From e571446481f7a7dc3d6aaf56812713ab05fa1c44 Mon Sep 17 00:00:00 2001 From: "robbberto88@gmail.com" Date: Mon, 27 Feb 2023 15:06:38 -0500 Subject: [PATCH 1/3] fix inputs prefixes from amr to mfix --- .../ManagingGridHierarchy_Chapter.rst | 2 +- .../getting_started/FirstSimulation.rst | 2 +- docs/source_docs/getting_started/Paraview.rst | 4 +- docs/source_docs/inputs/InputsCheckpoint.rst | 4 +- .../inputs/InputsInitialization.rst | 4 +- .../inputs/InputsLoadBalancing.rst | 2 +- docs/source_docs/inputs/InputsMonitors.rst | 34 +++--- docs/source_docs/inputs/InputsPICtoDEM.rst | 100 +++++++----------- docs/source_docs/inputs/InputsPlotFiles.rst | 12 +-- 9 files changed, 70 insertions(+), 94 deletions(-) diff --git a/docs/source_docs/ManagingGridHierarchy_Chapter.rst b/docs/source_docs/ManagingGridHierarchy_Chapter.rst index 41602ad..0ded985 100644 --- a/docs/source_docs/ManagingGridHierarchy_Chapter.rst +++ b/docs/source_docs/ManagingGridHierarchy_Chapter.rst @@ -21,7 +21,7 @@ grids to MPI ranks, i.e. defining the :cpp:`DistributionMapping` with which MFIX-Exa also allows for the "dual grid approach", in which mesh and particle data are allocated on different box layouts with different mappings to MPI ranks. This option is enabled -by setting :cpp:`amr.dual_grid = 1` in the inputs file. +by setting :cpp:`mfix.dual_grid = 1` in the inputs file. See :ref:`sec:dual_grid` for more about this approach. When running on multicore machines with OpenMP, we can also control the distribution of diff --git a/docs/source_docs/getting_started/FirstSimulation.rst b/docs/source_docs/getting_started/FirstSimulation.rst index 14ef716..4a4a02e 100644 --- a/docs/source_docs/getting_started/FirstSimulation.rst +++ b/docs/source_docs/getting_started/FirstSimulation.rst @@ -6,7 +6,7 @@ we will run a simple example that contains fluid, particles, and embedded boundaries. This particular example is particles flowing down a cylinder. First, edit ``path/to/mfix/benchmarks/05-cyl-fluidbed/Size0001/inputs`` -so that ``mfix.write_eb_surface = true`` and ``amr.plot_int = 1``. +so that ``mfix.write_eb_surface = true`` and ``mfix.plot_int = 1``. Then, run the example with: .. highlight:: console diff --git a/docs/source_docs/getting_started/Paraview.rst b/docs/source_docs/getting_started/Paraview.rst index 22ec659..7e8fcf6 100644 --- a/docs/source_docs/getting_started/Paraview.rst +++ b/docs/source_docs/getting_started/Paraview.rst @@ -26,9 +26,9 @@ Visualize the particles ----------------------- The solver will write plot files if one of the write frequency options is set -(``amr.plot_int``, ``amr.plot_per_exact``, or ``amr.plot_per_approx``) in +(``mfix.plot_int``, ``mfix.plot_per_exact``, or ``mfix.plot_per_approx``) in directories that are prefixed with the prefix specified in the inputs file -(``amr.plot_file = 'plt'``). To visualize these particles in Paraview, press +(``mfix.plot_file = 'plt'``). To visualize these particles in Paraview, press the open button. In the file dialog, browse to the simulation directory and select the directory group corresponding to the specified prefix. In this example, the director group is displayed as ``plt...``. If only one plot diff --git a/docs/source_docs/inputs/InputsCheckpoint.rst b/docs/source_docs/inputs/InputsCheckpoint.rst index 3cb29fb..a7d4fc3 100644 --- a/docs/source_docs/inputs/InputsCheckpoint.rst +++ b/docs/source_docs/inputs/InputsCheckpoint.rst @@ -3,7 +3,7 @@ Checkpoint/Restart ================== -The following inputs must be preceded by "amr" and control checkpoint/restart. +The following inputs must be preceded by "mfix" and control checkpoint/restart. +-------------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -16,7 +16,7 @@ The following inputs must be preceded by "amr" and control checkpoint/restart. | check_file | Prefix to use for checkpoint output | String | chk | +-------------------------+-----------------------------------------------------------------------+-------------+-----------+ | check_walltime | Write a check point file after the specified walltime (HH:MM:SS) | String | None | -| | has lapsed. For example, if amr.check_waltime = 00:10:00, then a | | | +| | has lapsed. For example, if mfix.check_walltime = 00:10:00, then a | | | | | checkpoint file is after a job has run for ten minutes. | | | +-------------------------+-----------------------------------------------------------------------+-------------+-----------+ | geom_chk_write | When True, writes the EB geometry data into geom_chk_file | bool | False | diff --git