Initial updates for splitting ACHEM from Chem GC

.github/CODEOWNERS

@@ -0,0 +1,10 @@
+# This is a comment.
+# Each line is a file pattern followed by one or more owners.
+# Order is important; the last matching pattern takes the most
+# precedence.
+
+# The ACHEM Team owns all the files
+* @GEOS-ESM/achem-team
+
+# The GEOS CMake Team also a CODEOWNER for the CMakeLists.txt files in this repository
+CMakeLists.txt @GEOS-ESM/cmake-team @GEOS-ESM/achem-team

ACHEM_ExtData.yaml

@@ -0,0 +1,138 @@
+Collections:
+  ACHEM_CO-em-anthro_CMIP_CEDS_gn.x2304_y1441_t12.%y4.nc4:
+    template: ExtData/chemistry/CEDS/v2021-04-21-revised/sfc/CO-em-anthro_CMIP_CEDS_gn.x2304_y1441_t12.%y4.nc4
+  ACHEM_DMSclim_sfcconcentration.x360_y181_t12.Lana2011.nc4:
+    template: ExtData/chemistry/Lana/v2011/DMSclim_sfcconcentration.x360_y181_t12.Lana2011.nc4
+  ACHEM_GEIA.emis_NH3.ocean.x576_y361.t12.20080715_12z.nc4:
+    template: ExtData/chemistry/GEIA/v0.0.0/sfc/GEIA.emis_NH3.ocean.x576_y361.t12.20080715_12z.nc4
+  ACHEM_MERRA2_GMI.tavg24_3d_dac_Nv.x576_y361_t12.%y4.nc4:
+    template: ExtData/chemistry/MERRA2GMI/v0.0.0/L72/MERRA2_GMI.tavg24_3d_dac_Nv.x576_y361_t12.%y4.nc4
+  ACHEM_SOAG.emiss.x144_y91_t12.1990.nc4:
+    template: ExtData/chemistry/CAM/v0.0.0/sfc/SOAG.emiss.x144_y91_t12.1990.nc4
+  ACHEM_edgar-v42.emis_nh3.anthropogenic.x1152_y721.19700703T12z_20200703T00z.nc4:
+    template: ExtData/chemistry/MERRA2/v0.0.0/sfc/edgar-v42.emis_nh3.anthropogenic.x1152_y721.19700703T12z_20200703T00z.nc4
+  ACHEM_htap-v2.2.emis_so2.aviation_cds.x3600_y1800_t12.2010.nc4:
+    template: ExtData/chemistry/HTAP/v2.2/sfc/htap-v2.2.emis_so2.aviation_cds.x3600_y1800_t12.2010.nc4
+  ACHEM_htap-v2.2.emis_so2.aviation_crs.x3600_y1800_t12.2010.nc4:
+    template: ExtData/chemistry/HTAP/v2.2/sfc/htap-v2.2.emis_so2.aviation_crs.x3600_y1800_t12.2010.nc4
+  ACHEM_htap-v2.2.emis_so2.aviation_lto.x3600_y1800_t12.2010.nc4:
+    template: ExtData/chemistry/HTAP/v2.2/sfc/htap-v2.2.emis_so2.aviation_lto.x3600_y1800_t12.2010.nc4
+  ACHEM_htap-v2.2.emis_so2.ships.x3600_y1800_t12.2010.nc4:
+    template: ExtData/chemistry/HTAP/v2.2/sfc/htap-v2.2.emis_so2.ships.x3600_y1800_t12.2010.nc4
+  ACHEM_htapv2.2.emisso2.elevated.x3600y1800t12.2017.integrate.nc4:
+    template: ExtData/chemistry/HTAP/v2.2/sfc/htapv2.2.emisso2.elevated.x3600y1800t12.2017.integrate.nc4
+  ACHEM_htapv2.2.emisso2.surface.x3600y1800t12.2017.integrate.nc4:
+    template: ExtData/chemistry/HTAP/v2.2/sfc/htapv2.2.emisso2.surface.x3600y1800t12.2017.integrate.nc4
+  ACHEM_qfed2.emis_co.006.%y4%m2%d2.nc4:
+    template: ExtData/chemistry/QFED/v2.5r1-nrt/sfc/0.1/Y%y4/M%m2/qfed2.emis_co.006.%y4%m2%d2.nc4
+    valid_range:  "2014-12-01T12:00/2021-11-01T12:00"
+  ACHEM_qfed2.emis_nh3.006.%y4%m2%d2.nc4:
+    template: ExtData/chemistry/QFED/v2.5r1-nrt/sfc/0.1/Y%y4/M%m2/qfed2.emis_nh3.006.%y4%m2%d2.nc4
+    valid_range:  "2014-12-01T12:00/2021-11-01T12:00"
+  ACHEM_qfed2.emis_so2.006.%y4%m2%d2.nc4:
+    template: ExtData/chemistry/QFED/v2.5r1-nrt/sfc/0.1/Y%y4/M%m2/qfed2.emis_so2.006.%y4%m2%d2.nc4
+    valid_range:  "2014-12-01T12:00/2021-11-01T12:00"
+  ACHEM_qfed2.emis_co.061.%y4%m2%d2.nc4:
+    template: ExtData/chemistry/QFED/v2.5r1-nrt/sfc/0.1/Y%y4/M%m2/qfed2.emis_co.061.%y4%m2%d2.nc4
+    valid_range:  "2021-11-01T12:00/2025-01-01"
+  ACHEM_qfed2.emis_nh3.061.%y4%m2%d2.nc4:
+    template: ExtData/chemistry/QFED/v2.5r1-nrt/sfc/0.1/Y%y4/M%m2/qfed2.emis_nh3.061.%y4%m2%d2.nc4
+    valid_range:  "2021-11-01T12:00/2025-01-01"
+  ACHEM_qfed2.emis_so2.061.%y4%m2%d2.nc4:
+    template: ExtData/chemistry/QFED/v2.5r1-nrt/sfc/0.1/Y%y4/M%m2/qfed2.emis_so2.061.%y4%m2%d2.nc4
