HEMCO_Config.rc

GEOS-Chem Classic relies on the Harmonized Emissions Component (aka HEMCO) for file I/O, regridding, and computing emissions fluxes. Settings for HEMCO can be updated in the HEMCO configuration file, which is named HEMCO_Config.rc.

The HEMCO online manual at hemco.readthedocs.io contains detailed instructions about the structure and contents of HEMCO_Config.rc, so we will not replicate that content in this Guide. Instead, we will provide a short summary with links to the relevant documentation.

General HEMCO settings

Define general simulation parameters in the Settings section of HEMCO_Config.rc. This includes data paths, global diagnostic options, and verbose output options.

###############################################################################
### BEGIN SECTION SETTINGS
###############################################################################

ROOT:                        /path/to/hemco/data/dir
METDIR:                      /path/to/hemco/met/dir
GCAPSCENARIO:                not_used
GCAPVERTRES:                 47
Logfile:                     *
DiagnFile:                   HEMCO_Diagn.rc
DiagnPrefix:                 ./OutputDir/HEMCO_diagnostics
DiagnFreq:                   00000000 010000
Wildcard:                    *
Separator:                   /
Unit tolerance:              1
Negative values:             0
Only unitless scale factors: false
Verbose:                     false
VerboseOnCores:              root       # Accepted values: root all

### END SECTION SETTINGS ###

Extension switches

Turn individual emissions inventories on/off in the Extension Switches section of HEMCO_Config.rc. Emission inventories are specified as either Base Emissions (i.e. read from files on disk) or Extensions (i.e. computed using meteorological inputs).

###############################################################################
### BEGIN SECTION EXTENSION SWITCHES
###############################################################################
# ExtNr ExtName                on/off  Species  Years avail.
0       Base                   : on    *
# ----- MAIN SWITCHES ---------------------------------------------------------
    --> EMISSIONS              :       true
    --> METEOROLOGY            :       true
    --> CHEMISTRY_INPUT        :       true
# ----- RESTART FIELDS --------------------------------------------------------
    --> GC_RESTART             :       true
    --> HEMCO_RESTART          :       true
# ----- NESTED GRID FIELDS ----------------------------------------------------
    --> GC_BCs                 :       false
# ----- REGIONAL INVENTORIES --------------------------------------------------
    --> APEI                   :       false    # 1989-2014
    --> NEI2016_MONMEAN        :       false    # 2002-2020
    --> DICE_Africa            :       false    # 2013
# ----- GLOBAL INVENTORIES ----------------------------------------------------
    --> CEDSv2                 :       true     # 1750-2019
    --> CEDS_GBDMAPS           :       false    # 1970-2017
    --> CEDS_GBDMAPS_byFuelType:       false    # 1970-2017

... etc ...

# -----------------------------------------------------------------------------
100     Custom                 : off   -
101     SeaFlux                : on    DMS/ACET/ALD2/MENO3/ETNO3/MOH
102     ParaNOx                : on    NO/NO2/O3/HNO3
    --> LUT data format        :       nc
    --> LUT source dir         :       $ROOT/PARANOX/v2015-02
103     LightNOx               : on    NO
    --> CDF table              :       $ROOT/LIGHTNOX/v2014-07/light_dist.ott2010.dat
104     SoilNOx                : on    NO
    --> Use fertilizer NOx     :       true

... etc ...

### END SECTION EXTENSION SWITCHES ###

Base emissions

Note

You do not have to edit this section if you just wish to run GEOS-Chem Classic with its default emissions configuration. But if your simulation start date does not match the date of the restart file, or if you simulation contains species not found in the restart file, then you must edit the restart file entry as described below.

Specify how emissions and other data sets will be read from disk in the Base Emissions section of HEMCO_Config.rc.

###############################################################################
### BEGIN SECTION BASE EMISSIONS
###############################################################################

# ExtNrName sourceFile sourceVar sourceTime C/R/E SrcDim SrcUnit Species ScalIDs Cat Hier

(((EMISSIONS

... etc ...

#==============================================================================
# --- CEDS_01x01 ---
#
# %%% This is the default global inventory.                            %%%
# %%% You may select either CEDS, EDGAR, HTAP or CMIP6_SFC_LAND_ANTHRO %%%
# %%% for the global base emissions.                                   %%%
#==============================================================================
(((CEDS_01x01
0 CEDS_NO_AGR  $ROOT/CEDS/v2024-06/$YYYY/CEDS_NO_0.1x0.1_$YYYY.nc  NO_agr  1980-2019/1-12/1/0 C xy   kg/m2/s NO  2401          1 5
0 CEDS_NO_ENE  $ROOT/CEDS/v2024-06/$YYYY/CEDS_NO_0.1x0.1_$YYYY.nc  NO_ene  1980-2019/1-12/1/0 C xyL* kg/m2/s NO  2401/706/315  1 5
0 CEDS_NO_IND  $ROOT/CEDS/v2024-06/$YYYY/CEDS_NO_0.1x0.1_$YYYY.nc  NO_ind  1980-2019/1-12/1/0 C xyL* kg/m2/s NO  2407/707/316  1 5
0 CEDS_NO_TRA  $ROOT/CEDS/v2024-06/$YYYY/CEDS_NO_0.1x0.1_$YYYY.nc  NO_tra  1980-2019/1-12/1/0 C xy   kg/m2/s NO  2411/711      1 5
0 CEDS_NO_RCO  $ROOT/CEDS/v2024-06/$YYYY/CEDS_NO_0.1x0.1_$YYYY.nc  NO_rco  1980-2019/1-12/1/0 C xy   kg/m2/s NO  2409/709      1 5
0 CEDS_NO_SLV  $ROOT/CEDS/v2024-06/$YYYY/CEDS_NO_0.1x0.1_$YYYY.nc  NO_slv  1980-2019/1-12/1/0 C xy   kg/m2/s NO  2407/707      1 5
0 CEDS_NO_WST  $ROOT/CEDS/v2024-06/$YYYY/CEDS_NO_0.1x0.1_$YYYY.nc  NO_wst  1980-2019/1-12/1/0 C xy   kg/m2/s NO  25            1 5

... etc ...