a/docs/source_docs/inputs/InputsInitialization.rst b/docs/source_docs/inputs/InputsInitialization.rst index 296b386..e4d8d04 100644 --- a/docs/source_docs/inputs/InputsInitialization.rst +++ b/docs/source_docs/inputs/InputsInitialization.rst @@ -3,13 +3,11 @@ Initialization ============== -The following inputs must be preceded by "amr" and determine how we initialize a calculation: +The following inputs must be preceded by "mfix" and determine how we initialize a calculation: +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | +======================+=======================================================================+=============+==============+ -| input_deck | Read physical data from this file | String | mfix.dat | -+----------------------+-----------------------------------------------------------------------+-------------+--------------+ | restart | If set, then restart from this file rather than from scratch | String | None | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | repl_x | Replicate initial data by this factor in the x-direction | Int | 1 | diff --git a/docs/source_docs/inputs/InputsLoadBalancing.rst b/docs/source_docs/inputs/InputsLoadBalancing.rst index ced491e..2faadf9 100644 --- a/docs/source_docs/inputs/InputsLoadBalancing.rst +++ b/docs/source_docs/inputs/InputsLoadBalancing.rst @@ -6,7 +6,7 @@ Gridding and Load Balancing =========================== -The following inputs must be preceded by "amr" and determine how we create the grids and how often we regrid. +The following inputs must be preceded by "mfix" and determine how we create the grids and how often we regrid. +----------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | diff --git a/docs/source_docs/inputs/InputsMonitors.rst b/docs/source_docs/inputs/InputsMonitors.rst index 8bda3ae..f3eb4f1 100644 --- a/docs/source_docs/inputs/InputsMonitors.rst +++ b/docs/source_docs/inputs/InputsMonitors.rst @@ -3,7 +3,7 @@ Spatial averages ================ -The following inputs must be preceded by "amr" and control whether to compute +The following inputs must be preceded by "mfix" and control whether to compute spatial averages, and how often to output the results. n is the number of spatial averages implicitly defined by the size of avg_region_x_w. @@ -52,7 +52,7 @@ A Monitor is a tool for capturing data from the solver about the model. Data (such as volume fraction, pressure, velocity, etc.) for a given monitor region is written to a CSV file while the solver is running. -To define monitors, the following inputs must be preceded by "amr." prefix. +To define monitors, the following inputs must be preceded by "mfix" prefix. +--------------------+------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -64,10 +64,10 @@ To define monitors, the following inputs must be preceded by "amr." prefix. .. code-block:: none - amr.monitors = my_monitor0 my_monitor1 + mfix.monitors = my_monitor0 my_monitor1 - amr.monitors.my_monitor0 = Eulerian::VolumeIntegral::MassWeightedIntegral - amr.monitors.my_monitor1 = Lagrangian::Average::VolumeWeightedAverage + mfix.monitors.my_monitor0 = Eulerian::VolumeIntegral::MassWeightedIntegral + mfix.monitors.my_monitor1 = Lagrangian::Average::VolumeWeightedAverage Region Selection @@ -76,7 +76,7 @@ Region Selection To define a monitor, there must be a region already defined in the regions inputs. A Monitor region is a single point, plane, or volume. Multiple regions cannot be combined for a monitor. The following inputs must be preceded by the -"amr.monitors." prefix. +"mfix.monitors" prefix. +------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -87,8 +87,8 @@ cannot be combined for a monitor. The following inputs must be preceded by the .. code-block:: none # regionA and regionB to be defined in the "regions" inputs section - amr.monitors.my_monitor0.region = regionA - amr.monitors.my_monitor1.region = regionB + mfix.monitors.my_monitor0.region = regionA + mfix.monitors.my_monitor1.region = regionB Monitor Output @@ -98,7 +98,7 @@ The monitor data will be output to a file with name given by the input "plot_file", and the extension ``.csv`` is automatically added. The monitor output file is in Comma Separated Value (CSV) format. The first line of the file provides header information. The following inputs must be preceded by the -"amr.monitors." prefix. +"mfix.monitors" prefix. +-------------------------------+----------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -128,18 +128,18 @@ provides header information. The following inputs must be preceded by the .. code-block:: none - amr.monitors.my_monitor0.plot_file = monitor0_output - amr.monitors.my_monitor0.plot_int = 10 + mfix.monitors.my_monitor0.plot_file = monitor0_output + mfix.monitors.my_monitor0.plot_int = 10 - amr.monitors.my_monitor1.plot_file = monitor1_output - amr.monitors.my_monitor1.plot_per_approx = 0.01 + mfix.monitors.my_monitor1.plot_file = monitor1_output + mfix.monitors.my_monitor1.plot_per_approx = 0.01 Monitor Variables ----------------- The variables to be monitored can be specified in the inputs by including the -following input preceded by the "amr.monitors." prefix. +following input preceded by the "mfix.monitors" prefix. +---------------------+--------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -149,9 +149,9 @@ following input preceded by the "amr.monitors." prefix. .. code-block:: none - amr.monitors.my_monitor0.variables = T_g vel_g p_g gp_y X_gk + mfix.monitors.my_monitor0.variables = T_g vel_g p_g gp_y X_gk - amr.monitors.my_monitor1.variables = density drag_y T_s txfr_vel_x + mfix.monitors.my_monitor1.variables = density drag_y T_s txfr_vel_x Eulerian Monitors @@ -642,7 +642,7 @@ Flow rates For Lagrangian monitors of type FlowRate, the flow plane must be specified in the inputs and it must be defined by one of the regions defined in the regions inputs. The following input for a monitor [monitor] of type FlowRate can be -used, preceeded by the "amr.monitors." prefix. +used, preceeded by the "mfix.monitors" prefix. +------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | diff --git a/docs/source_docs/inputs/InputsPICtoDEM.rst b/docs/source_docs/inputs/InputsPICtoDEM.rst index e2e5be5..ff2d5cd 100644 --- a/docs/source_docs/inputs/InputsPICtoDEM.rst +++ b/docs/source_docs/inputs/InputsPICtoDEM.rst @@ -17,64 +17,42 @@ Building the PIC to DEM tool using CMake (from inside the build directory): The following inputs must be preceded by "pic2dem". -+------------------+---------------------------------------------------+--------+---------+ -| | Description | Type | Default | -+==================+===================================================+========+=========+ -| refinement_ratio | The mesh refinement ratio that will be applied | int | 1 | -| | on each direction to obtain a refined mesh out of | | | -| | the one read form the PIC checkpoint file | | | -+------------------+---------------------------------------------------+--------+---------+ -| eps_tolerance | The threshold used for DEM particles generation | Real | 1.e-15 | -| | from the PIC solids volfrac distribution. If ep_s | | | -| | in a cell is below the threshold, no DEM solids | | | -| | will be generated in that cell | | | -+------------------+---------------------------------------------------+--------+---------+ -| eps_overflow | An artifact, like a knob, for the user to force | Real | 1.0 | -| | over-production (if value > 1), or | | | -| | under-production (if value < 1) of DEM particles | | | -+------------------+---------------------------------------------------+--------+---------+ - -The following inputs must be preceded by "eb2". - -+-----------------------+----------------------------------------------+--------+---------+ -| | Description | Type | Default | -+=======================+==============================================+========+=========+ -| refined_small_volfrac | This input gives the possibility to set a | Real | 0. | -| | small volfrac value just for the DEM refined | | | -| | case, while the standard small volfrac value | | | -| | will still be used for the PIC case read | | | -| | from the checkpoint file | | | -+-----------------------+----------------------------------------------+--------+---------+ - -The following inputs must be preceded by "amr". - -+-------------------------------+--------------------------------------+--------+---------+ -| | Description | Type | Default | -+===============================+======================================+========+=========+ -| refined_geom_chk_file | Name of the EB checkpoint file where | string | "" | -| | the DEM refined case geometry will | | | -| | be read or written | | | -+-------------------------------+--------------------------------------+--------+---------+ -| refined_geom_chk_refined_file | Name of the EB checkpoint file where | string | "" | -| | the finer levels of the geometry for | | | -| | the DEM refined case will be read or | | | -| | written | | | -+-------------------------------+--------------------------------------+--------+---------+ -| refined_geom_chk_write | Flag to turn on/off