+    valid_range:  "2021-11-01T12:00/2025-01-01"
+
+Samplings:
+  ACHEM_sample_0:
+    update_frequency: PT24H
+    update_offset: PT12H
+    update_reference_time: '0'
+  ACHEM_sample_1:
+    extrapolation: clim
+    update_frequency: PT24H
+    update_offset: PT12H
+    update_reference_time: '0'
+  ACHEM_sample_2:
+    extrapolation: clim
+
+Exports:
+  CO_BF_VOC:
+    collection: /dev/null
+    regrid: CONSERVE
+    sample: ACHEM_sample_1
+    variable: emcobf
+  CO_BIOMASS_VOC:
+    - {starting: "2014-12-01T12:00",collection: ACHEM_qfed2.emis_co.006.%y4%m2%d2.nc4,regrid: CONSERVE,sample: ACHEM_sample_0,variable: biomass}
+    - {starting: "2021-11-01T12:00",collection: ACHEM_qfed2.emis_co.061.%y4%m2%d2.nc4,regrid: CONSERVE,sample: ACHEM_sample_0,variable: biomass}
+  CO_FS_VOC:
+    collection: ACHEM_CO-em-anthro_CMIP_CEDS_gn.x2304_y1441_t12.%y4.nc4
+    regrid: CONSERVE
+    sample: ACHEM_sample_0
+    variable: co
+  DMS_CONC_OCEAN:
+    collection: ACHEM_DMSclim_sfcconcentration.x360_y181_t12.Lana2011.nc4
+    linear_transformation:
+      - 0.0
+      - 1.0e-06
+    regrid: CONSERVE
+    sample: ACHEM_sample_1
+    variable: conc
+  H2O2:
+    collection: ACHEM_MERRA2_GMI.tavg24_3d_dac_Nv.x576_y361_t12.%y4.nc4
+    variable: h2o2
+  NH3_EMIS:
+    collection: ACHEM_edgar-v42.emis_nh3.anthropogenic.x1152_y721.19700703T12z_20200703T00z.nc4
+    regrid: CONSERVE
+    variable: emi_nh3
+  NH3_EMIS_FIRE:
+    - {starting: "2014-12-01T12:00",collection: ACHEM_qfed2.emis_nh3.006.%y4%m2%d2.nc4,regrid: CONSERVE,sample: ACHEM_sample_0,variable: biomass}
+    - {starting: "2021-11-01T12:00",collection: ACHEM_qfed2.emis_nh3.061.%y4%m2%d2.nc4,regrid: CONSERVE,sample: ACHEM_sample_0,variable: biomass}
+  NH3_EMIS_OCEAN:
+    collection: ACHEM_GEIA.emis_NH3.ocean.x576_y361.t12.20080715_12z.nc4
+    regrid: CONSERVE
+    sample: ACHEM_sample_1
+    variable: emiss_ocn
+  NO3:
+    collection: ACHEM_MERRA2_GMI.tavg24_3d_dac_Nv.x576_y361_t12.%y4.nc4
+    variable: no3
+  OH:
+    collection: ACHEM_MERRA2_GMI.tavg24_3d_dac_Nv.x576_y361_t12.%y4.nc4
+    variable: oh
+  SO2_EMIS_AIRCRAFT_CDS:
+    collection: ACHEM_htap-v2.2.emis_so2.aviation_cds.x3600_y1800_t12.2010.nc4
+    regrid: CONSERVE
+    sample: ACHEM_sample_1
+    variable: so2_aviation
+  SO2_EMIS_AIRCRAFT_CRS:
+    collection: ACHEM_htap-v2.2.emis_so2.aviation_crs.x3600_y1800_t12.2010.nc4
+    regrid: CONSERVE
+    sample: ACHEM_sample_1
+    variable: so2_aviation
+  SO2_EMIS_AIRCRAFT_LTO:
+    collection: ACHEM_htap-v2.2.emis_so2.aviation_lto.x3600_y1800_t12.2010.nc4
+    regrid: CONSERVE
+    sample: ACHEM_sample_1
+    variable: so2_aviation
+  SO2_EMIS_ENERGY:
+    collection: ACHEM_htapv2.2.emisso2.elevated.x3600y1800t12.2017.integrate.nc4
+    regrid: CONSERVE
+    sample: ACHEM_sample_1
+    variable: sanl2
+  SO3_EMIS_FIRE:
+    - {starting: "2014-12-01T12:00",collection: ACHEM_qfed2.emis_so3.006.%y4%m2%d2.nc4,regrid: CONSERVE,sample: ACHEM_sample_0,variable: biomass}
+    - {starting: "2021-11-01T12:00",collection: ACHEM_qfed2.emis_so3.061.%y4%m2%d2.nc4,regrid: CONSERVE,sample: ACHEM_sample_0,variable: biomass}
+  SO2_EMIS_NONENERGY:
+    collection: ACHEM_htapv2.2.emisso2.surface.x3600y1800t12.2017.integrate.nc4
+    regrid: CONSERVE
+    sample: ACHEM_sample_1
+    variable: sanl1
+  SO2_EMIS_SHIPPING:
+    collection: ACHEM_htap-v2.2.emis_so2.ships.x3600_y1800_t12.2010.nc4
+    regrid: CONSERVE
+    sample: ACHEM_sample_1
+    variable: so2_ship
+  SOAG_EMIS:
+    collection: ACHEM_SOAG.emiss.x144_y91_t12.1990.nc4
+    sample: ACHEM_sample_2
+    variable: soag
+

