Loading docs/source_docs/references/eb/EBWalls.rst +1 −1 Changes for docs/source_docs/references/eb/EBWalls.rst: 1 added line, 1 removed line. Original line number Diff line number Diff line Loading @@ -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 | +-------------------------------+------------------------------------------------+ Loading docs/source_docs/user_guide/inputs/advanced.rst +10 −2 Changes for docs/source_docs/user_guide/inputs/advanced.rst: 10 added lines, 2 removed lines. Original line number Diff line number Diff line Loading @@ -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 Loading Loading @@ -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 Loading docs/source_docs/user_guide/inputs/domain.rst +3 −3 Changes for docs/source_docs/user_guide/inputs/domain.rst: 3 added lines, 3 removed lines. Original line number Diff line number Diff line Loading @@ -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 Loading docs/source_docs/user_guide/inputs/geometry.rst +20 −0 Changes for docs/source_docs/user_guide/inputs/geometry.rst: 20 added lines, 0 removed lines. Original line number Diff line number Diff line Loading @@ -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. | | | | | | | | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+ docs/source_docs/user_guide/inputs/gridding.rst +62 −11 Changes for docs/source_docs/user_guide/inputs/gridding.rst: 62 added lines, 11 removed lines. Original line number Diff line number Diff line Loading @@ -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. Loading Loading @@ -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. | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ Loading Loading
docs/source_docs/references/eb/EBWalls.rst +1 −1 Changes for docs/source_docs/references/eb/EBWalls.rst: 1 added line, 1 removed line. Original line number Diff line number Diff line Loading @@ -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 | +-------------------------------+------------------------------------------------+ Loading
docs/source_docs/user_guide/inputs/advanced.rst +10 −2 Changes for docs/source_docs/user_guide/inputs/advanced.rst: 10 added lines, 2 removed lines. Original line number Diff line number Diff line Loading @@ -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 Loading Loading @@ -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 Loading
docs/source_docs/user_guide/inputs/domain.rst +3 −3 Changes for docs/source_docs/user_guide/inputs/domain.rst: 3 added lines, 3 removed lines. Original line number Diff line number Diff line Loading @@ -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 Loading
docs/source_docs/user_guide/inputs/geometry.rst +20 −0 Changes for docs/source_docs/user_guide/inputs/geometry.rst: 20 added lines, 0 removed lines. Original line number Diff line number Diff line Loading @@ -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. | | | | | | | | +---------------------------------+-----------------------------------------------------------------------+-------------+--------------+
docs/source_docs/user_guide/inputs/gridding.rst +62 −11 Changes for docs/source_docs/user_guide/inputs/gridding.rst: 62 added lines, 11 removed lines. Original line number Diff line number Diff line Loading @@ -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. Loading Loading @@ -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. | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ Loading
