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Feature/psturm/kpp standalone interface #9

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Feature/psturm/kpp standalone interface #9

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690d6c2
Initial version of KPP Standalone Interface
Mar 26, 2024
2949d61
Initial version w revised header and cell name fix
Mar 27, 2024
8d7ca81
commenting out verbose diagnostic printing
Apr 2, 2024
12fcca1
Add chemistry operator splitting timestep
Apr 8, 2024
f26b7fb
Merge branch 'geos/develop' into feature/psturm/kpp_standalone_interface
Apr 15, 2024
e87964e
remove MODEL_GEOS ifdef
Apr 21, 2024
2075fe7
Add OutputDir as a backup default output directory
Apr 23, 2024
311a824
Fix early quit conditional so GNU fortran 10.2 stops tripping
Apr 23, 2024
2674a17
moved kpp_standalone_interface.yml to run/shared
Apr 23, 2024
60f0263
comment in the YAML file that output_dir must exist
Apr 23, 2024
d4e6111
fix KPP species name mapping
Apr 26, 2024
c6a6ee3
Merge branch 'geos/develop' into feature/psturm/kpp_standalone_interface
obin1 Apr 30, 2024
d21c1f6
write Hexit last step instead of future step
May 1, 2024
080f8d9
Merge branch 'geos/develop' into feature/psturm/kpp_standalone_interface
May 13, 2024
d33d931
three digit exponent, tip from @nicholasbalasus
May 14, 2024
cc18af8
Merge branch 'geos/develop' into feature/psturm/kpp_standalone_interface
viral211 May 22, 2024
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1 change: 1 addition & 0 deletions GeosCore/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -87,6 +87,7 @@ add_library(GeosCore
vdiff_mod.F90
wetscav_mod.F90
YuIMN_Code.F90
kpp_standalone_interface.F90

# Files only included for special cases
$<$<BOOL:${MODEL_CLASSIC}>:flexgrid_read_mod.F90 get_met_mod.F90 set_boundary_conditions_mod.F90>
Expand Down
60 changes: 59 additions & 1 deletion GeosCore/fullchem_mod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -140,6 +140,7 @@ SUBROUTINE Do_FullChem( Input_Opt, State_Chm, State_Diag, &
USE UCX_MOD, ONLY : SO4_PHOTFRAC
USE UCX_MOD, ONLY : UCX_NOX
USE UCX_MOD, ONLY : UCX_H2SO4PHOT
USE KPP_Standalone_Interface
#ifdef TOMAS
USE TOMAS_MOD, ONLY : H2SO4_RATE
USE TOMAS_MOD, ONLY : PSO4AQ_RATE
Expand Down Expand Up @@ -178,7 +179,7 @@ SUBROUTINE Do_FullChem( Input_Opt, State_Chm, State_Diag, &
INTEGER :: errorCount, origUnit
REAL(fp) :: SO4_FRAC, T, TIN
REAL(fp) :: TOUT, SR, LWC

REAL(dp) :: KPPH_before_integrate
! Strings
CHARACTER(LEN=255) :: errMsg, thisLoc

Expand Down Expand Up @@ -235,6 +236,8 @@ SUBROUTINE Do_FullChem( Input_Opt, State_Chm, State_Diag, &
! (assuming Rosenbrock solver). Define this locally in order to break
! a compile-time dependency. -- Bob Yantosca (05 May 2022)
INTEGER, PARAMETER :: Nhnew = 3
! Add Nhexit, the last timestep length -- Obin Sturm (30 April 2024)
INTEGER, PARAMETER :: Nhexit = 2

! Suppress printing out KPP error messages after this many errors occur
INTEGER, PARAMETER :: INTEGRATE_FAIL_TOGGLE = 20
Expand Down Expand Up @@ -431,6 +434,13 @@ SUBROUTINE Do_FullChem( Input_Opt, State_Chm, State_Diag, &
mapData => NULL()
ENDIF

!=======================================================================
! Should we print the full chemical state for any grid cell on this CPU?
! for use with the KPP Standalone
! (psturm, 03/22/24)
!=======================================================================
CALL Check_Domain( RC )

!========================================================================
! Set up integration convergence conditions and timesteps
! (cf. M. J. Evans)
Expand Down Expand Up @@ -507,6 +517,7 @@ SUBROUTINE Do_FullChem( Input_Opt, State_Chm, State_Diag, &
!$OMP DEFAULT( SHARED )&
!$OMP PRIVATE( I, J, L, N )&
!$OMP PRIVATE( ICNTRL, C_before_integrate )&
!$OMP PRIVATE( KPPH_before_integrate, local_RCONST )&
!$OMP PRIVATE( SO4_FRAC, IERR, RCNTRL, ISTATUS, RSTATE )&
!$OMP PRIVATE( SpcID, KppID, F, P, Vloc )&
!$OMP PRIVATE( Aout, Thread, RC, S, LCH4 )&
Expand Down Expand Up @@ -562,6 +573,12 @@ SUBROUTINE Do_FullChem( Input_Opt, State_Chm, State_Diag, &
! atmosphere if keepActive option is enabled. (hplin, 2/9/22)
CALL fullchem_AR_SetKeepActive( option=.TRUE. )