writing the EB | bool | false | -| | geometry checkpoint file for the DEM | | | -| | refined case | | | -+-------------------------------+--------------------------------------+--------+---------+ -| refined_geom_chk_read | Flag to turn on/off reading the EB | bool | false | -| | geometry checkpoint file for the DEM | | | -| | refined case | | | -+-------------------------------+--------------------------------------+--------+---------+ - -The following inputs must be preceded by "pic2dem". - -+-------------------+--------------------------------------------------+--------+---------+ -| | Description | Type | Default | -+===================+==================================================+========+=========+ -| geometry_filename | CSG filename that will be used for generating | string | "" | -| | the DEM refined geometry in case the PIC coarse | | | -| | geometry is read from a checkpoint file | | | -+-------------------+--------------------------------------------------+--------+---------+ ++------------------------+---------------------------------------------------+--------+---------+ +| | Description | Type | Default | ++========================+===================================================+========+=========+ +| refinement_ratio | The mesh refinement ratio that will be applied on | int | 1 | +| | each direction to obtain a refined mesh out of | | | +| | the one read form the PIC checkpoint file | | | ++------------------------+---------------------------------------------------+--------+---------+ +| eps_tolerance | The threshold used for DEM particles generation | Real | 1.e-15 | +| | from the PIC solids volfrac distribution. If ep_s | | | +| | in a cell is below the threshold, no DEM solids | | | +| | will be generated in that cell | | | ++------------------------+---------------------------------------------------+--------+---------+ +| eps_overflow | An artifact, like a knob, for the user to force | Real | 1.0 | +| | over-production (if value > 1), or | | | +| | under-production (if value < 1) of DEM particles | | | ++------------------------+---------------------------------------------------+--------+---------+ +| small_volfrac | This input gives the possibility to set a small | Real | 0. | +| | volfrac value just for the DEM refined case, | | | +| | while the standard small volfrac value will still | | | +| | be used for the PIC case read from the checkpoint | | | +| | file | | | ++------------------------+---------------------------------------------------+--------+---------+ +| geom_chk_file | Name of the EB checkpoint file where the DEM | string | "" | +| | refined case geometry will be read or written | | | ++------------------------+---------------------------------------------------+--------+---------+ +| geom_levelset_chk_file | Name of the EB checkpoint file where the levelset | string | "" | +| | geometry for the DEM refined case will be read or | | | +| | written | | | ++------------------------+---------------------------------------------------+--------+---------+ +| geom_chk_write | Flag to turn on/off writing the EB geometry | bool | false | +| | checkpoint file for the DEM refined case | | | ++------------------------+---------------------------------------------------+--------+---------+ +| geom_chk_read | Flag to turn on/off reading the EB geometry | bool | false | +| | checkpoint file for the DEM refined case | | | ++------------------------+---------------------------------------------------+--------+---------+ +| geometry_filename | CSG filename that will be used for generating the | string | "" | +| | DEM refined geometry in case the PIC coarse | | | +| | geometry is read from a checkpoint file | | | ++------------------------+---------------------------------------------------+--------+---------+ diff --git a/docs/source_docs/inputs/InputsPlotFiles.rst b/docs/source_docs/inputs/InputsPlotFiles.rst index 6aee3fe..ed00e0b 100644 --- a/docs/source_docs/inputs/InputsPlotFiles.rst +++ b/docs/source_docs/inputs/InputsPlotFiles.rst @@ -3,7 +3,7 @@ Plotfiles and Other Output ========================== -The following inputs must be preceded by "amr" and control frequency and naming of plotfile generation as well +The following inputs must be preceded by "mfix" and control frequency and naming of plotfile generation as well as whether the EB geometry or level set should be written out, and if the particles should be written out in Ascii format (for debugging). @@ -36,7 +36,7 @@ format (for debugging). +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -The