Difference between revisions of "List of diagnostics archived to netCDF format"
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Revision as of 17:36, 29 January 2018
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.
Contents
- 1 Mapping netCDF diagnostic names to the NDxx bpch diagnostics
- 2 Legend
- 3 Proposed diagnostic names for general quantities
- 4 Proposed diagnostic names for fields of the State_Chm object
- 5 Proposed diagnostic names for aerosols
- 6 Proposed diagnostic names for chemistry
- 7 Proposed diagnostic names for dry deposition
- 8 Proposed diagnostic names for advection and boundary layer mixing
- 9 Proposed diagnostic names for convection and wet scavenging
- 10 Proposed diagnostic names for specialty simulations
- 11 Diagnostics that are currently archived by HEMCO
- 12 Replicating the existing specialty diagnostics
- 13 Validating the netCDF diagnostics
Mapping netCDF diagnostic names to the NDxx bpch diagnostics
In the sections below, we present a list of naming conventions for netCDF diagnostics that we developed last year. GCST member Bob Yantosca will be working on the transition to netCDF diagnostics very soon so feel free to follow up with him on suggested names.
An introduction to netCDF diagnostics
Bob Yantosca has created an overview presentation about the new netCDF diagnostics for v11-02.
Further notes:
The new netCDF diagnostic package in GC-Classic is designed to mimic how the diagnostics already work in GCHP. GCHP uses the MAPL library’s "History" component to save output to netCDF files in High-Performance Computing environments with MPI parallelization.
- We have made the GC-Classic netCDF diagnostics use the same input file (called HISTORY.rc) as GCHP, with minor modifications.
- The new netCDF diagnostics in GC-Classic are “array” based rather than “point” based, just as the GCHP diagnostics already are.
Because of this, we do not plan on introducing netCDF diagnostic features into GC-Classic that are not also present in GCHP.
- For example, we will not have the ability to save out a series of points like the ND40 planeflight diagnostic (ASCII output) or ND48 point timeseries diagnostic (bpch output) in the new netCDF diagnostic package.
- That being said, we will “grandfather in” the ND40 planeflight diagnostic for GC-Classic. We will either keep it in ASCII format, or replace it with equivalent functionality, such as NOAA’s ObsPack code.
At present, the netCDF diagnostic output in GEOS-Chem “Classic” can save global fields.
- It would be easy to add in the capability to save a subset of fields (e.g. a horizontal region of the world).
- We plan to delay implementation of this until after all of the diagnostics required for benchmark simulations have been implemented as netCDF output.
Many of the emissions diagnostics in GEOS-Chem are archived by the HEMCO emissions component, and are manually written to bpch output. These diagnostics will be redirected to the HEMCO_diagnostics*.nc netCDF files once the bpch files are retired.)
For now the units of the new netCDF diagnostics will remain same as the existing diagnostics, as this will facilitate validation.
- But we also propose to implement area-independent units (e.g. [kg/m2/s] or [kg/m3/s], depending on the type of the diagnostic) once validation has been completed.
- Area-independent diagnostics will facilitate using GEOS-Chem to use any type of grid (e.g. GCHP cubed-sphere)
- Area-independent diagnostics facilitate comparing GEOS-Chem output on different types of grids (cubed-sphere vs. lat-lon).
The user will be able to set the archival frequency of the netCDF diagnostics to one of two options: Instantaneous or Time-Averaged. Several netCDF diagnostic "collections" can be created, each with its own archival frequency.
- To be clear, the column labeled FREQUENCY in the tables below refers to the archival frequency of the NDxx bpch diagnostics.
--Bob Yantosca (talk) 20:48, 14 November 2017 (UTC)
Naming convention
We shall use the following naming convention for netCDF diagnostics.
Diagnostic names may only consist of mixed-case letters, numbers, and single underscores. This will ensure that the netCDF files produced by GEOS-Chem will be consistent with both the COARDS and CF netCDF conventions.
Diagnostic names are case-insensitive. However, we recommend using “camel case” (i.e. mixed upper and lower case) to improve readability (e.g. ProdBCPIfromBCPO), etc.
"CHEM_" (case-insensitive) must precede the array name when archiving an array field from the State_Chm object. (e.g. CHEM_Species_NO, CHEM_AeroAreaSulf)
"MET_" (case-insensitive) must precede the array name when archiving an array field from the State_Met object. (e.g. MET_U10M, MET_T, MET_TROPP)
Single underscores may only be used in these instances:
- Separating the prefixes "CHEM_" and "MET_" from the rest of the variable name, as described above.
- Separating the diagnostic name from a wildcard or tag that can be included in a wildcard (e.g. SpeciesConc_NO, SpeciesConc_?ADV?).
You can use wildcards to request a subset of species or bins instead of having to list each diagnostic name individually. The set of acceptable wildcards is listed in the listed in the the Legend section below.
--Bob Yantosca (talk) 18:14, 28 November 2017 (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. The names for netCDF diagnostic quantities follow the naming convention listed above.