! Check if the current grid cell in this loop should have its
! full chemical state printed (concentrations, rates, constants)
! for use with the KPP Standalone
! (psturm, 03/22/24)
CALL Check_ActiveCell( I, J, L, State_Grid )

! Start measuring KPP-related routine timing for this grid box
IF ( State_Diag%Archive_KppTime ) THEN
call cpu_time(TimeStart)
Expand Down Expand Up @@ -983,6 +1000,11 @@ SUBROUTINE Do_FullChem( Input_Opt, State_Chm, State_Diag, &
! let us reset concentrations before calling "Integrate" a 2nd time.
C_before_integrate = C

! Do the same for the KPP initial timestep
! Save local rate constants too
KPPH_before_integrate = State_Chm%KPPHvalue(I,J,L)
local_RCONST = RCONST

! Call the Rosenbrock integrator
! (with optional auto-reduce functionality)
CALL Integrate( TIN, TOUT, ICNTRL, &
Expand Down Expand Up @@ -1253,6 +1275,26 @@ SUBROUTINE Do_FullChem( Input_Opt, State_Chm, State_Diag, &
State_Diag%KppTime(I,J,L) = TimeEnd - TimeStart
ENDIF

! Write chemical state to file for the kpp standalone interface
! No external logic needed, this subroutine exits early if the
! chemical state should not be printed (psturm, 03/23/24)
CALL Write_Samples( I, J, L, C_before_integrate, &
local_RCONST, KPPH_before_integrate, &
RSTATE(Nhexit), &
State_Grid, State_Chm, State_Met, &
Input_Opt, ISTATUS(3), RC )

! test the force write option on the root node
! example use case: printing chemical state under conditions
! without knowing where those conditions will happen
! IF ( Input_Opt%amIRoot .AND. L == 1 ) &
! CALL Write_Samples( I, J, L, C_before_integrate, &
! local_RCONST, KPPH_before_integrate, &
! RSTATE(Nhexit), &
! State_Grid, State_Chm, State_Met, &
! Input_Opt, ISTATUS(3), RC, &
! FORCE_WRITE = .TRUE., CELL_NAME = 'root')

!=====================================================================
! Check we have no negative values and copy the concentrations
! calculated from the C array back into State_Chm%Species%Conc
Expand Down Expand Up @@ -2635,6 +2677,7 @@ SUBROUTINE Init_FullChem( Input_Opt, State_Chm, State_Diag, RC )
USE State_Chm_Mod, ONLY : ChmState
USE State_Chm_Mod, ONLY : Ind_
USE State_Diag_Mod, ONLY : DgnState
USE KPP_Standalone_Interface, ONLY : Config_KPP_Standalone
!
! !INPUT PARAMETERS:
!
Expand Down Expand Up @@ -2915,6 +2958,16 @@ SUBROUTINE Init_FullChem( Input_Opt, State_Chm, State_Diag, RC )
ENDIF
ENDIF

!--------------------------------------------------------------------
! Initialize grid cells for input to KPP Standalone (Obin Sturm)
!--------------------------------------------------------------------
CALL Config_KPP_Standalone( Input_Opt, RC )
IF ( RC /= GC_SUCCESS ) THEN
ErrMsg = 'Error encountered in "KPP_Standalone"!'
CALL GC_Error( ErrMsg, RC, ThisLoc )
RETURN
ENDIF

END SUBROUTINE Init_FullChem
!EOC
!------------------------------------------------------------------------------
Expand All @@ -2934,6 +2987,7 @@ SUBROUTINE Cleanup_FullChem( RC )
! !USES:
!
USE ErrCode_Mod
USE KPP_Standalone_Interface, ONLY : Cleanup_KPP_Standalone
!
! !OUTPUT PARAMETERS:
!
Expand Down Expand Up @@ -2983,6 +3037,10 @@ SUBROUTINE Cleanup_FullChem( RC )
IF ( RC /= GC_SUCCESS ) RETURN
ENDIF

! Deallocate variables from kpp standalone module
! psturm, 03/22/2024
CALL Cleanup_KPP_Standalone( RC )

END SUBROUTINE Cleanup_FullChem
!EOC
END MODULE FullChem_Mod
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