following inputs must be preceded by "amr" and control what variables will be written in plotfiles. +The following inputs must be preceded by "mfix" and control what variables will be written in plotfiles. +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -117,7 +117,7 @@ i.e., set `amrex.the_arena_is_managed = true`. +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -The following inputs must be preceded by "amr.solids" and allow to write additional plotfiles which contain only solids variables in specific regions at fixed timesteps or approximated simulation times. All these parameters are user-defined. +The following inputs must be preceded by "mfix.solids" and allow to write additional plotfiles which contain only solids variables in specific regions at fixed timesteps or approximated simulation times. All these parameters are user-defined. +---------------------------+-----------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -177,7 +177,7 @@ region. .. code-block:: none - amr.solids.regions = my_region + mfix.solids.regions = my_region - amr.solids.my_region.plot_int = 10 - amr.solids.my_region.plt_vel_p = 1 + mfix.solids.my_region.plot_int = 10 + mfix.solids.my_region.plt_vel_p = 1 -- GitLab From a1346e5e65441a1686f5d3b02ad0319686d8e014 Mon Sep 17 00:00:00 2001 From: "robbberto88@gmail.com" Date: Mon, 27 Feb 2023 15:35:30 -0500 Subject: [PATCH 2/3] fix a mistake: max_grid_size and blocking_factor need amr prefix --- docs/source_docs/inputs/InputsLoadBalancing.rst | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/docs/source_docs/inputs/InputsLoadBalancing.rst b/docs/source_docs/inputs/InputsLoadBalancing.rst index 2faadf9..163a13c 100644 --- a/docs/source_docs/inputs/InputsLoadBalancing.rst +++ b/docs/source_docs/inputs/InputsLoadBalancing.rst @@ -6,14 +6,11 @@ Gridding and Load Balancing =========================== -The following inputs must be preceded by "mfix" and determine how we create the grids and how often we regrid. +The following inputs must be preceded by "amr" and determine how we create the grids. +----------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | +======================+=======================================================================+=============+===========+ -| regrid_int | How often to regrid (in number of steps at level 0) | Int | -1 | -| | if regrid_int = -1 then no regridding will occur | | | -+----------------------+-----------------------------------------------------------------------+-------------+-----------+ | max_grid_size_x | Maximum number of cells at level 0 in each grid in x-direction | Int | 32 | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ | max_grid_size_y | Maximum number of cells at level 0 in each grid in y-direction | Int | 32 | @@ -27,6 +24,15 @@ The following inputs must be preceded by "mfix" and determine how we create the | blocking_factor_z | Each grid must be divisible by blocking_factor_z in z-direction | Int | 8 | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ +The following inputs must be preceded by "mfix" and determine how often we regrid. + ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ +| | Description | Type | Default | ++======================+=======================================================================+=============+===========+ +| regrid_int | How often to regrid (in number of steps at level 0) | Int | -1 | +| | if regrid_int = -1 then no regridding will occur | | | ++----------------------+-----------------------------------------------------------------------+-------------+-----------+ + The following inputs must be preceded by "fabarray_mfiter" and determine how we create the logical tiles: +----------------------+-----------------------------------------------------------------------+----------+-------------+ -- GitLab From 9863f37972b70a0e53319bb09507d265200e051b Mon Sep 17 00:00:00 2001 From: "robbberto88@gmail.com" Date: Tue, 28 Feb 2023 18:18:19 -0500 Subject: [PATCH 3/3] minor fixes to inputs prefixes --- docs/source_docs/inputs/InputsCheckpoint.rst | 2 +- docs/source_docs/inputs/InputsInitialization.rst | 6 +++--- docs/source_docs/inputs/InputsLoadBalancing.rst | 10 +++++----- docs/source_docs/inputs/InputsMonitors.rst | 14 +++++++------- docs/source_docs/inputs/InputsMultigrid.rst | 6 +++--- docs/source_docs/inputs/InputsPICtoDEM.rst | 2 +- docs/source_docs/inputs/InputsPlotFiles.rst | 12 +++++++----- docs/source_docs/inputs/InputsTimeStepping.rst | 4 ++-- 8 files changed, 29 insertions(+), 27 deletions(-) diff --git a/docs/source_docs/inputs/InputsCheckpoint.rst b/docs/source_docs/inputs/InputsCheckpoint.rst index a7d4fc3..777b61a 100644 --- a/docs/source_docs/inputs/InputsCheckpoint.rst +++ b/docs/source_docs/inputs/InputsCheckpoint.rst @@ -3,7 +3,7 @@ Checkpoint/Restart ================== -The following inputs must be preceded by "mfix" and control checkpoint/restart. +The following inputs must be preceded by "mfix." and control checkpoint/restart. +-------------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | diff --git a/docs/source_docs/inputs/InputsInitialization.rst b/docs/source_docs/inputs/InputsInitialization.rst index e4d8d04..e2c4184 100644 --- a/docs/source_docs/inputs/InputsInitialization.rst +++ b/docs/source_docs/inputs/InputsInitialization.rst @@ -3,7 +3,7 @@ Initialization ============== -The following inputs must be preceded by "mfix" and determine how we initialize a calculation: +The following inputs must be preceded by "mfix." and determine how we initialize a calculation: +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | @@ -18,7 +18,7 @@ The following inputs must be preceded by "mfix" and determine how we initialize +----------------------+-----------------------------------------------------------------------+-------------+--------------+ -The following inputs must be preceded by "mfix" and determine how we initialize a calculation: +The following inputs must be preceded by "mfix." and determine how we initialize a calculation: +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | @@ -31,7 +31,7 @@ The following inputs must be preceded by "mfix" and determine how we initialize | initial_iterations | How many pressure iterations before starting the first timestep | Int | 3 | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ -The following inputs must be preceded by "particles." +The following inputs must be preceded by "particles.": +--------------------+---------------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | diff --git a/docs/source_docs/inputs/InputsLoadBalancing.rst b/docs/source_docs/inputs/InputsLoadBalancing.rst index 163a13c..ff41595 100644 --- a/docs/source_docs/inputs/InputsLoadBalancing.rst +++ b/docs/source_docs/inputs/InputsLoadBalancing.rst @@ -6,7 +6,7 @@ Gridding and Load Balancing =========================== -The following inputs must be preceded by "amr" and determine how we create the grids. +The following inputs must be preceded by "amr." and determine how we create the grids. +----------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -24,7 +24,7 @@ The following inputs must be preceded by "amr" and determine how we create the g | blocking_factor_z | Each grid must be divisible by blocking_factor_z in z-direction | Int | 8 | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -The following inputs must be preceded by "mfix" and determine how often we regrid. +The following inputs must be preceded by "mfix." and determine how often we regrid. +----------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -33,7 +33,7 @@ The following inputs must be preceded by "mfix" and determine how often we regri | | if regrid_int = -1 then no regridding will occur | | | +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -The following inputs must be preceded by "fabarray_mfiter" and determine how we create the logical tiles: +The following inputs must be preceded by "fabarray_mfiter." and determine how we create the logical tiles: +----------------------+-----------------------------------------------------------------------+----------+-------------+ | | Description | Type | Default | @@ -42,7 +42,7 @@ The following inputs must be preceded by "fabarray_mfiter" and determine how we | | (3D CPU-only) | | 1024000,8,8 | +----------------------+-----------------------------------------------------------------------+----------+-------------+ -The following inputs must be preceded by "particles" +The following inputs must be preceded by "particles." +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | @@ -68,7 +68,7 @@ the :cpp:`particles.max_grid_size` (in each direction) have no meaning. Therefor sizes should be set for particle load balancing. It may also be necessary to set the blocking factors to 1. -The following inputs must be preceded by "mfix" and determine how we load balance: +The following inputs must be preceded by "mfix." and determine how we load balance: +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | diff --git a/docs/source_docs/inputs/InputsMonitors.rst b/docs/source_docs/inputs/InputsMonitors.rst