List of diagnostics archived to netCDF format

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NOTE: we are reorganizing this page to be consistent with the latest GEOS-Chem netCDF diagnostics. This page will be in flux for the time being.

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On this page we list the information about the new netCDF diagnostics that will be introduced in GEOS-Chem v11-02.

NOTE: We will NOT retire the legacy bpch diagnostics in GEOS-Chem v11-02. We will preserve the bpch diagnostic output until we can find alternatives for specialty diagnostics, especially those which involve averaging in a local solar time window.

Overview

More information forthcoming

An introduction to netCDF diagnostics

Bob Yantosca has created an overview presentation about the new netCDF diagnostics for v11-02.

--Bob Yantosca (talk) 22:12, 8 February 2018 (UTC)

Sample HISTORY.rc diagnostic input file

Here is a sample HISTORY.rc file that is used to request netCDF diagnostic output from a GEOS-Chem “Classic” simulation. 

#===================================================================
# Declare collection names.  Disable collections by commenting
# each collection name out with a "#" character.
#===================================================================
COLLECTIONS: 'SpeciesConc',
             'ConcAfterChem',
::
#===================================================================
# Collection to save out GEOS-Chem species concentrations
#===================================================================
SpeciesConc.template:     '%y4%m2%d2_%h2%n2z.nc4',
SpeciesConc.frequency:    060000,
SpeciesConc.format:       'CFIO',
SpeciesConc.duration:     240000,
SpeciesConc.mode:         'instantaneous',
SpeciesConc.fields:       'SpeciesConc_?ADV?',  'GIGCchem',
::
#===================================================================
# Collection to save out concentrations after chemistry
# (from the FlexChem/KPP solver)
#===================================================================
ConcAfterChem.template:   '%y4%m2%d2_%h2%n2z.nc4',
ConcAfterChem.frequency:  000100 000000,
ConcAfterChem.format:     'CFIO',
ConcAfterChem.duration:   000100 000000,
ConcAfterChem.mode:       'time-averaged',
ConcAfterChem.fields:     'OHconcAfterChem',     'GIGCchem',
                          'HO2concAfterChem',    'GIGCchem',
                          'O1DconcAfterChem',    ‘GIGCchem’,
                          'O3PconcAfterChem',    ‘GIGCchem’,
::

In this HISTORY.rc file, we are requesting two collections, or types of netCDF file output.

Attribute Explanation
SpeciesConc Name of the first collection in this HISTORY.rc file. A collection is a series of files containing the same GEOS-Chem diagnostic quantities.
SpeciesConc.template Determines the date and time format for each netCDF file name belonging to the SpeciesConc collection.
  • The string %y4%m2%d2_%h2%n2z.nc4 will print 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.
SpeciesConc.frequency Determines how often the diagnostic quantities belonging to SpeciesConc collection will be saved to a netCDF file.
  • This can be specified as either "hhmmss" or "YYMMDD hhmmss".
  • In the above example, data belonging to the SpeciesConc 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: indicates the I/O library that will be used. This can be omitted for GEOS-Chem "Classic" simualations.
SpeciesConc.duration Determines how often a new SpeciesConc netCDF file will be created.
  • This can be specified as either hhmmss or YYMMDD hhmmss.
  • In the above example, a new SpeciesConc netCDF file will be created every 24 hours.
SpeciesConc.mode Determines the averaging method for the SpeciesConc collection
  • In this example, SpeciesConc is defined as an instantaneous (aka "time-series") collection.
  • Diagnostic quantities belonging to SpeciesConc will be written directly to disk without any temporal averaging, at the specified frequency.
SpeciesConc.fields Lists the diagnostic quantities to be included in the SpeciesConc collection.
  • In the above example, we are requesting to archive the concentrations of all advected species to the SpeciesConc collection.
  • The text 'GIGCchem' is only needed for GCHP simulations. It is ignored for GEOS-Chem "Classic" simulations. We keep the 'GIGCchem' in the file in order HISTORY.rc files to be interchanged between GEOS-Chem "Classic" and GCHP simulations.

See the sections below for in-depth descriptions of all possible diagnostic quantities that can be archived to netCDF format.

NOTE: You may use wildcards to request a subset of all possible chemical species. See the next section for more information about wildcards.

:: Signifies the end of the SpeciesConc definition section.
  • "::" may be placed at any column in the file.
ConcAfterChem Name of the second collection in this HISTORY.rc file.
ConcAfterChem.template Determines the date and time format for each netCDF file name belonging to the ConcAfterChem collection.
ConcAfterChem.frequency Determines the length of the period in which the diagnostic quantities belonging to ConcAfterChem collection will be temporally-averaged, before being saved to a netCDF file.
  • This can be can be specified as either "hhmmss" or "YYMMDD hhmmss".
  • In the above example, data belonging to the ConcAfterChem collection will be averaged into monthly mean output.
ConcAfterChem.format For GCHP simulations only: indicates the I/O library that will be used. This can be omitted for GEOS-Chem "Classic" simualations.
ConcAfterChem.duration Determines how often a new netCDF file belongng to the ConcAfterChem will be created.
  • The duration attribute can be specified as either hhmmss or YYMMDD hhmmss.
  • In the above example, a new ConcAfterChem netCDF file will be created at the start of each new month.
ConcAfterChem.mode Determines the averaging method for the ConcAfterChem collection
  • In the above example, ConcAfterChem is defined as an time-averaged collection.
  • Diagnostic quantities belonging to the ConcAfterChem collection will be temporally-averaged for a period whose length is specified by the frequency attribute before being written to a netCDF file.
ConcAfterChem.fields Lists the diagnostic quantities to be included in the ConcAfterChem collection.
  • In the above example, we are requesting to archive to the ConcAfterChem collection the concentrations of OH, HO2, O1D, and O3P upon exiting the FlexChem/KPP solver
  • The text 'GIGCchem' is only needed for GCHP simulations. It is ignored for GEOS-Chem "Classic" simulations. We keep the 'GIGCchem' in the file in order HISTORY.rc files to be interchanged between GEOS-Chem "Classic" and GCHP simulations.

See the sections below for in-depth descriptions of all possible diagnostic quantities that can be archived to netCDF format.

NOTE: You may use wildcards to request a subset of all possible species. See the next section for more information about wildcards.

:: Signifies the end of the ConcAfterChem definition section.
  • "::" may be placed at any column in the file.

For more examples, please see Bob Yantosca’s netCDF diagnostics overview presentation. We will also add more documentation to the GEOS-Chem wiki in the coming weeks.

--Bob Yantosca (talk) 22:12, 8 February 2018 (UTC)

Legend

This section contains a description of how the information about each diagnostic quantity is arranged in the sections below.

General information about each diagnostic

The tables below list the following parameters for each diagnostic that is archived to bpch format:

Diagnostic name The name of the given diagnostic quantity that will be archived to netCDF file format.
  • NOTE: Wildcards can be used with certain diagnostics. This will let you specify all possible species, wavelength bins, etc. for a given diagnostic instead of having to list them individually. See the next section for a list of all possible wildcards.
  • ALSO NOTE: At this time, wildcards are not allowed in GCHP simulations. We are working to resolve this.
Description A short overview of the given diagnostic.
Units The physical units of the given diagnostic quantity.
Wildcards A list of wildcards that can be used to specify all possible species, wavelength bins, etc. for the given diagnostic quantity. For a complete list of wildcards, please see the table below.
Simulations A list of simulations for which this particular diagnostic is valid.

