Archive output with the History diagnostics

Introduction

GEOS-Chem Classic and GCHP allow you to save various diagnostic fields to netCDF files via the History component. In the following sections you will learn how to schedule diagnostics for output using History.

Note

HEMCO has its own diagnostic archiving capability. Please see the HEMCO diagnostics chapter of The HEMCO User’s Guide more information.

The HISTORY.rc configuration file

You can request GEOS-Chem diagnostics by editing the HISTORY.rc configuration file. This file lists the groups of diagnostic outputs (called collections), and the parameters for each collection (frequency of archival, mode of archiving, fields per collection, etc.). GEOS-Chem will write netCDF files for each collection at the output intervals that you specify in HISTORY.rc.

The following is a stripped-down HISTORY.rc file example for illustration purposes. The HISTORY.rc file that you will find in your GEOS-Chem run directory will contain more collections than what is shown below.

#============================================================================
# EXPID allows you to specify the beginning of the file path corresponding
# to each diagnostic collection.  For example:
#
#   EXPID: ./GEOSChem
#      Will create netCDF files whose names begin "GEOSChem",
#      in this run directory.
#
#   EXPID: ./OutputDir/GEOSChem
#      Will create netCDF files whose names begin with "GEOSChem"
#      in the OutputDir sub-folder of this run directory.
#
#============================================================================
EXPID:  ./OutputDir/GEOSChem

#==============================================================================
# %%%%% COLLECTION NAME DECLARATIONS %%%%%
#
# To disable a collection, place a "#" character in front of its name.
#==============================================================================
COLLECTIONS: 'SpeciesConc',
             'SpeciesConcSubset',
             'ConcAfterChem',
::
#==============================================================================
# %%%%% THE SpeciesConc COLLECTION %%%%%
#
# GEOS-Chem species concentrations (default = advected species)
#
# Available for all simulations
#==============================================================================
SpeciesConc.template:           '%y4%m2%d2_%h2%n2z.nc4',
SpeciesConc.frequency:          00000000 060000
SpeciesConc.duration :          00000001 000000
SpeciesConc.format:             'CFIO',
SpeciesConc.mode:               'instantaneous',
SpeciesConc.fields:             'SpeciesConcVV_?ADV?',
                                'SpeciesConcMND_?ALL?',
::
#==============================================================================
# %%%%% THE SpeciesConcSubset COLLECTION %%%%%
#
# Same as the SpeciesConc collection, but will subset data in the horizontal
# and vertical dimensions so that the netCDF diagnostic files will cover
# a smaller region of the globe.  This can save disk space and memory.
#
# NOTE: This capability will be available in GEOS-Chem "Classic" 12.5.0
# and later versions.
#
# Available for all simulations
#==============================================================================
SpeciesConcSubset.template:     '%y4%m2%d2_%h2%n2z.nc4',
SpeciesConcSubset.frequency:    00000000 060000
SpeciesConcSubset.duration:     00000001 000000
SpeciesConcSubset.format:       'CFIO',
SpeciesConcSubset.mode:         'instantaneous',
SpeciesConcSubset.LON_RANGE:    -40.0 60.0,
SpeciesConcSubset.LAT_RANGE:    -10.0 50.0,
SpeciesConcSubset.levels:       1 2 3 4 5,
SpeciesConcSubset.fields:       'SpeciesConcVV_?ADV?',
::
#==============================================================================
# %%%%% THE ConcAfterChem COLLECTION %%%%%
#
# Concentrations of OH, HO2, O1D, O3P immediately after exiting the KPP solver
# or OH after the CH4 specialty-simulation chemistry routine.
#
# OH:       Available for all full-chemistry simulations and CH4 specialty sim
# HO2:      Available for all full-chemistry simulations
# O1D, O3P: Availalbe for full-chemistry simulations using UCX mechanism
#==============================================================================
ConcAfterChem.template:         '%y4%m2%d2_%h2%n2z.nc4',
ConcAfterChem.format:           'CFIO',
ConcAfterChem.frequency:        00000100 000000,
ConcAfterChem.duration:         00000100 000000,
ConcAfterChem.mode:             'time-averaged',
ConcAfterChem.fields:           'OHconcAfterChem',
                                'HO2concAfterChem',
                                'O1DconcAfterChem',
                                'O3PconcAfterChem',
::

In this HISTORY.rc file, we are requesting three collections, or types of netCDF file output. The table below explains in more detail parameters shown in the HISTORY.rc file above.

EXPID

This parameter controls the filename prefix. In this example,, EXPID is set to ./OutputDir/GEOSChem by default. This means that all diagnostic files will be written to the ./OutputDir subdirectory of the GEOS-Chem run directory, and will start with the prefix GEOSChem.

Note

Restart files are placed in the ./Restarts subdirectory of the run directory instead of ./OutputDir, which only contains diagnostic files.

COLLECTIONS:

The COLLECTIONS: tag specifies all of the diagnostic collections that you wish to activate during a GEOS-Chem simulation. Each collection represents a group of diagnostic quantities that will be written to disk in netCDF file format. The collection name will be automatically added to the netCDF file name along with the date/or time.

Each GEOS-Chem run directory will ship with its own customized HISTORY.rc configuration file. Only the diagnostic collections pertaining to a particular GEOS-Chem simulation will be included in the corresponding HISTORY.rc file.

Each collection name must be bracketed by single quotes, and be followed by a comma.

To disable an entire diagnostic collection, simply put a # comment character in front of the collection name in the COLLECTIONS: section.

GEOS-Chem will expect to find a collection definition section for each of the activated collections listed under the COLLECTIONS: section. In other words, if you have SpeciesConc listed under COLLECTIONS:, but there is no further information provided about the SpeciesConc collection, then GEOS-Chem will halt with an error message.

Note

You are not limited to the collections that are pre-defined in the HISTORY.rc configuration file. You may create additional diagnostic collections to suit your research purposes.

SpeciesConc

Name of the first collection in this HISTORY.rc file.

SpeciesConc.template

Determines the date and time format for the SpeciesConc collection filename suffix, as described below:

  • %y4%m2%d2_%h2%n2z.nc4 prints YYYYMMDD_hhmmz.nc4 to the end of each netCDF filename.

  • YYYYMMDD is the date in year/month/day format;

  • hhmm is the time in hour:minutes format.

  • z denotes “Zulu”, which is an abbreviation for UTC time.

  • .nc4 denotes that the data file is in the netCDF-4 format.

Note

For example, the complete file path for the SpeciesConc collection at 00:00 UTC on 2020/01/01 will be ./OutputDir/GEOSChem.SpeciesConc.20200101_0000z.nc4, where:

  • EXPID specifies the filename prefix (./OutputDir/GEOSChem)

  • SpeciesConc.template specifies the format of the filename suffix (.20200101_0000z.nc4).

SpeciesConc.frequency

Determines how often the diagnostic quantities belonging to the SpeciesConc collection will be saved to a netCDF file. This can be specified as either hhmmss or YYYYMMDD hhmmss.

In the above example, data belonging to the collection will be written to the file every 6 hours. Because SpeciesConc is an instantaneous collection, no time-averaging will be performed.

SpeciesConc.format

For GCHP simulations only. This tag indicates the I/O library that will be used.

SpeciesConc.duration

Determines how often a new SpeciesConc netCDF file will be created. Uses the same format as SpeciesConc.frequency.

SpeciesConc.mode

Determines the averaging method for the SpeciesConc collection. Allowable values are:

  • instantaneous: Archives instantaneous values at the interval specified by SpeciesConc.frequency.

  • time-averaged: Archives values averaged over the interval specified by SpeciesConc.frequency.

SpeciesConc.fields

Lists the diagnostic quantities to be archived in the SpeciesConc collection. Some diagnostic quantities (e.g. concentrations, fluxes, masses) may also have an extra dimension, which represents species, size bins, reaction numbers, etc.

For example, to request the ozone species concentration (in mixing ratio units) you may use the field name SpeciesConcVV_O3. The species name is separated from the quantity name by a single underscore.

Note

For GCHP, each diagnostic field must be followed by 'GCHPchem',. This indicates the ESMF Gridded Component to which the diagnostics belong.

If you are using GEOS-Chem Classic,you may also use a wildcard to specify a given category of species. In the above example SpeciesConcVV_?ADV? refers to all advected species and SpeciesConcVV_?ALL? refers to all species (both advected and non-advected).

Note

GCHP does not allow the use of wildcards. Each diagnostic quantity must be listed individually.

::

Signifies the end of the SpeciesConc definition section. :: may be placed at any column.

SpeciesConc.subset

Name of the second diagnostic collection specified in this sample HISTORY.rc configuration file. In this collection we will request output to be restricted to a subset of the horizontal grid.

The .template, .frequency, .duration, :mode, and .fields are described for the SpeciesConc collection above, so we will not repeat them here.

SpeciesConcSubset.LON_RANGE

Defines the longitude range (min max) where diagnostic data will be archived. Data outside of this range will be ignored. If this option is omitted, values at all longitudes (-180 180) will be included.

SpeciesConcSubset.LAT_RANGE

Defines the latitude range (min max) where diagnostic data will be archived. Data outside of this range will be ignored. If this option is omitted, values at all latitudes (-90 90) will be included.

SpeciesConcSubset.levels

Specifies the levels that you wish to be included in the diagnostic archiving. If omitted, data at all levels will be included.

Note

In GEOS-Chem Classic, all levels between the minimum and maximum level specified will be included in the diagnostic archival. This differs from the behavior in GCHP, which archives only the specified levels.

ConcAfterChem

Name of the third collection specified in this sample HISTORY.rc configuration file.

The .template, .frequency, .duration, :mode, and .fields are described for the SpeciesConc collection above, so we will not repeat them here.

ConcAftercChem.mode

In this example, the ConcAfterChem.mode setting indicates that the ConcAfterChem collection will contain time-averaged data. The averaging interval is set in the

Wildcards (GEOS-Chem Classic only)

For GEOS-Chem Classic diagnostic output, you can use the following wildcards with diagnostic quantities that have a species/bin/reaction dimension:

Wildcard

Description

Example

?ADV?

Advected species

SpeciesConcVV_?ADV?

?AER?

Aerosol species

SpeciesConcVV_?AER?

?ALL?

All species

SpeciesConcVV_?ALL?

?DRY?

Dry-deposited species

SpeciesConcVV_?DRY?

?DRYALT?

Species for the histguide-concabovechem collection

SpeciesConcVV_?DRYALT

?DUSTBIN?

Dust bin number

AODdust550nm_?DUSTBIN?

?FIX?

Fixed species in the KPP chemistry mechanism

SpeciesConcVV_?FIX?

?GAS?

Gas-phase species

SpeciesConcVV_?GAS?

?HYG?

Aerosol species that undergo hygroscopic growth (e.g. black carbon)

AODhyg550nm_?HYG?

?KPP?

All species (fixed + variable) in the KPP chemistry mechanism

SpeciesConcVV_?KPP?

?LOS?

Chemical loss species or families

SpeciesConcVV_?LOS?

?PHO?

Photolyzed species

SpeciesConcVV_?PHO?

?PRD?

Chemical production species or families

SpeciesConcVV_?PRD?

?RRTMG?

RRTMG-computed fluxes

RadAllSkywSurf_?RRTMG?

?RXN?

KPP reaction rates

RxnRate_?RXN?

?TOMASBIN?

TOMAS size bins

TomasH2SO4Mass_?TOMASBIN?

?UVFLX?

UV flux bins

UVFluxDiffuse_?UVFLX?

?VAR?

Variable species in the KPP mechanism

SpeciesConcVV_?VAR?

?WET?

Wet-deposited species

SpeciesConcVV_?WET

Prefixes

You may add any field from the State_Met and State_Chm objects to any diagnostic collection as well. These fields must be prefixed as described below:

Wildcard

Description

Example

Chem_

Request diagnostic output from the State_Chm object

Chem_pHCloud

Met_

Request diagnostic output from the State_Met object

Met_SPHU

File naming convention

As mentioned above, SpeciesConc.template, GEOS-Chem History files adhere to the following naming convention:

EXPID.collection-name.collection-template

e.g.

../OutputDir/GEOSChem.SpeciesConc.20200101_0000z.nc4

The duration tag of each collection in HISTORY.rc controls how often a new file will be written to disk, as we saw above:

SpeciesConc.duration:           00000001 000000     # Write a new file each day
SpeciesConcSubset.duration:     00000001 000000     # Write a new file each day
ConcAfterChem.duration:         00000100 000000     # Write a new file each month

Therefore, based on all of these settings in our example HISTORY.rc file, GEOS-Chem will write the following netCDF files to disk in the current run directory:

GEOSChem.SpeciesConc.20160101_0000z.nc4    GEOSChem.SpeciesConcSubset.20160101_0000z.nc4
GEOSChem.SpeciesConc.20160102_0000z.nc4    GEOSChem.SpeciesConcSubset.20160102_0000z.nc4
GEOSChem.SpeciesConc.20160103_0000z.nc4    GEOSChem.SpeciesConcSubset.20160102_0000z.nc4
GEOSChem.SpeciesConc.20160104_0000z.nc4    GEOSChem.SpeciesConcSubset.20160104_0000z.nc4
... etc ...

GEOSChem.ConcAfterChem.20160101_0000z.nc4
GEOSChem.ConcAfterChem.20160201_0000z.nc4
GEOSChem.ConcAfterChem.20160301_0000z.nc4
GEOSChem.ConcAfterChem.20160401_0000z.nc4
... etc ...

Vertical coordinates in netCDF files

All netCDF files produced by GEOS-Chem (i.e. diagnostic files and restart files) adhere to the the COARDS netCDF convention. for the lon, lat, and time dimensions.

