From 8a8c6e0c8eda3c91e052aa46bd3758eff318756c Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Tue, 10 Mar 2026 11:29:30 -0500 Subject: [PATCH 1/6] correct types --- docs/source_docs/user_guide/inputs/advanced.rst | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/advanced.rst b/docs/source_docs/user_guide/inputs/advanced.rst index 56dc646..cae2ed9 100644 --- a/docs/source_docs/user_guide/inputs/advanced.rst +++ b/docs/source_docs/user_guide/inputs/advanced.rst @@ -32,11 +32,11 @@ The following inputs must be preceded by the prefix ``amrex``: +------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +========================+=======================================================================+=============+==============+ -| fpe_trap_invalid | Abort if an invalid floating point exception is encountered. | Int | 0 | +| fpe_trap_invalid | Abort if an invalid floating point exception is encountered. | Bool | false | +------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| fpe_trap_zero | Abort if a division by zero is computed. | Int | 0 | +| fpe_trap_zero | Abort if a division by zero is computed. | Bool | false | +------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| fpe_trap_overflow | Abort if an overflow is detected. | Int | 0 | +| fpe_trap_overflow | Abort if an overflow is detected. | Bool | false | +------------------------+-----------------------------------------------------------------------+-------------+--------------+ GPU memory @@ -47,12 +47,12 @@ The following inputs must be preceded by the prefix ``amrex``: +----------------------------+-----------------------------------------------------------------------+-------------+---------------+ | | Description | Type | Default | +============================+=======================================================================+=============+===============+ -| the_arena_is_managed | Use managed memory for the main arena. | Int | 0 | +| the_arena_is_managed | Use managed memory for the main arena. | Bool | false | +----------------------------+-----------------------------------------------------------------------+-------------+---------------+ | the_arena_init_size | Initial size of main memory arena (bytes). If not specified, use | Int | Unspecified | | | 3/4 of system device memory. | | | +----------------------------+-----------------------------------------------------------------------+-------------+---------------+ -| abort_on_out_of_gpu_memory | Abort if free device memory is less than the amount an arena is | Int | 0 | +| abort_on_out_of_gpu_memory | Abort if free device memory is less than the amount an arena is | Bool | false | | | asked to allocate. | | | +----------------------------+-----------------------------------------------------------------------+-------------+---------------+ | use_gpu_aware_mpi | For GPU runs,controls the memory type used for AMReX's communication | Bool | false | -- GitLab From ce6516a5e46accb5e6e98b1fbacbc2fd50a9b72b Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Tue, 10 Mar 2026 11:29:37 -0500 Subject: [PATCH 2/6] add .model --- .../user_guide/inputs/chemical_reactions.rst | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/chemical_reactions.rst b/docs/source_docs/user_guide/inputs/chemical_reactions.rst index 86c25a4..f90a95e 100644 --- a/docs/source_docs/user_guide/inputs/chemical_reactions.rst +++ b/docs/source_docs/user_guide/inputs/chemical_reactions.rst @@ -176,10 +176,10 @@ to chemical reactions. #---------------------------------------------------------------------- species.solve = CH4 H2 CO H2O CO2 O2 N2 Fe2O3 FeO inert - species.diffusivity = constant + species.diffusivity.model = constant species.diffusivity.constant = 2.31000e-5 # m^2 / sec - species.specific_heat = NASA7-poly + species.specific_heat.model = NASA7-poly # Methane species.CH4.molecular_weight = 16.04276e-3 @@ -281,12 +281,12 @@ to chemical reactions. fluid.species = CH4 H2 CO H2O CO2 O2 N2 - fluid.viscosity = constant - fluid.viscosity.constant = 4.73e-5 #air @ 1200K + fluid.viscosity.molecular.model = constant + fluid.viscosity.molecular.constant = 4.73e-5 #air @ 1200K fluid.specific_heat = mixture - fluid.thermal_conductivity = constant + fluid.thermal_conductivity.model = constant fluid.thermal_conductivity.constant = 0.024 @@ -297,7 +297,7 @@ to chemical reactions. solids.species = Fe2O3 FeO inert - solids.specific_heat = mixture + solids.specific_heat.model = mixture # Chemistry model settings -- GitLab From a0c4528c85322953050b6159b6a13be757cbe3fe Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Tue, 10 Mar 2026 11:53:46 -0500 Subject: [PATCH 3/6] update Joule build instructions --- docs/source_docs/references/hpc/Joule3.rst | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/docs/source_docs/references/hpc/Joule3.rst b/docs/source_docs/references/hpc/Joule3.rst index 27f9c0f..f7e73fa 100644 --- a/docs/source_docs/references/hpc/Joule3.rst +++ b/docs/source_docs/references/hpc/Joule3.rst @@ -142,9 +142,9 @@ cmake export CSG_DIR=$CSG_INSTALL_DIR export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$CSG_DIR - export Boost_INCLUDE_DIR="-I/nfs/apps/Libraries/Boost/1.83.0/gnu/13.2.0/openmpi/4.1.5/include/" + export BOOST_ROOT="/nfs/apps/Libraries/Boost/1.83.0/gnu/13.2.0/openmpi/4.1.5/" - mkdir build; cd build + mkdir -p build; cd build cmake -DCMAKE_C_COMPILER=gcc \ -DCMAKE_CXX_COMPILER=g++ \ @@ -184,7 +184,6 @@ cmake cmake -DCMAKE_C_COMPILER=gcc \ -DCMAKE_CXX_COMPILER=g++ \ - -DBoost_INCLUDE_DIR="$BOOST_ROOT/include" \ -DMFIX_MPI=yes \ -DMFIX_OMP=no \ -DMFIX_CSG=yes \ @@ -414,7 +413,7 @@ prior to following any of the full build instructions above. module load boost/1.77.0_gnu9.3 - export Boost_INCLUDE_DIR="-I/nfs/apps/Libraries/Boost/1.83.0/gnu/13.2.0/openmpi/4.1.5/include" + export Boost_INCLUDE_DIR="/nfs/apps/Libraries/Boost/1.83.0/gnu/13.2.0/openmpi/4.1.5/include" export CSG_DIR=$CSG_INSTALL_DIR export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$CSG_DIR -- GitLab From fd3815819eaec060f27ac158f0e24e1af3aad613 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Tue, 10 Mar 2026 11:55:40 -0500 Subject: [PATCH 4/6] remove obsolete module load --- docs/source_docs/references/hpc/Joule3.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/source_docs/references/hpc/Joule3.rst b/docs/source_docs/references/hpc/Joule3.rst index f7e73fa..7f9dad2 100644 --- a/docs/source_docs/references/hpc/Joule3.rst +++ b/docs/source_docs/references/hpc/Joule3.rst @@ -179,7 +179,6 @@ cmake export CSG_DIR=$CSG_INSTALL_DIR export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$CSG_DIR - module load boost/1.77.0_gnu9.3 export BOOST_ROOT="/nfs/apps/Libraries/Boost/1.83.0/gnu/13.2.0/openmpi/4.1.5" cmake -DCMAKE_C_COMPILER=gcc \ -- GitLab From 788dc63ee22a6f17dd7d9a332094ea1c03de3f43 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 13 Mar 2026 09:05:07 -0500 Subject: [PATCH 5/6] make delp_dir an option list --- docs/source_docs/user_guide/inputs/boundary_conditions.rst | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/docs/source_docs/user_guide/inputs/boundary_conditions.rst b/docs/source_docs/user_guide/inputs/boundary_conditions.rst index 34890eb..77d5e13 100644 --- a/docs/source_docs/user_guide/inputs/boundary_conditions.rst +++ b/docs/source_docs/user_guide/inputs/boundary_conditions.rst @@ -19,6 +19,11 @@ The following inputs are defined using the prefix ``bc``: +---------------------+--------------------------------------------------------------------------+-------------+-----------+ | delp_dir | Direction for specified pressure drop. Note that this direction | Int | 0 | | | should also be periodic. | | | +| | | | | +| | Options: | | | +| | * ``0``: X | | | +| | * ``1``: Y | | | +| | * ``2``: Z | | | +---------------------+--------------------------------------------------------------------------+-------------+-----------+ | delp | Pressure drop (Pa) | Real | 0 | +---------------------+--------------------------------------------------------------------------+-------------+-----------+ -- GitLab From 267aa9214e2622754fee7b0f7404ca387883dfc9 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Fri, 13 Mar 2026 09:06:12 -0500 Subject: [PATCH 6/6] remove 0 defaults --- .../source_docs/user_guide/inputs/regions.rst | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/regions.rst