Difference between revisions of "GEOS-Chem diagnostic output files"

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__FORCETOC__
 
__FORCETOC__
'''''[[GEOS-Chem restart files|Previous]] | [[Guide_to_visualization_and_analysis_tools_for_GEOS-Chem|Next]] | [[Getting Started with GEOS-Chem]]'''''
+
'''''[[GEOS-Chem restart files|Previous]] | [[Python tools for use with GEOS-Chem|Next]] | [[Getting Started with GEOS-Chem]]'''''
#[[Minimum system requirements for GEOS-Chem|Minimum system requirements]]
+
#[[Minimum system requirements for GEOS-Chem|Minimum system requirements (and software installation)]]
 
#[[Configuring your computational environment]]
 
#[[Configuring your computational environment]]
 
#[[Downloading GEOS-Chem source code|Downloading source code]]
 
#[[Downloading GEOS-Chem source code|Downloading source code]]
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#*[[GEOS-Chem restart files|Restart files]]
 
#*[[GEOS-Chem restart files|Restart files]]
 
#*<span style="color:blue">'''Diagnostic output files'''</span>
 
#*<span style="color:blue">'''Diagnostic output files'''</span>
#[[Guide_to_visualization_and_analysis_tools_for_GEOS-Chem|Visualizing and processing output]]
+
#[[Python tools for use with GEOS-Chem]]
 
#[[GEOS-Chem_coding_and_debugging|Coding and debugging]]
 
#[[GEOS-Chem_coding_and_debugging|Coding and debugging]]
 
#[[GEOS-Chem_overview#Further_reading|Further reading]]
 
#[[GEOS-Chem_overview#Further_reading|Further reading]]
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!width="100px"|Format
 
!width="100px"|Format
 
!width="150px"|Collection
 
!width="150px"|Collection
!width="300px"|Created by
+
!width="300px"|For simulation(s)
 
!width="150px"|Added/Removed
 
!width="150px"|Added/Removed
  
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|[[History_collections_for_advection_and_mixing#The_AdvFluxVert_collection|AdvFluxVert]]
 
|[[History_collections_for_advection_and_mixing#The_AdvFluxVert_collection|AdvFluxVert]]
 
|
 
|
*All simulations
+
*fullchem_benchmark
*Typically used only with benchmark
+
 
|
 
|
*Added in [[GEOS-Chem 12#12.6.0|12.6.0]]
+
*<span style="color:darkgreen">'''Added in 12.6.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_aerosols#The_AerosolMass_collection|AerosolMass]]
 
|[[History_collections_for_aerosols#The_AerosolMass_collection|AerosolMass]]
 
|
 
|
*All full-chemistry simulations
+
*fullchem
*Aerosol-only simulations
+
*aerosol
 
|
 
|
*Added in [[GEOS-Chem 12#12.0.0|12.0.0]]
+
*<span style="color:darkgreen">'''Added in 12.0.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_aerosols#The_Aerosols_collection|Aerosols]]
 
|[[History_collections_for_aerosols#The_Aerosols_collection|Aerosols]]
 
|
 
|
*All full-chemistry simulations
+
*fullchem
*Aerosol-only simulations
+
*aerosol
 
|
 
|
*Added in [[GEOS-Chem 12#12.0.0|12.0.0]]
+
*<span style="color:darkgreen">'''Added in 12.0.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_species_concentrations#The_BoundaryConditions_collection|BoundaryConditions]]
 
|[[History_collections_for_species_concentrations#The_BoundaryConditions_collection|BoundaryConditions]]
 
|
 
|
*Can be created by all simulations
+
*can be created by: all simulations
*Can be read in by nested-grid simulations
+
*can be read by: nested-grid simulations
 
|
 
|
*Added in [[GEOS-Chem 12#12.4.0|12.4.0]]
+
*<span style="color:darkgreen">'''Added in 12.4.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_budgets#The_Budget_collection|Budget]]
 