For the vertical dimension, we have chosen to use the following coordinate variables, emulating the file format of the NCAR Community Earth System Model (CESM):

variables:
     double lev(lev) ;
         lev:long_name = "hybrid level at midpoints (1000*(A+B))" ;
         lev:units = "level" ;
         lev:positive = "down" ;\
         lev:standard_name = "atmosphere_hybrid_sigma_pressure_coordinate" ;
         lev:formula_terms = "a: hyam b: hybm p0: P0 ps: PS" ;
     double hyam(lev) ;
         hyam:long_name = "hybrid A coefficient at layer midpoints" ;
     double hybm(lev) ;
         hybm:long_name = "hybrid B coefficient at layer midpoints" ;
     double ilev(ilev) ;
         ilev:long_name = "hybrid level at interfaces (1000*(A+B))" ;
         ilev:units = "level" ;
         ilev:positive = "down" ;
         ilev:standard_name = "atmosphere_hybrid_sigma_pressure_coordinate" ;
         ilev:formula_terms = "a: hyai b: hybi p0: P0 ps: PS" ;
     double hyai(ilev) ;
         hyai:long_name = "hybrid A coefficient at layer interfaces" ;
     double hybi(ilev) ;
         hybi:long_name = "hybrid B coefficient at layer interfaces" ;
     double P0 ;
         P0:long_name = "reference pressure" ;

The lev variable is used for data that is placed on the midpoints between vertical levels. This is an “approximate” eta coordinate, which is close to 1 at the surface and close to zero at the atmosphere top.

lev = 0.99250002413, 0.97749990013, 0.962499776, 0.947499955, 0.93250006,
   0.91749991, 0.90249991, 0.88749996, 0.87249996, 0.85750006, 0.842500125,
   0.82750016, 0.8100002, 0.78750002, 0.762499965, 0.737500105, 0.7125001,
   0.6875001, 0.65625015, 0.6187502, 0.58125015, 0.5437501, 0.5062501,
   0.4687501, 0.4312501, 0.3937501, 0.3562501, 0.31279158, 0.26647905,
   0.2265135325, 0.192541016587707, 0.163661504087706, 0.139115, 0.11825,
   0.10051436, 0.085439015, 0.07255786, 0.06149566, 0.05201591, 0.04390966,
   0.03699271, 0.03108891, 0.02604911, 0.021761005, 0.01812435, 0.01505025,
   0.01246015, 0.010284921, 0.008456392, 0.0069183215, 0.005631801,
   0.004561686, 0.003676501, 0.002948321, 0.0023525905, 0.00186788,
   0.00147565, 0.001159975, 0.00090728705, 0.0007059566, 0.0005462926,
   0.0004204236, 0.0003217836, 0.00024493755, 0.000185422, 0.000139599,
   0.00010452401, 7.7672515e-05, 5.679251e-05, 4.0142505e-05, 2.635e-05,
   1.5e-05 ;

The lev variable may be used for quick plotting. To compute the actual pressure at the midpoint of the grid box (I,J,L), you will need to supply your own 2-D surface pressure field (e.g. saved from another diagnostic file):

Pmid = ( hyam(L) * PS(I,J) ) + hybm(L)

The ilev variable is used for data that is placed on vertical level edges or “interfaces” (hence the “i” in ilev). This is also an “approximate” eta coordinate.

ilev = 1, 0.98500004826, 0.969999752, 0.9549998, 0.94000011, 0.92500001,
   0.90999981, 0.89500001, 0.87999991, 0.86500001, 0.85000011, 0.83500014,
   0.82000018, 0.80000022, 0.77499982, 0.75000011, 0.7250001, 0.7000001,
   0.6750001, 0.6375002, 0.6000002, 0.5625001, 0.5250001, 0.4875001,
   0.4500001, 0.4125001, 0.3750001, 0.3375001, 0.28808306, 0.24487504,
   0.208152025, 0.176930008175413, 0.150393, 0.127837, 0.108663, 0.09236572,
   0.07851231, 0.06660341, 0.05638791, 0.04764391, 0.04017541, 0.03381001,
   0.02836781, 0.02373041, 0.0197916, 0.0164571, 0.0136434, 0.0112769,
   0.009292942, 0.007619842, 0.006216801, 0.005046801, 0.004076571,
   0.003276431, 0.002620211, 0.00208497, 0.00165079, 0.00130051, 0.00101944,
   0.0007951341, 0.0006167791, 0.0004758061, 0.0003650411, 0.0002785261,
   0.000211349, 0.000159495, 0.000119703, 8.934502e-05, 6.600001e-05,
   4.758501e-05, 3.27e-05, 2e-05, 1e-05 ;

To compute the actual pressure at the bottom and top edges of the grid box (I,J,L), you will need to supply your own 2-D surface pressure field (e.g. saved from another diagnostic file):

Pbot = ( hyai(L  ) * PS(I,J) ) + hybi(L  )
Ptop = ( hyai(L+1) * PS(I,J) ) + hybi(L+1)

Diagnostic collections

The diagnostic collections described in the sections below are used by default in GEOS-Chem simulations. You can create your own customized collections by modifying the HISTORY.rc file.

The only restriction is that you cannot mix data that is placed on grid box layer edges in the same collection as data placed on grid box layer centers. This violates the netCDF convention that all data variables have to be defined with the same vertical dimension.

Note

For diagnostic quantities that have a species/bin/reaction dimension, we will use the abbreviation <name|wc> to indicate a species/bin/reaction name or wildcard.

For example, SpeciesConcVV_<name|wc> means that the diagnostic quantity can be a single species (SpeciesConcVV_O3) or a wildcarded subset of species (SpeciesConcVV_?ADV?).

AdvFluxVert

The AdvFluxVert collection contains diagnostics for vertical transport in advection. In practice, this collection is only used to obtain the vertical flux of O3 from GEOS-Chem fullchem benchmark simulations. Most GEOS-Chem users will not need to activate this collection.

Sample definition section for HISTORY.rc

  AdvFluxVert.template:    '%y4%m2%d2_%h2%n2z.nc4',
  AdvFluxVert.frequency:   00000100 000000
  AdvFluxVert.duration:    00000100 000000
  AdvFluxVert.mode:        'time-averaged'
  AdvFluxVert.fields:      'AdvFluxVert_O3',
::

List of diagnostic fields in the AdvFluxVert collection

Diagnostic field

Description

Units

Wildcards

AdvFluxVert_<name|wc> [1]

Vertical flux of species in advection

kg/s

?ADV?

Footnotes

AerosolMass

The AerosolMass collection contains diagnostics for aerosol mass and particulate matter from full-chemistry simulations.

Sample definition section for HISTORY.rc

  AerosolMass.template:       '%y4%m2%d2_%h2%n2z.nc4',
  AerosolMass.frequency:      00000100 000000
  AerosolMass.duration:       00000100 000000
  AerosolMass.mode:           'time-averaged'
  AerosolMass.fields:         'AerMassASOA    ',
                              'AerMassBC      ',
                              'AerMassINDIOL  ',
                              'AerMassISN1OA  ',
                              'AerMassISOA    ',
                              'AerMassLVOCOA  ',
                              'AerMassNH4     ',
                              'AerMassNIT     ',
                              'AerMassOPOA    ',
                              'AerMassPOA     ',
                              'AerMassSAL     ',
                              'AerMassSO4     ',
                              'AerMassSOAGX   ',
                              'AerMassSOAIE   ',
                              'AerMassSOAME   ',
                              'AerMassSOAMG   ',
                              'AerMassTSOA    ',
                              'BetaNO         ',
                              'PM25           ',
                              'TotalBiogenicOA',
                              'TotalOA        ',
                              'TotalOC        ',
::

List of diagnostic fields in the AerosolMass collection

Diagnostic field

Description

Units

AerMassASOA[2]

Aerosol products of light aromatics + IVOC oxidation

\({\mu}g/m^3\)

AerMassBC

Aerosol products of light aromatics + IVOC oxidation

\({\mu}g/m^3\)

AerMassINDIOL[2]

Generic aerosol-phase organonitrate hydrolysis product

\({\mu}g/m^3\)

AerMassISN10A[2]

Aerosol phase 2nd generation hydroxynitrates formed from ISOP + NO3 rxn pathway

\({\mu}g/m^3\)

AerMassISOA[2]

Aerosol products of isoprene oxidation

\({\mu}g/m^3\)

AerMassLVOCOA[2]

Aerosol-phase low-volatility non-IEPOX product of ISOPOOH (RIP) oxidation

\({\mu}g/m^3\)

AerMassNH4

Ammonium

\({\mu}g/m^3\)

AerMassNIT

Inorganic nitrate aerosol

\({\mu}g/m^3\)

AerMassPOA[2]

Aerosols from SVOCs

\({\mu}g/m^3\)

AerMassOPOA[2]

Aerosols products of POG oxidation

\({\mu}g/m^3\)

AerMassSAL

Sea salt aerosol (SALA+SALC)

\({\mu}g/m^3\)

AerMassSO4

Sulfate

\({\mu}g/m^3\)

AerMassSOAGX[2]

Aerosol phase glyoxal

\({\mu}g/m^3\)

AerMassSOAIE[2]

Aerosol phase IEPOX

\({\mu}g/m^3\)

AerMassSOAME[2]

Aerosol phase IMAE

\({\mu}g/m^3\)

AerMassSOAMG[2]

Aerosol phase methylglyoxal

\({\mu}g/m^3\)

AerMassTSOA[2]

Aerosol products of terpene oxidation

\({\mu}g/m^3\)

BetaNO[2]

NO branching ratio

\({\mu}g/m^3\)

PM25

Particulate matter (d < 2.5 :math:{mu}m`)

\({\mu}g/m^3\)

TotalBiogenicOA[3]

Sum of all organic aerosol

\({\mu}g/m^3\)

TotalOA[2]

Sum of all organic aerosol

\({\mu}g/m^3\)

TotalOC

Sum of all organic carbon

\({\mu}g/m^3\)

Notes for the AerosolMass collection

Aerosols

The Aerosols collection contains diagnostics for aerosol optical depth and related quantities from full-chemistry simulations.

Note

Some diagnostic fields in the Aerosols collection may be computed at up to 3 wavelengths (WL1, WL2, WL3) as specified in this menu of the geoschem_config.yml file:

rrtmg_rad_transfer_model:
    ... etc ...
    aod_wavelengths_in_nm:
    - 550

For GEOS-Chem simulations that do not use the RRTMG radiative transfer model, you may specify only one wavelength WL1, which is set to a default value of 550 nm. For GEOS-Chem simulations using RRTMG, you may specify up to 2 more additional wavelengths (WL2 and WL3). GEOS-Chem will replace the tokens WL1, WL2, WL3 in diagnostic field names with the corresponding wavelength.

For example, these diagnostic fields:

AODHygWL1_BCPI
AODDustWL1_DST1
AODStratLiquidAerWL1
AODPolarStratCloudWL1
AODSOAfromAqIsopreneWL1
AODStratLiquidAerWL1
AODPolarStratCloudWL1

will be saved to the GEOSChem.Aerosols.YYYYMMDD_hhmmz.nc4 file(s) under these names:

AODHyg550nm_BCPI
AODDust550nm_DST1
AODStratLiquidAer550nm
AODPolarStratCloud550nm
AODSOAfromAqIsoprene550nm
AODStratLiquidAer550nm
AODPolarStratCloud550nm

Sample definition section for HISTORY.rc

  Aerosols.template:    '%y4%m2%d2_%h2%n2z.nc4',
  Aerosols.frequency:   00000100 000000
  Aerosols.duration:    00000100 000000
  Aerosols.mode:        'time-averaged'
  Aerosols.fields:      'AODDust                      ',
                        'AODDustWL1_?DUSTBIN?         ',
                        'AODHygWL1_?HYG?              ',
                        'AODSOAfromAqIsopreneWL1      ',
                        'AODStratLiquidAerWL1         ',
                        'AODPolarStratCloudWL1        ',
                        'AerHygroscopicGrowth_?HYG?   ',
                        'AerNumDensityStratLiquid     ',
                        'AerNumDensityStratParticulate',
                        'AerAqueousVolume             ',
                        'AerSurfAreaDust              ',
                        'AerSurfAreaHyg_?HYG?         ',
                        'AerSurfAreaStratLiquid       ',
                        'AerSurfAreaPolarStratCloud   ',
                        'Chem_AeroAreaMDUST1          ',
                        'Chem_AeroAreaMDUST2          ',
                        'Chem_AeroAreaMDUST3          ',
                        'Chem_AeroAreaMDUST4          ',
                        'Chem_AeroAreaMDUST5          ',
                        'Chem_AeroAreaMDUST6          ',
                        'Chem_AeroAreaMDUST7          ',
                        'Chem_AeroAreaSULF            ',
                        'Chem_AeroAreaBC              ',
                        'Chem_AeroAreaOC              ',
                        'Chem_AeroAreaSSA             ',
                        'Chem_AeroAreaSSC             ',
                        'Chem_AeroAreaBGSULF          ',
                        'Chem_AeroAreaICEI            ',
                        'Chem_AeroRadiMDUST1          ',
                        'Chem_AeroRadiMDUST2          ',
                        'Chem_AeroRadiMDUST3          ',
                        'Chem_AeroRadiMDUST4          ',
                        'Chem_AeroRadiMDUST5          ',
                        'Chem_AeroRadiMDUST6          ',
                        'Chem_AeroRadiMDUST7          ',
                        'Chem_AeroRadiSULF            ',
                        'Chem_AeroRadiBC              ',
                        'Chem_AeroRadiOC              ',
                        'Chem_AeroRadiSSA             ',
                        'Chem_AeroRadiSSC             ',
                        'Chem_AeroRadiBGSULF          ',
                        'Chem_AeroRadiICEI            ',
                        'Chem_WetAeroAreaMDUST1       ',
                        'Chem_WetAeroAreaMDUST2       ',
                        'Chem_WetAeroAreaMDUST3       ',
                        'Chem_WetAeroAreaMDUST4       ',
                        'Chem_WetAeroAreaMDUST5       ',
                        'Chem_WetAeroAreaMDUST6       ',
                        'Chem_WetAeroAreaMDUST7       ',
                        'Chem_WetAeroAreaSULF         ',
                        'Chem_WetAeroAreaBC           ',
                        'Chem_WetAeroAreaOC           ',
                        'Chem_WetAeroAreaSSA          ',
                        'Chem_WetAeroAreaSSC          ',
                        'Chem_WetAeroAreaBGSULF       ',
                        'Chem_WetAeroAreaICEI         ',
                        'Chem_WetAeroRadiMDUST1       ',
                        'Chem_WetAeroRadiMDUST2       ',
                        'Chem_WetAeroRadiMDUST3       ',
                        'Chem_WetAeroRadiMDUST4       ',
                        'Chem_WetAeroRadiMDUST5       ',
                        'Chem_WetAeroRadiMDUST6       ',
                        'Chem_WetAeroRadiMDUST7       ',
                        'Chem_WetAeroRadiSULF         ',
                        'Chem_WetAeroRadiBC           ',
                        'Chem_WetAeroRadiOC           ',
                        'Chem_WetAeroRadiSSA          ',
                        'Chem_WetAeroRadiSSC          ',
                        'Chem_WetAeroRadiBGSULF       ',
                        'Chem_WetAeroRadiICEI         ',
                        'Chem_StatePSC                ',
                        'Chem_KhetiSLAN2O5H2O         ',
                        'Chem_KhetiSLAN2O5HCl         ',
                        'Chem_KhetiSLAClNO3H2O        ',
                        'Chem_KhetiSLAClNO3HCl        ',
                        'Chem_KhetiSLAClNO3HBr        ',
                        'Chem_KhetiSLABrNO3H2O        ',
                        'Chem_KhetiSLABrNO3HCl        ',
                        'Chem_KhetiSLAHOClHCl         ',
                        'Chem_KhetiSLAHOClHBr         ',
                        'Chem_KhetiSLAHOBrHCl         ',
                        'Chem_KhetiSLAHOBrHBr         ',
::

