From f379eadbd270f549dcd60f6e6f26ed1786c28e9a Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 23 Feb 2026 12:34:02 -0600 Subject: [PATCH 01/15] update --- nonexistent-keys.txt | 37 +------------------------------------ 1 file changed, 1 insertion(+), 36 deletions(-) diff --git a/nonexistent-keys.txt b/nonexistent-keys.txt index de176cc..1f3d3bc 100644 --- a/nonexistent-keys.txt +++ b/nonexistent-keys.txt @@ -1,43 +1,8 @@ -bc.[region_name].[solid_name].bins -bc.[region_name].[solid_name].density.custom -bc.[region_name].[solid_name].density.max -bc.[region_name].[solid_name].density.mean -bc.[region_name].[solid_name].density.min -bc.[region_name].[solid_name].density.std -bc.[region_name].[solid_name].diameter -bc.[region_name].[solid_name].diameter.constant -bc.[region_name].[solid_name].diameter.custom -bc.[region_name].[solid_name].diameter.max -bc.[region_name].[solid_name].diameter.mean -bc.[region_name].[solid_name].diameter.min -bc.[region_name].[solid_name].diameter.std bc.[region_name].[solid_name].massflow -bc.[region_name].[solid_name].type -ic.[region_name].[solid_name].bins -ic.[region_name].[solid_name].type - -mac_proj.bottom_maxiter -mac_proj.bottom_verbose -mac_proj.maxiter -mac_proj.verbose -mfix.deposition_diffusion_coeff -mfix.plt_T_p -mfix.plt_drag_p -mfix.plt_omega_p -mfix.plt_phase -mfix.plt_radius -mfix.plt_ro_p -mfix.plt_statwt -mfix.plt_vel_p mfix.solids.[region_name].plt_cp_s mfix.solids.[region_name].plt_h_s_txfr mfix.solids.[region_name].plt_mass mfix.solids.[region_name].plt_mass_sn_txfr mfix.solids.[region_name].plt_omoi mfix.solids.[region_name].plt_vel_s_txfr -mfix.solids.[region_name].plt_volume -mfix.use_drag_coeff_in_proj_gp -nodal_proj.bottom_maxiter -nodal_proj.bottom_verbose -nodal_proj.maxiter -nodal_proj.verbose +mfix.solids.[region_name].plt_volume \ No newline at end of file -- GitLab From e935a828f795b6adc4d13039bd2da3dbc7ca4a55 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 23 Feb 2026 12:34:06 -0600 Subject: [PATCH 02/15] update --- undocumented-keys.txt | 15 +++------------ 1 file changed, 3 insertions(+), 12 deletions(-) diff --git a/undocumented-keys.txt b/undocumented-keys.txt index 0b4dd2c..73a1611 100644 --- a/undocumented-keys.txt +++ b/undocumented-keys.txt @@ -21,14 +21,12 @@ diffusion.verbose_solver eb2.extend_domain_face eb2.small_volfrac fab.format +fluid_name.thermal_conductivity hopper.center hopper.direction hopper.funnel_height hopper.funnel_radius hopper.orifice_radius -ic.[region_name].[solid_name].[property_name].bins -ic.[region_name].[solid_name].[property_name].interpolate -ic.[region_name].[solid_name].[property_name].type ic.[region_name].granular_temperature mfix.advect_momentum mfix.advect_tracer @@ -36,18 +34,11 @@ mfix.agg_grid_size mfix.ascent_on_restart mfix.checkpoint_files_output mfix.constraint.include_depdt -mfix.deposition.filter -mfix.deposition.filter.constant -mfix.deposition.filter.variable -mfix.deposition.filter.variable.min_eps mfix.geom_chk_ccse_regtest +mfix.grid_pruning mfix.monitors.[monitor_name].count mfix.overstep_end_time mfix.particle_sorting_bin -mfix.particles.enthalpy_source -mfix.particles.update_enthalpy -mfix.particles.update_mass -mfix.particles.update_momentum mfix.plt_D_g mfix.plt_MW_g mfix.plt_X_g @@ -72,11 +63,11 @@ mfix.solids.[region_name].plt_pft_neighbor_flags mfix.solids.[region_name].plt_ptype mfix.solids.[region_name].plt_vm_coeff mfix.sort_particle_int -mfix.stop_for_unused_inputs mfix.test_tracer_conservation mfix.use_new_depdt_algo particles.reduceGhostParticles pic2dem.convert +species.thermal_conductivity.model stl.internal_flow tracer tracer.diff_coeff \ No newline at end of file -- GitLab From e8a105997b80af39dc6d06a45fd4925c098917f1 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 23 Feb 2026 12:34:28 -0600 Subject: [PATCH 03/15] bool -> Bool --- docs/source_docs/references/size_distributions.