Move KPP standalone code to KPP/standalone folder

KPP/CMakeLists.txt - Calls the KPP/standalone/CMakeLists.txt file to build the KPP standalone executable when fullchem or custom mechanisms are selected KPP/standalone/kpp_standalone.F90 KPP/standalone/kpp_standalone_init.F90 - Moved from KPP/fullchem folder - Trimmed trailing whitespace KPP/standalone/sample_sites - Moved from KPP/fullchem/samples_kpp_standalone KPP/standalone/CMakeLists.txt - Compiles the kpp_standalone_init.F90 and kpp_standalone.F90 modules, linking it to the KPP library that is built (fullchem or custom) CHANGELOG.md - Updaetd accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
geoschem · Oct 8, 2024 · 38162aa · 38162aa
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,7 +17,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Added computation of water concentration to use in photolysis for application of UV absorption by water in Cloud-J v8
 - Added ACO3, ACR, ACRO2, ALK4N{1,2,O}2, ALK4P, ALK7, APAN, APINN, APINO2, APINP, AROCMCHO, AROMCO3, AROMPN, BPINN, BPINO2, BPINON, BPINOO2, BPINOOH, BPINP, BUTN, BUTO2, C4H6, C96N, C96O2, C9602H, EBZ, GCO3, HACTA, LIMAL, LIMKB, LIMKET, LIMKO2, LIMN, LIMNB, LIMO2H, LIMO3, LIMO3H, LIMPAN, MEKCO3, MEKPN, MYRCO, PHAN, PIN, PINAL, PINO3, PINONIC, PINPAN, R7N{1,2}, R7O2, R7P, RNO3, STYR, TLFUO2, TLFUONE, TMB, ZRO2 to `species_database.yml` following Travis et  al. 2024.
 - Added TSOIL1 field to `State_Met` for use in HEMCO soil NOx extension. This should only be read in when the `UseSoilTemperature` option is true in HEMCO config.
-- Added KPP standalone
+- Added KPP standalone; executable will be built when compiling for fullchem or custom mechanisms
 
 ### Changed
 - Copy values from `State_Chm%KPP_AbsTol` to `ATOL` and `State_Chm%KPP_RelTol` to `RTOL` for fullchem and Hg simulations

diff --git a/KPP/CMakeLists.txt b/KPP/CMakeLists.txt
@@ -6,6 +6,7 @@
 #-----------------------------------------------------------------------------
 if("${MECH}" STREQUAL fullchem)
   add_subdirectory(fullchem)
+  add_subdirectory(standalone)
 endif()
 
 #-----------------------------------------------------------------------------
@@ -20,6 +21,7 @@ endif()
 #-----------------------------------------------------------------------------
 if("${MECH}" STREQUAL custom)
   add_subdirectory(custom)
+  add_subdirectory(standalone)
 endif()
 
 #-----------------------------------------------------------------------------

diff --git a/KPP/standalone/CMakeLists.txt b/KPP/standalone/CMakeLists.txt
@@ -0,0 +1,23 @@
+# KPP/fullchem/CMakeLists.txt
+
+#----------------------------------------------------------------------------
+# Add libKPPStandalone.a -- KPP standalone executable
+#----------------------------------------------------------------------------
+add_library(KPPStandalone
+  STATIC EXCLUDE_FROM_ALL
+  kpp_standalone.F90
+  kpp_standalone_init.F90
+)
+
+# Dependencies
+target_link_libraries(KPPStandalone
+  PUBLIC
+  KPP
+)
+
+# Treat REAL as if it were REAL*8
+target_compile_options(KPPStandalone
+  PRIVATE ""
+  $<$<STREQUAL:"${CMAKE_Fortran_COMPILER_ID}","Intel">:-r8>
+  $<$<STREQUAL:"${CMAKE_Fortran_COMPILER_ID}","GNU">:-fdefault-real-8 -fdefault-double-8>
+)
diff --git a/KPP/fullchem/kpp_standalone.F90 → KPP/standalone/kpp_standalone.F90 b/KPP/fullchem/kpp_standalone.F90 → KPP/standalone/kpp_standalone.F90
@@ -1,26 +1,26 @@
 program main
 
 ! The KPP Standalone for GEOS-Chem Mechanism Analysis
-! 
-! 
+!
+!
 ! Program Description:
-! 
+!
 ! This program runs the GEOS-Chem KPP Standalone for a given set of initial conditions.
 ! It reads an input file generated by the KPP Standalone Interface that generates model
 ! output of the full chemical state of grid cells in 3D GEOS-Chem, GCHP, and GEOS-CF runs.
 ! The full mechanism is run to replicate the chemistry of the specified grid cell.
 ! Obin Sturm (psturm@usc.edu), Michael S Long, Christoph Keller
 
