History collections for mercury and POPs

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Previous | Next | Guide to GEOS-Chem History diagnostics

  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 MercuryChem collection

NOTE: This collection has not yet been validated and should be considered experimental.

The 'MercuryChem collection contains concentrations and prod/loss diagnostic outputs for the Hg specialty simulationl

Here is a sample definition section for the MercuryEmis 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.
  MercuryChem.template:       '%y4%m2%d2_%h2%n2z.nc4',
  MercuryChem.format:         'CFIO',
  MercuryChem.frequency:      00000000 040000
  MercuryChem.duration:       00000000 040000
  MercuryChem.mode:           'time-averaged'
  MercuryChem.fields:         'ConcBr                        ', 'GIGCchem',
                              'ConcBrO                       ', 'GIGCchem',
                              'LossHg2bySeaSalt              ', 'GIGCchem',
                              'LossRateHg2bySeaSalt          ', 'GIGCchem',
                              'PolarConcBr                   ', 'GIGCchem',
                              'PolarConcBrO                  ', 'GIGCchem',
                              'PolarConcO3                   ', 'GIGCchem',
                              'ProdHg2fromBr                 ', 'GIGCchem',
                              'ProdHg2fromBrY                ', 'GIGCchem',
                              'ProdHg2fromClY                ', 'GIGCchem',
                              'ProdHg2fromHg0                ', 'GIGCchem',
                              'ProdHg2fromHgBrPlusBr2        ', 'GIGCchem',
                              'ProdHg2fromHgBrPlusBrBrO      ', 'GIGCchem',
                              'ProdHg2fromHgBrPlusBrClO      ', 'GIGCchem',
                              'ProdHg2fromHgBrPlusBrHO2      ', 'GIGCchem',
                              'ProdHg2fromHgBrPlusBrNO2      ', 'GIGCchem',
                              'ProdHg2fromHgBrPlusBrOH       ', 'GIGCchem',
                              'ProdHg2fromO3                 ', 'GIGCchem',
                              'ProdHg2fromOH                 ', 'GIGCchem',
                              'ParticulateBoundHg            ', 'GIGCchem',
                              'ReactiveGaseousHg             ', 'GIGCchem',
::

The table below describes the diagnostic quantities belonging to the MercuryChem collection:

Diagnostic name Description Units Wildcards Simulations Notes Bpch equiv.
ConcBr Br concentration molec/cm3
  • Hg
  • tagHg
ConcBrO BrO concentration molec/cm3
  • Hg
  • tagHg
LossHg2bySeaSalt Loss of Hg2 by reaction with sea salt aerosols kg/s
  • Hg
  • tagHg
LossRateHg2bySeaSalt Rate of loss of Hg2 by reaction with sea salt aerosols 1/s
  • Hg
  • tagHg
PolarConcBr Br concentration in polar regions pptv
  • Hg
  • tagHg
PolarConcBrO BrO concentration in polar regions molec/cm3
  • Hg
  • tagHg
PolarConcO3 O3 concentration in polar regions molec/cm3
  • Hg
  • tagHg
ProdHg2fromBr Chemical production of Hg2 from Br kg/s
  • Hg
  • tagHg
ProdHg2fromBrY Chemical production of Hg2 from reaction with BrY kg/s
  • Hg
  • tagHg
ProdHg2fromClY Chemical production of Hg2 from reaction with ClY kg/s
  • Hg
  • tagHg
ProdHg2fromHg0 Chemical production of Hg2 from reaction with Hg0 kg/s
  • Hg
  • tagHg
ProdHg2fromHgBrPlusBr2 Chemical production of Hg2 from reaction with HgBr + Br2 kg/s
  • Hg
  • tagHg
ProdHg2fromHgBrPlusBrBrO Chemical production of Hg2 from reaction with HgBr + BrBrO kg/s
  • Hg
  • tagHg
ProdHg2fromHgBrPlusBrClO Chemical production of Hg2 from reaction with HgBr + BrClO kg/s
  • Hg
  • tagHg
ProdHg2fromHgBrPlusBrHO2 Chemical production of Hg2 from reaction with HgBr + BrHO2 kg/s
  • Hg
  • tagHg
ProdHg2fromHgBrPlusBrNO2 Chemical production of Hg2 from reaction with HgBr + BrNO2 kg/s
  • Hg
  • tagHg
ProdHg2fromHgBrPlusBrOH Chemical production of Hg2 from reaction with HgBr + BrOH kg/s
  • Hg
  • tagHg
ProdHg2fromO3 Chemical production of Hg2 from reaction with O3 kg/s
  • Hg
  • tagHg
ProdHg2fromO3 Chemical production of Hg2 from reaction with O3 kg/s
  • Hg
  • tagHg
ParticulateBoundHg Particulate bound mercury (PBM) pptv
  • Hg
  • tagHg
ParticulateBoundHg Reactive gaseous mercury pptv
  • Hg
  • tagHg

