History collections for chemistry and photolysis
Contents
The ConcAfterChem collection
The ConcAfterChem collection contains diagnostics for OH, HO2, etc. species immediately upon exiting the FlexChem solver.
Here is a sample definition section for the ConcAfterChem 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.
ConcAfterChem.template: '%y4%m2%d2_%h2%n2z.nc4', ConcAfterChem.format: 'CFIO', ConcAfterChem.frequency: 00000100 000000 ConcAfterChem.duration: 00000100 000000 ConcAfterChem.mode: 'time-averaged' ConcAfterChem.fields: 'OHconcAfterChem ', 'GIGCchem', 'HO2concAfterChem ', 'GIGCchem', 'O1DconcAfterChem ', 'GIGCchem', 'O3PconcAfterChem ', 'GIGCchem', ::
This table describes the diagnostic quantities belonging to the ConcAfterChem collection:
- NOTE: All fullchem refers to all simulations that use a full-chemistry mechanism (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).
- NOTE: UCX fullchem refers to all full-chemistry simulations that use UCX (i.e. benchmark, standard, aciduptake, marinePOA).
Diagnostic name | Description | Units | Wildcards | Simulations | Notes | Bpch equiv. |
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OHconcAfterChem | OH concentration immediately after exiting the FlexChem solver | molec/cm3 |
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HO2concAfterChem | HO2 concentration immediately after exiting the FlexChem solver | molec/cm3 |
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O1DconcAfterChem | O1D concentration immediately after exiting the FlexChem solver | molec/cm3 |
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O3PconcAfterChem | O3P concentration immediately after exiting the FlexChem solver | molec/cm3 |
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--Bob Yantosca (talk) 21:35, 18 July 2019 (UTC)
The JValues collection
The JValues collection contains diagnostics for photolysis rates for various chemical species, obtained from the FAST-JX photolysis mechanism.
Here is a sample definition section for the JValues 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.
JValues.template: '%y4%m2%d2_%h2%n2z.nc4', JValues.format: 'CFIO', JValues.frequency: 00000000 010000 JValues.duration: 00000000 010000 JValues.mode: 'instantaneous' JValues.fields: 'Jval_?PHO? ', 'GIGCchem', ::
This table describes the diagnostic quantities belonging to the JValues collection:
- NOTE: All fullchem refers to all simulations that use a full-chemistry mechanism (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).
Diagnostic name | Description | Units | Wildcards | Simulations | Notes | Bpch equiv. |
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Jval_<spcname> | Photolysis rates | 1/s |
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--Bob Yantosca (talk) 21:35, 18 July 2019 (UTC)
The ProdLoss Collection
The ProdLoss collection contains chemical production and loss rates.
Here is a sample definition section for the ProdLoss 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: This example is for the benchmark simulation. Some quantities in this collection are not applicable to certain simulations.
ProdLoss.template: '%y4%m2%d2_%h2%n2z.nc4', ProdLoss.format: 'CFIO', ProdLoss.frequency: 00000100 000000 ProdLoss.duration: 00000100 000000 ProdLoss.mode: 'time-averaged' ProdLoss.fields: 'Prod_?PRD? ', 'GIGCchem', 'ProdBCPIfromBCPO ', 'GIGCchem', 'ProdOCPIfromOCPO ', 'GIGCchem', 'ProdSO4fromH2O2inCloud ', 'GIGCchem', 'ProdSO4fromO2inCloudMetal ', 'GIGCchem', 'ProdSO4fromO3inCloud ', 'GIGCchem', 'ProdSO4fromO3inSeaSalt ', 'GIGCchem', 'ProdSO4fromHOBrInCloud ', 'GIGCchem', 'ProdSO4fromSRO3 ', 'GIGCchem', 'ProdSO4fromSRHObr ', 'GIGCchem', 'ProdSO4fromO3s ', 'GIGCchem', 'Loss_?LOS? ', 'GIGCchem', 'LossHNO3onSeaSalt ', 'GIGCchem', ::
The table below describes diagnostic quantities belonging to the ProdLoss collection.
- NOTE: All fullchem refers to all simulations that use a full-chemistry mechanism (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).