List of diagnostic fields in the Aerosols collection

Diagnostic field

Description

Units

Wildcard

AODDust[4]

Mineral dust optical depth @ WL1

1

AODDustWL1_<name|wc>[4]

AOD for each dust bin @ WL1

1

?DUSTBIN?

AODHygWL1_<name|wc>[4]

AOD @ WL1 for aerosol species

1

?HYG?

AODSOAfromAqIsopreneWL1[5]

Optical depth of SOA from aqueous isoprene @ WL1

1

AODStratLiquidAerWL1

Stratospheric liquid optical depth @ WL1

1

AODPolarStratCloudWL1

Polar stratospheric cloud type 1a/2 optical depth @ WL1

1

AerHygroscopicGrowth_<name|wc>[4]

Hygroscopic growth of aerosol species

1

?HYG?

AerNumDensityStratLiquid

Stratospheric liquid aerosol number density

1/cm3

AerNumDensityStratParticulate

Stratospheric particulate aerosol number density

1/cm3

AerAqueousVolume

Aqueous aerosol volume

cm2/cm3

AerSurfAreaDust

Surface area of mineral dust

cm2/cm3

AerSurfAreaHyg_<name|wc>

Surface area of aerosol species

cm2/cm3

?HYG?

AerSurfAreaStratLiquid

Stratospheric liquid surface area

cm2/cm3

AerSurfaceAreaPolarStratCloud

Polar stratospheric cloud type 1a/2 surface area

cm2/cm3

Chem_AeroAreaMDUST1[4]

Dry aerosol area for mineral dust (0.15 \({\mu}m\))

cm2/cm3

Chem_AeroAreaMDUST2[4]

Dry aerosol area for mineral dust (0.25 \({\mu}m\))

cm2/cm3

Chem_AeroAreaMDUST3[4]

Dry aerosol area for mineral dust (0.4 \({\mu}m\))

cm2/cm3

Chem_AeroAreaMDUST4[4]

Dry aerosol area for mineral dust (0.8 \({\mu}m\))

cm2/cm3

Chem_AeroAreaMDUST5[4]

Dry aerosol area for mineral dust (1.5 \({\mu}m\))

cm2/cm3

Chem_AeroAreaMDUST6[4]

Dry aerosol area for mineral dust (2.5 \({\mu}m\))

cm2/cm3

Chem_AeroAreaMDUST7[4]

Dry aerosol area for mineral dust (4.0 \({\mu}m\))

cm2/cm3

Chem_AeroAreaSULF[4]

Dry aerosol area for sulfate aerosol

cm2/cm3

Chem_AeroAreaBC[4]

Dry aerosol area for black carbon

cm2/cm3

Chem_AeroAreaOC[4]

Dry aerosol area for organic carbon

cm2/cm3

Chem_AeroAreaSSA[4]

Dry aerosol area for sea salt aerosol, accumulation mode

cm2/cm3

Chem_AeroAreaSSC[4]

Dry aerosol area for sea salt aerosol, coarse mode

cm2/cm3

Chem_AeroAreaBGSULF

Dry aerosol area for background stratospheric sulfate

cm2/cm3

Chem_AeroAreaICEI

Dry aerosol area for irregular ice cloud

cm2/cm3

Chem_AeroRadiMDUST1[4]

Dry aerosol radius for mineral dust (0.15 \({\mu}m\))

cm

Chem_AeroRadiMDUST2[4]

Dry aerosol radius for mineral dust (0.25 \({\mu}m\))

cm

Chem_AeroRadiMDUST3[4]

Dry aerosol radius for mineral dust (0.4 \({\mu}m\))

cm

Chem_AeroRadiMDUST4[4]

Dry aerosol radius for mineral dust (0.8 \({\mu}m\))

cm

Chem_AeroRadiMDUST5[4]

Dry aerosol radius for mineral dust (1.5 \({\mu}m\))

cm

Chem_AeroRAdiMDUST6[4]

Dry aerosol radius for mineral dust (2.5 \({\mu}m\))

cm

Chem_AeroRadiMDUST7[4]

Dry aerosol radius for mineral dust (4.0 \({\mu}m\))

cm

Chem_AeroRadiSULF[4]

Dry aerosol radius for sulfate aerosol

cm

Chem_AeroRadiBC[4]

Dry aerosol radius for black carbon

cm

Chem_AeroRadiOC[4]

Dry aerosol radius for organic carbon

cm

Chem_AeroRadiSSA[4]

Dry aerosol radius for sea salt aerosol, accumulation mode

cm

Chem_AeroRadiSSC[4]

Dry aerosol radius for sea salt aerosol, coarse mode

cm

Chem_AeroRadiBGSULF

Dry aerosol radius for background stratospheric sulfate

cm

Chem_AeroRadiICEI

Dry aerosol Radius for irregular ice cloud

cm

Chem_WetAeroAreaMDUST1[4]

Wet aerosol area for mineral dust (0.15 \({\mu}m\))

cm2/cm3

Chem_WetAeroAreaMDUST2[4]

Wet aerosol area for mineral dust (0.25 \({\mu}m\))

cm2/cm3

Chem_WetAeroAreaMDUST3[4]

Wet aerosol area for mineral dust (0.4 \({\mu}m\))

cm2/cm3

Chem_WetAeroAreaMDUST4[4]

Wet aerosol area for mineral dust (0.8 \({\mu}m\))

cm2/cm3

Chem_WetAeroAreaMDUST5[4]

Wet aerosol area for mineral dust (1.5 \({\mu}m\))

cm2/cm3

Chem_WetAeroAreaMDUST6[4]

Wet aerosol area for mineral dust (2.5 \({\mu}m\))

cm2/cm3

Chem_AeroAreaMDUST7[4]

Dry aerosol area for mineral dust (4.0 \({\mu}m\))

cm2/cm3

Chem_WetAeroAreaSULF[4]

Wet aerosol area for sulfate aerosol

cm2/cm3

Chem_WetAeroAreaBC[4]

Wet aerosol area for black carbon

cm2/cm3

Chem_WetAeroAreaOC[4]

Wet aerosol area for organic carbon

cm2/cm3

Chem_WetAeroAreaSSA[4]

Wet aerosol area for sea salt aerosol, accumulation mode

cm2/cm3

Chem_WetAeroAreaSSC[4]

Wet aerosol area for sea salt aerosol, coarse mode

cm2/cm3

Chem_WetAeroAreaBGSULF

Wet aerosol area for background stratospheric sulfate

cm2/cm3

Chem_WetAeroAreaICEI

Wet aerosol area for irregular ice cloud

cm2/cm3

Chem_WetAeroRadiMDUST1[4]

Wet aerosol radius for mineral dust (0.15 \({\mu}m\))

cm

Chem_WetAeroRadiMDUST2[4]

Wet aerosol radius for mineral dust (0.25 \({\mu}m\))

cm

Chem_WetAeroRadiMDUST3[4]

Wet aerosol radius for mineral dust (0.4 \({\mu}m\))

cm

Chem_WetAeroRadiMDUST4[4]

Wet aerosol radius for mineral dust (0.8 \({\mu}m\))

cm

Chem_WetAeroRadiMDUST5 [4]

Wet aerosol radius for mineral dust (1.5 \({\mu}m\))

cm

Chem_WetAeroRAdiMDUST6[4]

Wet aerosol radius for mineral dust (2.5 \({\mu}m\))

cm

Chem_WetAeroRadiMDUST7[4]

Wet aerosol radius for mineral dust (4.0 \({\mu}m\))

cm

Chem_WetAeroRadiSULF[4]

Wet aerosol radius for sulfate aerosol

cm

Chem_WetAeroRadiBC[4]

Wet aerosol radius for black carbon

cm

Chem_WetAeroRadiOC[4]

Wet aerosol radius for organic carbon

cm

Chem_WetAeroRadiSSA[4]

Wet aerosol radius for sea salt aerosol, accumulation mode

cm

Chem_WetAeroRadiSSC[4]

Wet aerosol radius for sea salt aerosol, coarse mode

cm

Chem_WetAeroRadiBGSULF

Wet aerosol radius for background stratospheric sulfate

cm

Chem_WetAeroRadiICEI

Wet aerosol Radius for irregular ice cloud

cm

Chem_KhetiSLAN2O5H2O

Sticking coefficient for N2O5 + H2O rxn

1

Chem_KhetiSLAN2O5HCl

Sticking coefficient for N2O5 + HCl rxn

1

Chem_KhetiSLACLNO3H2O

Sticking coefficient for ClNO3 + H2O rxn

1

Chem_KhetiSLACLNO3HCL

Sticking coefficient for ClNO3 + HCl rxn

1

Chem_KhetiSLACLNO3HBR

Sticking coefficient for ClNO3 + HBr rxn

1

Chem_KhetiSLABRNO3H2O

Sticking coefficient for BrNO3 + H2O rxn

1

Chem_KhetiSLABRNO3HCL

Sticking coefficient for BrNO3 + HCl rxn

1

Chem_KhetiSLAHOCLHCL

Sticking coefficient for HOCl + HCl rxn

1

Chem_KhetiSLAHOCLHBR

Sticking coefficient for HOCl + HBr rxn

1

Chem_KhetiSLAHOBRHCL

Sticking coefficient for HOBr + HCl rxn

1

Chem_KhetiSLAHOBRHBR

Sticking coefficient for HOBr + HBr rxn

1

Notes for the Aerosols colletion

BoundaryConditions

The BoundaryConditions diagnostic collection contains advected species concentrations (archived from a global simulation) that will be used by GEOS-Chen Classic nested-grid simulations as transport boundary conditions.

Sample definition section for HISTORY.rc

  BoundaryConditions.template:   '%y4%m2%d2_%h2%n2z.nc4',
  BoundaryConditions.frequency:  00000000 030000
  BoundaryConditions.duration:   00000100 000000
  BoundaryConditions.mode:       'instantaneous'
  BoundaryConditions.fields:     'SpeciesBC_?ADV?',
::

List of diagnostic fields in the BoundaryConditions collection

Diagnostic field

Description

Units

Wildcard

SpeciesBC_<name|wc>[6]

Advected species concentrations used as boundary conditions GEOS-Chem Classic nested-grid simulations

mol/mol dry air

?ADV?

Footnotes

Budget

The Budget diagnostic collection is a 2D diagnostic containing the mass tendencies per grid cell, in kg/s, for each species within a region of the column and across each GEOS-Chem component. The diagnostic is calculated by taking the difference in vertically summed column mass before and after major GEOS-Chem components.

There are three pre-defined column regions defined for this diagnostic: troposphere-only, PBL-only, and full column, as well as a user-defined column region. By post-processing this diagnostic you can calculate global mass change or mass change across regions by summing the diagnostic values for the relevant grid cells. You can also retrieve the mass change across a longer chunk of time by multiplying the time-averaged output by the number of seconds in the averaging period.

While there are seven major components in GEOS-Chem, there are only six implemented for the budget diagnostics. Emissions and dry deposition components are combined together for this diagnostic because of the way they are applied at the same time. Furthermore, if using non-local PBL mixing then the emissions and dry deposition budget diagnostic will not capture all fluxes from these sources and sinks. This is because emissions and dry deposition tendencies below the PBL are applied within mixing instead. When using full mixing, however, mixing and emissions/dry deposition budget diagnostics are fully separated.