|[[History_collections_for_budgets#The_Budget_collection|Budget]]
 
|
 
|
*All simulations
+
*all simulations
 
|
 
|
*Added in [[GEOS-Chem 12#12.1.0|12.1.0]]
+
*<span style="color:darkgreen">'''Added in 12.1.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_methane#The_CH4_collection|CH4]]
 
|[[History_collections_for_methane#The_CH4_collection|CH4]]
 
|
 
|
*CH4 simulations
+
*CH4
 +
*tagCH4
 
|
 
|
*Added in [[GEOS-Chem 12#12.1.0|12.1.0]]
+
*<span style="color:darkgreen">'''Added in 12.1.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_convection_and_wet_deposition#The_CloudConvFlux_collection|CloudConvFlux]]
 
|[[History_collections_for_convection_and_wet_deposition#The_CloudConvFlux_collection|CloudConvFlux]]
 
|
 
|
*All simulations
+
*all simulations
 
|
 
|
*Added in [[GEOS-Chem 12#12.0.0|12.0.0]]
+
*<span style="color:darkgreen">'''Added in 12.0.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_dry_deposition#The_ConcAboveSfc_collection|ConcAboveSfc]]
 
|[[History_collections_for_dry_deposition#The_ConcAboveSfc_collection|ConcAboveSfc]]
 
|
 
|
*Full-chemistry simulations
+
*fullchem
 
|
 
|
*Added in [[GEOS-Chem 12#12.6.0|12.6.0]]
+
*<span style="color:darkgreen">'''Added in 12.6.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_chemistry_and_photolysis#The_ConcAfterChem_collection|ConcAfterChem]]
 
|[[History_collections_for_chemistry_and_photolysis#The_ConcAfterChem_collection|ConcAfterChem]]
 
|
 
|
*All full-chemistry simulations
+
*fullchem
*CH4 simulation
+
*CH4
 +
*tagCH4
 
|
 
|
*Added in [[GEOS-Chem 12#12.0.0|12.0.0]]
+
*<span style="color:darkgreen">'''Added in 12.0.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_dry_deposition#The_DryDep_collection|DryDep]]
 
|[[History_collections_for_dry_deposition#The_DryDep_collection|DryDep]]
 
|
 
|
*All simulations with dry-depositing species
+
*simulations w/ drydep species
 
|
 
|
*Added in [[GEOS-Chem 12#12.0.0|12.0.0]]
+
*<span style="color:darkgreen">'''Added in 12.0.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_chemistry_and_photolysis#The_JValues_collection|JValues]]
 
|[[History_collections_for_chemistry_and_photolysis#The_JValues_collection|JValues]]
 
|
 
|
*All full-chemistry simulations
+
*fullchem
 
|
 
|
*Added in [[GEOS-Chem 12#12.0.0|12.0.0]]
+
*<span style="color:darkgreen">'''Added in 12.0.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_chemistry_and_photolysis#KppDiags|KppDiags]]
 
|[[History_collections_for_chemistry_and_photolysis#KppDiags|KppDiags]]
 
|
 
|
*All full-chemistry simulations
+
*fullchem
 
|
 
|
*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
+
*<span style="color:darkgreen">'''Added in 12.7.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_met_fields_and_related_quantities#The_LevelEdgeDiags_collection|LevelEdgeDiags]]
 
|[[History_collections_for_met_fields_and_related_quantities#The_LevelEdgeDiags_collection|LevelEdgeDiags]]
 
|
 
|
*All simulations
+
*all simulations
 
|
 
|
*Added in [[GEOS-Chem 12#12.0.0|12.0.0]]
+
*<span style="color:darkgreen">'''Added in 12.0.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_mercury_and_POPs#The_MercuryChem_collection|MercuryChem]]
 
|[[History_collections_for_mercury_and_POPs#The_MercuryChem_collection|MercuryChem]]
 