### END SECTION BASE EMISSIONS ###

GEOS-Chem Classic restart input via HEMCO

If your GEOS-Chem Classic simulation is configured to read the restart file via HEMCO, then your simulation will stop by default if:

The start date of your simulation does not match the restart file’s internal timestamp (as specified by the time:units netCDF attribute).
The restart file does not contain all of the species used by your simulation.

But you may force the simulation to proceed as follows. First, for the SPC_ entry in your HEMCO_Config.rc file. This may be found in the NON-EMISSIONS DATA subsection under the BASE EMISSIONS section:

* SPC_           ./Restarts/GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 SpeciesRst_?ALL?    $YYYY/$MM/$DD/$HH EFYO xyz 1 * - 1 1

Next, change the EFYO to either CYS or EY (both will work).

* SPC_           ./Restarts/GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 SpeciesRst_?ALL?    $YYYY/$MM/$DD/$HH CYS xyz 1 * - 1 1

This will allow your simulation to proceed without stopping.

Scale factors

Define scale factors for emissions inventories and other data sets in the Scale Factors section of HEMCO_Config.rc.

#==============================================================================
# --- Scale factors used for species conversions ---
#==============================================================================

# Units carbon to species conversions
# Factor = # carbon atoms * MW carbon) / MW species
40 CtoACET MATH:58.09/(3.0*12.0)   - - - xy unitless 1
41 CtoALD2 MATH:44.06/(2.0*12.0)   - - - xy unitless 1
42 CtoALK4 MATH:58.12/(4.3*12.0)   - - - xy unitless 1

... etc ...
# VOC speciations
(((RCP_3PD.or.RCP_45.or.RCP_60.or.RCP_85
50 KET2MEK    0.25  - - - xy unitless 1
51 KET2ACET   0.75  - - - xy unitless 1
)))RCP_3PD.or.RCP_45.or.RCP_60.or.RCP_85

... etc ...

### END SECTION SCALE FACTORS ###

Masks

Define masks for emissions and other data sets in the Masks section of HEMCO_Config.rc

  ###############################################################################
  ### BEGIN SECTION MASKS
  ###############################################################################

  # ScalID Name sourceFile sourceVar sourceTime C/R/E SrcDim SrcUnit Oper Lon1/Lat1/Lon2/Lat2

  (((EMISSIONS

  #==============================================================================
  # Country/region masks
  #==============================================================================
  (((APEI
  1002 CANADA_MASK $ROOT/MASKS/v2018-09/Canada_mask.geos.1x1.nc                  MASK     2000/1/1/0 C xy 1 1 -141/40/-52/85
  )))APEI

  (((NEI2016_MONMEAN
  1007 CONUS_MASK  $ROOT/MASKS/v2018-09/CONUS_Mask.01x01.nc                      MASK     2000/1/1/0 C xy 1 1 -140/20/-50/60
  )))NEI2016_MONMEAN

  ... etc ...

  )))EMISSIONS

  ### END SECTION MASKS ###

  ### END OF HEMCO INPUT FILE ###

.. _cfg-hco-gchp-gcc:

Usage differences between GCHP and GEOS-Chem Classic

HEMCO_Config.rc is used in GCHP for masking and scaling within HEMCO. The input file and read frequency information is not used because MAPL ExtData handles file input rather than HEMCO in GCHP. Items at the top of the file that are ignored include:

ROOT data directory path
METDIR path
DiagnPrefix
DiagnFreq
Wildcard

The ROOT data directory and METDIR paths are instead specified by the symbolic links in the run directory. Diagnostic filename and frequency information are specified in HISTORY.rc. Emissions diagnostics in GCHP are output in the same way and with the same file format as other diagnostic collections in GCHP. Please note, however, that all emissions diagnostics are vertically flipped relative to other diagnostics, with level 1 corresponding to top-of-atmosphere.

In the Base emissions section and beyond, columns that are ignored include:

sourceFile
sourceVar
sourceTime
C/R/E
SrcDim
SrcUnit

Because GCHP uses NASA MAPL code to read and regrid input files the file path, variable name, and data frequency are specified in GCHP config file ExtData.rc. Input data dimensions and units are not needed since they are taken directly from the file during read.

Note that some GEOS-Chem simulations require that all species be present in the restart file. For GEOS-Chem Classic you can get around this by updating the C/R/E flags in HEMCO_Config.rc. In GCHP that part of HEMCO_Config.rc is not used. To configure your run to allow missing species in the restart file you instead need to flip a switch in config file setCommonRunSettings.sh. Search for string Require_Species_in_Restart in the file. If set to 1 it will require species, and if set to 0 it will not.

Also beware that one entry in HEMCO_Config.rc is changed when script setCommonRunSettings.sh is executed in the run script prior to running GCHP. The online dust mass tuning factor gets replaced by a value specific to your configured grid resolution.

One entry also gets propagated to another configuration file by setCommonRunSettings.sh. Lightning entries in ExtData.rc get commented or uncommented depending on whether lightning climatology is turned on in HEMCO_Config.rc.