NOTE: all fullchem simulations are those that use one of the following full-chemistry mechanisms with the FlexChem/KPP solver:

  • benchmark
  • standard
  • tropchem
  • complexSOA
  • complesSOA_SVPOA
  • marinePOA
  • aciduptake
Bpch equivalent The NDxx diagnostic number (and slot) under which the same diagnostic is available as bpch output. See the List of diagnostics archived to bpch format wiki page for more information.
Notes Lists supplemental information for the given diagnostic.

Wildcards

The following terms are used in the tables below.

Term Explanation Example
<spcname> Short name of a GEOS-Chem species, used in several diagnostics listed below.

NOTES:

  1. The single-underscore (_) preceding the species name indicates that use of a species wildcard (e.g SpeciesConc_?ADV?, which only selects advected species) is possible.
  2. Allowable wild card values (case-insensitive) for species name are:
    • ?ADV?: Only the advected species
    • ?AER?: Only the aerosol species
    • ?ALL?: All GEOS-Chem species
    • ?DRY?: Only the dry-deposited species
    • ?FIX?: Only the inactive (aka "fixed") species in the KPP chemical mechanism
    • ?GAS?: Only the gas-phase species
    • ?KPP?: Only the KPP species
    • ?PHO: Only the photolyzed species
    • ?VAR?: Only the active (aka "variable") species in the KPP chemical mechanism
    • ?WET?: Only the wet-deposited species
    • ?PRODLOSS?: Only prod/loss diagnostic species
    • ?DUSTBIN: Only the dust bin number
  3. <spcname> should be case-insensitive. In most places where species names are compared, species names are first converted to uppercase and then a string match test is done. But because most species names represent a chemical formula (e.g. NO, CO),they will be mostly all uppercase. Some species names would have mixed-case, e.g. BrCl, Rn, Pb, Be7, etc.
 SpeciesConc_NO
SpeciesConc_CO
SpeciesConc_?ADV?
SpeciesConc_?AER?
SpeciesConc_?ALL?
SpeciesConc_?DRY?
SpeciesConc_?FIX?
SpeciesConc_?GAS?
SpeciesConc_?KPP?
SpeciesConc_?PHO?
SpeciesConc_?VAR?
SpeciesConc_?WET?
...etc...
<metname> Denotes a met field (or derived quantity such as total optical depth).

NOTES:

  1. MET_, Met_ or met_ (case-insensitive) must precede <metname>. This tells the diagnostic code to look for the corresponding field of the State_Met object.
 MET_U10M
MET_PS
MET_HFLUX
MET_T
...etc...
<photobin> Number of a given wavelength bin for FAST-JX photolysis 1-18 (with UCX on);
1-12 (with UCX off)
<aername> Aerosol quanatities included in the following array fields:
  1. State_Chm%AeroArea
  2. State_Chm%AeroRadi
  3. State_Chm%WetAeroArea
  4. State_Chm%WetAeroRadi

These do not always conform to GEOS-Chem species (for example, the mineral dust bins are the bins that are used as input for photolysis).

  1. MDUST1: Mineral dust (0.15μm)
  2. MDUST2: Mineral dust (0.25μm)
  3. MDUST3: Mineral dust (0.40μm)
  4. MDUST4: Mineral dust (0.80μm)
  5. MDUST5: Mineral dust (1.50μm)
  6. MDUST6: Mineral dust (2.50μm)
  7. MDUST7: Mineral dust (4.00μm)
  8. SULF: Sulfate
  9. BC: Black Carbon
  10. OC: Organic Carbon
  11. SSA: Sea salt aerosol, accumulation mode
  12. SSC: Sea salt aerosol, coarse mode
  13. BGSULF: Background stratospheric sulfate
  14. ICEI: Irregular ice cloud (Mischenko)
 CHEM_AeroAreaMDUST1
CHEM_WetAeroRadiSSA
...etc...


--Bob Yantosca (talk) 17:05, 9 February 2018 (UTC)

Collections

More information to be added

NOTE: The following collections 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 there can be only one vertical dimension per file.

The CloudConvFlux collection

A sample collection definition section is listed below. You may cut-and-paste this into your HISTORY.rc file and edit accordingly. 

 CloudConvFlux.template:     '%y4%m2%d2_%h2%n2z.nc4',
 CloudConvFlux.format:       'CFIO',
 CloudConvFlux.frequency:    010000
 CloudConvFlux.duration:     010000
 CloudConvFlux.mode:         'time-averaged'
 CloudConvFlux.fields:       'CloudConvFlux_?ADV?           ', 'GIGCchem',
 ::

Here follows a description of diagnostic quantities belonging to the CloudConvFlux collection.

Diagnostic name Description Units Wildcards Simulations Bpch equiv. Notes
CloudConvFlux_<spcname> Mass change due to cloud convection kg/s
  • ?ADV?
  • ?DRY?
  • ?GAS?
  • ?WET?
  • all simulations
  • Will be replaced by new flux diagnostics in v11-03

The ConcAfterChem collection

A sample collection definition section is listed below. You may cut-and-paste this into your HISTORY.rc file and edit accordingly. 

 ConcAfterChem.template:     '%y4%m2%d2_%h2%n2z.nc4',
 ConcAfterChem.format:       'CFIO',
 ConcAfterChem.frequency:    010000
 ConcAfterChem.duration:     010000
 ConcAfterChem.mode:         'time-averaged'
 ConcAfterChem.fields:       'OHconcAfterChem                ', 'GIGCchem',  
                             'HO2concAfterChem               ', 'GIGCchem',  
                             'O1DconcAfterChem               ', 'GIGCchem',  
                             'O3PconcAfterChem               ', 'GIGCchem',  
 ::

Here follows a description of diagnostic quantities belonging to the ConcAfterChem collection.

Diagnostic name Description Units Wildcards Simulations Bpch equiv. Notes
OHconcAfterChem OH concentration immediately after exiting the FlexChem solver molec/cm3
  • all fullchem
HO2concAfterChem HO2 concentration immediately after exiting the FlexChem solver molec/cm3
  • all fullchem
O1DconcAfterChem O1D concentration immediately after exiting the FlexChem solver molec/cm3
  • fullchem simuations using the UCX mechanism
O3PconcAfterChem O3P concentration immediately after exiting the FlexChem solver molec/cm3
  • fullchem simuations using the UCX mechanism

The SpeciesConc collection

A sample collection definition section is listed below. You may cut-and-paste this into your HISTORY.rc file and edit accordingly. 

 SpeciesConc.template:       '%y4%m2%d2_%h2%n2z.nc4',
 SpeciesConc.format:         'CFIO',
 SpeciesConc.frequency:      010000
 SpeciesConc.duration:       010000
 SpeciesConc.mode:           'time-averaged'
 SpeciesConc.fields:         'SpeciesConc_?ADV?             ', 'GIGCchem',
 ::

Here follows a description of diagnostic quantities belonging to the SpeciesConc collection.

Diagnostic name Description Units Wildcards Simulations Bpch equiv. Notes
SpeciesConc_<spcname> Chemical species concentrations mol/mol dry air
  • ?ADV?
  • ?AER?
  • ?ALL?
  • ?DRY?
  • ?FIX?
  • ?GAS?
  • ?KPP?
  • ?PHO?
  • ?VAR?
  • ?WET?
  • all simulations

--Bob Yantosca (talk) 22:45, 8 February 2018 (UTC)

Proposed diagnostic names for fields of the State_Chm object

The table below lists the available fields of the State_Chm chemistry state object that can be archived and sent to netCDF output files.

NOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability.

