History collections for species concentrations

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Revision as of 16:31, 19 July 2019 by Bmy (Talk | contribs) (The ConcAboveSfc collection)

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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

--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 ConcAfterChemcollection

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)