From e487f11d50b1fa6ecb39f7bd7d8c728fa38b1891 Mon Sep 17 00:00:00 2001 From: Aditi Vijayan Date: Mon, 23 Oct 2023 10:42:04 +1100 Subject: [PATCH 1/4] adding parseparam.rst to docs --- docs/parseparam.rst | 43 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 docs/parseparam.rst diff --git a/docs/parseparam.rst b/docs/parseparam.rst new file mode 100644 index 000000000..6051c1fc8 --- /dev/null +++ b/docs/parseparam.rst @@ -0,0 +1,43 @@ +#This document includes the details on the all the parse-able params in Quokka. +#These parameters are read in the readParameters() function in simulation.hpp. + + +---------------------------------------------------------------------------—————————————————————————- +| Param Name | Type | Param Description | +—————————————————————————---------------------------------------------------------------------------- +max_timesteps | Integer | Maximum time steps for the simulation | + | | +cfl | Float | Set the cfl number for the simulation | + | | +amr_interpolation_method | String | Sets how to interpolate between AMR levels??| + | | | +stop_time | Float | Stop time of the simulation | + | | | +ascent_interval | ??? | ??? | + | | | +plotfile_interval | Integer | The number of steps between plot file dumps | + | | | +projection_interval | ???? | ??? + | | | +statistics_interval | ???? | + | | | +checkpointtime_interval | ??? | ????? | + | | | +checkpoint_interval | Integer | The number of steps between successive checkpoint dumps | + | | | +do_reflux | ???? | | + | | | +suppress_output | ???? | ????? | + | | | +derived_vars | ???? | ???? | + | | | +regrid_interval |??? | ????? | + | | | +density_floor | Float | The floor on density values in the simulation. Enforced through EnforceLimits | + | | | +temperature_ceiling | Float | The ceiling on temperature values in the simulation. Enforced through EnforceLimits | + | | | +speed_ceiling | Float | The ceiling on the absolute value of speed in the simulation. Enforced through EnforceLimits. | + | | | +max_walltime | Float | The duration of the simulation. | + From 2ce3caca1453d3cf7306c8b228bc26da65091ab2 Mon Sep 17 00:00:00 2001 From: Aditi Vijayan Date: Tue, 24 Oct 2023 10:55:31 +1100 Subject: [PATCH 2/4] modify docs/paramparse --- docs/parseparam.rst | 82 ++++++++++++++++++++++----------------------- 1 file changed, 41 insertions(+), 41 deletions(-) diff --git a/docs/parseparam.rst b/docs/parseparam.rst index 6051c1fc8..840c199fe 100644 --- a/docs/parseparam.rst +++ b/docs/parseparam.rst @@ -1,43 +1,43 @@ -#This document includes the details on the all the parse-able params in Quokka. -#These parameters are read in the readParameters() function in simulation.hpp. +This document includes the details on the all the parse-able params in Quokka. +These parameters are read in the readParameters() function in simulation.hpp. ----------------------------------------------------------------------------—————————————————————————- -| Param Name | Type | Param Description | -—————————————————————————---------------------------------------------------------------------------- -max_timesteps | Integer | Maximum time steps for the simulation | - | | -cfl | Float | Set the cfl number for the simulation | - | | -amr_interpolation_method | String | Sets how to interpolate between AMR levels??| - | | | -stop_time | Float | Stop time of the simulation | - | | | -ascent_interval | ??? | ??? | - | | | -plotfile_interval | Integer | The number of steps between plot file dumps | - | | | -projection_interval | ???? | ??? - | | | -statistics_interval | ???? | - | | | -checkpointtime_interval | ??? | ????? | - | | | -checkpoint_interval | Integer | The number of steps between successive checkpoint dumps | - | | | -do_reflux | ???? | | - | | | -suppress_output | ???? | ????? | - | | | -derived_vars | ???? | ???? | - | | | -regrid_interval |??? | ????? | - | | | -density_floor | Float | The floor on density values in the simulation. Enforced through EnforceLimits | - | | | -temperature_ceiling | Float | The ceiling on temperature values in the simulation. Enforced through EnforceLimits | - | | | -speed_ceiling | Float | The ceiling on the absolute value of speed in the simulation. Enforced through EnforceLimits. | - | | | -max_walltime | Float | The duration of the simulation. | - ++----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ +| Param Name | Type | Param Description | ++----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ +max_timesteps | Integer | Maximum time steps for the simulation | ++----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ +cfl | Float | Set the cfl number for the simulation | ++----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ +amr_interpolation_method | String | Sets how to interpolate between AMR levels?? | ++----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ +stop_time | Float | Stop time of the simulation | ++----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ +ascent_interval | ??? | ??? | ++----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ +plotfile_interval | Integer | The number of steps between plot file dumps | ++----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ +projection_interval | ???? | ??? | ++----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ +statistics_interval | ???? | ????? | ++----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ +checkpointtime_interval | ??? | ????? | ++----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ +checkpoint_interval | Integer | The number of steps between successive checkpoint dumps | ++----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ +do_reflux | ???? | | ++----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ +suppress_output | ???? | ????? | ++----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ +derived_vars | ???? | ???? | ++----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ +regrid_interval |??? | ????? | ++----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ +density_floor | Float | The floor on density values in the simulation. Enforced through EnforceLimits | ++----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ +temperature_ceiling | Float | The ceiling on temperature values in the simulation. Enforced through EnforceLimits | ++----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ +speed_ceiling | Float | The ceiling on the absolute value of speed in the simulation. Enforced through EnforceLimits. | ++----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ +max_walltime | Float | The duration of the simulation. | ++----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ From 9029d9dc10665d6484e32bcac89c081e24755775 Mon Sep 17 00:00:00 2001 From: Ben Wibking Date: Thu, 30 Nov 2023 16:54:58 -0500 Subject: [PATCH 3/4] fix formatting --- docs/index.rst | 1 + docs/parameters.rst | 69 +++++++++++++++++++++++++++++++++++++++++++++ docs/parseparam.rst | 43 ---------------------------- 3 files changed, 70 insertions(+), 43 deletions(-) create mode 100644 docs/parameters.rst delete mode 100644 docs/parseparam.rst diff --git a/docs/index.rst b/docs/index.rst index 16b4adff2..e988c3cca 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -19,6 +19,7 @@ run with high performance on either CPUs or GPUs. equations flowchart tests/index + parameters api bibliography diff --git a/docs/parameters.rst b/docs/parameters.rst new file mode 100644 index 000000000..04c702393 --- /dev/null +++ b/docs/parameters.rst @@ -0,0 +1,69 @@ +.. Runtime parameters + +Runtime parameters +========================== + +This document lists all of the runtime parameters in Quokka. +Using the AMReX ParmParse object, these parameters are read in the `readParameters()` function in `simulation.hpp` from an input file or from command line arguments. + +.. list-table:: Table of runtime parameters. + :widths: 25 25 50 + :header-rows: 1 + + * - Parameter Name + - Type + - Description + * - max_timesteps + - Integer + - The maximum number of time steps for the simulation. + * - cfl + - Float + - Sets the CFL number for the simulation. + * - amr_interpolation_method + - Integer + - Selects the method used to interpolate from coarse to fine AMR levels. + * - stop_time + - Float + - The simulation time at which to stop evolving the simulation. + * - ascent_interval + - Integer + - The number of coarse timesteps between Ascent outputs. + * - plotfile_interval + - Integer + - The number of coarse timesteps between plotfile outputs. + * - projection_interval + - Integer + - The number of coarse timesteps between 2D projection outputs. + * - statistics_interval + - Integer + - The number of coarse timesteps between statistics outputs. + * - checkpointtime_interval + - Float + - The time interval (in simulated time) between checkpoint outputs. + * - checkpoint_interval + - Float + - The number of coarse timesteps between checkpoint outputs. + * - do_reflux + - Integer + - this turns on refluxing at coarse-fine boundaries (1) or turns it off (0). Except for debugging, this should always be on if AMR is used. + * - suppress_output + - Integer + - If set to 1, this disables output to stdout while the simulation is running. + * - derived_vars + - String + - A list of the names of derived variables that should be included in the plotfile and Ascent outputs. + * - regrid_interval + - Integer + - The number of timesteps between AMR regridding. + * - density_floor + - Float + - The minimum density value allowed in the simulation. Enforced through EnforceLimits. + * - temperature_ceiling + - Float + - The ceiling on temperature values in the simulation. Enforced through EnforceLimits. + * - speed_ceiling + - Float + - The ceiling on the absolute value of the fluid velocity in the simulation. Enforced through EnforceLimits. + * - max_walltime + - String + - The maximum walltime for the simulation in the format DD:HH:SS (days/hours/seconds). After 90% of this walltime elapses, the simulation will stop and exit. diff --git a/docs/parseparam.rst b/docs/parseparam.rst deleted file mode 100644 index 840c199fe..000000000 --- a/docs/parseparam.rst +++ /dev/null @@ -1,43 +0,0 @@ -This document includes the details on the all the parse-able params in Quokka. -These parameters are read in the readParameters() function