|
 
|
*Hg simulation
+
*Hg
*tagHg simulation
+
*tagHg
 
|
 
|
*Added in [[GEOS-Chem 12#12.0.0|12.0.0]]
+
*<span style="color:darkgreen">'''Added in 12.0.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_mercury_and_POPs#The_MercuryEmis_collection|MercuryEmis]]
 
|[[History_collections_for_mercury_and_POPs#The_MercuryEmis_collection|MercuryEmis]]
 
|
 
|
*Hg simulation
+
*Hg
*tagHg simulation
+
*tagHg
 
|
 
|
*Added in [[GEOS-Chem 12#12.0.0|12.0.0]]
+
*<span style="color:darkgreen">'''Added in 12.0.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_mercury_and_POPs#The_MercuryEmis_collection|MercuryOcean]]
 
|[[History_collections_for_mercury_and_POPs#The_MercuryEmis_collection|MercuryOcean]]
 
|
 
|
*Hg simulation
+
*Hg
*tagHg simulation
+
*tagHg
 
|
 
|
*Added in [[GEOS-Chem 12#12.0.0|12.0.0]]
+
*<span style="color:darkgreen">'''Added in 12.0.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_mercury_and_POPs#The_MercuryEmis_collection|POPs]]
 
|[[History_collections_for_mercury_and_POPs#The_MercuryEmis_collection|POPs]]
 
|
 
|
*Hg simulation
+
*Hg
*tagHg simulation
+
*tagHg
 
|
 
|
*Added in [[GEOS-Chem 12#12.0.0|12.0.0]]
+
*<span style="color:darkgreen">'''Added in 12.0.0'''</span>
 +
 
 +
|-valign="top"
 +
|<tt>GEOSChem.Metrics.YYYYMMDD_hhmmz.nc4</tt>
 +
|netCDF
 +
|[[History_collections_for_chemistry_and_photolysis#The_Metrics_collection|Metrics]]
 +
|
 +
*fullchem
 +
*CH4
 +
*tagCH4
 +
|
 +
*<span style="color:darkgreen">'''Added in 13.0.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_chemistry_and_photolysis#The_ProdLoss_Collection|ProdLoss]]
 
|[[History_collections_for_chemistry_and_photolysis#The_ProdLoss_Collection|ProdLoss]]
 
|
 
|
*All full-chemistry simulations
+
*fullchem
*Aerosol-only simulation
+
*aerosol
*tagCO simulation
+
*tagCO
*tagO3 simulation
+
*tagO3
 
|
 
|
*Added in [[GEOS-Chem 12#12.0.0|12.0.0]]
+
*<span style="color:darkgreen">'''Added in 12.0.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|netCDF
 
|netCDF
 
|[[History_collections_for_TransportTracers#The_RadioNuclide_Collection|RadioNuclide]]
 
|[[History_collections_for_TransportTracers#The_RadioNuclide_Collection|RadioNuclide]]
 
 
|
 
|
*TransportTraces simulation
+
*TransportTracers
 
|
 
|
*Added in [[GEOS-Chem 12#12.0.0|12.0.0]]
+
*<span style="color:darkgreen">'''Added in 12.0.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_species_concentrations#The_SpeciesConc_collection|SpeciesConc]]
 
|[[History_collections_for_species_concentrations#The_SpeciesConc_collection|SpeciesConc]]
 
|
 
|
*All simulations
+
*all simulations
 
|
 
|
*Added in [[GEOS-Chem 12#12.0.0|12.0.0]]
+
*<span style="color:darkgreen">'''Added in 12.0.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_chemistry_and_photolysis#The_StateChm_Collection|StateChm]]
 
|[[History_collections_for_chemistry_and_photolysis#The_StateChm_Collection|StateChm]]
 
|
 
|
*All simulations
+
*all simulations
 
|
 
|
*Added in [[GEOS-Chem 12#12.0.0|12.0.0]]
+
*<span style="color:darkgreen">'''Added in 12.0.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_met_fields_and_related_quantities#The_StateMet_collection|StateMet]]
 
