Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

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>

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>