + the averaged variable in the selected region: - .. math:: \sigma_{\phi} = \sqrt{\frac{ \sum_p w_p (\phi_p-\bar{\phi})^2 }{\sum_p w_p}} + .. math:: \sigma_{\phi} = \sqrt{\frac{ \sum_p w_p (\phi_p-\bar{\phi})^{2}}{\sum_p w_p}} Mass-weighted average +---------------------------------------------------+ -- GitLab From 8dba6b05d2ea7424142f62ec37a00f1fb7c5f102 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 4 May 2026 15:16:24 -0500 Subject: [PATCH 15/19] remove deleted keys --- .../user_guide/inputs/output/plotting.rst | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/output/plotting.rst b/docs/source_docs/user_guide/inputs/output/plotting.rst index 4c9aa3d..a9eb674 100644 --- a/docs/source_docs/user_guide/inputs/output/plotting.rst +++ b/docs/source_docs/user_guide/inputs/output/plotting.rst @@ -95,20 +95,10 @@ contain only solids variables in specific regions at fixed timesteps or approxim +--------------------------------+-----------------------------------------------------------------+-------------+-----------+ | [region_name].plt_regtest | Plot all variables (overrides all other plot flags). | Int | 0 | +--------------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region_name].plt_cp_s | Plot particle specific heat coefficient. | Int | 0 | -+--------------------------------+-----------------------------------------------------------------+-------------+-----------+ | [region_name].plt_drag_p | Plot particle drag force. | Int | 0 | +--------------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region_name].plt_h_s_txfr | Plot particle interphase enthalpy transfer. | Int | 0 | -+--------------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region_name].plt_mass | Plot particle mass. | Int | 0 | -+--------------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region_name].plt_mass_sn_txfr | Plot particle interphase mass transfer. | Int | 0 | -+--------------------------------+-----------------------------------------------------------------+-------------+-----------+ | [region_name].plt_omega_p | Plot particle angular velocity. | Int | 0 | +--------------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region_name].plt_omoi | Plot particle inverse momentum of inertia. | Int | 0 | -+--------------------------------+-----------------------------------------------------------------+-------------+-----------+ | [region_name].plt_phase | Plot particle phase. | Int | 0 | +--------------------------------+-----------------------------------------------------------------+-------------+-----------+ | [region_name].plt_radius | Plot particle radius. | Int | 0 | @@ -121,10 +111,6 @@ contain only solids variables in specific regions at fixed timesteps or approxim +--------------------------------+-----------------------------------------------------------------+-------------+-----------+ | [region_name].plt_vel_p | Plot particle velocity. | Int | 0 | +--------------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region_name].plt_vel_s_txfr | Plot particle interphase velocity transfer. | Int | 0 | -+--------------------------------+-----------------------------------------------------------------+-------------+-----------+ -| [region_name].plt_volume | Plot particle volume. | Int | 0 | -+--------------------------------+-----------------------------------------------------------------+-------------+-----------+ | [region_name].plt_X_s | Plot particle species mass fractions. | Int | 0 | +--------------------------------+-----------------------------------------------------------------+-------------+-----------+ -- GitLab From 61670d6bcc8defaa4c61769e570273c08ab4d5ce Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 4 May 2026 15:16:37 -0500 Subject: [PATCH 16/19] solids -> [solid_name] --- docs/source_docs/user_guide/inputs/solids_model.