NOTE: Each of the diagnostic quantities listed below must begin with the case-insensitive text CHEM_ (or Chem_ or chem_). This will tell the diagnostics modules to look for these quantities in the State_Chm object.

Proposed diagnostic name Description replaces
NDXX 		with
CATEGORY 		and
TRACERS 		and
FREQUENCY 		from this bpch file
CHEM_Species_<spcname> Species concentrations in State_Chm%Species, in native units.

NOTE: This diagnostic may be useful for debugging and/or checkpointing. We do not recommend normal use of this diagnostic, because the units of State_Chm%Species change throughout a GEOS-Chem simulation. We recommend that you use the SpeciesConc diagnostic, which will always have consistent units (i.e. [mol/mol dry air]).

ND45 IJ-AVG-$ 1-nAdvect Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ND47 IJ-24H-$ 1-nAdvect Daily trac_avg.YYYYMMDDhhmm.bpch
ND48 IJ-24H-$ 1-nAdvect Instantaneous stations.YYYYMMDDhh
ND49 IJ-AVG-$ 1-nAdvect Instantaneous ts.YYYYMMDDhh.bpch
ND50 IJ-AVG-$ 1-nAdvect Daily ts_24h_avg.YYYYMMDDhh.bpch
ND51 & ND51b IJ-AVG-$ 1-nAdvect User-defined time avg ts_24h_avg.YYYYMMDDhh.bpch
CHEM_AeroArea<aername> Dry aerosol area [cm2/cm3] for several aerosol types, stored in the State_Chm%AeroArea array. - - - - -
CHEM_AeroRadi<aername> Dry aerosol radii [cm] for several aerosol types, stored in the State_Chm%AeroRadi array. - - - - -
CHEM_WetAeroArea<aername> Wet aerosol area [cm2/cm3] for several aerosol types, stored in the State_Chm%WetAeroArea array. - - - - -
CHEM_WetAeroRadi<aername> Wet aerosol radii [cm] for several aerosol types, stored in the State_Chm%WetAeroRadi array. - - - - -
CHEM_StatePsc Polar stratospheric cloud type (cf Kirner et al, 2011, GMD) [1] - - - - -
CHEM_KhetiSlaN2O5H2O Sticking coefficient for N2O5 + H2O reaction [1] - - - - -
CHEM_KhetiSlaN2O5HCl Sticking coefficient for N2O5 + HCl reaction [1] - - - - -
CHEM_KhetiSlaClNO3H2O Sticking coefficient for ClNO3 + H2O reaction [1] - - - - -
CHEM_KhetiSlaClNO3HCl Sticking coefficient for ClNO3 + HCl reaction [1] - - - - -
CHEM_KhetiSlaClNO3HBr Sticking coefficient for ClNO3 + HBr reaction [1] - - - - -
CHEM_KhetiSlaBrNO3H2O Sticking coefficient for BrNO3 + H2O reaction [1] - - - - -
CHEM_KhetiSlaBrNO3HCl Sticking coefficient for BrNO3 + HCl reaction [1] - - - - -
CHEM_KhetiSlaHOClHCl Sticking coefficient for HOCl + HCl reaction [1] - - - - -
CHEM_KhetiSlaHOClHBr Sticking coefficient for HOCl + HBr reaction [1] - - - - -
CHEM_KhetiSlaHOBrHCl Sticking coefficient for HOBr + HCl reaction [1] - - - - -
CHEM_KhetiSlaHOBrHBr Sticking coefficient for N2O5 + H2O reaction - - - - -
CHEM_phSav ISORROPIA aerosol pH ND73 ISOROP-$ 1 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
CHEM_HplusSav ISORROPIA H+ concentration [M] ND73 ISOROP-$ 2 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
CHEM_WaterSav ISORROPIA aerosol water [μg m-3] ND73 ISOROP-$ 3 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
CHEM_SulRatSav ISORROPIA sulfate concentration [M] none (not archived in v11-01) " " " " " " " "
CHEM_NaRatSav ISORROPIA Na+ concentration [M] none (not archived in v11-01) " " " " " " " "
CHEM_AcidPurSav ISORROPIA acidpur ?? concentration [M] none (not archived in v11-01) " " " " " " " "
CHEM_BiSulSav ISORROPIA bisulfate (general acide) concentration [M] none (not archived in v11-01) " " " " " " " "
CHEM_phCloud Cloud PH [1] none (new in v11-02) " " " " " " " "
CHEM_SSAlk Sea salt alkalinity [1] none (new in v11-02) " " " " " " " "

--Bob Yantosca (talk) 18:55, 29 November 2017 (UTC)

Proposed diagnostic names for aerosols

Here is a list of our proposed netCDF diagnostic names for quantities archived in the GEOS-Chem aerosol modules. This list is by no means exhaustive or complete. Contact Bob Yantosca with any suggestions or concerns.

NOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability.

NOTE: We propose changing the units of prod and loss diagnostics to the area-independent units of [kg/m3/s].

Proposed diagnostic name Description replaces
NDXX 		with
CATEGORY 		and
TRACERS 		and
FREQUENCY 		from this bpch file
LossHNO3onSeaSalt Loss of NO3 by DMS [kg]
NOTE: Only archived for dust uptake simulations 		ND05 PL-SUL-$ 14 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
LossNO3byDMS Loss of NO3 by DMS [kg]
NOTE: Only archived for aerosol-only simulations 		ND05 PL-SUL-$ 10 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
LossOHbyDMS Loss of OH by DMS [kg]
NOTE: Only archived for aerosol-only simulations 		ND05 PL-SUL-$ 9 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ProdMSAfromDMS Production of MSA from DMS [kg]
NOTE: Only archived for aerosol-only simulations 		ND05 PL-SUL-$ 4 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ProdNITfromHNO3uptakeOnDust Production of NIT from HNO3 uptake on dust aerosols [kg N]
NOTE: Only archived for dust uptake simulations 		ND05 PL-SUL-$ 12 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ProdSO2fromDMS Total P(SO2) from DMS [kg S]
NOTE: Only archived for aerosol-only simulations 		ND05 PL-SUL-$ 3 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ProdSO2fromDMSandNO3 Production of SO2 from DMS + NO3 (in sulfate_mod.F) [kg S]
NOTE: Only archived for aerosol-only simulations 		ND05 PL-SUL-$ 2 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ProdSO2fromDMSandOH Production of SO2 from DMS + OH (in sulfate_mod.F) [kg S]
NOTE: Only archived for Aerosol-only simulations 		ND05 PL-SUL-$ 1 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ProdSO4fromGasPhase Production of SO4 in the gas phase [kg S] ND05 PL-SUL-$ 5 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ProdSO4fromH2O2inCloud Production of SO4 from aqueous oxidation of H2O2 in clouds [kg S] ND05 PL-SUL-$ 6 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ProdSO4fromHOBrinCloud Production of SO4 from aqueous oxidation of HOBr in clouds [kg S] ND05 PL-SUL-$ 15 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ProdSO4fromO3inCloud Production of SO4 from aqueous oxidation of O3 in clouds [kg S] ND05 PL-SUL-$ 7 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ProdSO4fromO3inSeaSalt Production of SO4 from O3 in sea salt [kg S] ND05 PL-SUL-$ 8 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ProdSO4fromO3s Production of SO4 from aqueous phase SO3-- loss by OH [kg S] ND05 PL-SUL-$ 18 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ProdSO4fromOxidationOnDust Production of SO4 from oxidation on dust aerosols [kg S]
NOTE: Only archived for dust uptake simulations 		ND05 PL-SUL-$ 11 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ProdSO4fromSRHOBr Production of SO4 from sulfur production rate of HOBr+O3 ND05 PL-SUL-$ 17 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ProdSO4fromSRO3r Production of SO4 from sulfur production rate of O3 ND05 PL-SUL-$ 16 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ProdSO4fromUptakeOfH2SO4g Production of SO4 from uptake of H2SO4(g) [kg S]
NOTE: Only archived for dust uptake simulations 		ND05 PL-SUL-$ 13 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ProdBCPIfromBCPO Hydrophilic BC that was converted from hydrophobic BC [kg] ND07 PL-BC-$ 4 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ProdOCPIfromOCPO Hydrophilic OC that was converted from hydrophobic OC [kg] ND07 PL-OC-$ 9 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch

--Bob Yantosca (talk) 15:44, 8 December 2017 (UTC)

Proposed diagnostic names for chemistry

Here is a list of our proposed netCDF diagnostic names for quantities archived in the GEOS-Chem chemistry modules. Contact Bob Yantosca with any suggestions or concerns.

NOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability.

Proposed diagnostic name Description replaces
NDXX 		with
CATEGORY 		and
TRACERS 		and
FREQUENCY 		from this bpch file
Jvalues_<spcname> J-values for photolyzing species, computed by FAST-JX [s-1] ND22 JV-MAP-$ 1-nPhoto Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
RxnRate_<spcname> Reaction rates from the KPP chemical solver [molec/cm3/s] none none 1-nKppSpc Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
OHconcAfterChem OH concentration immediately after exiting the FlexChem chemistry solver [molec/cm3] ND43 CHEM-L=$ 1 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ND48 TIME-SER 1 Hourly stations.YYYYMMDDhh
ND49 TIME-SER 1 Hourly tsYYYYMMDDh.bpch
ND50 TIME-SER 1 Daily ts_24h_avg.YYYYMMDDh.bpch
ND51 TIME-SER 1 Local-time avg ts_satellite.YYYYMMDDh.bpch
HO2concAfterChem HO2 concentration immediately after exiting the FlexChem chemistry solver [molec/cm3] ND43 CHEM-L=$ 3 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
O1DconcAfterChem O1D concentration immediately after exiting the FlexChem chemistry solver [molec/cm3] ND43 CHEM-L=$ 4 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
O3PconcAfterChem O3P concentration immediately after exiting the FlexChem chemistry solver [molec/cm3] ND43 CHEM-L=$ 5 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
UVFluxDiffuse_<photobin> Diffuse UV flux in each photolysis wavelength bin [W/m2] ND64 FJX-FLUX 1-18 (w/ UCX)
1-12 (w/o UCX) 		Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
UVFluxDirect_<photobin> Direct UV flux in each photolysis wavelength bin [W/m2] ND64 FJX-FLUX 1-18 (w/ UCX)
1-12 (w/o UCX) 		Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
UVFluxNet_<photobin> Net UV flux in each photolysis wavelength bin [W/m2] ND64 FJX-FLUX 1-18 (w/ UCX)
1-12 (w/o UCX) 		Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Prod_<prodlossname>
Loss_<prodlossname> 		Production and loss of families and/or species: [molec/cm3/s]
  • From the KPP solver (fullchem simulations)
  • From the tagged O3 simulation
  • From the tagged CO simulation
 ND65 PORL-L=$ 1-5 (fullchem)
1-nAdvect*2 (tagO3, tagCO) 		Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch

--Bob Yantosca (talk) 23:37, 30 November 2017 (UTC)

Proposed diagnostic names for dry deposition

Here is a list of our proposed netCDF diagnostic names for quantities archived in the GEOS-Chem chemistry and dry deposition modules. Contact Bob Yantosca with any suggestions or concerns.

NOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability.

NOTE: We propose changing the units of of dry deposition fluxes from [molec/cm2/s] to [kg/m2/s]. This will also consistent with the units of emission fluxes archived by HEMCO.

Proposed diagnostic name Description replaces
NDXX 		with
CATEGORY 		and
TRACERS 		and
FREQUENCY 		from this bpch file
DryDepChm_<spcname> Dry deposition fluxes, applied in chemistry [molec/cm2/s] ND44 DRYD-FLX 1-nDryDep Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
DryDepMix_<spcname> Dry deposition fluxes, applied in PBL mixing [molec/cm2/s]

NOTE: This needs to be archived separately, because PBL mixing is called each dynamic timestep, which done 2X as frequently as chemistry.

ND44 DRYD-FLX 1-nDryDep Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
DryDepVel_<spcname> Dry deposition velocities [cm/s] ND44 DRYD-FLX 1-nDryDep Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
DryDepRstRA Aerodynamic resistance [s/m] - - - - -
DryDepRstRB Aerodynamic resistance [s/m] - - - - -
DryDepRstRC_<spcname> Total resistance to deposition for dry-depositing species [s/m] - - - - -
DryDepRstRI Stomatal resistance [s/m] - - - - -

--Bob Yantosca (talk) 18:12, 21 November 2017 (UTC)

Proposed diagnostic names for advection and boundary layer mixing

Here is a list of our proposed netCDF diagnostic names for quantities archived in the GEOS-Chem transport and boundary layer mixing modules. This list is by no means exhaustive or complete. Contact Bob Yantosca with any suggestions or concerns.

NOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability.

NOTE: We propose changing the units of flux diagnostics from [kg/s] to the area-independent units [kg/m2/s]. This will also be consistent with the units of emission fluxes archived by HEMCO.

Proposed diagnostic name Description replaces
NDXX 		with
CATEGORY 		and
TRACERS 		and
FREQUENCY 		from this bpch file
AdvFluxZonal_<spcname> Advection of species in the E-W direction [kg/s] ND24 EW-FLX-$ 1-nAdvect Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
AdvFluxMerid_<spcname> Advection of species in the N-S direction [kg/s] ND25 NS-FLX-$ 1-nAdvect Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
AdvFluxVert_<spcname> Advection of species in the vertical direction [kg/s] ND26 UP-FLX-$ 1-nAdvect Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
PBLMixFrac Fraction of boundary layer occupied by level L [1]

NOTE: HEMCO appears to have disabled this diagnostic in GEOS-Chem v11-01. It is not yet clear how this can be restored.

ND02 EMDIS-BL 1-nAdvect Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
PBLFlux_<spcname> Species mass change due to boundary layer mixing [kg/s] ND15 TURBMC-$ 1-nAdvect Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch

--Bob Yantosca (talk) 20:35, 14 November 2017 (UTC)

Proposed diagnostic names for convection and wet scavenging

Here is a list of our proposed netCDF diagnostic names for quantities archived in the GEOS-Chem convection and wet scavenging modules. This list is by no means exhaustive or complete. Contact Bob Yantosca with any suggestions or concerns.

NOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability.

NOTE: We propose changing the units of flux diagnostics from [kg/s] to the area-independent units [kg/m2/s]. This will also be consistent with the units of emission fluxes archived by HEMCO.