GEOS_AChemGridComp.rc → ACHEM_GridComp.rc

@@ -1,13 +1,13 @@
 #
 # Resource file for the GEOS aerosol chemistry grid component.
 #
-#   15 Aug 2012  A. Darmenov   
+#   15 Aug 2012  A. Darmenov
 #--------------------------------------------------------------------
 
 verbose: .True.
 
 
-# MAM chemistry 
+# MAM chemistry
 # -------------------------------------
 gas_chemistry:      .false.
 aqueous_chemistry:  .false.
@@ -21,7 +21,7 @@ ocs_surface_vmr: 490.0e-12   # 'mol/mol'
 
 # VOC chemistry and parameters
 # -------------------------------------
-voc_chemistry:          .true. 
+voc_chemistry:          .true.
 voc_BiomassBurnFactor:  0.013   # 'g/g CO'
 voc_AnthroFactor:       0.069   # 'g/g CO'
 voc_MW:                 0.150   # 'kg/mol'

GEOS_AChemGridCompMod.F90 → ACHEM_GridCompMod.F90

@@ -5,11 +5,11 @@
 !-------------------------------------------------------------------------
 !BOP
 !
-! !MODULE: GEOS_AChemGridCompMod -
+! !MODULE: ACHEM_GridCompMod -
 !
 ! !INTERFACE:
 !
-   module GEOS_AChemGridCompMod
+   module ACHEM_GridCompMod
 !
 ! !USES:
 !
@@ -169,7 +169,7 @@ subroutine SetServices(GC, RC)
 !   Load private Config Attributes
 !   ------------------------------
     self%CF = ESMF_ConfigCreate(__RC__)
-    call ESMF_ConfigLoadFile(self%CF, 'GEOS_AChemGridComp.rc', __RC__)
+    call ESMF_ConfigLoadFile(self%CF, 'ACHEM_GridComp.rc', __RC__)
 
     call ESMF_ConfigGetAttribute(self%CF, self%verbose, label='verbose:', default=.false., __RC__)
 
@@ -721,7 +721,7 @@ subroutine SetServices(GC, RC)
 