index f3eb4f1..b065762 100644 --- a/docs/source_docs/inputs/InputsMonitors.rst +++ b/docs/source_docs/inputs/InputsMonitors.rst @@ -3,7 +3,7 @@ Spatial averages ================ -The following inputs must be preceded by "mfix" and control whether to compute +The following inputs must be preceded by "mfix." and control whether to compute spatial averages, and how often to output the results. n is the number of spatial averages implicitly defined by the size of avg_region_x_w. @@ -52,7 +52,7 @@ A Monitor is a tool for capturing data from the solver about the model. Data (such as volume fraction, pressure, velocity, etc.) for a given monitor region is written to a CSV file while the solver is running. -To define monitors, the following inputs must be preceded by "mfix" prefix. +To define monitors, the following inputs must be preceded by "mfix.": +--------------------+------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -75,8 +75,8 @@ Region Selection To define a monitor, there must be a region already defined in the regions inputs. A Monitor region is a single point, plane, or volume. Multiple regions -cannot be combined for a monitor. The following inputs must be preceded by the -"mfix.monitors" prefix. +cannot be combined for a monitor. The following inputs must be preceded by +"mfix.monitors.": +------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -97,8 +97,8 @@ Monitor Output The monitor data will be output to a file with name given by the input "plot_file", and the extension ``.csv`` is automatically added. The monitor output file is in Comma Separated Value (CSV) format. The first line of the file -provides header information. The following inputs must be preceded by the -"mfix.monitors" prefix. +provides header information. The following inputs must be preceded by +"mfix.monitors.": +-------------------------------+----------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -139,7 +139,7 @@ Monitor Variables ----------------- The variables to be monitored can be specified in the inputs by including the -following input preceded by the "mfix.monitors" prefix. +following input preceded by the "mfix.monitors.": +---------------------+--------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | diff --git a/docs/source_docs/inputs/InputsMultigrid.rst b/docs/source_docs/inputs/InputsMultigrid.rst index c9f1d25..6caaad5 100644 --- a/docs/source_docs/inputs/InputsMultigrid.rst +++ b/docs/source_docs/inputs/InputsMultigrid.rst @@ -9,7 +9,7 @@ different solvers called by MFIX-Exa. NOTE: the nodal solver settings are read in directly by AMReX, the MAC and diffusion settings by MFIX-Exa. -These control the nodal projection and must be preceded by "nodal_proj": +These control the nodal projection and must be preceded by "nodal_proj.": +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | @@ -42,7 +42,7 @@ These control the nodal projection and must be preceded by "nodal_proj": | | Options are ij, semi_structured or structured | | | +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ -These control the MAC projection and must be preceded by "mac_proj": +These control the MAC projection and must be preceded by "mac_proj.": +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | @@ -78,7 +78,7 @@ These control the MAC projection and must be preceded by "mac_proj": NOTE: If the :cpp:`nodal_proj` and :cpp:`mac_proj` :cpp:`hypre_namespace`'s are set, they must be distinct unless set to :cpp:`hypre`, in which case the default behavior is recovered in which case hypre settings apply to all solvers. -These control the diffusion solver and must be preceded by "diffusion": +These control the diffusion solver and must be preceded by "diffusion.": +-------------------------+-----------------------------------------------------------------------+-------------+--------------+ | | Description | Type | Default | diff --git a/docs/source_docs/inputs/InputsPICtoDEM.rst b/docs/source_docs/inputs/InputsPICtoDEM.rst index ff2d5cd..44b6b6a 100644 --- a/docs/source_docs/inputs/InputsPICtoDEM.rst +++ b/docs/source_docs/inputs/InputsPICtoDEM.rst @@ -15,7 +15,7 @@ Building the PIC to DEM tool using CMake (from inside the build directory): cmake --build ./ --target pic2dem -The following inputs must be preceded by "pic2dem". +The following inputs must be preceded by "pic2dem.": +------------------------+---------------------------------------------------+--------+---------+ | | Description | Type | Default | diff --git a/docs/source_docs/inputs/InputsPlotFiles.rst