Sample definition section for HISTORY.rc

  Budget.template:     '%y4%m2%d2_%h2%n2z.nc4',
  Budget.frequency:    00000100 000000
  Budget.duration:     00000100 000000
  Budget.mode:         'time-averaged'
  Budget.fields:       'BudgetChemistryFull_?ADV? ',
                       'BudgetChemistryPBL_?ADV?  ',
                       'BudgetChemistryTrop_?ADV? ',
                       'BudgetEmisDepFull_?ADV?   ',
                       'BudgetEmisDepTrop_?ADV?   ',
                       'BudgetEmisDepPBL_?ADV?    ',
                       'BudgetTransportFull_?ADV? ',
                       'BudgetTransportTrop_?ADV? ',
                       'BudgetTransportPBL_?ADV?  ',
                       'BudgetMixingFull_?ADV?    ',
                       'BudgetMixingTrop_?ADV?    ',
                       'BudgetMixingPBL_?ADV?     ',
                       'BudgetConvectionFull_?ADV?',
                       'BudgetConvectionTrop_?ADV?',
                       'BudgetConvectionPBL_?ADV? ',
                       'BudgetWetDepFull_?WET?    ',
                       'BudgetWetDepTrop_?WET?    ',
                       'BudgetWetDepPBL_?WET?     ',
::

List of diagnostic fields in the Budget collection

Diagnostic field

Mass tendency (kg/s) across …

Wildcard

BudgetChemistryFull_<name|wc>

Chemistry (full atmosphere)

?ADV?

BudgetChemistryLevs1to35_<name|wc>[7]

Chemistry (fixed level range)

?ADV?

BudgetChemistryPBL_<name|wc>

Chemistry (PBL only)

?ADV?

BudgetChemistryTrop_<name|wc>

Chemistry (troposphere only)

?ADV?

BudgetConvectionFull_<name|wc>

Convection (full atmosphere)

?ADV?

BudgetConvectionLevs1to35_<name|wc> [7]

Convection (fixed level range)

?ADV?

BudgetConvectionPBL_<name|wc>

Convection (PBL only)

?ADV?

BudgetConvectionTrop_<name|wc>

Convection (troposphere only)

?ADV?

BudgetEmisDepFull_<name|wc>[8]

Emissions & dry deposition (full atmosphere)

?ADV?

BudgetEmisDepLevs1to35_<name|wc>[7] [8]

Emissions & dry deposition (fixed level range)

?ADV?

BudgetEmisDepPBL_<name|wc>[8]

Emissions & dry deposition (PBL only)

?ADV?

BudgetEmisDepTrop_<name|wc>[8]

Emissions & dry deposition (troposphere only)

?ADV?

BudgetMixingFull_<name|wc> [9]

PBL mixing (full atmosphere)

?ADV?

BudgetMixingLevs1to35_<name|wc>[7] [9]

PBL mixing (full atmosphere) (fixed level range)

?ADV?

BudgetMixingPBL_<name|wc>[9]

PBL mixing (PBL only)

?ADV?

BudgetMixingTrop_<name|wc>[9]

PBL mixing (troposphere only)

?ADV?

BudgetTransportFull_<name|wc>

Transport (full attmosphere)

?ADV?

BudgetTransportLevs1to35_<name|wc>[7]

Transport (fixed level range)

?ADV?

BudgetTransportPBL_<name|wc>

Transport (PBL only)

?ADV?

BudgetTransportTrop_<name|wc>

Transport (troposphere only)

?ADV?

BudgetWetDepFull_<name|wc>

Wet deposition (full atmosphere)

?WET?

BudgetWetDepLevs1to35_<name|wc>[7]

Wet deposition (fixed level range)

?WET?

BudgetWetDepPBL_<name|wc>

Wet deposition (PBL only)

?WET

Notes for the Budget collection

Carbon

The Carbon collection contains diagnostic fields specific to the GEOS-Chem carbon gases simulation.

Sample definition section for HISTORY.rc

  Carbon.template:    '%y4%m2%d2_%h2%n2z.nc4',
  Carbon.frequency:   00000100 000000
  Carbon.duration:    00000100 000000
  Carbon.mode:        'time-averaged'
  Carbon.fields:      'OHconcAfterChem',
                      'ProdCOfromCH4  ',
                      'ProdCOfromNMVOC',
                      'ProdCO2fromCO  ',
::

List of diagnostic fields in the Carbon collection

Diagnostic field

Description

Units

OHconcAfterChem

OH concentration immediately after chemistry

molec/cm3

ProdCOfromCH4

Production of CO from CH4

molec/cm3

ProdCOfromNMVOC

Production of CO from non-methane VOCs

molec/cm3

ProdCO2fromCO

Production of CO2 from CO oxidation

molec/cm3

CH4

The CH4 collection contains diagnostics for loss of CH4 and OH concentration for the CH4 simulation.

Attention

This simulation is slated to be replaced by the GEOS-Chem carbon gases simulation. when this happens, the CH4 collection will be replaced by the Carbon collection.

Sample definition section for HISTORY.rc

  CH4.template:    '%y4%m2%d2_%h2%n2z.nc4',
  CH4.frequency:   00000100 000000
  CH4.duration:    00000100 000000
  CH4.mode:        'time-averaged'
  CH4.fields:      'OHconcAfterChem   ',
                   'LossCH4byClinTrop ',
                   'LossCH4byOHinTrop ',
                   'LossCH4inStrat    ',
::

List of diagnostic fields in the CH4 collection

Diagnostic field

Description

Units

LossCH4byClinTrop

Loss of CH4 by raction with Cl in the troposphere

kg/s

LossCH4byOHinTrop

Loss of CH4 by raction with OH in the troposphere

kg/s

LossCH4inStrat

Loss of CH4 in the stratosphere

kg/s

OHconcAfterChem

OH concentration after chemistry

kg/s

CloudConvFlux

The CloudConvFlux collection contains diagnostics for mass fluxes in cloud convection.

Sample definition section for HISTORY.rc

  CloudConvFlux.template:     '%y4%m2%d2_%h2%n2z.nc4',
  CloudConvFlux.frequency:    00000100 000000
  CloudConvFlux.duration:     00000100 000000
  CloudConvFlux.mode:         'time-averaged'
  CloudConvFlux.fields:       'CloudConvFlux_?ADV?',
::

List of diagnostic fields in the CloudConvFlux collection

Diagnostic field

Description

Units

Wildcards

CloudConvFlux_<name|wc>

Mass change due to cloud convection

kg/s

?ADV?
?GAS?
?WET?

CO

The CO collection contains diagnostic fields for the GEOS-Chem tagged CO simulation.

Attention

The tagged CO simulation is slated to be replaced by the GEOS-Chem carbon gases simulation. When this happens, the CO collection will be replaced with the Carbon collection.

  CO.template:   '%y4%m2%d2_%h2%n2z.nc4',
  CO.frequency:  00000100 000000
  CO.duration:   00000100 000000
  CO.mode:       'time-averaged'
  CO.fields:     'ProdCOfromCH4  ',
                 'ProdCOfromNMVOC',
::

List of diagnostic fields in the CO collection

Diagnostic field

Description

Units

ProdCOfromCH4

Production of CO from CH4

kg/s

ProdCOfromNMVOC

Production of CO from non-methane VOCs

kg/s

CO2

The CO2 collection contains diagnostic outputs from the GEOS-Chem CO2 simulation.

Attention

The CO2 simulation is slated to be replaced by the new GEOS-Chem carbon gases simulation. When this happens, the CO2 collection will be replaced with the Carbon collection.

Note

Several other diagnostics for the CO2 simulation are archived via HEMCO diagnostics.

Sample definition section for HISTORY.rc

  CO2.template:    '%y4%m2%d2_%h2%n2z.nc4',
  CO2.frequency:   00000100 000000
  CO2.duration:    00000100 000000
  CO2.mode:        'time-averaged'
  CO2.fields:      'ProdCO2fromCO',
::

List of diagnostic fields in the CO2 collection

Diagnostic field

Description

Units

ProdCO2fromCO

Chemical production of CO2 from CO oxidation

kg/m2/s

ConcAboveSfc

The ConcAboveSfc diagnostic collection uses dry deposition quantities (surface resistance, dry deposition velocity) to compute the species concentration of O3 and HNO3 at a given altitude (such as 10 m) above the surface. This will facilitate comparison between GEOS-Chem and observational networks (e.g. CASTNET), which often place instruments above the canopy at approx. 10m height.

Attention

If dry deposition is turned off in your simulation, then you must disable this collection, or else your run will stop with an error.

Sample definition section for HISTORY.rc

ConcAboveSfc.template:      '%y4%m2%d2_%h2%n2z.nc4',
ConcAboveSfc.mode:          'instantaneous'
ConcAboveSfc.fields:        'DryDepRaALT1             ',
                            'DryDepVelForALT1_?DRYALT?',
                            'SpeciesConcALT1_?DRYALT? ',
::

List of diagnostic fields in the ConcAboveSfc collection

Diagnostic field

Description

Units

Wildcard

DryDepRaALT1[10]

Dry deposition aerodynamic resistance at ALT1 meters above the surface

s/cm

DryDepVelForALT1_<name|wc>[10] [11]

Dry deposition velocity of species tagged with the ?DRYALT?wildcard

cm/s

?DRYALT?

SpeciesConcALT1_<name|wc>[10] [11]

Concentration of species tagged with the ?DRYALT? wildcard

mol/mol dry air

?DRYALT?

Notes about the ConcAboveSfc collection

ConcAfterChem

The ConcAfterChem collection contains diagnostics for OH, HO2, etc. species immediately upon exiting the chemical solver.

Sample definition section for HISTORY.rc

  ConcAfterChem.template:     '%y4%m2%d2_%h2%n2z.nc4',
  ConcAfterChem.frequency:    00000100 000000
  ConcAfterChem.duration:     00000100 000000
  ConcAfterChem.mode:         'time-averaged'
  ConcAfterChem.fields:       'OHconcAfterChem ',
                              'HO2concAfterChem',
                              'O1DconcAfterChem',
                              'O3PconcAfterChem',
                              'O3concAfterChem ',
                              'RO2concAfterChem',
::

List of diagnostic fields in the ConcAfterChem collection

Diagnostic field

Description

Units

HO2concAfterChem

HO2 immediately after exiting the chemical solver

mol/mol

O1DconcAfterChem

O1D immediately after exiting the chemical solver

molec/cm3

O3concAfterChem

O3 immediately after exiting the chemical solver

molec/cm3

O3PconcAfterChem

O3P immediately after exiting the chemical solver

molec/cm3

OHconcAfterChem

OH immediately after exiting the chemical solver

molec/cm3

RO2concAfterChem

RO2 immediately after exiting the chemical solver

molec/cm3

DryDep

The DryDep collection contains diagnostics for the flux and velocity of each species lost to dry-deposition.

Sample definition section for HISTORY.rc

  DryDep.template:     '%y4%m2%d2_%h2%n2z.nc4',
  DryDep.frequency:    00000100 000000
  DryDep.duration:     00000100 000000
  DryDep.mode:         'time-averaged'
  DryDep.fields:       'DryDepVel_?DRY?',
                       'DryDepMix_?DRY?',
                       'DryDepChm_?DRY?',
                       'DryDep_?DRY?   ',
::

List of diagnostic fields in the DryDep collection

Diagnostic field

Description

Units

Wildcard

DryDep_<name|wc>

Total dry deposition flux

molec/cm2/s

?DRY?

DryDepChm_<name|wc>

Dry deposition flux (computed in chemistry)

molec/cm2/s

?DRY?

DryDepMix_<name|wc>

Dry deposition flux (computed in the PBL)

molec/cm2/s

?DRY?

DryDepVel_<name|wc>

Dry deposition velocity

cm/s

?DRY?

JValues

The JValues collection contains diagnostics for photolysis rates for various chemical species, obtained from the photolysis mechanism.

Sample definition section for HISTORY.rc

  JValues.template:           '%y4%m2%d2_%h2%n2z.nc4',
  JValues.frequency:          00000100 000000
  JValues.duration:           00000100 000000
  JValues.mode:               'time-averaged'
  JValues.fields:             'Jval_?PHO?',
                              'JvalO3O1D ',
                              'JvalO3O3P ',
::

List of diagnostic fields in the JValues collection

Diagnostic field

Description

Units

Wildcard

Jval_<name|wc>

Photolysis rates

1/s

?PHO?

JvalO3O1D

Photolysis rate of O3 \(\rightarrow\) O1D

1/s

JvalO3O3P

Photolysis rate of O3 \(\rightarrow\) O3P

1/s

KppARDiags

The KppARDiags collection contains diagnostics for the KPP Rosenbrock solver with mechanism auto-reduction. You may leave this collection disabled unless you are interested in assessing the solver’s performance.

Sample definition section for HISTORY.rc

  KppARDiags.template:        '%y4%m2%d2_%h2%n2z.nc4',
  KppARDiags.frequency:       00000100 000000
  KppARDiags.duration:        00000100 000000
  KppARDiags.mode:            'time-averaged'
  KppARDiags.fields:          'KppAutoReducerNVAR',
                              'KppAutoReduceThres',
                              'KppcNONZERO       ',
::

List of diagnostic fields in the KppARDiags collection

Diagnostic field

Description

Units

KppAutoReducerNVAR

Number of species (rNVAR) in the auto-reduced mechanism

count

KppAutoReduceThres

Auto-reduction threshold

molec/cm3/s

KppcNONZERO

Number of nonzero elements (cNONZERO) in LU decomposition in the auto-reduced mechanism

count

KppDiags

The KppDiags collection contains KPP solver diagnostics. You may leave this collection disabled unless you are interested in assessing the solver’s performance.

