From 6bce34d9963c2169628d884374ee577994f1f7c7 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Thu, 26 Feb 2026 11:52:38 -0600 Subject: [PATCH 1/4] run doc_scanner --- undocumented-keys.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/undocumented-keys.txt b/undocumented-keys.txt index daaab1c..271defb 100644 --- a/undocumented-keys.txt +++ b/undocumented-keys.txt @@ -31,7 +31,6 @@ mfix.ascent_on_restart mfix.checkpoint_files_output mfix.constraint.include_depdt mfix.geom_chk_ccse_regtest -mfix.grid_pruning mfix.monitors.[monitor_name].count mfix.overstep_end_time mfix.particle_sorting_bin -- GitLab From cb4737862d4e981689016a01daefe75f305859f9 Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Thu, 26 Feb 2026 11:53:01 -0600 Subject: [PATCH 2/4] add mfix.grid_pruning --- .../user_guide/inputs/gridding.rst | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/gridding.rst b/docs/source_docs/user_guide/inputs/gridding.rst index c8eff24..3821b74 100644 --- a/docs/source_docs/user_guide/inputs/gridding.rst +++ b/docs/source_docs/user_guide/inputs/gridding.rst @@ -147,7 +147,6 @@ mesh refinement algorithm and are only applicable when ``amr.max_level > 0``. | | 1/2, 2/3, and 3/4, respectively. | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ - .. caution:: **Mesh refinement limitations:** @@ -158,14 +157,26 @@ See the `AMReX documentation 0``. +The following input is defined using the prefix ``mfix``. It only aplies to AMR level 0. + ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| | Description | Type | Default | ++======================+=======================================================================+=============+===========+ +| grid_pruning | Remove fully covered grids from the box array to avoid allocating | Bool | false | +| | memory to them or looping over them. | | | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ + + + +The following input is defined using the prefix ``mfix``. This inputs controls the automatic +mesh refinement algorithm and is only applicable when ``amr.max_level > 0``. +----------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +======================+=======================================================================+=============+===========+ | regrid_int | How often to regrid (in number of steps at level 0). | Int | 0 | -| | If regrid_int <= 0 then no regridding will occur. | | | +| | If regrid_int <= 0 then no regridding will occur. Only applies when | | | +| | ``amr.max_level > 0``. | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -- GitLab From 436d14859c1c025d19bfa1520bcfaaeef2aa200f Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Thu, 26 Feb 2026 12:00:41 -0600 Subject: [PATCH 3/4] add key docs from AMReX-Hydro --- .../user_guide/inputs/multigrid_solvers.rst | 203 ++++++++++-------- 1 file changed, 118 insertions(+), 85 deletions(-) diff --git a/docs/source_docs/user_guide/inputs/multigrid_solvers.rst b/docs/source_docs/user_guide/inputs/multigrid_solvers.rst index 97bb5e5..c52c7ab 100644 --- a/docs/source_docs/user_guide/inputs/multigrid_solvers.rst +++ b/docs/source_docs/user_guide/inputs/multigrid_solvers.rst @@ -3,6 +3,7 @@ Multigrid solvers ================= + Nodal projection ---------------- @@ -11,45 +12,54 @@ The following inputs are defined using the prefix ``nodal_proj``: +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +=========================+=======================================================================+=============+==============+ -| verbose | Verbosity of multigrid solver in nodal projection. | Int | 0 | +| verbose | Verbosity of multigrid solver in nodal projection. | Int | 0 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_verbose | Verbosity of BiCGStab solver in nodal projection. | Int | 0 | +| bottom_verbose | Verbosity of BiCGStab solver in nodal projection. | Int | 0 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_rtol | Relative tolerance in nodal projection. | Real | 1.e-11 | +| mg_rtol | Relative tolerance in nodal projection. | Real | 1.e-11 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_atol | Absolute tolerance in nodal projection. | Real | 1.e-14 | +| bottom_rtol | Relative tolerance of bottom solver. | Real | 1.0e-4 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| maxiter | Maximum number of iterations in the nodal projection. | Int | 100 | +| mg_atol | Absolute tolerance in nodal projection. | Real | 1.e-14 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_maxiter | Maximum number of iterations in the nodal projection | Int | 100 | -| | bottom solver if using ``bicg``, ``cg``, ``bicgcg``, or ``cgbicg``. | | | +| bottom_atol | Absolute tolerance of bottom solver, a negative number means it won't | Real | -1.0 | +| | be used. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_max_coarsening_level | Maximum number of coarser levels to allow in the nodal projection. | Int | 100 | -| | If set to 0, the bottom solver will be called at the current level. | | | +| maxiter | Maximum number of iterations in the nodal projection. | Int | 100 | ++-------------------------+-----------------------------------------------------------------------+-------------+--------------+ +| bottom_maxiter | Maximum number of iterations in the nodal projection | Int | 100 | +| | bottom solver if using ``bicg``, ``cg``, ``bicgcg``, or ``cgbicg``. | | | ++-------------------------+-----------------------------------------------------------------------+-------------+--------------+ +| mg_max_coarsening_level | Maximum number of coarser levels to allow in the nodal projection. | Int | 100 | +| | If set to 0, the bottom solver will be called at the current level. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_solver | Which bottom solver to use in the nodal projection. | String | bicgcg | +| bottom_solver | Which bottom solver to use in the nodal projection. | String | bicgcg | | | | | | -| | Options: | | | +| | Options: | | | | | | | | -| | * ``bicgcg`` | | | -| | * ``bicgstab`` | | | -| | * ``cg`` | | | -| | * ``cgbicg`` | | | -| | * ``hypre`` | | | -| | * ``smoother`` | | | +| | * ``bicgcg`` | | | +| | * ``bicgstab`` | | | +| | * ``cg`` | | | +| | * ``cgbicg`` | | | +| | * ``hypre`` | | | +| | * ``smoother`` | | | | | | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| hypre_namespace | Namespace to use in the nodal projection when using hypre | String | hypre | -| | to control hypre specific settings. It can be any string. | | | +| hypre_namespace | Namespace to use in the nodal projection when using hypre | String | hypre | +| | to control hypre specific settings. It can be any string. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| hypre_interface | Which interface to use in the nodal projection when using ``hypre``. | String | ij | +| hypre_interface | Which interface to use in the nodal projection when using ``hypre``. | String | ij | | | | | | +| | Options: | | | | | | | | -| | Options: | | | +| | * ``ij`` | | | +| | * ``semi-structured`` | | | +| | * ``structured`` | | | | | | | | -| | * ``ij`` | | | -| | * ``semi-structured`` | | | -| | * ``structured`` | | | ++-------------------------+-----------------------------------------------------------------------+-------------+--------------+ +| num_pre_smooth | Number of smoother iterations when going down the V-cycle | Int | 2 | ++-------------------------+-----------------------------------------------------------------------+-------------+--------------+ +| num_post_smooth | Number of smoother iterations when going up the V-cycle | Int | 2 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ @@ -61,45 +71,67 @@ The following inputs are defined using the prefix ``mac_proj``: +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +=========================+=======================================================================+=============+==============+ -| verbose | Verbosity of multigrid solver in MAC projection. | Int | 0 | +| verbose | Verbosity of multigrid solver in MAC projection. | Int | 0 | ++-------------------------+-----------------------------------------------------------------------+-------------+--------------+ +| bottom_verbose | Verbosity of BiCGStab solver in MAC projection. | Int | 0 | ++-------------------------+-----------------------------------------------------------------------+-------------+--------------+ +| mg_rtol | Relative tolerance in MAC projection. | Real | 1.e-11 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_verbose | Verbosity of BiCGStab solver in MAC projection. | Int | 0 | +| bottom_rtol | Relative tolerance of bottom solver. | Real | 1.0e-4 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_rtol | Relative tolerance in MAC projection. | Real | 1.e-11 | +| mg_atol | Absolute tolerance in MAC projection. | Real | 1.e-14 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_atol | Absolute tolerance in MAC projection. | Real | 1.e-14 | +| bottom_atol | Absolute tolerance of bottom solver, a negative number means it won't | Real | -1.0 | +| | be used. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| maxiter | Maximum number of iterations in the MAC projection. | Int | 200 | +| maxiter | Maximum number of iterations in the MAC projection. | Int | 200 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_maxiter | Maximum number of iterations in the MAC projection | Int | 200 | -| | bottom solver if using ``bicg``, ``cg``, ``bicgcg``, or ``cgbicg``. | | | +| maxorder | Sets the order of the cell-centered linear operator stencil at | Int | 3 | +| | physical boundaries with Dirichlet boundary conditions and at | | | +| | coarse-fine boundaries. In both of these cases, the boundary value is| | | +| | not defined at the center of the ghost cell. The order determines the| | | +| | number of interior cells that are used in the extrapolation of the | | | +| | boundary value from the cell face to the center of the ghost cell, | | | +| | where the extrapolated value is then used in the regular stencil. For| | | +| | example, ``maxorder = 2`` uses the boundary value and the first | | | +| | interior value to extrapolate to the ghost cell center and | | | +| | ``maxorder = 3`` uses the boundary value and the first two interior | | | +| | values. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_max_coarsening_level | Maximum number of coarser levels to allow in the MAC projection | Int | 100 | +| bottom_maxiter | Maximum number of iterations in the MAC projection | Int | 200 | +| | bottom solver if using ``bicg``, ``cg``, ``bicgcg``, or ``cgbicg``. | | | ++-------------------------+-----------------------------------------------------------------------+-------------+--------------+ +| mg_max_coarsening_level | aximum number of coarser levels to allow in the MAC projection | Int | 100 | | | If set to 0, the bottom solver will be called at the current level. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_solver | Which bottom solver to use in the MAC projection. | String | bicgcg | +| bottom_solver | Which bottom solver to use in the MAC projection. | String | bicgcg | +| | | | | +| | Options: | | | | | | | | -| | Options: | | | +| | * ``bicgcg`` | | | +| | * ``bicgstab`` | | | +| | * ``cg`` | | | +| | * ``cgbicg`` | | | +| | * ``hypre`` | | | +| | * ``smoother`` | | | | | | | | -| | * ``bicgcg`` | | | -| | * ``bicgstab`` | | | -| | * ``cg`` | | | -| | * ``cgbicg`` | | | -| | * ``hypre`` | | | -| | * ``smoother`` | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| hypre_namespace | Namespace to use in the MAC projection when using ``hypre`` | String | hypre | -| | to control hypre specific settings. It can be any string. | | | +| hypre_namespace | Namespace to use in the MAC projection when using ``hypre`` | String | hypre | +| | to control hypre specific settings. It can be any string. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| hypre_interface | Which interface to use in the MAC projection when using ``hypre``. | String | ij | +| hypre_interface | Which interface to use in the MAC projection when using ``hypre``. | String | ij | | | | | | -| | Options: | | | +| | Options: | | | +| | | | | +| | * ``ij`` | | | +| | * ``semi-structured`` | | | +| | * ``structured`` | | | | | | | | -| | * ``ij`` | | | -| | * ``semi-structured`` | | | -| | * ``structured`` | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ - +| num_pre_smooth | Number of smoother iterations when going down the V-cycle | Int | 2 | ++-------------------------+-----------------------------------------------------------------------+-------------+--------------+ +| num_post_smooth | Number of smoother iterations when going up the V-cycle | Int | 2 | ++-------------------------+-----------------------------------------------------------------------+-------------+--------------+ Diffusion @@ -110,31 +142,32 @@ The following inputs are defined using the prefix ``diffusion``: +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +=========================+=======================================================================+=============+==============+ -| verbose | Verbosity of linear solver for diffusion. | Int | 0 | +| verbose | Verbosity of linear solver for diffusion. | Int | 0 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_verbose | Verbosity of BiCGStab solver in diffusion. | Int | 0 | +| bottom_verbose | Verbosity of BiCGStab solver in diffusion. | Int | 0 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_rtol | Relative tolerance in diffusion solver. | Real | 1.e-11 | +| mg_rtol | Relative tolerance in diffusion solver. | Real | 1.e-11 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_atol | Absolute tolerance in diffusion solver. | Real | 1.e-14 | +| mg_atol | Absolute tolerance in diffusion solver. | Real | 1.e-14 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| maxiter | Maximum number of iterations in diffusion solver. | Int | 100 | +| maxiter | Maximum number of iterations in diffusion solver. | Int | 100 | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_maxiter | Maximum number of iterations in diffusion solver | Int | 100 | -| | bottom solver if using ``bicg``, ``cg``, ``bicgcg``, or ``cgbicg``. | | | +| bottom_maxiter | Maximum number of iterations in diffusion solver | Int | 100 | +| | bottom solver if using ``bicg``, ``cg``, ``bicgcg``, or ``cgbicg``. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| mg_max_coarsening_level | Maximum number of coarser levels to allow in diffusion solver. | Int | 100 | -| | If set to 0, the bottom solver will be called at the current level. | | | +| mg_max_coarsening_level | Maximum number of coarser levels to allow in diffusion solver. | Int | 100 | +| | If set to 0, the bottom solver will be called at the current level. | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| bottom_solver | Which bottom solver to use for diffusion. | String | bicgcg | +| bottom_solver | Which bottom solver to use for diffusion. | String | bicgcg | +| | | | | +| | Options: | | | | | | | | -| | Options: | | | +| | * ``bicgcg`` | | | +| | * ``bicgstab`` | | | +| | * ``cg`` | | | +| | * ``cgbigc`` | | | +| | * ``smoother`` | | | | | | | | -| | * ``bicgcg`` | | | -| | * ``bicgstab`` | | | -| | * ``cg`` | | | -| | * ``cgbigc`` | | | -| | * ``smoother`` | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ @@ -160,38 +193,38 @@ and `GMRES` for the linear solver. +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +===================================+=======================================================================+=============+==============+ -| hypre_preconditioner | Type of preconditioner when using ``hypre``. | String | none | +| hypre_preconditioner | Type of preconditioner when using ``hypre``. | String | none | | | | | | -| | Options: | | | +| | Options: | | | | | | | | -| | * ``none`` - no preconditioner | | | -| | * ``BoomerAMG`` | | | -| | * ``euclid`` | | | +| | * ``none`` - no preconditioner | | | +| | * ``BoomerAMG`` | | | +| | * ``euclid`` | | | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| recompute_preconditioner | Recompute preconditioner during runs. | Bool | true | +| recompute_preconditioner | Recompute preconditioner during runs. | Bool | true | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| hypre_solver | Type of hypre solver. | String | BoomerAMG | +| hypre_solver | Type of hypre solver. | String | BoomerAMG | | | | | | -| | Options: | | | +| | Options: | | | | | | | | -| | * ``BoomerAMG`` | | | -| | * ``GMRES`` | | | -| | * ``COGMRES`` | | | -| | * ``LGMRES`` | | | -| | * ``FlexGMRES`` | | | -| | * ``BiCGSTAB`` | | | -| | * ``PCG`` | | | -| | * ``Hybrid`` | | | +| | * ``BoomerAMG`` | | | +| | * ``GMRES`` | | | +| | * ``COGMRES`` | | | +| | * ``LGMRES`` | | | +| | * ``FlexGMRES`` | | | +| | * ``BiCGSTAB`` | | | +| | * ``PCG`` | | | +| | * ``Hybrid`` | | | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| verbose | Verbosity of hypre. | Int | 0 | +| verbose | Verbosity of hypre. | Int | 0 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| num_krylov | Number of iterations. | Int | 50 | +| num_krylov | Number of iterations. | Int | 50 | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| adjust_singular_matrix | Enable if the problem to be solved has a singular matrix. | Bool | false | +| adjust_singular_matrix | Enable if the problem to be solved has a singular matrix. | Bool | false | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| overwrite_existing_matrix_files | Overwrite existing matrix files. | Bool | false | +| overwrite_existing_matrix_files | Overwrite existing matrix files. | Bool | false | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ -| write_matrix_files | Write matrix into text files. | Bool | false | +| write_matrix_files | Write matrix into text files. | Bool | false | +-----------------------------------+-----------------------------------------------------------------------+-------------+--------------+ The following inputs are valid when using ``BoomerAMG`` as a preconditioner or solver. They must be defined using the -- GitLab From 876548a7f223c5378d73abac24f87bd2eb52b54a Mon Sep 17 00:00:00 2001 From: Charles G Waldman Date: Thu, 26 Feb 2026 12:04:49 -0600 Subject: [PATCH 4/4] typo --- docs/source_docs/user_guide/inputs/gridding.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source_docs/user_guide/inputs/gridding.rst b/docs/source_docs/user_guide/inputs/gridding.rst index 3821b74..4f7d462 100644 --- a/docs/source_docs/user_guide/inputs/gridding.rst +++ b/docs/source_docs/user_guide/inputs/gridding.rst @@ -157,7 +157,7 @@ See the `AMReX documentation