Difference between revisions of "History collections for chemistry and photolysis"

Revision as of 22:30, 8 December 2020

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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:

Diagnostic name	Description	Units	Simulations	Bpch equiv.
OHconcAfterChem	OH concentration immediately after exiting the FlexChem solver	molec/cm3	fullchem CH4	ND43, #1
HO2concAfterChem	HO2 concentration immediately after exiting the FlexChem solver	molec/cm3	fullchem	ND43, #3
O1DconcAfterChem	O1D concentration immediately after exiting the FlexChem solver	molec/cm3	fullchem	ND43, #4
O3PconcAfterChem	O3P concentration immediately after exiting the FlexChem solver	molec/cm3	fullchem	ND43, #5

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:

Diagnostic name	Description	Units	Wildcards	Simulations	Notes	Bpch equiv.
Jval_<spcname>	Photolysis rates	1/s	?PHO?	fullchem		ND22
JvalO3O1D	Photolysis rate of O3 -> O1D	1/s		fullchem	Added in 13.0.0
JvalO3O3P	Photolysis rate of O3 -> O3P	1/s		fullchem	Added in 13.0.0

The KppDiags collection

The KppDiags collection contains KPP solver diagnostics. You can leave this collection disabled unless you are interested in assessing the solver's performance.

Here is a sample definition section for the KppDiags 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.

 KppDiags.template:          '%y4%m2%d2_%h2%n2z.nc4',
 KppDiags.format:            'CFIO',
 KppDiags.frequency:         010000
 KppDiags.duration:          010000
 KppDiags.mode:              'time-averaged'
 KppDiags.fields:            'KppIntCounts                  ', 'GIGCchem',
                             'KppJacCounts                  ', 'GIGCchem',
                             'KppTotSteps                   ', 'GIGCchem',
                             'KppAccSteps                   ', 'GIGCchem',
                             'KppRejSteps                   ', 'GIGCchem',
                             'KppLuDecomps                  ', 'GIGCchem',
                             'KppSubsts                     ', 'GIGCchem',
                             'KppSmDecomps                  ', 'GIGCchem',
::

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

NOTE: 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	Simulations	Notes
KppIntCounts	Number of times the KPP integrator was called	count	fullchem	Added in 12.7.0
KppJacCounts	Number of times the Jacobian matrix was constructed	count	fullchem	Added in 12.7.0
KppTotSteps	Total number of integration timesteps	count	fullchem	Added in 12.7.0
KppAccSteps	Number of accepted integration timesteps	count	fullchem	Added in 12.7.0
KppRejSteps	Number of rejected integration timesteps	count	fullchem	Added in 12.7.0
KppLuDecomps	Number of LU decompositions performed	count	fullchem	Added in 12.7.0
KppSubsts	Number of matrix substitutions performed. Includes forward and backward substitutions.	count	fullchem	Added in 12.7.0
KppSmDecomps	Number of singular matrix decopositions performed. NOTE: For Rosenbrock solvers, this will be zero everywhere, because the Rosenbrock method utilizes LU decomposition.	count	fullchem	Added in 12.7.0

The Metrics collection

The Metrics collection contains diagnostics for computing OH metrics from a GEOS-Chem full chemistry simulation. To compute the OH metrics, you must run the Python script metrics.py that ships with each fullchem or CH4 run directory.

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.

  Metrics.template:    '%y4%m2%d2_%h2%n2z.nc4',
  Metrics.format:      'CFIO',
  Metrics.frequency:   'End',
  Metrics.duration:    'End',
  Metrics.mode:        'time-averaged'
  Metrics.fields:      'AirMassColumnFull             ', 'GIGCchem',
                       'CH4emission                   ', 'GIGCchem',
                       'CH4massColumnFull             ', 'GIGCchem'
                       'CH4massColumnTrop             ', 'GIGCchem',
                       'LossOHbyCH4columnTrop         ', 'GIGCchem',
                       'LossOHbyMCFcolumnTrop         ', 'GIGCchem',
                       'OHwgtByAirMassColumnFull      ', 'GIGCchem',
::