b/docs/source_docs/inputs/InputsPlotFiles.rst index ed00e0b..6418c80 100644 --- a/docs/source_docs/inputs/InputsPlotFiles.rst +++ b/docs/source_docs/inputs/InputsPlotFiles.rst @@ -3,7 +3,7 @@ Plotfiles and Other Output ========================== -The following inputs must be preceded by "mfix" and control frequency and naming of plotfile generation as well +The following inputs must be preceded by "mfix." and control frequency and naming of plotfile generation as well as whether the EB geometry or level set should be written out, and if the particles should be written out in Ascii format (for debugging). @@ -36,7 +36,7 @@ format (for debugging). +----------------------+-----------------------------------------------------------------------+-------------+-----------+ -The following inputs must be preceded by "mfix" and control what variables will be written in plotfiles. +The following inputs must be preceded by "mfix." and control what variables will be written in plotfiles. +---------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -85,7 +85,7 @@ The following inputs must be preceded by "mfix" and control what variables will +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -The following inputs must be preceded by "mfix" and control whether the EB geometry or level set should be written out. +The following inputs must be preceded by "mfix." and control whether the EB geometry or level set should be written out. +----------------------+-----------------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | @@ -102,7 +102,7 @@ The following inputs must be preceded by "mfix" and control whether the EB geome `Ascent `_ has been integrated into MFIX-Exa for *in situ* visualization. -For codes that have been built with Ascent support, the following inputs must be preceded by "ascent" +For codes that have been built with Ascent support, the following inputs must be preceded by "ascent." and specifies the ascent actions for fluid and/or particles. The frequency which these are called is controlled by `ascent_int` or `ascent_per_approx`, see above. Note that if an ascent pipeline is being included in a GPU build/run, then you must enable managed memory, @@ -117,7 +117,9 @@ i.e., set `amrex.the_arena_is_managed = true`. +---------------------+-----------------------------------------------------------------------+-------------+-----------+ -The following inputs must be preceded by "mfix.solids" and allow to write additional plotfiles which contain only solids variables in specific regions at fixed timesteps or approximated simulation times. All these parameters are user-defined. +The following inputs must be preceded by "mfix.solids." and allow to write additional plotfiles which +contain only solids variables in specific regions at fixed timesteps or approximated simulation times. +All these parameters are user-defined. +---------------------------+-----------------------------------------------------------------+-------------+-----------+ | | Description | Type | Default | diff --git a/docs/source_docs/inputs/InputsTimeStepping.rst b/docs/source_docs/inputs/InputsTimeStepping.rst index a90bed5..888c4f0 100644 --- a/docs/source_docs/inputs/InputsTimeStepping.rst +++ b/docs/source_docs/inputs/InputsTimeStepping.rst @@ -9,7 +9,7 @@ the simulation will stop when either the number of steps reaches max_step or tim In the case of unsteady flow, the simulation will stop when either the tolerance (difference between subsequent steps) is reached or the number of iterations reaches the maximum number specified. -The following inputs must be preceded by ``mfix``. +The following inputs must be preceded by "mfix.": +----------------------+-----------------------------------------------------------------------+-------------+--------------+ | Key | Description | Type | Default | @@ -29,7 +29,7 @@ The following inputs must be preceded by ``mfix``. | tcoll_ratio | DEM timestep equals the min collision time divided by this value | Real | 50.0 | +----------------------+-----------------------------------------------------------------------+-------------+--------------+ -The following inputs must be preceded by "mfix" and are only relevant if running a problem to steady state. +The following inputs must be preceded by "mfix." and are only relevant if running a problem to steady state. Currently, the criterion for setting "steady_state" to true is if "dt" is undefined in mfix.dat +-----------------------+-----------------------------------------------------------------------+-------------+------------+ -- GitLab