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source_docs/references/size_distributions.rst b/docs/source_docs/references/size_distributions.rst index 514020e..058a049 100644 --- a/docs/source_docs/references/size_distributions.rst +++ b/docs/source_docs/references/size_distributions.rst @@ -707,7 +707,7 @@ A user-defined ``custom`` distribution can be specified by providing discrete pr +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +=====================+=======================================================================+=============+===========+ -| custom | File name of user-defined distribution | string | N/A | +| custom | File name of user-defined distribution | String | N/A | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | min | Minimum particle diameter. Drawn samples below ``min`` are discarded | Real | N/A | | | and a new sample is drawn. | | | @@ -715,7 +715,7 @@ A user-defined ``custom`` distribution can be specified by providing discrete pr | max | Maximum particle diameter. Drawn samples above ``max`` are discarded | Real | N/A | | | and a new sample is drawn. | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -| interpolate | Enable linear interpolation between discrete bins. This option is | bool | false | +| interpolate | Enable linear interpolation between discrete bins. This option is | Bool | false | | | only available when the initial distribution probability is zero. | | | +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -- GitLab From 58e0dd8486fc86ef548d707ee340e8a9a1058a0e Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 23 Feb 2026 12:34:49 -0600 Subject: [PATCH 04/15] downcase --- docs/source_docs/user_guide/inputs/fluid_model.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/fluid_model.rst b/docs/source_docs/user_guide/inputs/fluid_model.rst index 67c85b2..71194ba 100644 --- a/docs/source_docs/user_guide/inputs/fluid_model.rst +++ b/docs/source_docs/user_guide/inputs/fluid_model.rst @@ -223,7 +223,7 @@ The following inputs are defined using the prefix ``[fluid_name]``: -Specific Heat +Specific heat ------------- The following inputs are defined using the prefix ``[fluid_name].specific_heat``: -- GitLab From e9312b26e95bb82e9b649b3e5b6b10fac8996381 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Mon, 23 Feb 2026 12:34:55 -0600 Subject: [PATCH 05/15] add interpolate --- .../user_guide/inputs/boundary_conditions.rst | 12 ++++++++++-- .../user_guide/inputs/initial_conditions.rst | 8 ++++++++ 2 files changed, 18 insertions(+), 2 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/boundary_conditions.rst b/docs/source_docs/user_guide/inputs/boundary_conditions.rst index 6c71775..c4c3a7d 100644 --- a/docs/source_docs/user_guide/inputs/boundary_conditions.rst +++ b/docs/source_docs/user_guide/inputs/boundary_conditions.rst @@ -195,7 +195,6 @@ please refer to :ref:`ReferenceParticleDistributions Date: Wed, 25 Feb 2026 15:42:06 -0600 Subject: [PATCH 06/15] levelset__refinement -> levelset_refinement --- docs/source_docs/references/eb/EBWalls.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/references/eb/EBWalls.rst b/docs/source_docs/references/eb/EBWalls.rst index 9e840c3..99dcee2 100644 --- a/docs/source_docs/references/eb/EBWalls.rst +++ b/docs/source_docs/references/eb/EBWalls.rst @@ -30,7 +30,7 @@ the level-set creation: | | has two levels (one additional level with | | | higher refinement). | +-------------------------------+------------------------------------------------+ -| ``mfix.levelset__refinement`` | If ``amr.max_level > 1`` this parameter is | +| ``mfix.levelset_refinement`` | If ``amr.max_level > 1`` this parameter is | | | ignored. Otherwise it sets the maximum | | | refinement of the level-set | +-------------------------------+------------------------------------------------+ -- GitLab From 22242780fb2618bb41f183c72ace2679c9edd3b2 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Wed, 25 Feb 2026 15:43:09 -0600 Subject: [PATCH 07/15] use_gpu_aware_mpi --- docs/source_docs/user_guide/inputs/advanced.rst | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/advanced.rst b/docs/source_docs/user_guide/inputs/advanced.rst index 39aeedf..b044fe6 100644 --- a/docs/source_docs/user_guide/inputs/advanced.rst +++ b/docs/source_docs/user_guide/inputs/advanced.rst @@ -18,8 +18,8 @@ The following inputs must be preceded