Diagnostic name | Description | Units | Wildcards | Simulations | Notes | Bpch equiv. |
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Diagnostics applicable only to the aciduptake simulation | ||||||
ProdSO4fromOxidationOnDust | Production of SO4 from oxidation on dust aerosols | kg S/s |
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ProdNITfromHNO3uptakeOnDust | Production of NIT from HNO3 uptake on dust aerosols | kg N/s |
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ProdSO4fromUptakeOfH2SO4g | Production of SO4 from uptake of H2SO4(g) | kg S/s |
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Diagnostics applicable only to the aerosol-only simulation | ||||||
ProdSO2fromDMSandOH | Production of SO2 from DMS + OH (in sulfate_mod.F) | kg S/s |
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ProdSO2fromDMSandNO3 | Production of SO2 from DMS + NO3R | kg S/s |
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ProdSO2fromDMS | Total P(SO2) from DMS | kg S/s |
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ProdMSAfromDMS | Production of MSA from DMS | kg S/s |
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ProdSO4fromGasPhase | Production of SO4 in the gas phase | kg S/s |
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Diagnostics applicable only to the aerosol-only and all fullchem simulations | ||||||
ProdBCPIfromBCPO | Production of hydrophilic BC from hydrophobic BCs | kg |
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ProdOCPIfromOCPO | Production of hydrophilic BC from hydrophobic BCs | kg |
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ProdSO4fromH2O2inCloud | Production of SO4 from aqueous oxidation of H2O2 in clouds | kg S/s |
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ProdSO4fromO2inCloudMetal | Production of SO4 from aqueous oxidation of O2 from metals in cloud | kg S/s |
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ProdSO4fromO3inCloud | Production of SO4 from aqueous oxidation of O3 in clouds | kg S/s |
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ProdSO4fromO3inSeaSalt | Production of SO4 from O3 in sea salt | kg S/s |
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ProdSO4fromO3s | Production of SO4 from aqueous phase SO3-- loss by OH | kg S/s |
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ProdSO4fromSRO3 | Production of SO4 from sulfur production rate of O3 | kg S/s |
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LossHNO3onSeaSalt | Loss of HNO3 on sea salt aerosols | kg S/s |
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Diagnostics applicable only to full-chemistry simulations | ||||||
ProdSO4fromHOBrinCloud | Production of SO4 from aqueous oxidation of HOBr in clouds | kg S/s |
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ProdSO4fromSRHOBr | Production of SO4 from sulfur production rate of HOBr+O3 | kg S/s |
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Diagnostics for production and loss of species or chemical families (e.g. Ox) | ||||||
Prod_<spcname> | Chemical production for a given species or family | molec/cm3/s |
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Loss_<spcname> | Chemical loss for a given species or family | molec/cm3/s |
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--Bob Yantosca (talk) 19:25, 17 May 2018 (UTC)
The StateChm Collection
The StateChm collection contains quantities from State_Chm, the Chemistry state object (other than the species concentrations, which are stored in the SpeciesConc collection).
Here is a sample definition section for the StateChm 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.
- Other fields of the State_Chm object can be added to this collection by prefixing the field name with Chem_.
- Please see our Legend for History diagnostics page for more information about each of the collection tags.
StateChm.template: '%y4%m2%d2_%h2%n2z.nc4', StateChm.format: 'CFIO', StateChm.frequency: 00000100 000000 StateChm.duration: 00000100 000000 StateChm.mode: 'time-averaged' StateChm.fields: 'Chem_phSav ', 'GIGCchem', 'Chem_HplusSav ', 'GIGCchem', 'Chem_WaterSav ', 'GIGCchem', 'Chem_SulRatSav ', 'GIGCchem', 'Chem_NaRatSav ', 'GIGCchem', 'Chem_AcidPurSav ', 'GIGCchem', 'Chem_BiSulSav ', 'GIGCchem', 'Chem_pHCloud ', 'GIGCchem', 'Chem_SSAlk', ', 'GIGCchem', 'Chem_HSO3AQ ', 'GIGCchem', 'Chem_SO3AQ ', 'GIGCchem', 'Chem_fupdateHOBr ', 'GIGCchem', ::
The table below describes diagnostic quantities belonging to the StateChm collection.
- NOTE: All fullchem refers to all simulations that use a full-chemistry mechanism (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).
Diagnostic name | Description | Units | Wildcards | Simulations | Notes | Bpch equiv. |
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Chem_phSav | ISORROPIA aerosol pH | 1 |
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Chem_HplusSav | ISORROPIA H+ concentration | M |
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Chem_WaterSav | ISORROPIA aerosol water | μg/m3 |
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Chem_SulRatSav | ISORROPIA sulfate concentration | M |
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Chem_NaRatSav | ISORROPIA Na+ concentration | M |
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Chem_AcidPurSav | ISORROPIA acidpur ?? concentration | M |
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Chem_BiSulSav | ISORROPIA bisulfate (general acid) concentration | M |
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Chem_phCloud | Cloud PH | 1 |
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Chem_SSAlk | Sea salt alkalinity | 1 |
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Chem_HSO3AQ | Cloud bisulfite concentration | mol/L |
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Chem_SO3AQ | Cloud sulfite concentration | mol/L |
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Chem_fupdateHOBr | Correction factor for HOBr removal by SO2 | mol/L |
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--Bob Yantosca (talk) 19:55, 17 May 2018 (UTC)