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,,
EXPIDis set to./OutputDir/GEOSChemby default. This means that all diagnostic files will be written to the./OutputDirsubdirectory of the GEOS-Chem run directory, and will start with the prefixGEOSChem.Note
Restart files are placed in the
./Restartssubdirectory 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.rcconfiguration file. Only the diagnostic collections pertaining to a particular GEOS-Chem simulation will be included in the correspondingHISTORY.rcfile.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 theCOLLECTIONS: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 haveSpeciesConclisted underCOLLECTIONS:, but there is no further information provided about theSpeciesConccollection, then GEOS-Chem will halt with an error message.Note
You are not limited to the collections that are pre-defined in the
HISTORY.rcconfiguration file. You may create additional diagnostic collections to suit your research purposes.
SpeciesConc
Name of the first collection in this
HISTORY.rcfile.
SpeciesConc.template
Determines the date and time format for the
SpeciesConccollection filename suffix, as described below:
%y4%m2%d2_%h2%n2z.nc4printsYYYYMMDD_hhmmz.nc4to the end of each netCDF filename.
YYYYMMDDis the date in year/month/day format;
hhmmis the time inhour:minutesformat.
zdenotes “Zulu”, which is an abbreviation for UTC time.
.nc4denotes that the data file is in the netCDF-4 format.Note
For example, the complete file path for the
SpeciesConccollection at 00:00 UTC on 2020/01/01 will be./OutputDir/GEOSChem.SpeciesConc.20200101_0000z.nc4, where:
EXPIDspecifies the filename prefix (./OutputDir/GEOSChem)
SpeciesConc.templatespecifies the format of the filename suffix (.20200101_0000z.nc4).
SpeciesConc.frequency
Determines how often the diagnostic quantities belonging to the
SpeciesConccollection will be saved to a netCDF file. This can be specified as eitherhhmmssorYYYYMMDD hhmmss.In the above example, data belonging to the collection will be written to the file every 6 hours. Because
SpeciesConcis 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
SpeciesConcnetCDF file will be created. Uses the same format asSpeciesConc.frequency.
SpeciesConc.mode
Determines the averaging method for the
SpeciesConccollection. Allowable values are:
instantaneous: Archives instantaneous values at the interval specified bySpeciesConc.frequency.
time-averaged: Archives values averaged over the interval specified bySpeciesConc.frequency.
SpeciesConc.fields
Lists the diagnostic quantities to be archived in the
SpeciesConccollection. 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 andSpeciesConcVV_?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.rcconfiguration file. In this collection we will request output to be restricted to a subset of the horizontal grid.The
.template,.frequency,.duration,:mode, and.fieldsare described for theSpeciesConccollection 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.rcconfiguration file.The
.template,.frequency,.duration,:mode, and.fieldsare described for theSpeciesConccollection above, so we will not repeat them here.