by the prefix ``mfix``: | only_print_grid_report | Do not time-march the simulation. Simply generate the grid report | Bool | false | | | and exit. | | | +------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| stop_for_unused_inputs | Do not time-march the simulation if any keyword in the inputs file | Bool | false | -| | has not been used. This is useful in catching input errors. | | | +| stop_for_unused_inputs | Do not start the simulation if any keywords in the inputs file | Bool | false | +| | have not been used. This is useful for catching input errors. | | | +------------------------+-----------------------------------------------------------------------+-------------+--------------+ To assist in verifying the breakdown of fluid grids created before running a full simulation, an input option @@ -55,6 +55,14 @@ The following inputs must be preceded by the prefix ``amrex``: | abort_on_out_of_gpu_memory | Abort if free device memory is less than the amount an arena is | Int | 0 | | | asked to allocate. | | | +----------------------------+-----------------------------------------------------------------------+-------------+---------------+ +| use_gpu_aware_mpi | For GPU runs,controls the memory type used for AMReX's communication | Bool | false | +| | buffers. When ``true``, AMReX uses GPU device memory for communication| | | +| | data in MPI function calls. When ``false`, the data is placed in | | | +| | pinned memory. Note that this flag does not enable GPU-aware MPI by | | | +| | itself. Enabling GPU-aware MPI is system dependent. Users should | | | +| | consult their system's documentation for instructions on setting up | | | +| | the environment and linking to GPU-aware MPI libraries. | | | ++----------------------------+-----------------------------------------------------------------------+-------------+---------------+ Load balancing -- GitLab From 78541498c3f015eea220a80e7efc3effd9618361 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Wed, 25 Feb 2026 15:43:24 -0600 Subject: [PATCH 08/15] run doc_scanner --- undocumented-keys.txt | 4 ---- 1 file changed, 4 deletions(-) diff --git a/undocumented-keys.txt b/undocumented-keys.txt index 73a1611..daaab1c 100644 --- a/undocumented-keys.txt +++ b/undocumented-keys.txt @@ -1,11 +1,9 @@ [fluid_name].trac0 -amrex.use_gpu_aware_mpi catalyst.catalyst_on_restart catalyst.enabled catalyst.implementation catalyst.library_path catalyst.script -chemistry.solids.density dem.PolyNeighSearch dem.PolyNumTypes dem.PolyRefRatios @@ -19,9 +17,7 @@ diffusion.mg_max_fmg_iter diffusion.rtol diffusion.verbose_solver eb2.extend_domain_face -eb2.small_volfrac fab.format -fluid_name.thermal_conductivity hopper.center hopper.direction hopper.funnel_height -- GitLab From f9afcb2dce07c93f751303d0fc06b4a8c6e723d8 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Wed, 25 Feb 2026 15:43:34 -0600 Subject: [PATCH 09/15] CC -> $CXX --- .../user_guide/quick_start/BuildingMFIX.rst | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/source_docs/user_guide/quick_start/BuildingMFIX.rst b/docs/source_docs/user_guide/quick_start/BuildingMFIX.rst index 30e89e6..44d21d3 100644 --- a/docs/source_docs/user_guide/quick_start/BuildingMFIX.rst +++ b/docs/source_docs/user_guide/quick_start/BuildingMFIX.rst @@ -293,21 +293,21 @@ for an available AMReX installation. -Few more notes on building MFIX-Exa with cmake -<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +A few more notes on building MFIX-Exa with CMake +<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -The system defaults compilers can be overwritten as follows: +The system default compilers can be overridden as follows: .. code:: shell > cmake -DCMAKE_CXX_COMPILER= [options] .. When building on a platform that uses the ``module`` utility, use either -the above command (with full path to the compilers) or the following: +the above command (with full path to the compiler) or the following: .. code:: shell - > cmake -DCMAKE_CXX_COMPILER=CC [options] .. + > cmake -DCMAKE_CXX_COMPILER=$CXX [options] .. MFIX-Exa uses the same compiler flags used to build AMReX, unless ``CMAKE_CXX_FLAGS`` is explicitly provided, or -- GitLab From eb163dd1d28612b638f9224136685e1988d9a986 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Wed, 25 Feb 2026 15:43:44 -0600 Subject: [PATCH 10/15] fix LaTeX for PDF --- docs/source_docs/user_guide/inputs/model_options.