KPP standalone interface from Obin Sturm #2482
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added 12 commits
September 26, 2024 14:44
lizziel
added
category: Feature Request
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
|
Hi Lizzie, thanks for getting this started! I'm still working on redoing a few c360 runs with the new compute resources on Discover before we can write up the manuscript about this tool and species-level tolerances. I will keep you all posted when that's out as a preprint, and thanks again for moving this PR upstream |
yantosca
added
the
topic: Chemical Mechanisms
lizziel
changed the base branch from
dev/14.5.0
to
dev/no-diff-to-benchmark
run/shared/kpp_standalone_interface.yml - Fixed typo: "output_dir" -> "output_directory" Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
GeosCore/fullchem_mod.f90 - Use keyword arguments, for clarity GeosCore/kpp_standalone_interface.F90 - Remove Active_Cell and Active_Cell_Name from KPP_Standalone_YAML - Add new derived type KPP_Standalone_ActiveCell_Type, which is now declared with !$OMP THREADPRIVATE. This contains the Active_Cell and Active_Cell_Name fields. - Added new variable KPP_Standalone_ActiveCell, based on new KPP_Standalone_ActiveCell_Type NOTE: The KPP_Standalone_YAML is initialized outside of a parallel loop, so it does not need to be declared !$OMP THREADPRIVATE. But the choice of whether an (I,J,L) location corresponds to one of the "active_cells" (listed in the kpp_standalone_interface.yml file) happens within a parallelized loop. Thus we need to move the Active_Cell and Active_Cell_Name fields out of KPP_Standalone_YAML and into KPP_Standalone_ActiveCell. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
run/shared/kpp_standalone_interface.yml - Reorganize file so that "settings:" comes first, then "active_cells:", and then "locations:" - Add "settings:activate" YAML tag to toggle the KPP standalone interface on or off GeosCore/kpp_standalone_interface.F90 - Add call to QFYAML_Add_Get to parse the "settings:activate" YAML tag - Set KPP_Standalone_YAML%SkipIt to .TRUE. if "settings:activate" is false. This will cause the code to ignore saving out the state of the model for the KPP standalone even if kpp_standalone_interface.yml is present in the run directory. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
run/GCClassic/createRunDir.sh
- Copy run/shared/kpp_standalone_interface.yml to fullchem rundirs
run/shared/cleanRunDir.sh
- Skip removing bpch files (and {diag,tracer}info.dat files), we no
longer generate bpch output
- Add comments and usage examples
- Remove all fort.* files
- Remove OututDir/*.txt files as well (these are KPP standalone
interface files)
CHANGELOG.md
- Updated accordingly
Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
.gitignore - Also ignore *.exe files GeosCore/fullchem_mod.F90 - Remove State_Grid from call to Check_ActiveCell GeosCore/kpp_standalone_interface.F90 - Updated subroutine header comments - Added cosmetic changes for clarity (mostly making code fit within 80 characters, for better readability) - Removed Active_Cell and Active_Cell_name from the KPP_Standalone_Interface_Type (should have been done previously) - Remove State_Grid argument from Check_ActiveCell, this was only used for debugging. Also removed commented out debug prints. - Use Format statements with write statments where expedient - Echo a message when the KPP standalone interface is manually disabled (i.e. when settings:activate = false) - Added display of location names and lon/lats at end of the routine Config_KPP_Standalone - In routine Write_Samples, wrap file I/O in an !$OMP CRITICAL block, in order to prevent more than one thread from writing to each file. - Removed RETURN statement from within !$OMP CRITICAL block, this is not allowed. - Bug fix: Write Kpp_Standalone_ActiveCell%Active_Cell_Name to file, and not Kpp_Standalone_YAML%Active_Cell_Name (which has been removed). Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
GeosCore/kpp_standalone_interface.F90 - Moved to kppsa_interface_mod.F90 GeosCore/kppsa_interface_mod.F90 - Moved from kpp_standalone_interface - Renamed types, variables and routines using "KppSa" prefix: - KPP_Standalone_Interface_Type -> KppSa_Interface_Type - KPP_Standalone_ActiveCell_Type -> KppSa_ActiveCell_Type - KPP_Standalone_YAML -> KppSa_State - KPP_Standalone_ActiveCell -> KppSa_ActiveCell - Check_Domain -> KppSa_Check_Domain - Check_ActiveCell -> KppSa_Check_ActiveCell - Config_KPP_Standalone -> KppSa_Config - Write_Samples -> KppSa_Write_Samples - Cleanup_KPP_Standalone -> KppSa_Cleanup - Added KppSa_Check_Time function to determine if it is time to write KPP standalone output. This allows you to only write output e.g. at the end of a run instead of for each timestep. - Added KppSa_State%SkipWriteAtThisTime field, which is used to determine if we need to exit a routine early. GeosCore/fullchem_mod.F90 - "USE Kpp_Standalone_Interface" -> "USE KppSa_Interface_Mod" - Call renamed routines from kppsa_interface_mod.F90 - Now call KppSa_Check_Domain only if it is the first call to DO_FULLCHEM. This is to avoid repeated computations. - Now call KppSa_Check_Time to determine if we are in the time window when the model state should be archived to disk. - Updated comments and comment headers run/shared/kpp_standalone_interface.yml - Added "start_output_at" to denote starting date time for archiving model state - Added "stop_output_at" to denote ending date time for archiving model state - Updated comments CHANGELOG.md GeosCore/CMakeLists.txt - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
GeosCore/kppsa_interface_mod.F90
- In routine KppSa_Check_Time:
- rRmoved leftover debug print statements
- In routine Kpp_Check_ActiveCell
- Added an IF statement to exit after setting KppSa_State%Active_Cell to .FALSE.