|[[History_collections_for_met_fields_and_related_quantities#The_StateMet_collection|StateMet]]
 
|
 
|
*All simulations
+
*all simulations
 
|
 
|
*Added in [[GEOS-Chem 12#12.0.0|12.0.0]]
+
*<span style="color:darkgreen">'''Added in 12.0.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_advection_and_mixing#The_Transport_collection|Transport]]
 
|[[History_collections_for_advection_and_mixing#The_Transport_collection|Transport]]
 
|
 
|
*All simulations
+
*Typically used for fullchem_benchmark
*Typicaly only used with benchmark
+
*Moved to StateMet in 13.0.0
 
|
 
|
*Added in [[GEOS-Chem 12#12.2.0|12.2.0]]
+
*<span style="color:darkgreen">'''Added in 12.2.0'''</span>
 +
*<span style="color:red">'''Removed in 13.0.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_convection_and_wet_deposition#The_WetLossConv_collection|WetLossConv]]
 
|[[History_collections_for_convection_and_wet_deposition#The_WetLossConv_collection|WetLossConv]]
 
|
 
|
*All simulations with soluble species
+
*simulations w/ wetdep species
 
|
 
|
 +
*<span style="color:darkgreen">'''Added in 12.0.0'''</span>
  
 
|-valign="top"
 
|-valign="top"
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|[[History_collections_for_convection_and_wet_deposition#The_WetLossLS_collection|WetLossLS]]
 
|[[History_collections_for_convection_and_wet_deposition#The_WetLossLS_collection|WetLossLS]]
 
|
 
|
*All simulations with soluble species
+
*simulations w/ wetdep species
 
|
 
|
*Added in [[GEOS-Chem 12#12.0.0|12.0.0]]
+
*<span style="color:darkgreen">'''Added in 12.0.0'''</span>
  
 
|}
 
|}
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:13, 13 December 2019 (UTC)
 
  
 
== HEMCO diagnostic ouptut ==
 
== HEMCO diagnostic ouptut ==
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== Planeflight diagnostic output ==
 
== Planeflight diagnostic output ==
 
<span style="color:red">'''''NOTE: To use the Planeflight Diagnostic, you must compile GEOS-Chem with the BPCH_DIAG=y option.'''''</span>
 
  
 
By default, the planefight diagnostic output files will be created in your top-level run directory.  You can change this setting by modifying the output file name setting in [[The_input.geos_file#Planeflight_diagnostic|the Planeflight Menu of <tt>input.geos</tt>]].  For more information, please see our ''[[Planeflight diagnostic]]'' page.
 
By default, the planefight diagnostic output files will be created in your top-level run directory.  You can change this setting by modifying the output file name setting in [[The_input.geos_file#Planeflight_diagnostic|the Planeflight Menu of <tt>input.geos</tt>]].  For more information, please see our ''[[Planeflight diagnostic]]'' page.
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|}
 
|}
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:34, 13 December 2019 (UTC)
 
  
 
== ObsPack diagnostic output ==
 
== ObsPack diagnostic output ==
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----
 
----
'''''[[GEOS-Chem restart files|Previous]] | [[Guide_to_visualization_and_analysis_tools_for_GEOS-Chem|Next]] | [[Getting Started with GEOS-Chem]]'''''
+
'''''[[GEOS-Chem restart files|Previous]] | [[Python tools for use with GEOS-Chem|Next]] | [[Getting Started with GEOS-Chem]]'''''

Latest revision as of 15:27, 4 August 2022

Previous | Next | Getting Started with GEOS-Chem

  1. Minimum system requirements (and software installation)
  2. Configuring your computational environment
  3. Downloading source code
  4. Downloading data directories
  5. Creating run directories
  6. Configuring runs
  7. Compiling
  8. Running
  9. Output files
  10. Python tools for use with GEOS-Chem
  11. Coding and debugging
  12. Further reading


On this page, we list the files that are generated by GEOS-Chem's various diagnostic packages.