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/model_options.rst b/docs/source_docs/user_guide/inputs/model_options.rst index b40827a..bfd00b7 100644 --- a/docs/source_docs/user_guide/inputs/model_options.rst +++ b/docs/source_docs/user_guide/inputs/model_options.rst @@ -187,12 +187,12 @@ 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` - +- .. |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:`\begin{split}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\}\end{split}` +--------------------------+-------------------------------------------------------------------------------------------+-----------+-----------+ | | Description | Type | Default | -- GitLab From 0ac3a89db30b78612f1c1aac16ec42767486b915 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Wed, 25 Feb 2026 15:43:54 -0600 Subject: [PATCH 11/15] fix LaTeX for PDF --- docs/source_docs/user_guide/inputs/domain.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/domain.rst b/docs/source_docs/user_guide/inputs/domain.rst index f5fc9af..baf6614 100644 --- a/docs/source_docs/user_guide/inputs/domain.rst +++ b/docs/source_docs/user_guide/inputs/domain.rst @@ -50,9 +50,9 @@ number of cells. The mesh spacing is required to be the same in all directions: .. math:: - \frac{\text{prob_hi[0] - prob_lo[0]}}{\text{n_cell[0]}} - = \frac{\text{prob_hi[1] - prob_lo[1]}}{\text{n_cell[1]}} - = \frac{\text{prob_hi[2] - prob_lo[2]}}{\text{n_cell[2]}} + \frac{\text{prob\_hi[0] - prob\_lo[0]}}{\text{n\_cell[0]}} + = \frac{\text{prob\_hi[1] - prob\_lo[1]}}{\text{n\_cell[1]}} + = \frac{\text{prob\_hi[2] - prob\_lo[2]}}{\text{n\_cell[2]}} The inputs for defining the mesh for a single-level simulation are demonstrated in the -- GitLab From 1ef0077582af38d84c2d45090badf2be53962341 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Wed, 25 Feb 2026 15:44:01 -0600 Subject: [PATCH 12/15] add some eb2 keys --- .../user_guide/inputs/geometry.rst | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/docs/source_docs/user_guide/inputs/geometry.rst b/docs/source_docs/user_guide/inputs/geometry.rst index b1f0242..deb7152 100644 --- a/docs/source_docs/user_guide/inputs/geometry.rst +++ b/docs/source_docs/user_guide/inputs/geometry.rst @@ -369,3 +369,23 @@ The following inputs are defined using the prefix ``mfix``: | | resolution | | | +------------------------+-------------------------------------------------------------------------------+----------+---------------------+ +Embedded boundary +^^^^^^^^^^^^^^^^^ + +The following inputs are defined using the prefix ``eb2``: + ++---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ +| Key | Description | Type | Default | ++=================================+=======================================================================+=============+==============+ +| cover_multiple_cuts | If ``true``, multi-cut cells will be converted to covered cells. | Bool | false | +| | Because AMReX currently does not support multi-cut cells, it | | | +| | would be a runtime error if multi-cut cells are left unfixed. | | | ++---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ +| maxiter | Fixing small and multi-cut cells is an iterative process. This | Int | 32 | +| | parameter specifies the maximum number of iterations for the fix-up | | | +| | process. | | | ++---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ +| small_volfrac | Specifies the threshold for small cells that will be converted to | Real | 1e-14 | +| | covered cells, as a fraction of the total cell volume. | | | +| | | | | ++---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -- GitLab From a88c2a36b5f9414d78b733f2c096619a127b2156 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Wed, 25 Feb 2026 15:44:15 -0600 Subject: [PATCH 13/15] add some amr keys --- .../user_guide/inputs/gridding.rst | 73 ++++++++++++++++--- 1 file changed, 62 