Sample definition section for HISTORY.rc

 KppDiags.template:   '%y4%m2%d2_%h2%n2z.nc4',
 KppDiags.frequency:  00000100 000000
 KppDiags.duration:   00000100 000000
 KppDiags.mode:       'time-averaged'
 KppDiags.fields:     'KppIntCounts',
                      'KppJacCounts',
                      'KppTotSteps ',
                      'KppAccSteps ',
                      'KppRejSteps ',
                      'KppLuDecomps',
                      'KppSubsts   ',
                      'KppSmDecomps',
::

List of diagnostic fields in the KppDiags collection

Diagnostic field

Description

Units

KppAccSteps

Number of accepted integration timesteps

count

KppIntCounts

Number of times the KPP integrator was called

count

KppJacCounts

Number of times the KPP Jacobian matrix was constructed

count

KppLuDecomps

Number of LU decompositions performed

count

KppSmDecomps[12]

Number of singular matrix decompositions performed

count

KppSubsts

Number of matrix substitutions performed (both forward & backward substitutions)

count

KppRejSteps

Number of rejected integration timesteps

count

KppTotSteps

Total number of integration timesteps

count

Footnotes

LevelEdgeDiags

The LevelEdgeDiags collection contains diagnostics for quantities (mostly met fields) that are defined on the vertical edges of each grid box. According to the COARDS convention, all of the data variables in a netCDF file must be defined with the same vertical dimension.

Sample definition section for HISTORY.rc

  LevelEdgeDiags.template:    '%y4%m2%d2_%h2%n2z.nc4',
  LevelEdgeDiags.frequency:   00000100 000000
  LevelEdgeDiags.duration:    00000100 000000
  LevelEdgeDiags.mode:        'time-averaged'
  LevelEdgeDiags.fields:      'Met_CMFMC   ',
                              'Met_PEDGE   ',
                              'Met_PEDGEDRY',
                              'Met_PFICU   ',
                              'Met_PFILSAN ',
                              'Met_PFLCU   ',
                              'Met_PFLLSAN ',
::

List of diagnostic fields in the LevelEdgeDiags collection

Diagnostic field

Description

Units

Met_CMFMC

Upward moist convective mass flux

kg/m2/s

Met_PEDGE

Surface pressure at level edges (based on moist air)

hPa

Met_PEDGEDRY

Surface pressure at level edges (based on dry air)

hPa

Met_PFICU

3d flux of ice convective precipitation

kg/m2/s

Met_PFILSAN

3d flux of ice non-convective precipitation

kg/m2/s

Met_PFLCU

3d flux of liquid convective precipitation

kg/m2/s

Met_PFLLSAN

3d flux of liquid non-convective precipitation

kg/m2/s

MercuryChem

The MercuryChem collection contains concentrations and prod/loss diagnostic outputs for the GEOS-Chem mercury simulation.

Sample definition section for HISTORY.rc

  MercuryChem.template:    '%y4%m2%d2_%h2%n2z.nc4',
  MercuryChem.frequency:   ${RUNDIR_HIST_TIME_AVG_FREQ}
  MercuryChem.duration:    ${RUNDIR_HIST_TIME_AVG_DUR}
  MercuryChem.mode:        'time-averaged'
  MercuryChem.fields:      'HgBrAfterChem  ',
                           'HgClAfterChem  ',
                           'HgOHAfterChem  ',
                           'HgBrOAfterChem ',
                           'HgClOAfterChem ',
                           'HgOHOAfterChem ',
                           'Hg2GToHg2P     ',
                           'Hg2PToHg2G     ',
                           'Hg2GasToHg2StrP',
                           'Hg2GasToSSA    ',
::

List of diagnostic fields in the MercuryChem collection

Diagnostic field

Description

Units

Hg2GToHg2P

Hg2 gas transferred to Hg2P

molec/cm3/s

Hg2GasToHg2StrP

Hg2 gas transferred to Hg2StrP

molec/cm3/s

Hg2GasToSSA

Hg2 gas transferred to sea salt aerosol

molec/cm3/s

Hg2PToHg2G

Hg2P transferred to Hg2 gas

molec/cm3/s

HgBrAfterChem

HgBr concentration immediately after chemistry

mol/mol

HgBrOAfterChem

HgBrO concentration immediately after chemistry

mol/mol

HgClAfterChem

HgCl concentration immediately after chemistry

mol/mol

HgClOAfterChem

HgClO concentration immediately after chemistry

mol/mol

HgOHAfterChem

HgOH concentration immediately after chemistry

mol/mol

HgOHOAfterChem

HgOHO concentration immediately after chemistry

mol/mol

MercuryEmis

The MercuryEmis collection contains emission diagnostics for the GEOS-Chem mercury simulation.

Note

Several other mercury emission diagnostics are archived via HEMCO diagnostics.

Sample definition section for HISTORY.rc

  MercuryEmis.template:   '%y4%m2%d2_%h2%n2z.nc4',
  MercuryEmis.frequency:  00000100 000000
  MercuryEmis.duration:   00000100 000000
  MercuryEmis.mode:       'time-averaged'
  MercuryEmis.fields:     'EmisHg0land ',
                          'EmisHg0ocean',
                          'EmisHg0soil ',
                          'EmisHg0snow ',
::

List of diagnostic fields in the MercuryEmis collection

Diagnostic field

Description

Units

EmisHg0land

Re-emission of Hg0 from land

kg/s

EmisHg0ocean

Emissions of Hg0 from oceans

kg/s

EmisHg0snow

Emission of Hg0 from snowpack

kg/s

EmisHg0soil

Emissions of Hg0 from soils

kg/s

MercuryOcean

The MercuryOcean collection contains diagnostics from the mercury ocean model, used in the GEOS-Chem mercury simulation.

Sample definition section for HISTORY.rc

  MercuryOcean.template:    '%y4%m2%d2_%h2%n2z.nc4',
  MercuryOcean.frequency:   00000000 040000
  MercuryOcean.duration:    00000000 040000
  MercuryOcean.mode:        'time-averaged'
  MercuryOcean.fields:      'FluxHg0fromAirToOcean   ',
                            'FluxHg0fromOceanToAir   ',
                            'FluxHg2HgPfromAirToOcean',
                            'FluxHg2toDeepOcean      ',
                            'FluxOCtoDeepOcean       ',
                            'MassHg0inOcean          ',
                            'MassHg2inOcean          ',
                            'MassHgPinOcean          ',
                            'MassHgTotalInOcean      ',
::

List of diagnostic fields in the MercuryOcean collection

Diagnostic field

Description

Units

FluxHg0fromAirToOcean

Deposition flux of Hg0 from the atmosphere to the ocean

kg/s

FluxHg0fromOceanToAir

Volatization flux of Hg0 from the ocean to the atmosphere

kg/s

FluxHg2HgPfromAirToOcean

Deposition flux of Hg2 + HgP from atmosphere to ocean

kg/s

FluxHg2toDeepOcean

Flux of Hg2 sunk to the deep ocean

kg/s

MassHg0inOcean

Total mass of oceanic Hg0

kg

MassHg2inOcean

Total mass of oceanic Hg2

kg

MassHgPinOcean

Total mass of oceanic HgP

kg

MassHgTotalInOcean

Total mass of all organic mercury

kg

Metrics

The Metrics collection contains diagnostics for computing OH metrics from a GEOS-Chem full chemistry simulation (needed for benchmarking).

To compute the OH metrics, you must run the Python script metrics.py that ships with each fullchem or CH4 run directory.

Sample definition section for HISTORY.rc

  Metrics.template:    '%y4%m2%d2_%h2%n2z.nc4',
  Metrics.frequency:   'End',
  Metrics.duration:    'End',
  Metrics.mode:        'time-averaged'
  Metrics.fields:      'AirMassColumnFull       ',
                       'LossOHbyCH4columnTrop   ',
                       'LossOHbyMCFcolumnTrop   ',
                       'OHwgtByAirMassColumnFull',
::

List of diagnostic fields in the Metrics collection

Diagnostic field

Description

Units

AirMassColumnFull

Air mass column (full atmosphere)

kg

LossOHbyCH4columnTrop

Loss rate of CH4 by OH (tropospheric column sums)

molec/cm3

LossOHbyMCFcolumnTrop

Loss rate of CH4 by CH3CCl3 aka MCF (tropospheric column sums)

molec/cm3

OHwgtByAirMassColumnFull

Airmass-weighted OH concentration (full atmosphere column sums)

kg air/kg OH/m3

ProdLoss

The ProdLoss collection contains chemical production and loss rates.

Sample definition section for HISTORY.rc

  ProdLoss.template:   '%y4%m2%d2_%h2%n2z.nc4',
  ProdLoss.frequency:  00000100 000000
  ProdLoss.duration:   00000100 000000
  ProdLoss.mode:       'time-averaged'
  ProdLoss.fields:     'Prod_?PRD?                  ',
                       'ProdBCPIfromBCPO            ',
                       'ProdOCPIfromOCPO            ',
                       'ProdHMSfromSO2andHCHOinCloud',
                       'ProdSO2andHCHOfromHMSinCloud',
                       'ProdSO4fromHMSinCloud       ',
                       'ProdSO4fromH2O2inCloud      ',
                       'ProdSO4fromO2inCloudMetal   ',
                       'ProdSO4fromO3inCloud        ',
                       'ProdSO4fromO3inSeaSalt      ',
                       'ProdSO4fromHOBrInCloud      ',
                       'ProdSO4fromSRO3             ',
                       'ProdSO4fromSRHObr           ',
                       'ProdSO4fromO3s              ',
                       'Loss_?LOS?                  ',
                       'LossHNO3onSeaSalt           ',
                       'ProdCOfromCH4               ',
                       'ProdCOfromNMVOC             ',
::

List of diagnostic fields in the ProdLoss collection

Diagnostic field

Description

Units

Wildcard

Loss_<name|wc>

Chemical loss for a given species or family

molec/cm3

?LOS?

LossHNO3onSeaSalt[15]

L(HNO3) on sea salt aerosols

kg S/s

Prod_<name|wc>

Chemical production for a given species or family

molec/cm3

?PRD?

ProdBCPIfromBCPO[15]

Production of hydrophilic BC from hydrophobic BC

kg

ProdCOfromCH4[16]

P(CO) from CH4

molec/cm3

ProdCOfromNMVOC[16]

P(CO) from NMVOCs SO3– loss by OH

molec/cm3

ProdOCPIfromOCPO[15]

Production of hydrophilic OC from hydrophobic OC

kg

ProdMSAfromDMS[14]

P(MSA) from DMS

kg S/s

ProdNITfromHNO3uptakeOnDust[13]

P(NIT) from HNO3 uptake on dust aerosols

kg N/s

ProdSO2fromDMS[14]

Total P(SO2) from DMS

kg S/s

ProdSO2fromDMSandNO3[14]

P(SO2) from DMS + NO3

kg S/s

ProdSO2fromDMSandOH[14]

P(SO2) from DMS + OH

kg S/s

ProdSO2fromOxidationOnDust[13]

P(SO2) from DMS+OH on dust aerosols

kg S/s

ProdSO4fromGasPhase[14]

P(SO4) in gas phase

kg S/s

ProdSO4fromH2O2inCloud[15]

P(SO4) from aqueous oxidation of H2O2 in clouds

kg S/s

ProdSO4fromHOBrinCloud[16]

P(SO4) from aqueous oxidation of HOBr in clouds

kg S/s

ProdSO4fromO2inCloudMetal[15]

P(SO4) from aqueous oxidation of O2 from metals in cloud

kg S/s

ProdSO4fromO3inCloud[15]

P(SO4) from aqueous oxidation of O3 in clouds

kg S/s

ProdSO4fromO3inSeaSalt[15]

P(SO4) from O3 in sea salt

kg S/s

ProdSO4fromO3s[15]

P(SO4) from aqueous phase SO3– loss by OH

kg S/s

ProdSO4fromSRHOBR[16]

P(SO4) from sulfur production rate of HOBr + O3

kg S/s

ProdSO4fromSRO3[15]

P(SO4) from sulfur production rate of O3

kg S/s

ProdSO4fromUptakeOfH2SO4g[13]

P(SO4) from H2SO4 uptake on dust aerosols

kg S/s

Notes for the ProdLoss collection

RadioNuclide

The RadioNuclide collection contains diagnostic outputs for radionuclide species in the GEOS-Chem TransportTracers simulation.

Note

Emissions of Rn222, Be7, and Be10 species are archived to diagnostic output by HEMCO diagnostics, and are thus not contained in this collection.

Sample definition section for HISTORY.rc

  RadioNuclide.template:    '%y4%m2%d2_%h2%n2z.nc4',
  RadioNuclide.format:      'CFIO',
  RadioNuclide.frequency:   00000100 000000
  RadioNuclide.duration:    00000100 000000
  RadioNuclide.mode:        'time-averaged'
  RadioNuclide.fields:      'PbFromRnDecay  ',
                            'RadDecay_Rn222 ',
                            'RadDecay_Pb210 ',
                            'RadDecay_Pb210s',
                            'RadDecay_Be7   ',
                            'RadDecay_Be7s  ',
                            'RadDecay_Be10  ',
                            'RadDecay_Be10s ',
::

List of diagnostic fields in the RadioNuclide collection

Diagnostic field

Description

Units

PbFromRnDecay

Pb210 created from radioactive decay

kg/s

RadDecay_Be7

Loss of Be7 due to radioactive decay

kg/s

RadDecay_Be7s

Loss of Be7 (produced in the stratosphere) due to radioactive decay

kg/s

RadDecay_Be10

Loss of Be10 due to radioactive decay

kg/s

RadDecay_Be10s

Loss of Be10 (produced in the stratosphere) due to radioactive decay

kg/s

RadDecay_Pb210

Loss of Pb210 due to radioactive decay

kg/s

RadDecay_Pb210s

Loss of Pb210 (produced in the stratosphere) due to radioactive decay

kg/s

RadDecay_Rn222

Loss of Rn222 due to readioactive decay

kg/s

Restart

The Restart diagnostic collection contains fields for saving out to the GEOS-Chem restart file. This type of diagnostic output is used in all GEOS-Chem simulations; therefore, we have listed Restart first in the HISTORY.rc files that ship with each GEOS-Chem run directory.