ConcAftercChem.mode
In this example, the
ConcAfterChem.modesetting indicates that theConcAfterChemcollection 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 |
Chem_pHCloud |
Met_ |
Request diagnostic output
from the |
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? |
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? |
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? |
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 |
|
Dry deposition velocity of species tagged with the ?DRYALT?wildcard |
cm/s |
?DRYALT? |
|
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 ( |
count |
KppAutoReduceThres |
Auto-reduction threshold |
molec/cm3/s |
KppcNONZERO |
Number of nonzero elements
( |
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 |
?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 |
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
|
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 |
|
TomasAQOXmass_<name|wc> |
TomasAQOX mass rate |
kg/kg/s |
|
TomasAQOXnumber_<name|wc> |
TomasAQOX number rate |
#/kg/s |
|
TomasCOAG |
Tomas coagulation rate |
1 |
|
TomasCOAGmass_<name|wc> |
TOMASCOAG mass rate |
kg/kg/s |
|
TomasCOAGnumber_<name|wc> |
TomasCOAG number rate |
#/kg/s |
|
TomasH2SO4 |
Tomas condensation rate |
1 |
|
TomasH2SO4mass_<name|wc> |
TomasH2SO4 mass rate |
kg/kg/s |
|
TomasH2SO4number_<name|wc> |
TomasH2SO4 number rate |
#/kg/s |
|
TomasMNFIX |
Tomas error rate |
1 |
|
TomasMNFIXmass_<name|wc> |
TomasMNFIX mass rate |
kg/kg/s |
|
TomasMNFIXnumber_<name|wc> |
TomasMNFIX number rate |
#/kg/s |
|
TomasMNFIXaqoxmass_<name|wc> |
TOMASMNFIXAQOX mass rate |
kg/kg/s |
|
TomasMNFIXaqoxnumber_ <name|wc> |
TOMASMNFIXAQOX number rate |
#/kg/s |
|
TomasMNFIXcoagmass_<name|wc> |
TomasMNFIXCOAG mass rate |
kg/kg/s |
|
TomasMNFIXcoagnumber_<name|wc> |
TomasMNFIXCOAG number rate |
#/kg/s |
|
TomasMNFIXcheck1mass_<name|wc> |
TOMASMNFIXCHECK1 mass rate |
kg/kg/s |
|
TomasMNFIXcheck1number_<name|wc> |
TOMASMNFIXCHECK1 number rate |
#/kg/s |
|
TomasMNFIXcheck2mass_<name|wc> |
TOMASMNFIXCHECK2 mass rate |
kg/kg/s |
|
TomasMNFIXcheck2number_<name|wc> |
TOMASMNFIXCHECK2 number rate |
#/kg/s |
|
TomasMNFIXcheck3mass_<name|wc> |
TOMASMNFIXCHECK3 mass rate |
kg/kg/s |
|
TomasMNFIXcheck3number_<name|wc> |
TOMASMNFIXCHECK3 number rate |
#/kg/s |
|
TomasMNFIXezwat1mass_<name|wc> |
TOMASMNFIXEZWAT1 mass rate |
kg/kg/s |
|
TomasMNFIXezwat1number_<name|wc> |
TOMASMNFIXEZWAT1 number rate |
#/kg/s |
|
TomasMNFIXezwat2mass_<name|wc> |
TOMASMNFIXEZWAT2 mass rate |
kg/kg/s |
|
TomasMNFIXezwat2number_<name|wc> |
TOMASMNFIXEZWAT2 number rate |
#/kg/s |
|
TomasMNFIXezwat3mass_<name|wc> |
TOMASMNFIXEZWAT3 mass rate |
kg/kg/s |
|
TomasMNFIXezwat3number_<name|wc> |
TOMASMNFIXEZWAT3 number rate |
#/kg/s |
|
TomasMNFIXh2so4mass_<name|wc> |
TomasMNFIXH2SO4 mass rate |
kg/kg/s |
|
TomasMNFIXh2so4number_<name|wc> |
TomasMNFIXH2SO4 number rate |
#/kg/s |
|
TomasNUCL |
Tomas nucleation rate |
1 |
|
TomasNUCLmass_<name|wc> |
TomasNUCL mass rate |
kg/kg/s |
|
TomasNUCLnumber_<name|wc> |
TomasNUCL number rate |
#/kg/s |
|
TomasSOA |
TomasSOA rate |
1 |
|
TomasSOAmass_<name|wc> |
TomasSOA mass rate |
kg/kg/s |
|
TomasSOAnumber_<name|wc> |
TomasSOA number rate |
#/kg/s |
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:
Declare diagnostic array at top of module.
Set diagnostic array pointer to null in
Zero_State_Diagsubroutine.
Create a section in
Init_State_Diagsubroutine to allocate and register the array.
Deallocate the diagnostic array in subroutine
Cleanup_State_Diag.
Add an
IFblock for the diagnostic within subroutineGet_Metadata_State_Diagto 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.