insertions(+), 11 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/gridding.rst b/docs/source_docs/user_guide/inputs/gridding.rst index fdf2fe8..be6c52a 100644 --- a/docs/source_docs/user_guide/inputs/gridding.rst +++ b/docs/source_docs/user_guide/inputs/gridding.rst @@ -12,22 +12,38 @@ The following inputs are defined using the prefix ``amr``: +----------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +======================+=======================================================================+=============+===========+ -| max_grid_size_x | Maximum number of cells at level 0 in each grid in *X* | Ints | 32 | +| max_grid_size_x | Maximum number of cells in each grid in *X*. Can be specified | Ints | 32 | +| | per-level. | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| max_grid_size_y | Maximum number of cells at level 0 in each grid in *Y* | Ints | 32 | +| max_grid_size_y | Maximum number of cells in each grid in *Y*. Can be specified | Ints | 32 | +| | per-level. | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| max_grid_size_z | Maximum number of cells at level 0 in each grid in *Z* | Ints | 32 | +| max_grid_size_z | Maximum number of cells in each grid in *Z*. Can be specified | Ints | 32 | +| | per-level. | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| blocking_factor_x | Each grid in *X* must be divisible by ``blocking_factor_x`` | Ints | 8 | +| blocking_factor_x | Each grid in *X* must be divisible by ``blocking_factor_x``. Can be | Ints | 8 | +| | specified per-level. | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| blocking_factor_y | Each grid in *Y* must be divisible by ``blocking_factor_y`` | Ints | 8 | +| blocking_factor_y | Each grid in *Y* must be divisible by ``blocking_factor_y``. Can be | Ints | 8 | +| | specified per-level. | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| blocking_factor_z | Each grid in *Z* must be divisible by ``blocking_factor_z`` | Ints | 8 | +| blocking_factor_z | Each grid in *Z* must be divisible by ``blocking_factor_z``.Can be | Ints | 8 | +| | specified per-level. | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| refine_grid_layout | If true, AMReX will attempt to chop new grids into smaller chunks | Bool | true | -| | ensuring at least one grid per MPI process, provided this does not | | | -| | violate the blocking factor constraint. | | | +| refine_grid_layout_x | If set, AMReX will attempt to chop new grids into smaller chunks along| Bool | true | +| | the x axis, ensuring at least one grid per MPI process, provided this | | | +| | does not violate the blocking factor constraint. | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| refine_grid_layout_y | If set, AMReX will attempt to chop new grids into smaller chunks along| Bool | true | +| | the y axis, ensuring at least one grid per MPI process, provided this | | | +| | does not violate the blocking factor constraint. | | | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| refine_grid_layout_z | If set AMReX will attempt to chop new grids into smaller chunks along | Bool | true | +| | the z axis, ensuring at least one grid per MPI process, provided this | | | +| | does not violate the blocking factor constraint. | | | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ + + Note, the default for ``max_grid_size`` is 64 for GPU runs. @@ -92,8 +108,43 @@ mesh refinement algorithm and are only applicable when ``amr.max_level > 0``. | grid_eff | Threshold value to ensure grids do not contain too large a fraction | Real | 0.7 | | | of untagged cells. | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -| n_error_buf | Controls the number of tagged cells before grids are defined. Used | Ints | 0 | -| | to ensure coarse/fine boundaries are not too close to tagged cells. | | | +| n_error_buf | Controls how many extra cells will be tagged around every tagged cell.