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

Diagnostic name	Description	Units	Simulations	Notes
AirMassColumnFull	Air mass, full atmosphere column sums	kg	fullchem CH4 tagCH4	Added in 13.0.0
LossOHbyCH4columnTrop	Loss rate of CH4 by OH, tropospheric column sums	molec cm-3	fullchem CH4 tagCH4	Added in 13.0.0
LossOHbyMCFcolumnTrop	Loss rate of CH3CCl3 (aka MCF) by OH, tropospheric column sums	molec cm-3	fullchem CH4 tagCH4	Added in 13.0.0
OHwgtByAirMassColumnFull	Airmass-weighted mean OH concentration, full-atmosphere column sums	kg air kg OH m-3	fullchem CH4 tagCH4	Added in 13.0.0
Diagnostics applicable only to the CH4 or tagCH4 simulations
CH4emission	CH4 emission, used for computing OH metrics	kg s-1	CH4 tagCH4	Added in 13.0.0
CH4massColumnFull	Airmass-weighted CH4 concentration, full-atmosphere column sums	kg air kg CH4 m-3	CH4 tagCH4	Added in 13.0.0
CH4massColumnTrop	Airmass-weighted CH4 concentration, troposphere-only column sums	kg air kg CH4 m-3	CH4 tagCH4	Added in 13.0.0

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',
                              'ProdCOfromCH4                 ', 'GIGCchem',
                              'ProdCOfromNMVOC               ', 'GIGCchem',
::

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

NOTE: 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.
Diagnostics applicable only to the fullchem simulation with the aciduptake option
ProdSO4fromOxidationOnDust	Production of SO4 from oxidation on dust aerosols	kg S/s		fullchem w/ aciduptake		ND05 #12
ProdNITfromHNO3uptakeOnDust	Production of NIT from HNO3 uptake on dust aerosols	kg N/s		fullchem w/ aciduptake		ND05 #13
ProdSO4fromUptakeOfH2SO4g	Production of SO4 from uptake of H2SO4(g)	kg S/s		fullchem w/ aciduptake		ND05 #14
Diagnostics applicable only to the aerosol-only simulation
ProdSO2fromDMSandOH	Production of SO2 from DMS + OH (in sulfate_mod.F)	kg S/s		aerosol-only		ND05 #1
ProdSO2fromDMSandNO3	Production of SO2 from DMS + NO3R	kg S/s		aerosol-only		ND05 #2
ProdSO2fromDMS	Total P(SO2) from DMS	kg S/s		aerosol-only		ND05 #3
ProdMSAfromDMS	Production of MSA from DMS	kg S/s		aerosol-only		ND05 #4
ProdSO4fromGasPhase	Production of SO4 in the gas phase	kg S/s		aerosol-only		ND05 #5
Diagnostics applicable only to the aerosol-only and fullchem simulations
ProdBCPIfromBCPO	Production of hydrophilic BC from hydrophobic BCs	kg		aerosol-only fullchem		ND07 #4
ProdOCPIfromOCPO	Production of hydrophilic BC from hydrophobic BCs	kg		aerosol-only fullchem		ND07 #9
ProdSO4fromH2O2inCloud	Production of SO4 from aqueous oxidation of H2O2 in clouds	kg S/s		aerosol-only fullchem		ND05 #6
ProdSO4fromO2inCloudMetal	Production of SO4 from aqueous oxidation of O2 from metals in cloud	kg S/s		aerosol-only fullchem	New in 12.0.0	ND05 #8
ProdSO4fromO3inCloud	Production of SO4 from aqueous oxidation of O3 in clouds	kg S/s		aerosol-only fullchem		ND05 #7
ProdSO4fromO3inSeaSalt	Production of SO4 from O3 in sea salt	kg S/s		aerosol-only fullchem		ND05 #9
ProdSO4fromO3s	Production of SO4 from aqueous phase SO3-- loss by OH	kg S/s		aerosol-only fullchem	New in 12.0.0	ND05 #19
ProdSO4fromSRO3	Production of SO4 from sulfur production rate of O3	kg S/s		aerosol-only fullchem	New in 12.0.0	ND05 #17
LossHNO3onSeaSalt	Loss of HNO3 on sea salt aerosols	kg S/s		aerosol-only fullchem		ND07 #15
Diagnostics applicable only to full-chemistry simulations
ProdSO4fromHOBrinCloud	Production of SO4 from aqueous oxidation of HOBr in clouds	kg S/s		fullchem	Added in 12.0.0	ND05 #16
ProdSO4fromSRHOBr	Production of SO4 from sulfur production rate of HOBr+O3	kg S/s		fullchem	Added in 12.0.0	ND05 #18
ProdCOfromCH4	Production of CO from CH4	molec cm-3 s-1		fullchem	Added in 12.0.0
ProdCOfromNMVOC	Production of CO from NMVOCs	molec cm-3 s-1		fullchem	Added in 12.0.0
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	?PRD?	fullchem tagCO tagO3		ND65
Loss_<spcname>	Chemical loss for a given species or family	molec/cm3/s	?LOS?	fullchem tagCO tagO3		ND65