COLLECTIONS: 'inst', 'avg’, :: inst.filename: './GEOSChem.inst.%y4%m2%d2.nc4', inst.frequency: 060000, inst.duration: 240000, inst.mode: 'instantaneous', inst.fields: 'SpeciesConc_?ADV?', 'GIGCchem', 'Met_T', 'GIGCchem', 'DryDepVel_?DRY?', 'GIGCchem', 'WetLossLS_?WET?', ‘GIGCchem’, :: avg.filename: './GEOSChem.avg.%y4%m2%d2.nc4', avg.frequency: 000100 000000, avg.duration: 000100 000000, avg.mode: 'time-averaged', avg.fields: 'SpeciesConc_?ADV?', 'GIGCchem', 'Met_PEDGE', 'GIGCchem', 'Jval_?PHO?', 'GIGCchem', 'WetLossLS_?WET?', ‘GIGCchem’, 'OHconcAfterChem', ‘GIGCchem’, ::
In this HISTORY.rc file, we are requesting two collections, or types of netCDF file output.
- The first collection (inst) is instantaneous (aka timeseries) output with a 6-hour frequency. A new file will be created every 24 hours.
- The second collection (avg) is time-averaged output. Data will be updated at the dynamic timestep (= 10 minutes for most GEOS-Chem simulations) by default and averaged into monthly-mean output. A new file will be created at the start of each new month.
- The diagnostic quantities (aka "fields") that will be archived in each collection are listed after the “fields” tag. These diagnostic quantities follow the naming convention described in the previous section.
- For GEOS-Chem “Classic” simulations, you may use wildcards to request a multiple quantities. For example, instead of listing SpeciesConc_NO, SpeciesConc_O3, SpeciesConc_PAN, SpeciesConc_CO, etc. individually, you can use SpeciesConc_?ADV? to request all of the advected GEOS_Chem species.
- The "GIGCchem" text is only relevant for GCHP and will be ignored for GEOS-Chem “Classic” simulations.
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) 21:33, 28 November 2017 (UTC)
Legend
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:
|
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:
|
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:
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).
|
CHEM_AeroAreaMDUST1 CHEM_WetAeroRadiSSA ...etc... |
nAdvect | Number of advected GEOS-Chem species | |
nDryDep | Number of dry-depositing GEOS-Chem species | |
nKppSpc | Number of species in the KPP chemistry mechanism | |
nPhoto | Number of photolyzing GEOS-Chem species | |
nTomas | Number of size-resolved TOMAS species | IBINS*(ICOMP-IDIAG+1) |
nWetDep | Number of soluble, wet-depositing GEOS-Chem species |
--Bob Yantosca (talk) 20:32, 14 November 2017 (UTC)
Proposed diagnostic names for general quantities
Here is a list of our proposed netCDF diagnostic names for species concentrations and other general diagnostic quantities. 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.
Proposed diagnostic name | Description | replaces NDXX |
with CATEGORY |
and TRACERS |
and FREQUENCY |
from this bpch file |
---|---|---|---|---|---|---|
SpeciesConc_<spcname> | Species concentrations in State_Chm%SPECIES, converted from native units to [mol/mol dry air].
NOTE: You should always use this diagnostic instead of obtaining the species concentrations directly from State_Chm%Species (i.e. diagnostic name CHEM_SPC_<spcname>). Species concentrations in State_Chm%Species are converted between units in different locations in the code (and also the units will differ between GEOS-Chem "Classic" and GCHP). Using SpeciesConc_<spcname> will always ensure that the units will be the same (mol/mol dry). |
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 | ||
MET_<metname> | Met fields and derived quantites, which are contained in the State_Met object.
NOTE: The names for each of these diagnostic quantities must begin with MET_ (case-insensitive, so Met_ and met_ are also allowed.) This will tell the diagnostics modules to look for these quantities in the State_Met object. |
ND30 | LANDMAP | 1 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
ND31 | PEDGE-$ | 1 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch | ||
ND48 | TIME-SER | 1-8 | Instantaneous | stations.YYYYMMDDhh | ||
ND49 | TIME-SER | 1-8 | Instantaneous | ts.YYYYMMDD.bpch | ||
ND50 | TIME-SER | 1-8 | Daily | ts_24h_avg.YYYYMMDDhh.bpch | ||
ND50 & ND51b | TIME-SER | 1-8 | User-defined time avg | ts_satellite.YYYYMMDDhh.bpch | ||
ND55 | TR-PAUSE | 1-3 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch | ||
ND57 | THETA-$ | 1 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch | ||
ND66 | DAO-3D-$ | 1-6 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch | ||
ND67 | DAO-FLDS | 1-23 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch | ||
ND68 | BXHGHT-$ | 1-8 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch | ||
TimeInChemGrid | Amount of time a given grid box was in the chemistry grid (i.e. below the tropopause or mesopause, depending on the type of simulation). Is this even needed anymore? |
ND54 | TIME_TPS | 1 | Daily Monthly |
trac_avg.YYYYMMDDhhmm.bpch |
--Bob Yantosca (talk) 14:32, 18 October 2017 (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]
|
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:
- 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
- Specify instantaneous output:
- 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:
- 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
- Specify time-averaged output:
- 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)