and KppSa_Active_Cell_Name to '' if we are outside of the time
window specified in the kpp_standalone_interface.yml fiel.
- This will ensure that we only archive model state to disk during
the specified time window, which helps with computatonal efficiency.
- In routine KppSa_Config:
- Now write starting & ending date of archival window to log file
Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
run/GCHP/createRunDir.sh - Added an if statement to copy run/shared/kpp_standalone_interface.yml to GCHP fullchem run directories (any option) Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
obin1
reviewed
Oct 10, 2024
|
@obin1 @lizziel: FYI I have also modified this PR to save out the Now that we have per-species ATOL settings in GEOS-Chem 14.5.0, I will add another fix to save that out. This will be needed to set the ATOL for family/dummy species to a high value so as to keep them out of the error norm computations. |
GeosCore/fullchem_mod.F90 - Pass KPP integrator arguments ICNTRL and RCNTRL to KppSa_Write_Samples so that we can include it in the KPP standalone output. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
GeosCore/CMakeLists.txt - Changed permission from chmod 755 to chmod 644 GeosCore/kppsa_interface_mod.F90 - Now accept ICNTRL and RCNTRL as inputs to routine KppSa_Write_Samples - Change number of header lines from 48 to 60 - Better separate Meteorological metadata and KPP parameters for readability - Write out ICNTRL as 2 lines of format 10i6 - Write out RCNTRL as 4 lines of format 5f13.6 - Changed format e25.16e3 to es25.16e3, which changes the output from e.g. 0.5e1 to 5.0e0, etc., which is more standard - Write out ATOL after the species concentration with format es10.2e2 - Cosmetic changes (indentation, comments) Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
GeosCore/kppsa_interface_mod.F90 - In routine KppSa_Write_Samples: - Added a "," in between the concentration and abs tolerance output - Simplified FORMAT statements 120 and 130 - Added FORMAT statements 140 and 150 Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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Name and Institution (Required)
Name: Lizzie Lundgren
Institution: Harvard University
Describe the update
This draft PR contains updates for KPP standalone interface from Obin Sturm (GMAO) contained in GEOS-ESM#9. That original PR is built off of branch geos/develop in the GEOS-Chem fork in GMAO's GitHub. That version is not mergable into the standard model so this PR will be used instead.
Tagging @obin1, @yantosca
Expected changes
I have pushed several updates to this PR:
kpp_standalone_interface.ymlconfiguration file:GeosCore/kpp_standalone_interface.ymlhas been renamed toGeosCore/kppsa_interface_mod.F90. All derived types, variables, and public-facing routines have been renamed to use the prefixKppSa_, for consistency. Derived-typeobject
Kpp_Standalone_YAMLhas new been renamed toKppSa_Statefor brevity.We have added a new derived-type object
KppSa_ActiveCellto hold theActiveCelllogical flag andActive_Cell_Namefields. This is declared with!$OMP THREADPRIVATEbecause it is updated within the main parallel loop within theDO_FULLCHEMroutine.In the
KppSa_Write_Samplesroutine (formerlyWrite_Samples), we have placed the I/O code within an!$OMP CRITICALblock. This will prevent other threads from trying to write to the file, which can cause incomplete and/or corrupted files.We have added a new function
KppSa_Check_Timeto determine if we are within the time window for archiving model state specified in the YAML file. This updates a new flagKppSa_State%SkipWriteAtThisTime, which is used to determine if we need to skip writing output on this timestep.We now print the following output at initialization:
Reference(s)
None
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