| Ints | 1 | +| | For example, if set to ``2`` then tagging cell ``(i,j,k)`` will tag | | | +| | cells from ``(i-2,j-2,k-2(`` to ``(i+2,j+2,k+2)``. | | | +| | Used to ensure coarse-fine boundaries are not too close to tagged | | | +| | cells. Can be specified per-level. | | | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| n_error_buf_x | Controls how many extra cells will be tagged around every tagged cell | Ints | 1 | +| | along the x axis. For example, if set to ``2`` then tagging cell | | | +| | ``(i,j,k)`` will tag cells from ``i-2`` to ``i+2``. Used to ensure | | | +| | coarse-fine boundaries are not too close to tagged cells. Can be | | | +| | specified per-level. | | | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| n_error_buf_y | Controls how many extra cells will be tagged around every tagged cell | Ints | 1 | +| | along the y axis. For example, if set to ``2`` then tagging cell | | | +| | ``(i,j,k)`` will tag cells from ``j-2`` to ``j+2``. Used to ensure | | | +| | coarse-fine boundaries are not too close to tagged cells. Can be | | | +| | specified per-level. | | | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| n_error_buf_z | Controls how many extra cells will be tagged around every tagged cell | Ints | 1 | +| | along the z axis. For example, if set to ``2`` then tagging cell | | | +| | ``(i,j,k)`` will tag cells from ``k-2`` to ``k+2``. Used to ensure | | | +| | coarse-fine boundaries are not too close to tagged cells. Can be | | | +| | specified per-level. | | | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| ref_ratio_vect | If specified, sets thee refinement ratios between AMR levels. It's an | Ints | | +| | error if the size of the integer array, if presetn, is less than | | | +| | ``max_level*3``. The first three numbers specify the refinement ratios| | | +| | in three dimensions between levels 0 and 1, the next three numbers | | | +| | specify the ratios for levels 1 and 2, etc. | | | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| ref_ratio | If ``ref_ratio_vect`` is not specified, this parameter will be used to| Ints | 2 | +| | set the refinement ratios between AMR levels. If there are more AMR | | | +| | levels than the size of the integer parameter array, the last integer | | | +| | will be used as the refinement ratio for the unspecified levels. For | | | +| | example, if ``max_level`` is 4 and the provided ``amr.ref_ratio`` | | | +| | is ``2 4``, the refinement ratios are 2, 4, 4 and 4, for levels 0/1, | | | +| | 1/2, 2/3, and 3/4, respectively. | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -- GitLab From 47a43ca1a91534985602fe6af208bce310f5e52f Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Wed, 25 Feb 2026 15:48:17 -0600 Subject: [PATCH 14/15] fix LaTeX for PDF --- 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 bfd00b7..c821d94 100644 --- a/docs/source_docs/user_guide/inputs/model_options.rst +++ b/docs/source_docs/user_guide/inputs/model_options.rst @@ -188,9 +188,9 @@ 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` -- + .. |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\}` -- GitLab From 6ee4798aa12ed50290d2c2ed4dffd3131d76704a Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Wed, 25 Feb 2026 15:48:25 -0600 Subject: [PATCH 15/15] use_gpu_aware_mpi --- docs/source_docs/user_guide/inputs/advanced.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/advanced.rst b/docs/source_docs/user_guide/inputs/advanced.rst index b044fe6..d243a99 100644 --- a/docs/source_docs/user_guide/inputs/advanced.rst +++ b/docs/source_docs/user_guide/inputs/advanced.rst @@ -57,7 +57,7 @@ The following inputs must be preceded by the prefix ``amrex``: +----------------------------+-----------------------------------------------------------------------+-------------+---------------+ | use_gpu_aware_mpi | For GPU runs,controls the memory type used for AMReX's communication | Bool | false | | | buffers. When ``true``, AMReX uses GPU device memory for communication| | | -| | data in MPI function calls. When ``false`, the data is placed in | | | +| | data in MPI function calls. When ``false``, the data is placed in | | | | | pinned memory. Note that this flag does not enable GPU-aware MPI by | | | | | itself. Enabling GPU-aware MPI is system dependent. Users should | | | | | consult their system's documentation for instructions on setting up | | | -- GitLab