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/solids_model.rst b/docs/source_docs/user_guide/inputs/solids_model.rst index bfc0c1b..4a4d6f5 100644 --- a/docs/source_docs/user_guide/inputs/solids_model.rst +++ b/docs/source_docs/user_guide/inputs/solids_model.rst @@ -22,7 +22,7 @@ models. The following inputs are defined with the prefix ``solids``: Molecular weight ---------------- -The following inputs are defined with the prefix ``solids``: +The following input are defined with the prefix ``[solid_name]``: +----------------------------+--------------------------------------------------------------+----------+----------+ | | Description | Type | Default | @@ -36,7 +36,7 @@ Specific heat ------------- -The following inputs are defined with the prefix ``solids.specific_heat``: +The following inputs are defined with the prefix ``[solid_name].specific_heat``: +----------------------------+----------------------------------------------------------------+----------+----------+ | | Description | Type | Default | @@ -93,7 +93,7 @@ The following inputs are defined with the prefix ``solids.specific_heat``: | | not provided. | | | +----------------------------+----------------------------------------------------------------+----------+----------+ -The following inputs are defined with the prefix ``solids``: +The following inputs are defined with the prefix ``[solid_name]``: +------------------------+----------------------------------------------------------------+--------+----------+ -- GitLab From 9ee81a8d883d89c6b56af2ac1cfd85b5263c9e27 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 4 May 2026 15:16:44 -0500 Subject: [PATCH 17/19] cleanup equation --- docs/source_docs/user_guide/inputs/solids_model.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/solids_model.rst b/docs/source_docs/user_guide/inputs/solids_model.rst index 4a4d6f5..a0d4a47 100644 --- a/docs/source_docs/user_guide/inputs/solids_model.rst +++ b/docs/source_docs/user_guide/inputs/solids_model.rst @@ -111,9 +111,9 @@ The following inputs are defined with the prefix ``[solid_name]``: Thermal conductivity -------------------- -.. |Sutherland_k_Eq| replace:: :math:`\kappa(T) = \kappa_{ref}\left(\frac{T}{T_{ref}}\right)^{3/2}\frac{T_{ref} + S}{T+S}` +.. |Sutherland_k_Eq| replace:: :math:`\displaystyle\kappa(T) = \kappa_{ref}\left(\frac{T}{T_{ref}}\right)^{3/2}\times\frac{(T_{ref}+S)}{(T+S)}` -.. |PowerLaw_k_Eq| replace:: :math:`\kappa(T) = \left( \frac{T}{T_{ref}} \right)^n` +.. |PowerLaw_k_Eq| replace:: :math:`\displaystyle\kappa(T) = \left(\frac{T}{T_{ref}}\right)^n` The following inputs are defined using the prefix ``[solid_name].thermal_conductivity``. -- GitLab From 57984ab91ad573b7d3aa021d69798071e4632e5f Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 4 May 2026 15:16:57 -0500 Subject: [PATCH 18/19] code-block --- docs/source_docs/user_guide/inputs/species.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/species.rst b/docs/source_docs/user_guide/inputs/species.rst index 0b40d44..0089db0 100644 --- a/docs/source_docs/user_guide/inputs/species.rst +++ b/docs/source_docs/user_guide/inputs/species.rst @@ -227,7 +227,7 @@ The fluid energy equation is not solved, and because we are not updating fluid d local species concentrations do not affect the fluid. -.. code-block:: bash +.. code-block:: text :caption: Snippet of inputs defining species as passive tracers. This is not a complete input file. mfix.constraint = IncompressibleFluid @@ -301,7 +301,7 @@ equation of state is used to compute density from temperature, fluid composition and the thermodynamic pressure. The thermodynamic pressure is taken as the outflow boundary condition pressure which is set here to 1 atmosphere. -.. code-block:: bash +.. code-block:: text :caption: Snippet of inputs defining fluid as a mixture with ``NASA7-poly`` specific heat model. This is not a complete input file. mfix.constraint = IdealGasOpenSystem -- GitLab From 97aecf4b32182052b6ebc4d909e23d309914be93 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 4 May 2026 15:19:51 -0500 Subject: [PATCH 19/19] default no highlight for code-block --- docs/source_docs/conf.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source_docs/conf.py b/docs/source_docs/conf.py index c6b0495..5693c69 100644 --- a/docs/source_docs/conf.py +++ b/docs/source_docs/conf.py @@ -20,8 +20,8 @@ extensions = ['sphinx.ext.mathjax', # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] -# No highligting unless specified - highlight_language = 'none' +# No highlighting unless specified +highlight_language = 'none' # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: -- GitLab