in simulation.hpp. - - -+----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ -| Param Name | Type | Param Description | -+----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ -max_timesteps | Integer | Maximum time steps for the simulation | -+----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ -cfl | Float | Set the cfl number for the simulation | -+----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ -amr_interpolation_method | String | Sets how to interpolate between AMR levels?? | -+----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ -stop_time | Float | Stop time of the simulation | -+----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ -ascent_interval | ??? | ??? | -+----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ -plotfile_interval | Integer | The number of steps between plot file dumps | -+----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ -projection_interval | ???? | ??? | -+----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ -statistics_interval | ???? | ????? | -+----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ -checkpointtime_interval | ??? | ????? | -+----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ -checkpoint_interval | Integer | The number of steps between successive checkpoint dumps | -+----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ -do_reflux | ???? | | -+----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ -suppress_output | ???? | ????? | -+----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ -derived_vars | ???? | ???? | -+----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ -regrid_interval |??? | ????? | -+----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ -density_floor | Float | The floor on density values in the simulation. Enforced through EnforceLimits | -+----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ -temperature_ceiling | Float | The ceiling on temperature values in the simulation. Enforced through EnforceLimits | -+----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ -speed_ceiling | Float | The ceiling on the absolute value of speed in the simulation. Enforced through EnforceLimits. | -+----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ -max_walltime | Float | The duration of the simulation. | -+----------------------------------+--------------------------+-----------------------------------------------------------------------------------------------+ From d094c825b9ccbb62c81b65ec9f5a92829deeebd5 Mon Sep 17 00:00:00 2001 From: Ben Wibking Date: Sat, 2 Dec 2023 11:57:58 -0500 Subject: [PATCH 4/4] Update parameters.rst --- docs/parameters.rst | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/docs/parameters.rst b/docs/parameters.rst index 04c702393..322fcb57f 100644 --- a/docs/parameters.rst +++ b/docs/parameters.rst @@ -21,7 +21,7 @@ Using the AMReX ParmParse object, these parameters are read in the `readParamete - Sets the CFL number for the simulation. * - amr_interpolation_method - Integer - - Selects the method used to interpolate from coarse to fine AMR levels. + - Selects the method (piecewise constant or piecewise linear with limiters) used to interpolate from coarse to fine AMR levels. Except for debugging, this should not be changed. * - stop_time - Float - The simulation time at which to stop evolving the simulation. @@ -31,21 +31,24 @@ Using the AMReX ParmParse object, these parameters are read in the `readParamete * - plotfile_interval - Integer - The number of coarse timesteps between plotfile outputs. + * - plottime_interval + - Float + - The time interval (in simulated time) between plotfile outputs. * - projection_interval - Integer - The number of coarse timesteps between 2D projection outputs. * - statistics_interval - Integer - The number of coarse timesteps between statistics outputs. - * - checkpointtime_interval - - Float - - The time interval (in simulated time) between checkpoint outputs. * - checkpoint_interval - Float - The number of coarse timesteps between checkpoint outputs. + * - checkpointtime_interval + - Float + - The time interval (in simulated time) between checkpoint outputs. * - do_reflux - Integer - - this turns on refluxing at coarse-fine boundaries (1) or turns it off (0). Except for debugging, this should always be on if AMR is used. + - this turns on refluxing at coarse-fine boundaries (1) or turns it off (0). Except for debugging, this should always be on when AMR is used. * - suppress_output - Integer - If set to 1, this disables output to stdout while the simulation is running. @@ -66,4 +69,4 @@ Using the AMReX ParmParse object, these parameters are read in the `readParamete - The ceiling on the absolute value of the fluid velocity in the simulation. Enforced through EnforceLimits. * - max_walltime - String - - The maximum walltime for the simulation in the format DD:HH:SS (days/hours/seconds). After 90% of this walltime elapses, the simulation will stop and exit. + - The maximum walltime for the simulation in the format DD:HH:SS (days/hours/seconds). After 90% of this walltime elapses, the simulation will automatically stop and exit.