History collections for species concentrations

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  1. Overview of History diagnostics
  2. Legend for History diagnostics
  3. Collections for History diagnostics
  4. History collections for advection and mixing
  5. History collections for aerosols
  6. History collections for budgets
  7. History collections for chemistry and photolysis
  8. History collections for convection and wet deposition
  9. History collections for dry deposition
  10. History collections for mercury and POPs
  11. History collections for met fields and related quantities
  12. History collections for methane
  13. History collections for species concentrations
  14. History collections for TransportTracers
  15. Replicating the behavior of the prior timeseries diagnostics
  16. Adding new History diagnostics


The BoundaryConditions collection

NOTE: If you are not setting up for a nested-grid simulation, then you can disable this collection.

The BoundaryConditions diagnostic collection contains advected species concentrations (archived from a global simulation) that will be used by nested-grid simulations as transport boundary conditions. Like SpeciesConc, it archives data with units of mol/mol dry air.

Here is a sample definition section for the SpeciesConc collection.

  • If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.
  • To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.
  • Please see our Legend for History diagnostics page for more information about each of the collection tags.
  BoundaryConditions.template:   '%y4%m2%d2_%h2%n2z.nc4',
  BoundaryConditions.format:     'CFIO',
  BoundaryConditions.frequency:  00000000 030000
  BoundaryConditions.duration:   00000100 000000
  BoundaryConditions.mode:       'instantaneous'
  BoundaryConditions.fields:     'SpeciesBC_?ADV?             ', 'GIGCchem',
::

This table describes the diagnostic quantities belonging to the BoundaryConditions collection:

Diagnostic name Description Units Wildcards Simulations Notes
SpeciesBC_<spcname> Advected species concentrations used as boundary conditions for nested-grid simulations mol/mol dry air
  • ?ADV?
  • all simulations
Added in 12.4.0

--Bob Yantosca (talk) 20:54, 18 July 2019 (UTC)

The ConcAboveSfc collection

The ConcAboveSfc collection is listed on our History collections for dry deposition page.

--Bob Yantosca (talk) 21:24, 18 July 2019 (UTC)

The ConcAfterChem collection

The ConcAfterChem collection is listed on our History collections for chemistry and photolysis page.

--Bob Yantosca (talk) 14:21, 19 July 2019 (UTC)

The Restart collection

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

Here is a sample definition section for the Restart collection.

  • If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.
  • To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.
  • Please see our Legend for History diagnostics page for more information about each of the collection tags.

NOTE: The restart file will be created in the GEOS_Chem run directory, not in the OutputDir sub-folder.

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

This table describes the diagnostic quantities belonging to the SpeciesConc collection:

Diagnostic name Description Units Wildcards Simulations Notes
SpeciesRst_<spcname> Instantaneous chemical species concentrations for use in starting subsequent GEOS-Chem simulations mol/mol dry air
  • ?ALL?
  • all simulations
  • Use ?ALL? to make sure all species get archived
  • Variables renamed from SPC_ to SpeciesRst_ in 12.1.0
Chm_H2O2AfterChem Concentration of H2O2 after sulfate chemistry v/v
  • aerosol only
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • standard
  • tropchem
  • New addition to GEOS-Chem restart file in 12.1.0
  • Replaced local array H2O2s in wetscav_mod.F
Chm_SO2AfterChem Concentration of SO2 after sulfate chemistry v/v
  • aerosol only
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • standard
  • tropchem
  • New in 12.1.0
  • Replaced local array SO2s in wetscav_mod.F
Chm_DryDepNitrogen Dry deposited nitrogen molec/cm2/s
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • standard
  • tropchem
  • New in 12.1.0
  • Replaced local array DRY_TOTN in get_ndep_mod.F
Chm_WetDepNitrogen Wet deposited nitrogen molec/cm2/s
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • standard
  • tropchem
  • New in 12.1.0
  • Replaced local array WET_TOTN in get_ndep_mod.F
Chm_KPPHvalue H-value for Rosenbrock solver unitless
  • benchmark
  • complexSOA
  • complexSOA_SVPOA
  • standard
  • tropchem
  • New in 12.1.0
  • Replaced local array HSAVE_KPP in flexchem_mod.F90
Chm_StatePSC Polar stratospheric cloud type count
  • benchmark
  • standard
  • Moved to Restart collection from HEMCO restart file in 12.1.0
Met_DELPDRY Delta-pressure across grid box (dry air) hPa
  • all simulations
Met_PS1WET Wet surface pressure at dt start hPa
  • all simulations
Met_PS1DRY Dry surface pressure at dt start hPa
  • all simulations
Met_SPHU1 Instantaneous specific humidity at time=T g kg-1
  • all simulations
Met_TMPU1 Instantaneous temperature at time=T K
  • all simulations

--Melissa Sulprizio (talk) 16:05, 7 November 2018 (UTC)

The SpeciesConc collection

The SpeciesConc diagnostic collection contains advected species concentrations. This type of diagnostic output is used in all GEOS-Chem simulations.

Here is a sample definition section for the SpeciesConc collection.

  • If this collection is not already present in the HISTORY.rc file in the GEOS-Chem run directory for your selected simulation, you can copy and paste this into your HISTORY.rc file and edit accordingly.
  • To prevent an individual field from being included in the diagnostic output, place a comment character # in front of the field name.
  • Please see our Legend for History diagnostics page for more information about each of the collection tags.
  SpeciesConc.template:       '%y4%m2%d2_%h2%n2z.nc4',
  SpeciesConc.format:         'CFIO',
  SpeciesConc.frequency:      00000100 000000
  SpeciesConc.duration:       00000100 000000
  SpeciesConc.mode:           'time-averaged'
  SpeciesConc.fields:         'SpeciesConc_?ADV?             ', 'GIGCchem',
::

This table describes the diagnostic quantities belonging to the SpeciesConc collection:

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

--Bob Yantosca (talk) 20:36, 18 July 2019 (UTC)



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