 ! The KPP Standalone is adapted from a box model used in the following publication:
-! Lin, H., Long, M. S., Sander, R., Sandu, A., Yantosca, R. M., Estrada, L. A., et al. (2023). 
-!  An adaptive auto-reduction solver for speeding up integration of chemical kinetics in atmospheric chemistry models: 
-!  Implementation and evaluation in the Kinetic Pre-Processor (KPP) version 3.0.0. 
+! Lin, H., Long, M. S., Sander, R., Sandu, A., Yantosca, R. M., Estrada, L. A., et al. (2023).
+!  An adaptive auto-reduction solver for speeding up integration of chemical kinetics in atmospheric chemistry models:
+!  Implementation and evaluation in the Kinetic Pre-Processor (KPP) version 3.0.0.
 !  Journal of Advances in Modeling Earth Systems, 15, e2022MS003293. https://doi.org/10.1029/2022MS003293
 
 ! Updates:
 !  - 2024/05/06, Obin Sturm: Simplification of the code for the GEOS-Chem KPP Standalone,
 !                            removed all autoreduce and convergence criteria testing.
-!                            The more general tool just runs one operator timestep 
+!                            The more general tool just runs one operator timestep
 !                            and then prints out the results to an output file.
 
   USE GCKPP_GLOBAL
@@ -52,7 +52,7 @@ program main
 
   LOGICAL              :: OUTPUT
   LOGICAL              :: ReInit
-  
+
 
   ! Vars for reading files
   character(len=256) :: inputfile
@@ -64,7 +64,7 @@ program main
      ! Get the first argument
      call get_command_argument(1, inputfile)
      print*, 'Processing sample: ', trim(inputfile)
-   else 
+   else
     print*, 'No sample provided. Exiting.'
     stop
    endif
@@ -87,7 +87,6 @@ program main
   call read_input(inputfile, R, Cinit, SPC_NAMES, Hstart, Hexit, cosSZA, level, fileTotSteps, OperatorTimestep)
 
 
-
   ! Run the full mechanism
   call fullmech(RTOL_VALUE=0.5e-2_dp)
 
@@ -110,7 +109,7 @@ subroutine fullmech(RTOL_VALUE)
 
     ! Set OPTIONS
     IERR      = 0                 ! Success or failure flag
-    ISTATUS   = 0                 ! Rosenbrock output 
+    ISTATUS   = 0                 ! Rosenbrock output
     RCNTRL    = 0.0_dp            ! Rosenbrock input
     RCNTRL(3) = Hstart
     ! write(*,'(a,f10.2)') " Hstart: ", Hstart
@@ -121,7 +120,7 @@ subroutine fullmech(RTOL_VALUE)
     ICNTRL(3) = 4
     ICNTRL(7) = 1
     ICNTRL(15) = -1
-    
+
     ! Tolerances
     ATOL      = 1e-2_dp
     RTOL      = RTOL_VALUE ! default in GEOS-CF 2.0 is 0.5e-2_dp
@@ -131,7 +130,7 @@ subroutine fullmech(RTOL_VALUE)
     TIN  = T
     TOUT = T + OperatorTimestep
     TEMP = 298.
-        
+
     full_avg     = 0.
     full_sumtime = 0.
     start        = 0.
@@ -163,7 +162,7 @@ subroutine fullmech(RTOL_VALUE)
     endif
 
     ! Run the RTOL variation loop
-    DO I=1,NRTOL       
+    DO I=1,NRTOL
        call Initialize()
        C(1:NSPEC) = Cinit(1:NSPEC)
 
@@ -200,7 +199,7 @@ subroutine write_output(inputfile, outputfile)
     ! Write meteo data lines of the input to the output file
     open(20, file=outputfile)
     open(10, file=inputfile, status='old')
-    
+
     ! Write the header lines to the output file
     write(20, '(A)') "30"
     write(20, '(A)') "==========================================================================="
@@ -237,4 +236,3 @@ subroutine write_output(inputfile, outputfile)
  end subroutine write_output
 
 end program main
-
diff --git a/KPP/fullchem/kpp_standalone_init.F90 → KPP/standalone/kpp_standalone_init.F90 b/KPP/fullchem/kpp_standalone_init.F90 → KPP/standalone/kpp_standalone_init.F90
@@ -49,7 +49,7 @@ subroutine read_input(filename, R, C, SPC_NAMES, Hstart, Hexit, cosSZA, level, f
   do i = 1, NHEADER
      read(file_unit, '(A)', iostat=ierr) line
      if (ierr /= 0)  then
-      print *, "Error reading line", i 
+      print *, "Error reading line", i
       exit
      end if
      ! Get level
@@ -91,7 +91,7 @@ subroutine read_input(filename, R, C, SPC_NAMES, Hstart, Hexit, cosSZA, level, f
   do i = 1, NSPEC
      read(file_unit, '(A)', iostat=ierr) line
      if (ierr /= 0)  then
-      print *, "Error reading line", i+NHEADER 
+      print *, "Error reading line", i+NHEADER
       exit
      end if
      idx = index(line, ',') + 1
@@ -108,7 +108,7 @@ subroutine read_input(filename, R, C, SPC_NAMES, Hstart, Hexit, cosSZA, level, f
   do i = 1, NREACT
      read(file_unit, '(A)', iostat=ierr) line
      if (ierr /= 0)  then
-      print *, "Error reading line", i+NSPEC+NHEADER 
+      print *, "Error reading line", i+NSPEC+NHEADER
       exit
      end if
      idx = index(line, ',') + 1
@@ -120,4 +120,3 @@ subroutine read_input(filename, R, C, SPC_NAMES, Hstart, Hexit, cosSZA, level, f
 end subroutine read_input
 