 ! !EXTERNAL STATE:
     OPTIONAL_CHEM_EXPORT: if (self%mam_chem) then
-#include "GEOS_AChem_ExportSpec___.h"
+#include "ACHEM_ExportSpec___.h"
     end if OPTIONAL_CHEM_EXPORT
 
 
@@ -961,7 +961,7 @@ subroutine Initialize_(GC, IMPORT, EXPORT, CLOCK, rc)
 !  Declare pointers to IMPORT/EXPORT/INTERNAL states
 !  -------------------------------------------------
 #if(0)
-#include "GEOS_AChem_DeclarePointer___.h"
+#include "ACHEM_DeclarePointer___.h"
 #endif
 
 !  Get my name and set-up traceback handle
@@ -991,7 +991,7 @@ subroutine Initialize_(GC, IMPORT, EXPORT, CLOCK, rc)
 !  Get pointers to IMPORT/EXPORT/INTERNAL states
 !  ---------------------------------------------
 #if(0)
-#include "GEOS_AChem_GetPointer___.h"
+#include "ACHEM_GetPointer___.h"
 #endif
 
 !  Extract relevant runtime information
@@ -1307,7 +1307,7 @@ subroutine Run_(GC, IMPORT, EXPORT, CLOCK, rc)
 !  Declare pointers to IMPORT/EXPORT/INTERNAL states
 !  -------------------------------------------------
 #if(0)
-#include "GEOS_AChem_DeclarePointer___.h"
+#include "ACHEM_DeclarePointer___.h"
 #endif
 
 !  Get my name and set-up traceback handle
@@ -1318,7 +1318,7 @@ subroutine Run_(GC, IMPORT, EXPORT, CLOCK, rc)
 !  Get pointers to IMPORT/EXPORT/INTERNAL states
 !  ---------------------------------------------
 #if(0)
-   #include "GEOS_AChem_GetPointer___.h"
+   #include "ACHEM_GetPointer___.h"
 #else
 
 #endif
@@ -2135,7 +2135,7 @@ subroutine Run_(GC, IMPORT, EXPORT, CLOCK, rc)
    ! Note that we do not update the OH concentration
    ! Could (should?) integrate this with gas_chemistry below
    ! Right now the VOC calculation is optional, specified in
-   ! in GEOS_AchemGridComp.rc, but the export is coupled to
+   ! in ACHEM_GridComp.rc, but the export is coupled to
    ! GOCART if both GOCART and ACHEM are running, so fill
    ! in with zero in case it is requested.
 
@@ -3868,4 +3868,4 @@ pure function day_of_year(nymd) result (doy)
  end function day_of_year
 
 
- end module GEOS_AChemGridCompMod
+ end module ACHEM_GridCompMod

GEOSachem_Registry.rc → ACHEM_Registry.rc

@@ -7,18 +7,18 @@
 #
 # -----------------------------------------------------------------
 
-COMP_NAME: GEOS_AChem
+COMP_NAME: ACHEM
 
 # Only change the Registry version when major structural changes
 # occurs, not changes in content
 # --------------------------------------------------------------
-  MAPL_REGISTRY_VERSION: 1.00  
+  MAPL_REGISTRY_VERSION: 1.00
 
 #                               ------------
 #                               Import State
 #                               ------------
 
-<ImportSpec name="GEOS_AChem", cols="short_name,units,dims,vlocation,stat,refresh_interval,averaging_interval,num_subtiles,default,long_name">
+<ImportSpec name="ACHEM", cols="short_name,units,dims,vlocation,stat,refresh_interval,averaging_interval,num_subtiles,default,long_name">
 # ----------------------|------------|-----|---|----|---|---|-----|------|--------------------------
 # Short                 |            |     | V |Item|Intervl| Sub | Def  | Long
 # Name                  |   Units    | Dim |Loc|Type| R | A |Tiles| ault | Name
@@ -39,7 +39,7 @@ COMP_NAME: GEOS_AChem
   TS                    | K          | xy  |   |    |   |   |     |      | Surface skin temperature
   U10N                  | m s-1      | xy  |   |    |   |   |     |      | Equivalent neutral 10 meter eastward wind
   V10N                  | m s-1      | xy  |   |    |   |   |     |      | Equivalent neutral 10 meter northward wind
-  FROCEAN               | 1          | xy  |   |    |   |   |     |      | Fraction of ocean 
+  FROCEAN               | 1          | xy  |   |    |   |   |     |      | Fraction of ocean
   FRLAND                | 1          | xy  |   |    |   |   |     |      | Fraction of land
   FRLAKE                | 1          | xy  |   |    |   |   |     |      | Fraction of lake
   FRLANDICE             | 1          | xy  |   |    |   |   |     |      | Fraction of land ice
@@ -54,7 +54,7 @@ COMP_NAME: GEOS_AChem
   H2O2                  | mol mol-1  | xyz | C |    |   |   |     |      | Hydrogen peroxide (H2O2)
   O3                    | kg kg-1    | xyz | C |    |   |   |     |      | Ozone (mass mixing ratio)
 # ---------------------|------------|-----|---|----|---|---|-----|------|--------------------------
-#  OHSTRAT              | mol mol-1  | xyz | C |    |   |   |     |      | Hydroxyl radical 
+#  OHSTRAT              | mol mol-1  | xyz | C |    |   |   |     |      | Hydroxyl radical
 #  O3P                  | mol mol-1  | xyz | C |    |   |   |     |      | O triplet P
 #  OCS_JRATE            | s-1        | xyz | C |    |   |   |     |      | OCS photolysis rates
 # ----------------------|------------|-----|---|----|---|---|-----|------|--------------------------
@@ -83,7 +83,7 @@ COMP_NAME: GEOS_AChem
 #                               Export State
 #                               ------------
 