Proposed diagnostic name Description replaces
NDXX 		with
CATEGORY 		and
TRACERS 		and
FREQUENCY 		from this bpch file
CloudConvFlux_<spcname> Mass change due to cloud convection [kg/s] ND14 CV-FLX-$ 1-nAdvect Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
WetLossConv_<spcname> Loss of soluble species in convective updrafts [kg/s] ND38 WETDCV-$ 1-nWetDep Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
WetLossLS_<spcname> Loss of soluble species in large-scale rainout/washout [kg/s] ND39 WETDLS-$ 1-nWetDep Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
PrecipFracLS Fraction of grid box undergoing large-scale precipitation [1] ND16 WD-FRC-$ 1 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
RainFracLS_<spcname> Fraction of soluble species lost to rainout in large-scale precipitation [1] ND17 WD-LSR-$ 1-nWetDep Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
WashFracLS_<spcname> Fraction of soluble species lost to washout in large-scale precipitation [1] ND18 WD-LSW-$ 1-nWetDep Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch

--Bob Yantosca (talk) 18:52, 15 November 2017 (UTC)

Proposed diagnostic names for specialty simulations

Here is a list of our proposed netCDF diagnostic names for quantities archived in the GEOS-Chem specialty simulations. This list is by no means exhaustive or complete. Contact Bob Yantosca with any suggestions or concerns.

CH4 simulation

NOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability.

Proposed diagnostic name Description replaces
NDXX 		with
CATEGORY 		and
TRACERS 		and
FREQUENCY 		from this bpch file
LossCH4byOH CH4 removal by OH (for the CH4 specialty simualtion) [kg] ND19 CH4-LOSS 1 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
OHconcAfterChem OH concentration immediately after chemistry [molec/cm3] ND43 CHEM-L=$ 1 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch

--Bob Yantosca (talk) 18:57, 21 November 2017 (UTC)

CO2 simulation

NOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability.

NOTE: For consistency with the HEMCO emissions diagnostics, we propose changing the units of these diagnostics from [atoms C/cm2/s] to [kg/m2/s].

Proposed diagnostic name Description replaces
NDXX 		with
CATEGORY 		and
TRACERS 		and
FREQUENCY 		from this bpch file
BalanceBiosph_<spcname> CO2 balanced biospheres [atoms C/cm2/s]

NOTE: For tagged CO2 simuations you may specify all of the advected species.

ND04 CO2-SRCE 3 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ChemSource_<spcname> CO2 chemical source [atoms C/cm2/s] ND04 CO2-SRCE 9 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ChemSurfaceCorr_<spcname> CO2 chemical source surface correction [atoms C/cm2/s] ND04 CO2-SRCE 10 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
EmisAircraft_<spcname> CO2 aircraft emissions [atoms C/cm2/s]

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND04 CO2-SRCE 8 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
EmisAnthro_<spcname> CO2 anthropogenic emissions [atoms C/cm2/s]

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND04 CO2-SRCE 1 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
EmisBiofuel_<spcname> CO2 biofuel emissions [atoms C/cm2/s]

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND04 CO2-SRCE 5 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Emis_Biomass_<spcname> CO2 biomass burning emissions [atoms C/cm2/s]

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND04 CO2-SRCE 4 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
EmisOcean_<spcname> CO2 ocean emissions [atoms C/cm2/s]

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND04 CO2-SRCE 2 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
EmisShip_<spcname> CO2 ship emissions [atoms C/cm2/s]

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND04 CO2-SRCE 7 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
NetTerrExch_<spcname> CO2 net terrestrial exchange [atoms C/cm2/s] ND04 CO2-SRCE 6 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch

--Bob Yantosca (talk) 15:42, 15 November 2017 (UTC)

Hg simulation

NOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability. ALSO NOTE: We will eliminate underscore characters within the variable name (except to separate the name from the species name or wildcard) at a later date.

NOTE: We will probably delay implementation of new diagnostics for the Hg simulation until we receive updated Hg simulation source code from the Hg and POPs Working Group. Also we look to the Hg and POPs working group to inform us if any of these diagnostics are no longer necessary.

Proposed diagnostic name Description replaces
NDXX 		with
CATEGORY 		and
TRACERS 		and
FREQUENCY 		from this bpch file
Emis_Anthro_Hg0 Anthropogenic Hg0 emissions

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND03 HG-SRCE 1 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Mass_Ocean_Hg0 Mass of oceanic Hg0 ND03 HG-SRCE 2 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Emis_Ocean_Hg0 Oceanic Hg0 emissions

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND03 HG-SRCE 3 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Emis_LandReem_Hg0 Land Hg0 re-emission

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND03 HG-SRCE 4 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Emis_Natural_Hg0 Natural Hg0 emissions (from land)

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND03 HG-SRCE 5 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Emis_Anthro_Hg2 Anthropogenic Hg2 emissions

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND03 HG-SRCE 6 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Mass_Ocean_Hg2 Oceanic Hg2 mass ND03 HG-SRCE 7 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Sink_Ocean_Hg2 Sink of Hg2 into deep ocean ND03 HG-SRCE 8 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Emis_Anthro_HgP Anthropogenic HgP emissions

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND03 HG-SRCE 9 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Mass_Total_Hg Mass of oceanic Hg ND03 HG-SRCE 10 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Mass_Ocean_HgP Mass of oceanic HgP ND03 HG-SRCE 11 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Emis_Ocean_OC Sink of organic carbon to the ocean

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND03 HG-SRCE 12 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Emis_Biomass_Hg0 Hg0 emissions from biomass burning

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND03 HG-SRCE 13 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Emis_Vegetation_Hg0 Hg0 emissions from vegetation

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND03 HG-SRCE 14 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Emis_Soil_Hg0 Hg0 emissions from soils

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND03 HG-SRCE 15 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Hg0_Flux_from_Ocean Upwelling flux of Hg0 volatized from the ocean ND03 HG-SRCE 16 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Hg0_Flux_to_Ocean Drydep flux of Hg0 to the ocean ND03 HG-SRCE 17 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Emis_Snow_Hg Emission of Hg from snowpack

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND03 HG-SRCE 18 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Hg2_Prod_from_Hg0 Production of Hg2 from Hg0 ND03 PL-HG2-$ 19 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Hg2_Prod_from_OH Production of Hg2 from rxn with OH ND03 PL-HG2-$ 20 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Hg2_Prod_from_O3 Production of Hg2 from rxn with O3 ND03 PL-HG2_$ 21 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Hg2_Loss_by_Seasalt Loss of Hg2 from reaction with sea salt ND03 PL-HG2-$ 22 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
RxnRate_Seasalt_Hg2 Loss rate of Hg2 from rxn with sea salt ND03 PL-HG2-$ 23 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Br2_Prod_from_Br Production of Br2 from Br ND03 PL-Hg2-$ 24 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Concentration_Br Br concentration
NOTE: We can probably get this from the species concentration diagnostic; maybe no need to replicate it here. 		ND03 HG-SRCE 25 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Concentration_BrO BrO concentration
NOTE: We can probably get this from the species concentration diagnostic; maybe no need to replicate it here. 		ND03 HG-SRCE 26 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Concentration_HgP Particulate bound mercury

NOTE: Is this any different from the HgP species?'

ND03 PL-HG2-$ 27 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Concentratioin_RGM Reactive gaseous mercury

NOTE: Can this be obtained by summing Hg0 + Hg2?'

ND03 PL-HG2-$ 28 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Mass_Ocean_Hg0 Mass of oceanic Hg0

Is this needed anymore? Does the Hg simulation still need the slab ocean?

ND03 OCEAN-HG 29 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Mass_Ocean_Hg2 Mass of oceanic Hg2

Is this needed anymore? Does the Hg simulation still need the slab ocean?

ND03 OCEAN-Hg 30 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Mass_Ocean_HgP Mass of oceanic Hg

Is this needed anymore? Does the Hg simulation still need the slab ocean?

ND03 HG-SRCE 31 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Mass_SnowPack_Hg Mass of Hg in snowpack

Is this needed anymore? Does the Hg simulation still need the slab ocean?