Note

The restart file will be created in the Restarts/ subdirectory of the run directory, not in OutputDir/.

Sample definition section for HISTORY.rc

  Restart.filename:   './GEOSChem.Restart.%y4%m2%d2_%h2%n2z.nc4',
  Restart.frequency:  'End',
  Restart.duration:   'End',
  Restart.mode:       'instantaneous'
  Restart.fields:     'SpeciesRst_?ALL?   ',
                      'Chem_H2O2AfterChem ',
                      'Chem_SO2AfterChem  ',
                      'Chem_DryDepNitrogen',
                      'Chem_WetDepNitrogen',
                      'Chem_KPPHvalue     ',
                      'Met_DELPDRY        ',
                      'Met_PS1WET         ',
                      'Met_PS1DRY         ',
                      'Met_SPHU1          ',
                      'Met_TMPU1          ',
::

List of diagnostic fields in the Restart collection

Diagnostic field

Description

Units

Chm_DryDepNitrogen

Dry deposited nitrogen

molec/cm2/s

Chm_H2O2AfterChem

Concentration of H2O2 after sulfate chemistry

v/v

Chm_KPPHvalue

H-value for Rosenbrock solver

unitless

Chm_SO2AfterChem

Concentration of SO2 after sulfate chemistry

v/v

Chm_StatePSC

Polar stratospheric cloud type

count

Chm_WetDepNitrogen

Wet deposited nitrogen

molec/cm2/s

Met_DELPDRY

Delta-pressure across grid box (dry air)

hPa

Met_PS1WET

Wet surface pressure at dt start

hPa

Met_PS1DRY

Dry surface pressure at dt start

hPa

Met_SPHU1

Instantaneous specific humidity at time=T

g kg-1

Met_TMPU1

Instantaneous temperature at time=T

K

SpeciesRst_?ALL?

Instantaneous chemical species concentrations for use in starting subsequent GEOS-Chem simulations

mol/mol dry air

RRTMG

The RRTMG collection contains radiative flux diagnostics computed by the RRTMG radiative transfer model. You can leave this collection disabled unless your simulation uses RRTMG.

Note

You may compute RRTMG diagnostic quantities at up to 3 wavelengths (WL1, WL2, WL3). Specify the wavelengths in this menu of the geoschem_config.yml file:

rrtmg_rad_transfer_model:
    activate: true
    aod_wavelengths_in_nm:
    - 550 700 1000
    ... etc ...

GEOS-Chem will replace the tokens WL1, WL2, WL3 in diagnostic field names with the corresponding wavelength. For example:

RadAODWL1_SU
RadAODWL2_SU
RadAODWL3_SU

will be saved to the GEOSChem.RRTMG.YYYYMMDD_hhmmz.nc4 file(s) under these names:

RadAOD550nm_SU
RadAOD700nm_SU
RadAOD1000nm_SU

Sample definition section for HISTORY.rc

#==============================================================================
# %%%%% THE RRTMG COLLECTION %%%%%
#
# Outputs for different species from the RRTMG radiative transfer model:
# (See http://wiki.geos-chem.org/Coupling_GEOS-Chem_with_RRTMG)
#
#    0=BA (Baseline    )  1=O3 (Ozone          )   2=ME (Methane   )
#    3=SU (Sulfate     )  4=NI (Nitrate        )   5=AM (Ammonium  )
#    6=BC (Black carbon)  7=OA (Organic aerosol)   8=SS (Sea Salt  )
#    9=DU (Mineral dust) 10=PM (All part. matter) 12=ST (Strat aer., UCX only)
#
# NOTES:
# (1) Only request diagnostics you need to reduce the overall run time.
# (2) The ?RRTMG? wildcard includes all output except ST (strat aerosols).
#     However, if ST is included explicitly for one diagnostic then it
#     will be included for all others that use the wildcard.
# (3) Only enable ST if running with UCX.
# (4) Optics diagnostics have a reduced set of output species (no BASE, O3, ME)
#==============================================================================
  RRTMG.template:    %y4%m2%d2_%h2%n2z.nc4',
  RRTMG.frequency:   00000100 000000
  RRTMG.duration:    00000100 000000
  RRTMG.mode:        time-averaged'
  RRTMG.fields:      'RadClrSkyLWSurf_?RRTMG?',
                     'RadAllSkyLWSurf_?RRTMG?',
                     'RadClrSkySWSurf_?RRTMG?',
                     'RadAllSkySWSurf_?RRTMG?',
                     'RadClrSkyLWTOA_?RRTMG? ',
                     'RadAllSkyLWTOA_?RRTMG? ',
                     'RadClrSkySWTOA_?RRTMG? ',
                     'RadAllSkySWTOA_?RRTMG? ',
                     'RadAODWL1_?RRTMG?      ',
                     'RadAsymWL1_?RRTMG?     ',
::

List of diagnostic fields in the RRTMG collection

Diagnostic field

Description

Units

Wildcard

DynHeating

Dynamic heating rate in baseline simulation

K/day

?RRTMG?

DtRad

Temperature change due to radiative heating

K

?RRTMG?

RadAODWL1_<name|wc>

Aerosol optical depth computed @ WL1

1

?RRTMG?

RadAODWL2_<name|wc>

Aerosol optical depth computed @ WL2

1

?RRTMG?

RadAODWL3_<name|wc>

Aerosol optical depth computed @ WL3

1

?RRTMG?

RadAsymWL1_<name|wc>

Asymmetry parameter computed @ WL1

1

?RRTMG?

RadAsymWL2_<name|wc>

Asymmetry parameter computed @ WL2

1

?RRTMG?

RadAsymWL3_<name|wc>

Asymmetry parameter computed @ WL3

1

?RRTMG?

RadAllSkyLWSurf_<name|wc>

All-sky longwave radiation at the surface

W/m2

?RRTMG?

RadAllSkyLWTOA_<name|wc>

All-sky longwave radiation at top-of-atmosphere

W/m2

?RRTMG?

RadAllSkyLWTrop_<name|wc>

All-sky longwave radiation at the tropopause

W/m2

?RRTMG?

RadAllSkySWSurf_<name|wc>

All-sky shortwave radiation at the surface

W/m2

?RRTMG?

RadAllSkySWTOA_<name|wc>

All-sky shortwave radiation at top-of-atmosphere

W/m2

?RRTMG?

RadAllSkySWTrop_<name|wc>

All-sky shortwave radiation at the tropopause

W/m2

?RRTMG?

RadClrSkyLWSurf_<name|wc>

Clear-sky longwave radiation at the surface

W/m2

?RRTMG?

RadClrSkyLWTOA_<name|wc>

Clear-sky longwave radiation at top-of-atmosphere

W/m2

?RRTMG?

RadClrSkyLWTrop_<name|wc>

Clear-sky longwave radiation at the tropopause

W/m2

?RRTMG?

RadClrSkySWSurf_<name|wc>

Clear-sky shortwave radiation at the surface

W/m2

?RRTMG?

RadClrSkySWTOA_<name|wc>

Clear-sky shortwave radiation at top-of-atmosphere

W/m2

?RRTMG?

RadClrSkySWTrop_<name|wc>

Clear-sky shortwave radiation at the tropopause

W/m2

?RRTMG?

RadSSAWL1_<name|wc>

Single-scattering albedo computed @ WL1

1

?RRTMG?

RadSSAWL2_<name|wc>

Single-scattering albedo computed @ WL2

1

?RRTMG?

RadSSAWL3_<name|wc>

Single-scattering albedo computed @ WL3

1

?RRTMG?

RxnConst

The RxnConst collection contains reaction rate constants from the KPP solver.

  # It is best to list individual reactions to avoid using too much memory.
  # Reactions should be listed as "RxnConst_EQnnn", where nnn is the reaction
  # index as listed in KPP/fullchem/gckpp_Monitor.F90 (pad zeroes as needed).
  #
  # The units of reaction rate constants vary according to the number of reactants
  # in the reaction.
  #
  # Available for the fullchem simulations.
  RxnConst.template:   '%y4%m2%d2_%h2%n2z.nc4',
  RxnConst.frequency:  ${RUNDIR_HIST_TIME_AVG_FREQ}
  RxnConst.duration:   ${RUNDIR_HIST_TIME_AVG_DUR}
  RxnConst.mode:       'time-averaged'
  RxnConst.fields:     'RxnConst_EQ001                          ',
                       'RxnConst_EQ002                          ',
::

List of diagnostic fields in the RxnRate collection

Units are

Diagnostic field

Description

Units

Wildcard

RxnConst_EQnnn[17]

Rate constant for KPP reaction nnn

[18]

?RXN?

Notes for the RxnRates collection

RxnRates

The RxnRates collection contains reaction rates *aka equation rates) from the chemical mechanism (as computed by the KPP-generated solver code). For example, in the case of the NO + O3 → NO2 + O2 reaction the returned quantity is k[NO][O3] in molec/cm3/s.

Here is a sample definition section for the RxnRates collection.

Sample definition section for HISTORY.rc

  #
  # It is best to list individual reactions to avoid using too much memory.
  # Reactions should be listed as "RxnRate_EQnnn", where nnn is the reaction
  # index as listed in KPP/fullchem/gckpp_Monitor.F90,
  # KPP/carbon/gckpp_Monitor.F90, and KPP/Hg/gckpp_monitor.F90
  # (pad zeroes as needed)
  #
  RxnRates.template:   '%y4%m2%d2_%h2%n2z.nc4',
  RxnRates.frequency:  00000000 010000
  RxnRates.duration:   00000000 010000
  RxnRates.mode:       'time-averaged'
  RxnRates.fields:     'RxnRate_EQ001                           ',
                       'RxnRate_EQ002                           ',
::

List of diagnostic fields in the RxnRate collection

Diagnostic field

Description

Units

Wildcard

RxnRate_EQnnn[19]

Rate for KPP reaction nnn

molec/cm3/s

?RXN?

Notes for the RxnRates collection

SatDiagn

The SatDiagn collection contains diagnostic quantities that will be sampled within a specified local time range. This is to mimic the overpass sampling times of sun-synchronus satellite instruments.

Tip

Set the the hours (local time) for the averaging interval with:

SatDiagn.hrrange:    11.98 15.02

Sample definition section for HISTORY.rc

  SatDiagn.template:   '%y4%m2%d2_%h2%n2z.nc4',
  SatDiagn.frequency:  00000001 000000
  SatDiagn.duration:   00000100 000000
  SatDiagn.hrrange:    11.98 15.02
  SatDiagn.mode:       'time-averaged'
  SatDiagn.fields:     'SatDiagnConc_O3      ',
                       'SatDiagnOH           ',
                       'SatDiagnRH           ',
                       'SatDiagnAirDen       ',
                       'SatDiagnBoxHeight    ',
                       'SatDiagnPEdge        ',
                       'SatDiagnTROPP        ',
                       'SatDiagnPBLHeight    ',
                       'SatDiagnPBLTop       ',
                       'SatDiagnTAir         ',
                       'SatDiagnGWETROOT     ',
                       'SatDiagnGWETTOP      ',
                       'SatDiagnPARDR        ',
                       'SatDiagnPARDF        ',
                       'SatDiagnPRECTOT      ',
                       'SatDiagnSLP          ',
                       'SatDiagnSPHU         ',
                       'SatDiagnTS           ',
                       'SatDiagnPBLTOPL      ',
                       'SatDiagnMODISLAI     ',
                       'SatDiagnWetLossLS_   ',
                       'SatDiagnWetLossConv_ ',
                       'SatDiagnJval_        ',
                       'SatDiagnJvalO3O1D    ',
                       'SatDiagnJvalO3O3P    ',
                       'SatDiagnDryDep_      ',
                       'SatDiagnDryDepVel_   ',
                       'SatDiagnOHreactivity ',
                       'SatDiagnColEmis_     ',
                       'SatDiagnSurfFlux_    ',
                       'SatDiagnProd_?PRD?   ',
                       'SatDiagnLoss_?LOS?   ',
                       'SatDiagnRxnRate_EQnnn',
::

List of diagnostic fields in the SatDiagn collection

Diagnostic field

Description

Units

Wildcards

SatDiagnAirDen

Air density

molec/cm3

SatDiagnBoxHeight

Grid box height

m

SatDiagnColEmis_<name|wc>

Column emissions

kg/m2/s

?ADV?

SatDiagnConc_<name|wc>

Dry mixing ratio of species

mol/mol

?ADV?

SatDiagnDryDep_<name|wc>

Dry deposition flux of species

molec/cm2/s

?DRY?

SatDiagnDryDepVel_<name|wc>

Dry deposition velocity of species

cm/s

?DRY?

SatDiagnGWETROOT

Root zone soil moisture

1

SatDiagnGWETTOP

Topsoil moisture (or

1

SatDiagnJVal_<name|wc>

Photolysis rate

1/s

?PHO?

SatDiagnJvalO3O1D

Photolysis rate for O3 \(\rightarrow\) O1D

1/s

SatDiagnJvalO3O3P

Photolysis rate for O3 \(\rightarrow\) O1D

1/s

SatDiagnLoss_<name|wc>

Chemical loss of species or families

molec/cm3/s

?LOS?