--Bob Yantosca (talk) 16:39, 19 July 2019 (UTC)

The MercuryEmis Collection

NOTE: This collection has not yet been validated and should be considered experimental.

The MercuryEmis collection contains emission diagnostics for the Hg specialty simulation.

Here is a sample definition section for the MercuryEmis 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.
  MercuryEmis.template:       '%y4%m2%d2_%h2%n2z.nc4',
  MercuryEmis.format:         'CFIO',
  MercuryEmis.frequency:      00000000 040000
  MercuryEmis.duration:       00000000 040000
  MercuryEmis.mode:           'time-averaged'
  MercuryEmis.fields:         'EmisHg0anthro                 ', 'GIGCchem',
                              'EmisHg0biomass                ', 'GIGCchem',
                              'EmisHg0geogenic               ', 'GIGCchem',
                              'EmisHg0land                   ', 'GIGCchem',
                              'EmisHg0ocean                  ', 'GIGCchem',
                              'EmisHg0soil                   ', 'GIGCchem',
                              'EmisHg0snow                   ', 'GIGCchem',
                              'EmisHg0vegetation             ', 'GIGCchem',
                              'EmisHg2HgPanthro              ', 'GIGCchem',
                              'EmisHg2snowToOcean            ', 'GIGCchem',
                              'EmisHg2rivers                 ', 'GIGCchem',
                              'FluxHg2HgPfromAirToSnow       ', 'GIGCchem',
::

The table below describes the diagnostic quantities belonging to the MercuryEmis collection:

Diagnostic name Description Units Wildcards Simulations Notes Bpch equiv.
EmisHg0anthro Emission of Hg0 from anthropogenic sources kg/s
  • Hg
  • tagHg
EmisHg0biomass Emissions of Hg0 from biomass burning kg/s
  • Hg
  • tagHg
EmisHg0geogenic Emissions of Hg0 from geogenic sources kg/s
  • Hg
  • tagHg
EmisHg0land Re-emission of Hg0 from land kg/s
  • Hg
  • tagHg
EmisHg0ocean Emissions of Hg0 from oceans kg/s
  • Hg
  • tagHg
EmisHg0snow Emission of Hg0 from snowpack kg/s
  • Hg
  • tagHg
EmisHg0soil Emissions of Hg0 from soils kg/s
  • Hg
  • tagHg
EmisHg0vegetation Emission of Hg0 from vegetation kg/s
  • Hg
  • tagHg
EmisHg2HgPanthro Emission of Hg2 + HgP from anthropogenic sources kg/s
  • Hg
  • tagHg
  • NOTE: HgP is emitted as Hg2 in HEMCO_Config.rc.
EmisHg2snowToOcean Hg2 delivered to oceans from melting snow kg/s
  • Hg
  • tagHg
EmisHg2rivers Emissions of Hg2 from delivered to oceans from melting snow kg/s
  • Hg
  • tagHg
FluxHg2HgPfromAirToSnow Deposition flux of Hg2 + HgP from the atmosphere onto snow kg/s
  • Hg
  • tagHg

--Bob Yantosca (talk) 16:43, 19 July 2019 (UTC)

The MercuryOcean collection

NOTE: This collection has not yet been validated and should be considered experimental.

The MercuryOcean collection contains diagnostics from the mercury ocean model, used in the Hg specialty simulaton.