ND03 <ttOCEAN_Hg</tt> 32 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch

--Bob Yantosca (talk) 16:57, 20 October 2017 (UTC)

POPs simulation

NOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability.

NOTE: We will probably delay implementation of new diagnostics for the POPs simulation until we receive updated Hg simulation source code from the Hg and POPs Working Group.

Proposed diagnostic name Description replaces
NDXX 		with
CATEGORY 		and
TRACERS 		and
FREQUENCY 		from this bpch file
Emis_POP Total POPs emissions ND53 PG-SRCE 1 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Emis_POPOC POP OC emissions

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND53 PG-SRCE 2 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Emis_POPBC POP BC emissions

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND53 PG-SRCE 3 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Emis_POPG Gas-phase POPs emissions

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND53 PG-SRCE 4 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Emis_Soil_POP Secondary emissions from soil

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND53 PG-SRCE 5 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Emis_Lake_POP Secondary emissions from lakes

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND53 PG-SRCE 6 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Emis_Vegetation_POP Secondary emissions from vegetation (leaves)

NOTE: Could we use HEMCO's diagnostic capability to archive this?

ND53 PG-SRCE 7 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
FluxFromSoil_Pos_POP Secondary positive soil flux ND53 PG-SRCE 8 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
FluxFromSoil_Neg_POP Secondary negative soil flux ND53 PG-SRCE 9 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
FluxFromLake_Pos_POP Secondary positive lake flux ND53 PG-SRCE 10 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
FluxFromLake_Neg_POP Secondary negative lake flux ND53 PG-SRCE 11 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
FluxFromVegetation_Pos_POP Secondary positive vegetation flux ND53 PG-SRCE 12 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
FluxFromVegetation_Neg_POP Secondary negative leaf flux ND53 PG-SRCE 13 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Fugacity_Soil_Air Fugacity ratio: soil / air ND53 PG-SRCE 14 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Fugacity_Lake_Air Fugacity ratios: lake/air ND53 PG-SRCE 15 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Fugacity_Leaf_Air Fugacity ratios: leaf/air ND53 PG-SRCE 16 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
POPOC_Loss_to_Gas Gross POPOC lost to gas ND53 PG-PP 17 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
POPOC_Prod_from_Gas Gross POPOC formed from gas ND53 PG-PP 18 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
POPBC_Loss_to_Gas Gross POPBC lost to gas ND53 PG-PP 19 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
POPBC_Prod_from_Gas Gross POPBC formed from gas ND53 PG-PP 20 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
POPG_Prod_from_OH Production of oxidized POPG from reaction with OH ND53 PG-PP 21 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
POPPOCPO_Prod_from_O3 Production of oxidized POPPOCPO from reaction with O3 ND53 PG-PP 22 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
POPPPOCPI_Prod_from_O3 Production of oxidized POPPOCPI from reaction with O3 ND53 PG-PP 23 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
POPPBCPO_Prod_from_O3 Production of oxidized POPPBCPO from reaction with O3 ND53 PG-PP 24 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
POPPBCPI_Prod_from_O3 Production of oxidized POPBCPI from reaction with O3 ND53 PG-PP 25 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
POPPOCPO_Prod_from_NO3 Production of oxidized POPPOCPO from reaction with NO3 ND53 PG-PP 26 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
POPPOCPI_Prod_from_NO3 Production of oxidized POPPOCPI from reaction with NO3 ND53 PG-PP 27 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
POPPBCPO_Prod_from_NO3 Production of oxidized POPPBCPO from reaction with NO3 ND53 PG-PP 28 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
POPPBCPI_Prod_from_NO3 Production of oxidized POPPBCPI from reaction with NO3 ND53 PG-PP 29 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch

--Bob Yantosca (talk) 17:02, 20 October 2017 (UTC)

Rn-Pb-Be simulation

NOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability.

NOTE: We propose changing the units of emissions diagnostics from [kg/s] to the area-independent units [kg/m2/s], and decay diagnostics from [kg/s] to the area-independent units [kg/m3/s].

Proposed diagnostic name Description replaces
NDXX 		with
CATEGORY 		and
TRACERS 		and
FREQUENCY 		from this bpch file
EMIS_Be7_COSMIC Source of Be7 by cosmic rays [kg/m2/s]
(Archived by HEMCO) 		ND02 RN--SRCE 3 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
EMIS_Rn_SOIL Emission of Rn222 from soils [kg/m2/s]
(Archived by HEMCO) 		ND01 RN--SRCE 1 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
PbFromRadDecay Emission of Pb210 from Rn222 decay [kg/s] ND01 RN--SRCE 2 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
RadDecay_<spcname> Radioactive decay of Rn, Pb, or Be7 [kg/s] ND02 RN-DECAY 1-3 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch

--Bob Yantosca (talk) 20:38, 14 November 2017 (UTC)

RRTMG radiative transfer model

NOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability.

Proposed diagnostic name Description replaces
NDXX 		with
CATEGORY 		and
TRACERS 		and
FREQUENCY 		from this bpch file
RadAllSkyLWSurf All-sky long-wave radiation @ surface [W/m2] ND72 RADMAP-$ 4 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
RadAllSkyLWTOA All-sky long-wave radiation @ top of atm [W/m2] ND72 RADMAP-$ 3 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
RadAllSkySWSurf All-sky short-wave radiation @ surface [W/m2] ND72 RADMAP-$ 2 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
RadAllSkySWTOA All-sky short-wave radiation @ top of atm [W/m2] ND72 RADMAP-$ 1 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
RadClrSkyLWSurf Clear-sky long-wave radiation @ surface [W/m2] ND72 RADMAP-$ 8 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
RadClrSkyLWTOA Clear-sky long-wave radiation @ top of atm [W/m2] ND72 RADMAP-$ 7 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
RadClrSkySWSurf Clear-sky short-wave radiation @ surface [W/m2] ND72 RADMAP-$ 6 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
RadClrSkySWTOA Clear-sky short-wave radiation @ top of atm [W/m2] ND72 RADMAP-$ 5 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch

--Bob Yantosca (talk) 15:44, 2 November 2017 (UTC)

TOMAS aerosol microphysics

NOTE: Diagnostic names are case-insensitive, but we recommend that you use mixed-case to improve readability.

NOTE: We invite the TOMAS team to review these diagnostic names for accuracy.

Proposed diagnostic name Description replaces
NDXX 		with
CATEGORY 		and
TRACERS 		and
FREQUENCY 		from this bpch file
RateCond_<spcname> Condensation rate ND60 TMS-COND 1-nTomas Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
RateCoag_<spcname> Coagulation rate ND60 TMS-COAG 1-nTomas Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
RateNucl_<spcname> Nucleation rate ND60 TMS-NUCL 1-nTomas Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
RateAqOx_<spcname> Aqueous oxidation rate ND60 TMS-NUCL 1-nTomas Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
ErrorAccumFix_<spcname> Accumulated error fixed ND60 AERO-FIX 1-nTomas Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
RateCond_SOA SOA condensation rate ND60 TMS-SOA 1-nTomas Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Rate3dForm Formation of particles with a diameter > 10nm ND61 TOMAS-3D 1 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch
Rate3dNucl Nucleation rate (cluster size) ND61 TOMAS-3D 2 Daily
Monthly 		trac_avg.YYYYMMDDhhmm.bpch

--Bob Yantosca (talk) 20:43, 14 November 2017 (UTC)

Diagnostics that are currently archived by HEMCO

The following is a list of diagnostics that are archived by HEMCO. Usually, these diagnostics are written to the bpch file trac_avg_YYYYMMDDhhmm.bpch. But they can also be sent to the HEMCO_diagnostics.YYYYMMDDhhmm.nc file if you list them specifically in the HEMCO_Diagnostics.rc file.