SatDiagnMODISLAI

MODIS daily LAI

m2/m2

SatDiagnOH

OH number density

molec/cm3

SatDiagnOHreactivity

OH reactivity

1/s

SatDiagnPARDF

Diffuse photosynthetically active radiation

W/m2

SatDiagnPARDR

Direct photosynthetically active radiation

W/m2

SatDiagnPBLHeight

PBL Height

m

SatDiagnPBLTop

PBL Top

m

SatDiagnPBLTOPL

PBL top height

level

SatDiagnPRECTOT

Total precipitation at surface

mm/day

SatDiagnProd_<name|wc>

Chemical production of species or families

molec/cm3/s

?PRD?

SatDiagnRH

Relative humidity

%

SatDiagnRxnRate_EQnnn

Rate for chemical reaction `nnn`

molec/cm3/s

?RXN?

SatDiagnSLP

Sea level pressure

hPa

SatDiagnSPHU

Specific humidity interpolated to current time

g H2O/kg air

SatDiagnSurfFlux_<name|wc>

Total surface fluxes (emis - drydep) from surface to top of PBL

kg/m2/s

?ADV?

SatDiagnTAir

Air temperature

K

SatDiagnTROPP

Tropopause pressure

hPa

SatDiagnTS

Surface temperature at 2m

K

SatDiagnWetLossConv_<name|wc>

Loss of soluble species in convective updrafts

kg/s

?WET?

SatDiagnWetLossLS_<name|wc>

Loss of soluble species in large-scale precipitation

kg/s

?WET?

SatDiagnEdge

The SatDiagn collection contains diagnostic quantities (placed on level edges) that will be sampled within a specified local time range. This is to mimic the overpass sampling times of sun-synchronus satellite instruments.

Tip

Set the the hours (local time) for the averaging interval with:

SatDiagn.hrrange:    11.98 15.02

Sample definition section for HISTORY.rc

  SatDiagnEdge.template:      '%y4%m2%d2_%h2%n2z.nc4',
  SatDiagnEdge.frequency:     00000001 000000
  SatDiagnEdge.duration:      00000100 000000
  SatDiagnEdge.hrrange:       11.98 15.02
  SatDiagnEdge.mode:          'time-averaged'
  SatDiagnEdge.fields:        'SatDiagnConc_PEDGE',
::

List of diagnostic fields in the SatDiagnEdge collection

Diagnostic field

Description

Units

SatDiagnPEDGE

Pressure at grid box edges

hPa

SpeciesConc

The SpeciesConc diagnostic collection contains species concentrations.

Sample definition section for HISTORY.rc

  SpeciesConc.template:       '%y4%m2%d2_%h2%n2z.nc4',
  SpeciesConc.format:         'CFIO',
  SpeciesConc.frequency:      00000100 000000
  SpeciesConc.duration:       00000100 000000
  SpeciesConc.mode:           'time-averaged'
  SpeciesConc.fields:         'SpeciesConcVV_?ALL?',
                              'SpeciesConcMND_?ALL?',
::

List of diagnostic fields in the SpeciesConc collection

Diagnostic field

Description

Units

Wildcards

SpeciesConcMND_<name|wc>

Species concentration

molec/cm3

can be used with all wildcards

SpeciesConcVV_<name|wc>

Species concentration

mol/mol dry air

can be used with all wildcards

StateChm

The ‘’’StateChm ‘’’ collection contains quantities from State_Chm, the Chemistry State object (other than the species concentrations, which are stored in the SpeciesConc collection).

Sample definition section for HISTORY.rc

  StateChm.template:    '%y4%m2%d2_%h2%n2z.nc4',
  StateChm.frequency:   00000100 000000
  StateChm.duration:    00000100 000000
  StateChm.mode:        'time-averaged'
  StateChm.fields:      'Chem_phSav      ', 'GIGCchem',
                        'Chem_HplusSav   ', 'GIGCchem',
                        'Chem_WaterSav   ', 'GIGCchem',
                        'Chem_SulRatSav  ', 'GIGCchem',
                        'Chem_NaRatSav   ', 'GIGCchem',
                        'Chem_AcidPurSav ', 'GIGCchem',
                        'Chem_BiSulSav   ', 'GIGCchem',
                        'Chem_pHCloud    ', 'GIGCchem',
                        'Chem_SSAlk',    ', 'GIGCchem',
                        'Chem_HSO3AQ     ', 'GIGCchem',
                        'Chem_SO3AQ      ', 'GIGCchem',
                        'Chem_fupdateHOBr', 'GIGCchem',
::

List of diagnostic fields in the StateChm collection

Diagnostic field

Description

Units

Chm_AcidPurSav

ISORROPIA acidpur concentration

M

Chm_BiSulSav

ISORROPIA bisulfate general acid concentration

M

Chm_fupdateHOBr

Correction factor for HOBr removal by SO2 grid box (wet air)

mol/L

Chm_HplusSav

ISORROPIA H+ concentration

M

Chm_HSO3AQ

Cloud bisulfite concentration

mol/L

Chm_NaRatSav

ISORROPIA Na+ concentration

M

Chm_phCloud

Cloud pH

1

Chm_phSav

ISORROPIA aerosol pH

1

Chm_SO3AQ

Cloud sulfite concentration

mol/L

Chm_SulRatSav

ISORROPIA sulfate concentration

M

Chm_SSalk

Sea salt alkalinity

Chm_WaterSav

ISORROPIA aerosol water

\({\mu}g/m3\)

StateMet

The StateMet collection contains met fields and other derived quantities that are carried in the State_Met object.

Sample definition section for HISTORY.rc

  StateMet.template:    '%y4%m2%d2_%h2%n2z.nc4',
  StateMet.frequency:   00000100 000000
  StateMet.duration:    00000100 000000
  StateMet.mode:        'time-averaged'
  StateMet.fields:      'Met_AD         ',
                        'Met_AIRDEN     ',
                        'Met_AIRVOL     ',
                        'Met_ALBD       ',
                        'Met_AREAM2     ',
                        'Met_AVGW       ',
                        'Met_BXHEIGHT   ',
                        'Met_ChemGridLev',
                        'Met_CLDF       ',
                        'Met_CLDFRC     ',
                        'Met_CLDTOPS    ',
                        'Met_DELP       ',
                        'Met_DQRCU      ',
                        'Met_DQRLSAN    ',
                        'Met_DTRAIN     ',
                        'Met_EFLUX      ',
                        'Met_FRCLND     ',
                        'Met_FRLAKE     ',
                        'Met_FRLAND     ',
                        'Met_FRLANDIC   ',
                        'Met_FROCEAN    ',
                        'Met_FRSEAICE   ',
                        'Met_FRSNO      ',
                        'Met_GWETROOT   ',
                        'Met_GWETTOP    ',
                        'Met_HFLUX      ',
                        'Met_LAI        ',
                        'Met_LWI        ',
                        'Met_PARDR      ',
                        'Met_PARDF      ',
                        'Met_PBLTOPL    ',
                        'Met_PBLH       ',
                        'Met_PHIS       ',
                        'Met_PMID       ',
                        'Met_PMIDDRY    ',
                        'Met_PRECANV    ',
                        'Met_PRECCON    ',
                        'Met_PRECLSC    ',
                        'Met_PRECTOT    ',
                        'Met_PS1DRY     ',
                        'Met_PS1WET     ',
                        'Met_PS2DRY     ',
                        'Met_PS2WET     ',
                        'Met_PSC2WET    ',
                        'Met_PSC2DRY    ',
                        'Met_QI         ',
                        'Met_QL         ',
                        'Met_OMEGA      ',
                        'Met_OPTD       ',
                        'Met_REEVAPCN   ',
                        'Met_REEVAPLS   ',
                        'Met_SLP        ',
                        'Met_SNODP      ',
                        'Met_SNOMAS     ',
                        'Met_SPHU       ',
                        'Met_SPHU1      ',
                        'Met_SPHU2      ',
                        'Met_SUNCOS     ',
                        'Met_SUNCOSmid  ',
                        'Met_SWGDN      ',
                        'Met_T          ',
                        'Met_TAUCLI     ',
                        'Met_TAUCLW     ',
                        'Met_THETA      ',
                        'Met_TMPU1      ',
                        'Met_TMPU2      ',
                        'Met_TO3        ',
                        'Met_TropHt     ',
                        'Met_TropLev    ',
                        'Met_TropP      ',
                        'Met_TS         ',
                        'Met_TSKIN      ',
                        'Met_TV         ',
                        'Met_U          ',
                        'Met_U10M       ',
                        'Met_USTAR      ',
                        'Met_UVALBEDO   ',
                        'Met_V          ',
                        'Met_V10M       ',
                        'Met_Z0         ',
::

List of diagnostic fields in the StateMet collection

Diagnostic field

Description

Units

Met_AD

Dry air mass

kg

Met_AIRDEN

Dry air density

kg/m3

Met_AIRVOL

Grid box volume, dry air

m3

Met_ALBD

Surface albedo

1

Met_AREAM2

Grid box area

m2

Met_AVGW

Water vapor volume mixing ratio

vol H2O/vol dry air

Met_BXHEIGHT

Grid box height

m

Met_ChemGridLev

Chemistry grid level

1

Met_CLDF

3-D cloud fraction

Met_CLDFRC

Column cloud fraction

1

Met_CLDTOPS

Maximum cloud top height

1

Met_DELP

Delta-pressure between top and bottom edges of grid box (wet air)

hPa

Met_DQRCU

Convective precipitation production rate (dry air)

kg/kg/s

Met_DTRAIN

Detrainment flux

kg/m2/s

Met_EFLUX

Latent heat flux

W/m2

Met_FRCLND

Olson land fraction

1

Met_FRLAKE

Fraction of grid box covered by lakes

1

Met_FRLAND

Fraction of grid box covered by land

1

Met_FRLANDIC

Fraction of grid box covered by land ice

1

Met_FROCEAN

Fraction of grid box covered by ocean

1

Met_FRSEAICE

Fraction of grid box covered by sea ice

1

Met_FRSNO

Fraction of grid box covered by snow

1

Met_GWETROOT

Root soil moisture

1

Met_GWETTOP

Topsoil moisture

1

Met_HFLUX

Sensible heat flux

W/m2

Met_LAI

Leaf area index from met field archive

m2/m2

Met_LWI

Land-water-ice indices

1

Met_PARDF

Diffuse photosynthetically active radiation

W/m2

Met_PARDR

Diffuse photosynthetically active radiation

W/m2

Met_PBLTOPL

PBL top layer

1

Met_PBLH

PBL height

m

Met_PHIS

Surface geopotential height

m

Met_PMID

Pressure at midpoint of model layers, defined as arithmetic average of edge pressures (wet air)

hPa

Met_PMIDDRY

Pressure at midpoint of model layers, defined as arithmetic average of edge pressures (dry air)

hPa

Met_PRECANV

Anvil precipitation (at surface)

mm/day

Met_PRECCON

Convective precipitation (at surface)

mm/day

Met_PRECLSC

Large-scale precipitation (at surface)

mm/day

Met_PRECTOT

Total precipitation (at surface)

mm/day

Met_PS1DRY

Instantaneous surface pressure at start of 3-hr met field interval (dry air)

hPa

Met_PS2DRY

Instantaneous surface pressure at end of 3-hr met field interval (dry air)

hPa

Met_PSC2DRY

Surface pressure interpolated to current time (dry air)

hPa

Met_PS1WET

Instantaneous surface pressure at start of 3-hr met field interval (wet air)

hPa

Met_PS2WET

Instantaneous surface pressure at end of 3-hr met field interval (wet air)

hPa

Met_PSC2WET

Surface pressure interpolated to current time (wet air)

hPa

Met_QI

Ice mixing ratio (dry air)

kg/kg dry air

Met_QL

Liquid water mixing ratio (dry air)

kg/kg dry air

Met_OMEGA

Updraft velocity

Pa/s

Met_OPTD

Visible optical depth

1

Met_REEVAPCN

Evaporation of convective precipitation (dry air)

kg/kg/s

Met_REEVAPLS

Evaporation of large-scale + anvil precipitation (dry air)

kg/kg/s

Met_SLP

Sea level pressure

hPa

Met_SNODP

Snow depth

m

Met_SNOMAS

Snow mass

kg/m2

Met_SPHU1

Instantaneous specific humidity at start of 3 hr met field interval (wet air)

kg/kg

Met_SPHU2

Instantaneous specific humidity at end of 3-hr met field interval (wet air)

kg/kg

Met_SPHU

Specific humidity interpolated to current time (wet air)

g H2O/kg air

Met_SUNCOS

Cosine of solar zenith angle at current time

1

Met_SUNCOSMID

Cosine of solar zenith angle at midpoint of chemistry timestep

1

Met_SWGDN

Incident shortwave radiation at ground

W/m2

Met_TAUCLI

Visible optical depth of ice clouds

1

Met_TAUCLW

Visible optical depth of water clouds

1

Met_THETA

Potential temperature

K

Met_TMPU1

Instantaneous temperature at start of 3-hr met field interval

K

Met_TMPU2

Instantaneous temperature at end of 3-hr met field interval

K

Met_T

Temperature interpolated to current time

K

Met_TO3

Total overhead ozone column

Dobsons

Met_TropHt

Tropopause height

u

Met_TropLev

Tropopause level

1

Met_TROPP

Tropopause pressure

hPa

Met_TS

Surface temperature

K

Met_TSKIN

Surface skin temperature

K

Met_U

East-west ccomponent of wind

m/s

Met_U10M

East-west component of wind at 10 m height above surface

m/s

Met_USTAR

Friction velocity

m/s

Met_UVALBEDO

Ultraviolet surface albedo

1

Met_V

North-south ccomponent of wind

m/s

Met_V10M

North-south component of wind at 10 m height above surface

m/s

Met_Z0

Surface roughness height

m

FracOfTimeInTrop

Fraction of time spent in the troposphere

1

StratBM

The StratBM collection contains diagnostic fields for GEOS-Chem 10-year stratospheric benchmark simulations. Unless you are involved with benchmarking GEOS-Chem, you may leave this collection deactivated.