Here is a sample definition section for the MercuryOcean 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.
  MercuryOcean.template:      '%y4%m2%d2_%h2%n2z.nc4',
  MercuryOcean.format:        'CFIO',
  MercuryOcean.frequency:     00000000 040000
  MercuryOcean.duration:      00000000 040000
  MercuryOcean.mode:          'time-averaged'
  MercuryOcean.fields:        'FluxHg0fromAirToOcean         ', 'GIGCchem',
                              'FluxHg0fromOceanToAir         ', 'GIGCchem',
                              'FluxHg2HgPfromAirToOcean      ', 'GIGCchem',
                              'FluxHg2toDeepOcean            ', 'GIGCchem',
                              'FluxOCtoDeepOcean             ', 'GIGCchem',
                              'MassHg0inOcean                ', 'GIGCchem',
                              'MassHg2inOcean                ', 'GIGCchem',
                              'MassHgPinOcean                ', 'GIGCchem',
                              'MassHgTotalInOcean            ', 'GIGCchem',
::

The table below describes diagnostic quantities belonging to the MercuryOcean collection

Diagnostic name Description Units Wildcards Simulations Notes Bpch equiv.
FluxHg0fromAirToOcean Deposition flux of Hg0 from the atmosphere to the ocean kg/s
  • Hg
  • tagHg
FluxHg0fromOceanToAir Volatilizatoin flux of Hg0 from the ocean to the atmosphere kg/s
  • Hg
  • tagHg
FluxHg2HgPfromAirToOcean Deposition flux of Hg2 + HgP from the atmosphere to the ocean kg/s
  • Hg
  • tagHg
FluxHg2toDeepOcean Flux of Hg2 sunk to the deep ocean kg/s
  • Hg
  • tagHg
MassHg0inOcean Total mass of oceanic Hg0 kg
  • Hg
  • tagHg
MassHg2inOcean Total mass of oceanic Hg2 kg
  • Hg
  • tagHg
MassHgPinOcean Total mass of oceanic Hg2 kg
  • Hg
  • tagHg
MassHgTotalInOcean Total mass of all organic mercury kg
  • Hg
  • tagHg

The POPS collection

NOTE: This collection has not yet been validated and should be considered experimental.

The POPS collection contains diagnostic quantities for the Persistent Organic Pollutants (aka POPs) specialty simulation.

Here is a sample definition section for the POPS 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.
  POPS.template:         '%y4%m2%d2_%h2%n2z.nc4',
  POPS.format:           'CFIO',
  POPS.frequency:        00000100 000000
  POPS.duration:         00000100 000000
  POPS.mode:             'time-averaged'
  POPS.fields:           'EmisPOPPOCPO                       ', 'GIGCchem',
                         'EmisPOPPBCPO                       ', 'GIGCchem',
                         'EmisPOPG                           ', 'GIGCchem',
                         'EmisPOPGfromSoil                   ', 'GIGCchem',
                         'EmisPOPGfromLake                   ', 'GIGCchem',
                         'EmisPOPGfromLeaf                   ', 'GIGCchem',
                         'FluxPOPGfromSoilToAir              ', 'GIGCchem',
                         'FluxPOPGfromAirToSoil              ', 'GIGCchem',
                         'FluxPOPGfromLakeToAir              ', 'GIGCchem',
                         'FluxPOPGfromAirtoLake              ', 'GIGCchem',
                         'FluxPOPGfromLeafToAir              ', 'GIGCchem',
                         'FluxPOPGfromAirToLeaf              ', 'GIGCchem',
                         'FugacitySoilToAir                  ', 'GIGCchem',
                         'FugacityLakeToAir                  ', 'GIGCchem',
                         'FugacityLeafToAir                  ', 'GIGCchem',
                         'LossPOPPOCPObyGasPhase             ', 'GIGCchem',
                         'ProdPOPPOCPOfromGasPhase           ', 'GIGCchem',
                         'LossPOPPBPOCbyGasPhase             ', 'GIGCchem',
                         'ProdPOPPBCPOfromGasPhase           ', 'GIGCchem',
                         'ProdPOPGfromOH                     ', 'GIGCchem',
                         'ProdPOPPOCPOfromO3                 ', 'GIGCchem',
                         'ProdPOPPOCPIfromO3                 ', 'GIGCchem',
                         'ProdPOPPBCPIfromO3                 ', 'GIGCchem',
                         'ProdPOPPBCPOfromO3                 ', 'GIGCchem',
                         'ProdPOPPOCPOfromNO3                ', 'GIGCchem',
                         'ProdPOPPOCPIfromNO3                ', 'GIGCchem',
                         'ProdPOPPBCPIfromNO3                ', 'GIGCchem',
                         'ProdPOPPBCPOfromNO3                ', 'GIGCchem',
  :: 