We will preserve the HEMCO diagnostic naming structure for the time being.

Current HEMCO diagnostic name Description saved to
NDXX 		with
CATEGORY 		and
TRACERS 		and
FREQUENCY
EMIS_<spcname>_ANTH Anthropogenic emissions [kg/m2/s] ND36 ANTHSRCE NO, CO, ALK4, ACET, MEK, ALD2, RCHO, MACR, PRPE, C3H8, CH2O, C2H6, NO2, HNO2, BENZ, TOLU, XYLE, EOH Daily
Monthly
ND03 HG-SRCE Hg0, Hg2, HgP Daily
Monthly
ND04 CO2-SRCE CO2 Daily
Monthly
ND07 BC-ANTH
OC-ANTH 		BCPI, BCPO
OCPI, OCPO 		Daily
Monthly
ND13 SO2-AN-$
SO4-AN-$
NH3-AN-$ 		SO2
SO4
NH3 		Daily
Monthly
ND29 CO--SRCE CO Daily
Monthly
ND32 NO-AN-$ NO Daily
Monthly
ND58 CH4-EMIS CH4 Daily
Monthly
EMIS_<spcname>_BIOF Biofuel emissions [kg/m2/s]

NOTE: some emissions inventories lump biofuel emissions in with the anthropogenic emissions. For these inventories, the anthropogenic emissions diagnostics will contain the contribution from biofuels, and the biofuel emissions diagnostics will be zeroed out.

ND34 BIOFSRCE NO, CO, ALK4, ACET, MEK, ALD2, RCHO, MACR, PRPE, C3H8, CH2O, C2H6, NO2, HNO2, BENZ, TOLU, XYLE, EOH Daily
Monthly
ND04 CO2-SRCE CO2 Daily
Monthly
ND07 BC-BIOF
OC-BIOF 		BCPI, BCPO
OCPI, OCPO 		Daily
Monthly
ND13 SO2-BIOF
SO4-BIOF
NH3-BIOF 		SO2
SO4
NH3 		Daily
Monthly
ND29 CO--SRCE CO Daily
Monthly
ND32 NO-BIOF NO Daily
Monthly
ND58 CH4-EMIS CH4 Daily
Monthly
EMIS_<spcname>_BIOB Biomass burning emissions [kg/m2/s] ND28 BIOBSRCE NO, CO, ALK4, ACET, MEK, ALD2, PRPE, C3H8, CH2O, C2H6, SO2, NH3, BC, OC, CH4, BENZ, TOLU, XYLE, EOH, MGLY Daily
Monthly
ND03 HG-SRCE Hg0 Daily
Monthly
ND04 CO2-SRCE CO2 Daily
Monthly
ND07 BC-BIOB
OC-BIOB 		BCPI
OCPI 		Daily
Monthly
ND13 SO2-BIOB
NH3-BIOB 		SO2
NH3 		Daily
Monthly
ND29 CO--SRCE CO Daily
Monthly
ND32 NO-BIOB NO Daily
Monthly
ND58 CH4-EMIS CH4 Daily
Monthly
EMIS_<spcname>_BIOG Biogenic emissions [kg/m2/s] ND46 BIOGSRCE ISOP, ACET, PRPE, MONX, MBOX, C2H4, APIN, BPIN, LIMO, SABI, MYRC, CARE, OCIM, FAXX, AAXX, ALD2, OMON, MOHX, EOH, FARN, BCAR, OSQT Daily
Monthly
ND07 OC-BIOG OCPI Daily
Monthly
ND11 ACETSRCE ACET Daily
Monthly
EMIS_<spcname>_NATU Natural emissions [kg/m2/s] ND03 HG-SRCE Hg0 Daily
Monthly
ND13 NH3-NATU NH3 Daily
Monthly
ND06 DSTSRCE DST1-4 Daily
Monthly
ND08 SALTSRCE SALA, SALC Daily
Monthly
EMIS_<spcname>_SHIP Ship emissions [kg/m2/s] ND04 CO2-SRCE CO2 Daily
Monthly
ND13 SO2-SHIP SO2 Daily
Monthly
ND29 CO--SRCE CO Daily
Monthly
ND32 NO-AN-$ NO Daily
Monthly
EMIS_<spcname>_AIRC Aircraft emissions [kg/m2/s] ND04 CO2-SRCE CO2 Daily
Monthly
ND13 SO2-AC-$ SO2 Daily
Monthly
ND29 CO--SRCE CO Daily
Monthly
ND32 NO-AC-$ NO Daily
Monthly
EMIS_<spcname>_OCEAN Emissions from oceans [kg/m2/s] ND03 HG-SRCE Hg0, Hg2, HgP Daily
Monthly
ND04 CO2-SRCE CO2 Daily
Monthly
ND11 ACETSRCE ACET Daily
Monthly
ND13 DMS-BIOG DMS Daily
Monthly
ND46 BIOGSRCE ALD2, CHBr3, CH2Br2 Daily
Monthly
EMIS_<spcname>_SEN Emissions from senescing plants ND46 BIOGSRCE ALD2, EOH Daily
Monthly
EMIS_<spcname>_EVOL Emissions from eruptive volcanoes ND13 SO2-EV-$ SO2 Daily
Monthly
EMIS_<spcname>_NVOL Emissions from degassing (non-eruptive) volcanoes ND13 SO2-NV-$ SO2 Daily
Monthly
EMIS_<spcname>_FERT Fertilizer emissions ND32 NO-FERT NO Daily
Monthly
EMIS_<spcname>_SOIL Soil emissions [kg/m2/s] ND32 NO-SOIL NO Daily
Monthly
ND01 RN--SRCE Rn Daily
Monthly
EMIS_<spcname>_LGHTN Lightning emissions [kg/m2/s] ND32 NO-LI-$ NO Daily
Monthly
EMIS_<spcname>_MONO Produced from monoterpenes [kg/m2/s] ND11 ACETSRCE ACET Daily
Monthly
ND29 CO--SRCE CO Daily
Monthly
EMIS_ACET_MBO Acetone emissions from methyl butenol [kg/m2/s] ND11 ACETSRCE ACET Daily
Monthly
EMIS_Be7_COSMIC Source of Be7 from cosmic rays [kg/m2/s] ND01 RN--SRCE Be7 Daily
Monthly
EMIS_<spcname>_TOTAL Total emissions [kg/m2/s] 1-nEmis Daily
Monthly

--Bob Yantosca (talk) 14:16, 19 October 2017 (UTC)

Replicating the existing specialty diagnostics

Here we discuss our plans to replicate specialty diagnostic outputs (timeseries, local-time diagnostics, etc.) in the new GEOS-Chem netCDF diagnostic package.

NOTE: We will NOT retire the legacy bpch diagnostics in GEOS-Chem v11-02. We will preserve the bpch diagnostic output until we can find alternatives for specialty diagnostics, especially those which involve averaging in a local solar time window.

ND40 planeflight diagnostic

Tomas Sherwen wrote:

Please could I ask if there is s position on/plan for restoring the chemical rate tracking (REA_??) functionality of the planeflight diagnostic?

In v11-01/ v11-02d REA_?? has been deactivated due to FlexChem.

I use this functionality (and I suspect many others do) for tracking rates (e.g. JNO2) along plane/ship/station tracks/timeseries at instrument resolution.