b/docs/source_docs/user_guide/inputs/regions.rst index 73f981f..4fbb0aa 100644 --- a/docs/source_docs/user_guide/inputs/regions.rst +++ b/docs/source_docs/user_guide/inputs/regions.rst @@ -30,9 +30,9 @@ For each box region, the inputs are defined using the compound prefix ``regions. +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +==========================+=======================================================================+=============+===========+ -| lo | Low corner of physical region (physical, not index space) | Reals<3> | 0 0 0 | +| lo | Low corner of physical region (physical, not index space) | Reals<3> | | +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ -| hi | High corner of physical region (physical, not index space) | Reals<3> | 0 0 0 | +| hi | High corner of physical region (physical, not index space) | Reals<3> | | +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ Below is an example for specifying two regions. @@ -61,9 +61,9 @@ For each region, the inputs are defined using the compound prefix ``regions.[reg +==========================+=======================================================================+=============+===========+ | radius | cylinder radius | Real | None | +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ -| start | Coordinates of the cylinder's bottom cap | Reals<3> | 0 0 0 | +| start | Coordinates of the cylinder's bottom cap | Reals<3> | | +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ -| end | Coordinates of the cylinder's top cap | Reals<3> | 0 0 0 | +| end | Coordinates of the cylinder's top cap | Reals<3> | | +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ @@ -77,7 +77,7 @@ For each region, the inputs are defined using the compound prefix ``regions.[reg +==========================+=======================================================================+=============+===========+ | radius | Cylinder radius | Real | None | +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ -| center | Coordinates of the sphere's center | Reals<3> | 0 0 0 | +| center | Coordinates of the sphere's center | Reals<3> | | +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ @@ -89,9 +89,9 @@ For each region, the inputs are defined using the compound prefix ``regions.[reg +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +==========================+=======================================================================+=============+===========+ -| lo | Low corner of physical region (physical, not index space) | Reals<3> | 0 0 0 | +| lo | Low corner of physical region (physical, not index space) | Reals<3> | | +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ -| hi | High corner of physical region (physical, not index space) | Reals<3> | 0 0 0 | +| hi | High corner of physical region (physical, not index space) | Reals<3> | | +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ @@ -104,11 +104,11 @@ For each region, the inputs are defined using the compound prefix ``regions.[reg +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +==========================+=======================================================================+=============+===========+ -| radius | Disk radius | Real | None | +| radius | Disk radius | Real | | +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ -| center | Coordinates of the disk's center | Reals<3> | 0 0 0 | +| center | Coordinates of the disk's center | Reals<3> | | +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ -| normal | Surface normal | Reals<3> | 0 0 0 | +| normal | Surface normal | Reals<3> | | +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ @@ -120,5 +120,5 @@ For each region, the inputs are defined using the compound prefix ``regions.[reg +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +==========================+=======================================================================+=============+===========+ -| center | Coordinate of point | Reals<3> | 0 0 0 | +| center | Coordinate of point | Reals<3> | | +--------------------------+-----------------------------------------------------------------------+-------------+-----------+ -- GitLab