The table below describes diagnostic quantities belonging to the POPS collection.

Diagnostic name Description Units Wildcards Simulations Notes Bpch equiv.
EmisPOPPOCPO Particulate (hydrophobic organic carbon) POPS emissions kg/m2/s
  • POPs
EmisPOPPBCPO Particulate (hydrophobic black carbon) POPS emissions kg/m2/s
  • POPs
EmisPOPG POPG (gas-phase) POPS emissions kg/m2/s
  • POPs
EmisPOPGfromSoil Secondary emission of POPG from soils kg/s
  • POPs
EmisPOPGfromLake Secondary emission of POPG from lakes kg/s
  • POPs
EmisPOPGfromLeaf Secondary emission of POPG from leaves kg/m2/s
  • POPs
FluxPOPGfromSoilToAir Secondary (positive) flux of POPG from soils to air ng/m2/day
  • POPs
FluxPOPGfromAirToSoil Secondary (negative) flux of POPG from air to soil ng/m2/day
  • POPs
FluxPOPGfromLakeToAir Secondary (positive) flux of POPG from lakes to air ng/m2/day
  • POPs
FluxPOPGfromAirToLake Secondary (negative) flux of POPG from air to lakes ng/m2/day
  • POPs
FluxPOPGfromLeafToAir Secondary (positive) flux of POPG from leaves to air ng/m2/day
  • POPs
FluxPOPGfromAirToLeaf Secondary (negative) flux of POPG from air to leaves ng/m2/day
  • POPs
FugacitySoilToAir Fugacity ratio: soil/air 1
  • POPs
FugacityLakeToAir Fugacity ratio: lake/air 1
  • POPs
FugacityLeafToAir Fugacity ratio: leaf/air 1
  • POPs
LossPOPPOCPObyGasPhase Gross POP OC lost to gas kg/s
  • POPs
LossPOPPOCPObyGasPhase Gross POP OC produced from gas kg/s
  • POPs
LossPOPPBCPObyGasPhase Gross POP BC lost to gas kg/s
  • POPs
LossPOPPBCPObyGasPhase Gross POP BC produced from gas kg/s
  • POPs
ProdPOPGfromOH Production of oxidized POPG from reaction with OH kg/s
  • POPs
ProdPOPPOCPOfromO3 Production of oxidized POPPOCPO from reaction with O3 kg/s
  • POPs
ProdPOPPOCPIfromO3 Production of oxidized POPPOCPI from reaction with O3 kg/s
  • POPs
ProdPOPPBCPOfromO3 Production of oxidized POPPBCPO from reaction with O3 kg/s
  • POPs
ProdPOPPBCPIfromO3 Production of oxidized POPPBCPI from reaction with O3 kg/s
  • POPs
ProdPOPPOCPOfromNO3 Production of oxidized POPPOCPO from reaction with NO3 kg/s
  • POPs
ProdPOPPOCPIfromNO3 Production of oxidized POPPOCPI from reaction with NO3 kg/s
  • POPs
ProdPOPPBCPOfromNO3 Production of oxidized POPPBCPO from reaction with NO3 kg/s
  • POPs
ProdPOPPBCPIfromNO3 Production of oxidized POPPBCPI from reaction with NO3 kg/s
  • POPs

--Bob Yantosca (talk) 16:46, 19 July 2019 (UTC)



Previous | Next | Guide to GEOS-Chem History diagnostics

  1. Overview of History diagnostics