Melissa Sulprizio replied:

Yes, we will eventually restore the chemical rates in the planeflight diagnostic. One issue is that we're currently developing netCDF diagnostics and that will mess up the planeflight diagnostics even more. Bob wrote to the GCSC:
For the “planeflight” diagnostic, we will investigate using a separate package (such as NOAA ObsPack, as recommended by Andy Jacobsen at IGC8) that can more efficiently store point data. Then new diagnostic package we are developing works well for array data but not as well for point data.
Once the netCDF diagnostics are in place, we will reconsider how to fix/update planeflight_mod.F. If you need these diagnostics in the meantime, you should be able to hack it into the chemical mechanism by adding dummy species to the reactions you want to track and then rebuilding the mechanism based on these instructions. In flexchem_mod.F90, you can then obtain the rate from KPP using the C array (e.g. Rate = C(ind_NEWSPC) / DT to get molec/cm3/s).

Mat Evans replied:

I’ve had a quick look at obspack. I’m not sure its well suited to our needs.
I personally don’t see much need to update the plane flight files. They are easy to understand at the moment and easy to manipulate being in ascii. The biggest problem at the moment is that the rate constants have fallen out of them because of the move to FlexChem. If we can get that sorted I don’t think there is a pressing need to update the format.

--Bob Yantosca (talk) 16:20, 15 November 2017 (UTC)

ND48 station diagnostics

We will keep the current ND48 station diagnostics (bpch format) in GEOS-Chem v11-02 until we can find a suitable replacement.

Jenny Fisher wrote:

It seems we are losing compatibility for both ND48 (station) and ND51 (satellite) diagnostics. These are probably the two my group uses most frequently (and replacing with e.g. hourly output everywhere will require a lot of extra disk space). If we are going to have regional subsetting of diagnostics available, then ND48 can probably be dealt with by subsetting down to the level of a single box – but ND51 is harder.

ND49 instantaneous timeseries diagnostic

You can replicate the ND49 bpch diagnostic (instantaneous timeseries) as follows:

  1. Define a diagnostic collection in HISTORY.rc:
    • Specify instantaneous output:
      • Set mode: instantaneous
    • Specify the desired output frequency:
      • Set frequency: 010000 for hourly output
      • Set frequency: 030000 for 3-hourly output
      • Set frequency: 120000 for 12-hourly output, etc.
    • Specify that a new netCDF file should be created every 24 hours:
      • Set duration: 240000
  2. Within this diagnostic collection, you can add archive any available quantity from the State_Met, State_Chm, or State_Diag objects.

Example: 

COLLECTIONS: inst3hr',
            ::
  inst3hr.filename:      './GEOSChem.inst3hr.%y4%m2%d2.nc4',
  inst3hr.frequency:      030000,
  inst3hr.duration:       240000,
  inst3hr.mode:          'instantaneous',
  inst3hr.fields:        'SpeciesConc_?ADV?', 'GIGCchem',
                         'Met_T',             'GIGCchem',
                         'DryDepVel_?DRY?',   'GIGCchem',

--Bob Yantosca (talk) 15:57, 15 November 2017 (UTC)

ND50 24-hr average timeseries diagnostic

You can replicate the ND50 bpch diagnostic (24-hr average timeseries) as follows:

  1. Define a diagnostic collection in HISTORY.rc:
    • Specify time-averaged output:
      • Set mode: time-averaged
    • Specify daily output frequency. This will also set the averaging interval to be daily.
      • Set frequency: 240000
    • Specify that a new netCDF file should be created every 24 hours:
      • Set duration: 240000
  2. Within this diagnostic collection, you can add archive any available quantity from the State_Met, State_Chm, or State_Diag objects.

Example: 

COLLECTIONS: avg24hr',
            ::
  avg24hr.filename:      './GEOSChem.avg24hr.%y4%m2%d2.nc4',
  avg24hr.frequency:      240000,
  avg24hr.duration:       240000,
  avg24hr.mode:          'time-averaged',
  avg24hr.fields:        'SpeciesConc_?ADV?', 'GIGCchem',
                         'Met_T',             'GIGCchem',
                         'DryDepVel_?DRY?',   'GIGCchem',

--Bob Yantosca (talk) 16:06, 15 November 2017 (UTC)

ND51 satellite diagnostic

Aaron van Donkelaar wrote:

I wanted to double check about how the satellite-overpass diagnostic (ND51) was being included. There was some mention of it within the (netCDF diagnostic) presentation, but I wasn’t clear to me how the time-averaged netcdf collection could be made to output something similar to the current ND51.

My main concern was that ND51 samples between two defined local times once each day. From what I understood of the time-averaged collection via netcdf, it could be set to regularly sample between a defined interval of time (e.g. every six hours), but I didn’t understand how this could be set to sample between, say, 10am-12pm local time each day. Neither local time, nor once per day seemed an option.

Apologies if I’ve just misunderstood, but I thought I should check that an ND51-type output would still be possible.

Bob Yantosca replied:

At this time we don't yet have a good substitute for the ND51 satellite timeseries diagnostics. We may be able to replicate this with some type of satellite simulator package, but that remains to be seen as of yet. Right now we are focusing our efforts on implementing the netCDF diagnostics that are required for benchmarking. (Specialty diagnostics will be added later.)

We have designed the netCDF diagnostics for GC-Classic to replicate the behavior of the diagnostics in GCHP. Having the diagnostics work the same way in both configurations of GC facilitates benchmarking and comparing GC-Classic to GCHP. It also makes it easier for users to switch between GC-Classic to GCHP. But GCHP does not allow for local-time diagnostics. GCHP relies on the MAPL library, and its diagnostic package (aka "History") only allows for instantaneous or time-averaged output.

One could save e.g hourly timeseries, along with a local time field, to netCDF, and apply the local time comparison in post-processing. This would be doable but it would also end up generating a ton of output.

The good news is that we will preserve the bpch diagnostics in v11-02 (I need to update the wiki better to reflect that). We will not remove the bpch diagnostics until we have found a suitable replacement for the local-time diagnostics. So for the time being you can still rely on ND51.

--Bob Yantosca (talk) 15:33, 15 November 2017 (UTC)

Validating the netCDF diagnostics

In GEOS-Chem Classic

We invite you to view the the presentation NetCDF diagnostic validation in GEOS-Chem "Classic" by Bob Yantosca and the GCST which summarizes the initial validation process. A more robust validation will take place shortly.

One of the take-aways of the validation is that the timestep at which diagnostics are update could cause non-negligble differences. For example, several GEOS-Chem time-averaged diagnostics are updated on each chemistry timestep, which is 20 minutes for most GEOS-Chem simulations. But the default behavior of the new netCDF diagnostics in GEOS-Chem updates time-averaged diagnostic quantities every "heartbeat" timestep, which is 10 minutes for most simulations. Therefore, the netCDF diagnostics will capture the state of the atmopshere on those timesteps where chemistry does not happen. As shown in the presentation, this could cause non-negligible differences when comparing to the legacy diagnostics.

The GCST recommends that time-averaged diagnostic quantities in GEOS-Chem "Classic" be updated on each "heartbeat" timestep, as this mimics the behavior the diagnostics in GCHP.

--Bob Yantosca (talk) 20:14, 27 November 2017 (UTC)

In GCHP

Lizzie Lundgren (GCST) and Colin Lee (Dalhousie) are validating the new diagnostics in GCHP. Stay tuned for more information.

--Bob Yantosca (talk) 20:14, 27 November 2017 (UTC)

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