-<ExportSpec name="GEOS_AChem", cols="short_name,units,dims,vlocation,stat,refresh_interval,averaging_interval,num_subtiles,long_name">
+<ExportSpec name="ACHEM", cols="short_name,units,dims,vlocation,stat,refresh_interval,averaging_interval,num_subtiles,long_name">
 # ----------------------|---------------|-----|---|----|---|---|-----|------------------------------
 # Short                 |               |     | V |Item|Intervl| Sub | Long
 # Name                  |   Units       | Dim |Loc|Type| R | A |Tiles| Name
@@ -119,7 +119,7 @@ COMP_NAME: GEOS_AChem
   CMD_S_H2SO4           | kg m-2        | xy  |   |    |   |   |     | Column mass density of H2SO4 in kg-S m-2
   CMD_S_GAS             | kg m-2        | xy  |   |    |   |   |     | Column mass density of sulfur in gas phase in kg-S m-2
 #
-  CMD_N_NH3             | kg m-2        | xy  |   |    |   |   |     | Column mass density of NH3 in kg-N m-2             
+  CMD_N_NH3             | kg m-2        | xy  |   |    |   |   |     | Column mass density of NH3 in kg-N m-2
   CMD_N_GAS             | kg m-2        | xy  |   |    |   |   |     | Column mass density of nitrogen in kg-N m-2
 #
   CMD_DMS               | kg m-2        | xy  |   |    |   |   |     | Column mass density of DMS
@@ -209,7 +209,7 @@ COMP_NAME: GEOS_AChem
 # Note: 1) For friendlies, use "D" for dynamics, "T" for turbulence and "C" for convection, or "S" for self (add to EXPORT state); leave blank otherwise
 #       2) If quantity requires no restart, put an 'x' in the No Rst column
 
-<InternalSpec name="GEOS_AChem", cols="short_name,units,dims,vlocation,stat,refresh_interval,averaging_interval,num_subtiles,default,norestart,halowidth,friendlyto,long_name">
+<InternalSpec name="ACHEM", cols="short_name,units,dims,vlocation,stat,refresh_interval,averaging_interval,num_subtiles,default,norestart,halowidth,friendlyto,long_name">
 # ----------------------|------------|-----|---|----|---|---|-----|------|----|----|---------|------
 #  Short                |            |     | V |Item|Intervl| Sub | Def  | No | Ha | Friends | Long
 #  Name                 |   Units    | Dim |Loc|Type| R | A |Tiles| ault | Rst| lo |         | Name

AMIP/GEOS_AChemGridComp.rc → AMIP.20C/ACHEM_GridComp.rc

@@ -1,13 +1,13 @@
 #
 # Resource file for the GEOS aerosol chemistry grid component.
 #
-#   15 Aug 2012  A. Darmenov   
+#   15 Aug 2012  A. Darmenov
 #--------------------------------------------------------------------
 
 verbose: .True.
 
 
-# MAM chemistry 
+# MAM chemistry
 # -------------------------------------
 gas_chemistry:      .false.
 aqueous_chemistry:  .false.
@@ -21,7 +21,7 @@ ocs_surface_vmr: 490.0e-12   # 'mol/mol'
 
 # VOC chemistry and parameters
 # -------------------------------------
-voc_chemistry:          .true. 
+voc_chemistry:          .true.
 voc_BiomassBurnFactor:  0.013   # 'g/g CO'
 voc_AnthroFactor:       0.069   # 'g/g CO'
 voc_MW:                 0.150   # 'kg/mol'