 end module kpp_standalone_init
-
diff --git a/...p_standalone/Beijing_L1_20200106_1345.txt → ...sample_sites/Beijing_L1_20200106_1345.txt b/...p_standalone/Beijing_L1_20200106_1345.txt → ...sample_sites/Beijing_L1_20200106_1345.txt
@@ -1,30 +1,30 @@
-48                                                                         
+48
 ===========================================================================
-                                                                           
-                  KPP Standalone Atmospheric Chemical State                
-File Description:                                                          
-This file contains model output of the atmospheric chemical state          
-as simulated by the GEOS-Chem chemistry module in a 3D setting.            
-Each grid cell represents the chemical state of an individual location,    
-suitable for input into a separate KPP Standalone program which will       
-replicate the chemical evolution of that grid cell for mechanism analysis. 
-Note that the KPP Standalone will only use concentrations, rate constants, 
+
+                  KPP Standalone Atmospheric Chemical State
+File Description:
+This file contains model output of the atmospheric chemical state
+as simulated by the GEOS-Chem chemistry module in a 3D setting.
+Each grid cell represents the chemical state of an individual location,
+suitable for input into a separate KPP Standalone program which will
+replicate the chemical evolution of that grid cell for mechanism analysis.
+Note that the KPP Standalone will only use concentrations, rate constants,
 and KPP-specific fields. All other fields are for reference. The first line
-contains the number of lines in this header. If wanting to use this output 
-for other analysis, a Python class to read these fields is available by    
-request, contact Obin Sturm (psturm@usc.edu).                              
-                                                                           
-Generated by the GEOS-Chem Model                                           
-       (https://geos-chem.org/)                                            
-Using the KPP Standalone Interface                                         
-github.com/GEOS-ESM/geos-chem/tree/feature/psturm/kpp_standalone_interface 
-     With contributions from:                                              
-        Obin Sturm (psturm@usc.edu)                                        
-        Christoph Keller                                                   
-        Michael Long                                                       
-        Sam Silva                                                          
-                                                                           
-Meteorological and general grid cell metadata    
+contains the number of lines in this header. If wanting to use this output
+for other analysis, a Python class to read these fields is available by
+request, contact Obin Sturm (psturm@usc.edu).
+
+Generated by the GEOS-Chem Model
+       (https://geos-chem.org/)
+Using the KPP Standalone Interface
+github.com/GEOS-ESM/geos-chem/tree/feature/psturm/kpp_standalone_interface
+     With contributions from:
+        Obin Sturm (psturm@usc.edu)
+        Christoph Keller
+        Michael Long
+        Sam Silva
+
+Meteorological and general grid cell metadata
 Location:                                        Beijing
 Timestamp:                                       2020/01/06 13:45
 Longitude (degrees):                                117.0185
@@ -36,17 +36,17 @@ Dry air density (molec/cm3):                      0.2646E+20
 Water vapor mixing ratio (vol H2O/vol dry air):   0.3956E-02
 Cloud fraction:                                   0.0000E+00
 Cosine of solar zenith angle:                    -0.8279E+00
-KPP Integrator-specific parameters               
+KPP Integrator-specific parameters
 Init KPP Timestep (seconds):                        268.3002
 Exit KPP Timestep (seconds):                         32.4352
 Chemistry operator timestep (seconds):              900.0000
 Number of internal timesteps:                        28
-CSV data of full chemical state, including species concentrations,    
-rate constants (R) and instantaneous reaction rates (A).              
-All concentration units are in molecules/cc and rates in molec/cc/s.  
-                                                                           
+CSV data of full chemical state, including species concentrations,
+rate constants (R) and instantaneous reaction rates (A).
+All concentration units are in molecules/cc and rates in molec/cc/s.
+
 ===========================================================================
-Name,   Value                                                              
+Name,   Value
 CH2I2,   0.5229637490161687E+06
 CH2IBr,   0.5401741649323440E+06
 CH2ICl,   0.2389579494513276E+07
@@ -2130,4 +2130,3 @@ A891,   0.0000000000000000E+00
 A892,   0.0000000000000000E+00
 A893,   0.0000000000000000E+00
 A894,   0.0000000000000000E+00
-