History diagnostics output

The following files, which correspond to the default History diagnostic collections, will be created in the OutputDir/ folder in your GEOS-Chem run directory. You can prevent any of these files from being created by commenting out the collection name in the HISTORY.rc configuration file. You can also add your own new collections (i.e. requesting species concentrations for both time-averaged and instantaneous averaging modes) by updating HISTORY.rc. For more information, please see our Guide to GEOS-Chem History diagnostics.

In the table below, YYYYMMDD and hhmms corresponds to the simulation date and time at which the file was created. The z indicates UTC (sometimes called "Zulu" time).

History diagnostic file name Format Collection For simulation(s) Added/Removed
GEOSChem.AdvFluxVert.YYYYMMDD_hhmmz.nc4 netCDF AdvFluxVert
  • fullchem_benchmark
  • Added in 12.6.0
GEOSChem.AerosolMass.YYYYMMDD_hhmmz.nc4 netCDF AerosolMass
  • fullchem
  • aerosol
  • Added in 12.0.0
GEOSChem.Aerosols.YYYYMMDD_hhmmz.nc4 netCDF Aerosols
  • fullchem
  • aerosol
  • Added in 12.0.0
GEOSChem.BoundaryConditions.YYYYMMDD_hhmmz.nc4 netCDF BoundaryConditions
  • can be created by: all simulations
  • can be read by: nested-grid simulations
  • Added in 12.4.0
GEOSChem.Budget.YYYYMMDD_hhmmz.nc4 netCDF Budget
  • all simulations
  • Added in 12.1.0
GEOSChem.CH4.YYYYMMDD_hhmmz.nc4 netCDF CH4
  • CH4
  • tagCH4
  • Added in 12.1.0
GEOSChem.CloudConvFlux.YYYYMMDD_hhmmz.nc4 netCDF CloudConvFlux
  • all simulations
  • Added in 12.0.0
GEOSChem.ConcAboveSfc.YYYYMMDD_hhmmz.nc4 netCDF ConcAboveSfc
  • fullchem
  • Added in 12.6.0
GEOSChem.ConcAfterChem.YYYYMMDD_hhmmz.nc4 netCDF ConcAfterChem
  • fullchem
  • CH4
  • tagCH4
  • Added in 12.0.0
GEOSChem.DryDep.YYYYMMDD_hhmmz.nc4 netCDF DryDep
  • simulations w/ drydep species
  • Added in 12.0.0
GEOSChem.Jvalues.YYYYMMDD_hhmmz.nc4 netCDF JValues
  • fullchem
  • Added in 12.0.0
GEOSChem.KppDiags.YYYYMMDD_hhmmz.nc4 netCDF KppDiags
  • fullchem
  • Added in 12.7.0
GEOSChem.LevelEdgeDiags.YYYYMMDD_hhmmz.nc4 netCDF LevelEdgeDiags
  • all simulations
  • Added in 12.0.0
GEOSChem.MercuryChem.YYYYMMDD_hhmmz.nc4 netCDF MercuryChem
  • Hg
  • tagHg
  • Added in 12.0.0
GEOSChem.MercuryEmis.YYYYMMDD_hhmmz.nc4 netCDF MercuryEmis
  • Hg
  • tagHg
  • Added in 12.0.0
GEOSChem.MercuryOcean.YYYYMMDD_hhmmz.nc4 netCDF MercuryOcean
  • Hg
  • tagHg
  • Added in 12.0.0
GEOSChem.POPs.YYYYMMDD_hhmmz.nc4 netCDF POPs
  • Hg
  • tagHg
  • Added in 12.0.0
GEOSChem.Metrics.YYYYMMDD_hhmmz.nc4 netCDF Metrics
  • fullchem
  • CH4
  • tagCH4
  • Added in 13.0.0
GEOSChem.ProdLoss.YYYYMMDD_hhmmz.nc4 netCDF ProdLoss
  • fullchem
  • aerosol
  • tagCO
  • tagO3
  • Added in 12.0.0
GEOSChem.RadioNuclide.YYYYMMDD_hhmmz.nc4 netCDF RadioNuclide
  • TransportTracers
  • Added in 12.0.0
GEOSChem.SpeciesConc.YYYYMMDD_hhmmz.nc4 netCDF SpeciesConc
  • all simulations
  • Added in 12.0.0
GEOSChem.StateChm.YYYYMMDD_hhmmz.nc4 netCDF StateChm
  • all simulations
  • Added in 12.0.0
GEOSChem.StateMet.YYYYMMDD_hhmmz.nc4 netCDF StateMet
  • all simulations
  • Added in 12.0.0
GEOSChem.Transport.YYYYMMDD_hhmmz.nc4 netCDF Transport
  • Typically used for fullchem_benchmark
  • Moved to StateMet in 13.0.0
  • Added in 12.2.0
  • Removed in 13.0.0
GEOSChem.WetLossConv.YYYYMMDD_hhmmz.nc4 netCDF WetLossConv
  • simulations w/ wetdep species
  • Added in 12.0.0
GEOSChem.WetLossLS.YYYYMMDD_hhmmz.nc4 netCDF WetLossLS
  • simulations w/ wetdep species
  • Added in 12.0.0