Sample definition section for the StratBM collection

  StratBM.template:       '%y4%m2%d2_%h2%n2z.nc4',
  StratBM.frequency:      00000000 010000
  StratBM.duration:       00000001 000000
  StratBM.mode:           'time-averaged'
  StratBM.fields:         'SpeciesConcVV_NO2                 ',
                          'SpeciesConcVV_O3                  ',
                          'SpeciesConcVV_ClO                 ',
                          'Met_PSC2WET                       ',
                          'Met_BXHEIGHT                      ',
                          'Met_AIRDEN                        ',
                          'Met_AD                            ',
::

List of diagnostic fields in the StateMet collection

Diagnostic field

Description

Units

Met_AD

Dry air mass

kg

Met_AIRDEN

Dry air density

kg/m3

Met_BXHEIGHT

Grid box height

m

Met_PSC2WET

Surface pressure interpolated to current time (wet air)

hPa

SpeciesConcVV_ClO

ClO concentration

mol/mol dry air

SpeciesConcVV_NO2

NO2 concentration

mol/mol dry air

SpeciesConcVV_O3

O3 concentration

mol/mol dry air

Tomas

The TOMAS collection contains diagnostic fields for fullchem simulations with TOMAS aerosol microphysics.

  Tomas.template:       '%y4%m2%d2_%h2%n2z.nc4',
  Tomas.format:         'CFIO',
  Tomas.timestampStart: .true.
  Tomas.monthly:        0
  Tomas.frequency:      010000
  Tomas.duration:       010000
  Tomas.mode:           'time-averaged'
  Tomas.fields:         'TomasH2SO4                        ',
                        'TomasH2SO4mass_?TOMASBIN?         ',
                        #----------------------------------------------
                        # NOTE: for GEOS-Chem Classic you can use the
                        # ?TOMASBIN? wildcard.  For GCHP you will need
                        # to list each diagnostic field individually
                        # such as is shown below:
                        #'TomasH2SO4mass_bin01             ',
                        #'TomasH2SO4mass_bin02             ',
                        #'TomasH2SO4mass_bin03             ',
                        #'TomasH2SO4mass_bin04             ',
                        #'TomasH2SO4mass_bin05             ',
                        #'TomasH2SO4mass_bin06             ',
                        #'TomasH2SO4mass_bin07             ',
                        #'TomasH2SO4mass_bin08             ',
                        #'TomasH2SO4mass_bin09             ',
                        #'TomasH2SO4mass_bin10             ',
                        #'TomasH2SO4mass_bin11             ',
                        #'TomasH2SO4mass_bin12             ',
                        #'TomasH2SO4mass_bin13             ',
                        #'TomasH2SO4mass_bin14             ',
                        #'TomasH2SO4mass_bin15             ',
                        #----------------------------------------------
                        'TomasH2SO4number_?TOMASBIN?      ',
                        'TomasCOAG                        ',
                        'TomasCOAGmass_?TOMASBIN          ',
                        'TomasCOAGnumber_?TOMASBIN?       ',
                        'TomasNUCL                        ',
                        'TomasNUCRATEFN                   ',
                        'TomasNUCLmass_?TOMASBIN?         ',
                        'TomasNUCLnumber_?TOMASBIN?       ',
                        'TomasNUCRATEnumber_?TOMASBIN?    ',
                        'TomasAQOX                        ',
                        'TomasAQOXmass_?TOMASBIN?         ',
                        'TomasAQOXnumber_?TOMASBIN?       ',
                        'TomasMNFIX                       ',
                        'TomasMNFIXmass_?TOMASBIN?        ',
                        'TomasMNFIXnumber_?TOMASBIN?      ',
                        'TomasMNFIXh2so4mass_?TOMASBIN?   ',
                        'TomasMNFIXh2so4number_?TOMASBIN? ',
                        'TomasMNFIXcoagmass_?TOMASBIN?    ',
                        'TomasMNFIXcoagnumber_?TOMASBIN?  ',
                        'TomasMNFIXaqoxmass_?TOMASBIN?    ',
                        'TomasMNFIXaqoxnumber_?TOMASBIN?  ',
                        'TomasMNFIXezwat1number_?TOMASBIN?',
                        'TomasMNFIXezwat2mass_?TOMASBIN?  ',
                        'TomasMNFIXezwat2number_?TOMASBIN?',
                        'TomasMNFIXezwat3mass_?TOMASBIN?  ',
                        'TomasMNFIXezwat3number_?TOMASBIN?',
                        'TomasMNFIXcheck1mass_?TOMASBIN?  ',
                        'TomasMNFIXcheck1number_?TOMASBIN?',
                        'TomasMNFIXcheck2mass_?TOMASBIN?  ',
                        'TomasMNFIXcheck2number_?TOMASBIN?',
                        'TomasMNFIXcheck3mass_?TOMASBIN?  ',
                        'TomasMNFIXcheck3number_?TOMASBIN?',
                        'TomasSOA                         ',
                        'TomasSOAmass_?TOMASBIN?          ',
                        'TomasSOAnumber_?TOMASBIN?        ',
::

List of diagnostic fields for the Tomas collection

Diagnostic field

Description

Units

Wildcard

TomasAQOX

Tomas aqueous oxidation rate

1

[20]

TomasAQOXmass_<name|wc>

TomasAQOX mass rate

kg/kg/s

[20]

TomasAQOXnumber_<name|wc>

TomasAQOX number rate

#/kg/s

[20]

TomasCOAG

Tomas coagulation rate

1

[20]

TomasCOAGmass_<name|wc>

TOMASCOAG mass rate

kg/kg/s

[20]

TomasCOAGnumber_<name|wc>

TomasCOAG number rate

#/kg/s

[20]

TomasH2SO4

Tomas condensation rate

1

[20]

TomasH2SO4mass_<name|wc>

TomasH2SO4 mass rate

kg/kg/s

[20]

TomasH2SO4number_<name|wc>

TomasH2SO4 number rate

#/kg/s

[20]

TomasMNFIX

Tomas error rate

1

[20]

TomasMNFIXmass_<name|wc>

TomasMNFIX mass rate

kg/kg/s

[20]

TomasMNFIXnumber_<name|wc>

TomasMNFIX number rate

#/kg/s

[20]

TomasMNFIXaqoxmass_<name|wc>

TOMASMNFIXAQOX mass rate

kg/kg/s

[20]

TomasMNFIXaqoxnumber_ <name|wc>

TOMASMNFIXAQOX number rate

#/kg/s

[20]

TomasMNFIXcoagmass_<name|wc>

TomasMNFIXCOAG mass rate

kg/kg/s

[20]

TomasMNFIXcoagnumber_<name|wc>

TomasMNFIXCOAG number rate

#/kg/s

[20]

TomasMNFIXcheck1mass_<name|wc>

TOMASMNFIXCHECK1 mass rate

kg/kg/s

[20]

TomasMNFIXcheck1number_<name|wc>

TOMASMNFIXCHECK1 number rate

#/kg/s

[20]

TomasMNFIXcheck2mass_<name|wc>

TOMASMNFIXCHECK2 mass rate

kg/kg/s

[20]

TomasMNFIXcheck2number_<name|wc>

TOMASMNFIXCHECK2 number rate

#/kg/s

[20]

TomasMNFIXcheck3mass_<name|wc>

TOMASMNFIXCHECK3 mass rate

kg/kg/s

[20]

TomasMNFIXcheck3number_<name|wc>

TOMASMNFIXCHECK3 number rate

#/kg/s

[20]

TomasMNFIXezwat1mass_<name|wc>

TOMASMNFIXEZWAT1 mass rate

kg/kg/s

[20]

TomasMNFIXezwat1number_<name|wc>

TOMASMNFIXEZWAT1 number rate

#/kg/s

[20]

TomasMNFIXezwat2mass_<name|wc>

TOMASMNFIXEZWAT2 mass rate

kg/kg/s

[20]

TomasMNFIXezwat2number_<name|wc>

TOMASMNFIXEZWAT2 number rate

#/kg/s

[20]

TomasMNFIXezwat3mass_<name|wc>

TOMASMNFIXEZWAT3 mass rate

kg/kg/s

[20]

TomasMNFIXezwat3number_<name|wc>

TOMASMNFIXEZWAT3 number rate

#/kg/s

[20]

TomasMNFIXh2so4mass_<name|wc>

TomasMNFIXH2SO4 mass rate

kg/kg/s

[20]

TomasMNFIXh2so4number_<name|wc>

TomasMNFIXH2SO4 number rate

#/kg/s

[20]

TomasNUCL

Tomas nucleation rate

1

[20]

TomasNUCLmass_<name|wc>

TomasNUCL mass rate

kg/kg/s

[20]

TomasNUCLnumber_<name|wc>

TomasNUCL number rate

#/kg/s

[20]

TomasSOA

TomasSOA rate

1

[20]

TomasSOAmass_<name|wc>

TomasSOA mass rate

kg/kg/s

[20]

TomasSOAnumber_<name|wc>

TomasSOA number rate

#/kg/s

[20]

Notes for the Tomas collection

UVFlux

The UVFlux diagnostic contains diffuse, direct, and net UV fluxes at each of the photolysis wavelength bins.

Sample definition section for HISTORY.rc

  UVFlux.template:    '%y4%m2%d2_%h2%n2z.nc4',
  UVFlux.frequency:   00000100 000000
  UVFlux.duration:    00000100 000000
  UVFlux.mode:        'time-averaged'
  UVFlux.template:    'UVFluxDiffuse_?UVFLX?',
                      'UVFluxDirect_?UVFLX? ',
                      'UVFluxNet_?UVFLX?    ',
::

List of diagnostic fields in the UvFlux collection

Diagnostic field

Description

Units

Wildcards

UVFluxDiffuse_<name|wc>

Diffuse UV flux in wavelength bin

W/m2

?UVFLX?

UVFluxDirect_<name|wc>

Direct UV flux in wavelength bin

W/m2

?UVFLX?

UVFluxNet_<name|wc>

Net UV flux in wavelength bin

W/m2

?UVFLX?

WetLossConv

The WetLossConv collection contains diagnostics fluxes of soluble species lost to wet scavenging in convective updrafts.

Sample definition section for HISTORY.rc

  WetLossConv.template:    '%y4%m2%d2_%h2%n2z.nc4',
  WetLossConv.frequency:   00000100 000000
  WetLossConv.duration:    00000100 000000
  WetLossConv.mode:        'time-averaged'
  WetLossConv.fields:      'WetLossConv_?WET?    ',
                           'WetLossConvFrac_?WET?',
::

List of diagnostic fields in the WetLossConv collection

Diagnostic field

Description

Units

Wildcard

WetLossConv_<name|wc>

Loss of soluble species scavenged by cloud updrafts in moist convection

kg/s

?WET?

WetLossConvFrac_<name|wc>

Fraction of species scavenged by cloud updrafts in moist convection

1

?WET?

WetLossLS

The WetLossLS collection contains diagnostics fluxes of soluble species lost to rainout and washout in large-scale wet deposition.

Sample definition section for HISTORY.rc

  WetLossLS.template:     '%y4%m2%d2_%h2%n2z.nc4',
  WetLossLS.frequency:    00000100 000000
  WetLossLS.duration:     00000100 000000
  WetLossLS.mode:         'time-averaged'
  WetLossLS.fields:       'WetLossLS_?WET?',
::

List of diagnostic fields in the WetLossLS collection

Diagnostic field

Description

Units | Wildcard

WetLossLS_<name|wc>

Loss of soluble species in large-scale precipitation

kg/s

?WET?

Adding new History diagnostics

To add your own diagnostics we recommend that you find a similar existing diagnostic and use its implementation as a template. Most of the work is done in Headers/state_diag_mod.F90. Briefly, the following updates to that file are essential for adding in your own netCDF diagnostics:

  1. Declare diagnostic array at top of module.

  2. Set diagnostic array pointer to null in Zero_State_Diag subroutine.

  3. Create a section in Init_State_Diag subroutine to allocate and register the array.

  4. Deallocate the diagnostic array in subroutine Cleanup_State_Diag.

  5. Add an IF block for the diagnostic within subroutine Get_Metadata_State_Diag to define its metadata, making sure to list the diagnostic name with all capital letters.

Good diagnostics to use as templates are SpeciesConcVV for 3-dimensional arrays that are for all species and DryDepVel for 2-dimensional arrays that are for a subset of species. If your diagnostic is not per species then AODDust is a good diagnostic to look at. Search the file Headers/state_diag_mod.F90 for any of these strings to find all instances of code related to their implementation.

Note that information about the dimensions and species collection the diagnostic will include must be specified when allocating the array in Init_State_Diag and in Get_Metadata_State_Diag. In the lattersubroutine the Rank is the integer number of dimensions of the diagnostic (not including species) and the TagID string, if any, specifies the species collection to output the diagnostic per. TagIDs are defined in subroutine Get_TagInfo. Each TagID string can also be used as a wildcard within HISTORY.rc to simplify diagnostic name specification (for GEOS-Chem Classic only).

Once you have implemented your diagnostic in Headers/state_diag_mod.F90, try adding it to HISTORY.rc and running. You should get your diagnostic output in the netCDF output file as all zeros. The next step is to populate the array with whatever value you want to output. You should do this by passing the State_Diag array to the location where you want to set the values. Then write code to fill the array. A simple test of your understanding is to initially set values to a constant other than zero and see if the output matches what you set the arrays to.

For additional help implementing your own GEOS-Chem diagnostics please contact the GEOS-Chem Support Team.