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: 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	Simulations	Notes	Bpch equiv.
Chem_phSav	ISORROPIA aerosol pH	1	fullchem		ND73 #1
Chem_HplusSav	ISORROPIA H+ concentration	M	fullchem		ND73 #2
Chem_WaterSav	ISORROPIA aerosol water	μg/m3	fullchem		ND73 #3
Chem_SulRatSav	ISORROPIA sulfate concentration	M	fullchem
Chem_NaRatSav	ISORROPIA Na+ concentration	M	fullchem
Chem_AcidPurSav	ISORROPIA acidpur ?? concentration	M	fullchem
Chem_BiSulSav	ISORROPIA bisulfate (general acid) concentration	M	fullchem
Chem_phCloud	Cloud PH	1	fullchem	Added in 12.0.0
Chem_SSAlk	Sea salt alkalinity	1	fullchem	Added in 12.0.0
Chem_HSO3AQ	Cloud bisulfite concentration	mol/L	fullchem	Added in 12.0.0
Chem_SO3AQ	Cloud sulfite concentration	mol/L	fullchem	Added in 12.0.0
Chem_fupdateHOBr	Correction factor for HOBr removal by SO2	mol/L	fullchem	Added in 12.0.0

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Difference between revisions of "History collections for chemistry and photolysis"

Revision as of 22:30, 8 December 2020

Contents

The ConcAfterChem collection

The JValues collection

The KppDiags collection

The Metrics collection

The ProdLoss Collection

The StateChm Collection

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@@ Line 49: / Line 49: @@
 !width="80px"|Wildcards
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-!width="150px"|Notes
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 !width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
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 |}
---[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:35, 18 July 2019 (UTC)
 == The JValues collection ==
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 *fullchem
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---[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:01, 3 June 2020 (UTC)
 == The KppDiags collection ==
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 *fullchem
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-*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
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 *fullchem
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-*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
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 *fullchem
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-*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
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-*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
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 *fullchem
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-*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
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 |}
---[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:59, 13 December 2019 (UTC)
 == The Metrics collection ==
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 !width="80px"|Wildcards
 !width="150px"|Simulations
-!width="150px"|Notes
+!width="175px"|Notes
 !width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
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 *tagCH4
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-*To be added in 13.0.0
+*<span style="color:darkgreen">'''Added in 13.0.0'''</span>
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 *tagCH4
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-*To be added in 13.0.0
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 *tagCH4
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-*To be added in 13.0.0
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 *tagCH4
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-*To be added in 13.0.0
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 *tagCH4
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-*To be added in 13.0.0
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 *tagCH4
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-*To be added in 13.0.0
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 *tagCH4
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-*To be added in 13.0.0
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 |}
---[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 13:51, 6 October 2020 (UTC)
 == The ProdLoss Collection ==
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 !width="80px"|Wildcards
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-!width="150px"|Notes
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 !width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
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 *fullchem
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-*New in [[GEOS-Chem 12#12.0.0|12.0.0]]
+*<span style="color:darkgreen">'''Added in 12.0.0'''</span>
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 *[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #16]]
@@ Line 703: / Line 697: @@
 *fullchem
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-*New in [[GEOS-Chem 12#12.0.0|12.0.0]]
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 *[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #18]]
@@ Line 715: / Line 709: @@
 *fullchem
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-*New in [[GEOS-Chem 12#12.0.0|12.0.0]]
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 *fullchem
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-*New in [[GEOS-Chem 12#12.0.0|12.0.0]]
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 |-valign=top"
@@ Line 762: / Line 755: @@
 |}
---[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 13:55, 6 October 2020 (UTC)
 == The StateChm Collection ==
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 !width="80px"|Wildcards
 !width="150px"|Simulations
-!width="150px"|Notes
+!width="175px"|Notes
 !width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
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 *fullchem
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-*New in [[GEOS-Chem 12#12.0.0|12.0.0]]
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 *fullchem
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-*New in [[GEOS-Chem 12#12.0.0|12.0.0]]
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-*New in [[GEOS-Chem 12#12.0.0|12.0.0]]
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 *fullchem
 |
-*New 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]]) 19:55, 17 May 2018 (UTC)
 ----
 '''''[[History collections for budgets|Previous]] | [[History collections for convection and wet deposition|Next]] | [[Guide to GEOS-Chem History diagnostics]]'''''