HEMCO diagnostic ouptut

The HEMCO diagnostic output files will be created in the OutputDir/ folder in your GEOS-Chem run directory. For more information, please see our The HEMCO User's Guide: Diagnostics.

In the table below, YYYYMMDD and hhmms corresponds to the simulation date and time at which the file was created.

HEMCO diagnostic file name Format Collections Created by
HEMCO_diagnostics.YYYYMMDDhhmm.nc netCDF Diagnostic quantities requested in HEMCO_Diagn.rc
  • All simulations

--Bob Yantosca (talk) 16:07, 13 December 2019 (UTC)

Planeflight diagnostic output

By default, the planefight diagnostic output files will be created in your top-level run directory. You can change this setting by modifying the output file name setting in the Planeflight Menu of input.geos. For more information, please see our Planeflight diagnostic page.

In the table below, YYYYMMDD corresponds to the simulation date and time at which the file was created.

Planeflight diagnostic file name Format Collections Created by
plane.log.YYYYMMDD text Point diagnostics requested in Planeflight.dat
  • All simulations

ObsPack diagnostic output

By default, the ObsPack output files will be created in your top-level run directory. You can change this setting by modifying the output file name setting in the ObsPack Menu of input.geos. For more information, please see our ObsPack diagnostic page.

In the table below, YYYYMMDD and hhmms corresponds to the simulation date and time at which the file was created. The z indicates UTC (sometimes called "Zulu" time).

Obspack diagnostic file name Format Collections Created by
GEOSChem.ObsPack.YYYYMMDD_hhmmz.nc4 netCDF Point diagnostics at locations specified in an ObsPack format netCDF file
  • All simulations

--Bob Yantosca (talk) 16:41, 13 December 2019 (UTC)

Satellite timeseries diagnostic output in bpch format

NOTE: To use the satellite timeseries diagnostics, you must compile GEOS-Chem with the BPCH_DIAG=y option.

By default, the satellite timeseries files will be created in your top-level run directory. You can change by modifying the output file name setting in the ND51 MENU and/or ND51b MENU of input.geos.

In the table below, YYYYMMDD and hhmms corresponds to the simulation date and time at which the file was created.

Timeseries file name Format Collections Created by
ts_satellite.YYYYMMDDhh.bpch bpch Diagnostics requested in the ND51 MENU and/or ND51b MENU of input.geos.
  • All simulations



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