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

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(→‎The RxnRates Collection)
(→‎The RxnRates Collection)
 
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                               'O1DconcAfterChem              ', 'GIGCchem',   
 
                               'O1DconcAfterChem              ', 'GIGCchem',   
 
                               'O3PconcAfterChem              ', 'GIGCchem',   
 
                               'O3PconcAfterChem              ', 'GIGCchem',   
 +
                              'O3concAfterChem                ', 'GIGCchem', 
 +
                              'RO2concAfterChem              ', 'GIGCchem', 
 
  ::
 
  ::
  
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|HO2concAfterChem
 
|HO2concAfterChem
 
|HO2 concentration immediately after exiting the FlexChem solver
 
|HO2 concentration immediately after exiting the FlexChem solver
−
|molec/cm3
+
|v/v
 
|
 
|
 
|
 
|
Line 98: Line 100:
 
*[[List of diagnostics archived to bpch format|ND43]], #5
 
*[[List of diagnostics archived to bpch format|ND43]], #5
  
−
|}
+
|-valign="top"
 +
|O3concAfterChem
 +
|O3 concentration immediately after exiting the FlexChem solver
 +
|molec/cm3
 +
|
 +
|
 +
*fullchem
 +
|
 +
|
 +
*None
  
 +
|-valign="top"
 +
|RO2concAfterChem
 +
|RO2 concentration immediately after exiting the FlexChem solver
 +
|molec/cm3
 +
|
 +
|
 +
*fullchem
 +
|
 +
|
 +
*None
 +
 +
|}
  
 
== The JValues collection ==
 
== The JValues collection ==
Line 759: Line 782:
 
== The RxnRates Collection ==
 
== The RxnRates Collection ==
  
−
The '''RxnRates''' collection contains reaction rates that are used in solving the chemical mechanism.
+
The '''RxnRates''' collection contains reaction rates from the chemical mechanism (as computed by the KPP-generated solver code). For example, in the case of the NO + O<sub>3</sub> &rarr; NO<sub>2</sub> + O<sub>2</sub> reaction the returned quantity is k[NO][O<sub>3</sub>] in molec/cm<sup>3</sup>/s.
  
 
Here is a sample definition section for the RxnRates collection.
 
Here is a sample definition section for the RxnRates collection.
Line 769: Line 792:
 
   # It is best to list individual reactions to avoid using too much memory.
 
   # It is best to list individual reactions to avoid using too much memory.
 
   # Reactions should be listed as "RxnRate_EQnnn", where nnn is the reaction
 
   # Reactions should be listed as "RxnRate_EQnnn", where nnn is the reaction
−
   # index as listed in KPP/fullchem/gckpp_Monitor.F90 (pad zeroes as needed).
+
   # index as listed in KPP/fullchem/gckpp_Monitor.F90 or KPP/Hg/gckpp_monitor.F90
−
  #
+
  # (pad zeroes as needed)
−
  # Available for the fullchem simulations (and Hg simulation in 13.4.0 and later)
+
 
   #
 
   #
 
   RxnRates.template:  '%y4%m2%d2_%h2%n2z.nc4',
 
   RxnRates.template:  '%y4%m2%d2_%h2%n2z.nc4',
Line 797: Line 819:
 
|-valign=top"  
 
|-valign=top"  
 
!colspan="7" bgcolor="#CCFFFF"|Diagnostics applicable only to the fullchem simulation with the  aciduptake option
 
!colspan="7" bgcolor="#CCFFFF"|Diagnostics applicable only to the fullchem simulation with the  aciduptake option
−
 
−
|-valign="top"
 
−
|ProdSO4fromOxidationOnDust
 
−
|Production of SO4 from oxidation on dust aerosols
 
−
|kg S/s
 
−
|
 
−
|
 
−
*fullchem w/ aciduptake
 
−
|
 
−
|
 
−
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #12]]
 
  
 
|-valign="top"  
 
|-valign="top"  
 
|RxnRate_EQnnn
 
|RxnRate_EQnnn
−
|Rate for reaction nnn (see <tt>KPP/fullchem/gckpp_Monitor.F90</tt> or <tt>KPP/Hg/gckpp_Monitor.F90</tt> for the index number of each reaction.
+
|Rate for reaction nnn (see <tt>gckpp_Monitor.F90</tt> for the reaction number.
−
|1/s
+
|s<sup>-1</sup>
 
|
 
|
 +
*?RXN?
 
|
 
|
 
*fullchem
 
*fullchem
 
*Hg (in 13.4.0 and later)
 
*Hg (in 13.4.0 and later)
 +
*carboncycle (in 14.1.0 and later)
 
|
 
|
 
|
 
|

Latest revision as of 15:32, 30 August 2023

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. History collections for CO2
  16. Replicating the behavior of the prior timeseries diagnostics
  17. Adding new History diagnostics


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',  
                              'O3concAfterChem                ', 'GIGCchem',  
                              'RO2concAfterChem               ', 'GIGCchem',  
::

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


Diagnostic name Description Units Wildcards Simulations Notes Bpch equiv.
OHconcAfterChem OH concentration immediately after exiting the FlexChem solver molec/cm3
  • fullchem
  • CH4
HO2concAfterChem HO2 concentration immediately after exiting the FlexChem solver v/v
  • fullchem
O1DconcAfterChem O1D concentration immediately after exiting the FlexChem solver molec/cm3
  • fullchem
O3PconcAfterChem O3P concentration immediately after exiting the FlexChem solver molec/cm3
  • fullchem
O3concAfterChem O3 concentration immediately after exiting the FlexChem solver molec/cm3
  • fullchem
  • None
RO2concAfterChem RO2 concentration immediately after exiting the FlexChem solver molec/cm3
  • fullchem
  • None

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
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 Wildcards Simulations Notes Bpch equiv.
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 Wildcards Simulations Notes Bpch equiv.
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
ProdNITfromHNO3uptakeOnDust Production of NIT from HNO3 uptake on dust aerosols kg N/s
  • fullchem w/ aciduptake
ProdSO4fromUptakeOfH2SO4g Production of SO4 from uptake of H2SO4(g) kg S/s
  • fullchem w/ aciduptake
Diagnostics applicable only to the aerosol-only simulation
ProdSO2fromDMSandOH Production of SO2 from DMS + OH (in sulfate_mod.F) kg S/s
  • aerosol-only
ProdSO2fromDMSandNO3 Production of SO2 from DMS + NO3R kg S/s
  • aerosol-only
ProdSO2fromDMS Total P(SO2) from DMS kg S/s
  • aerosol-only
ProdMSAfromDMS Production of MSA from DMS kg S/s
  • aerosol-only
ProdSO4fromGasPhase Production of SO4 in the gas phase kg S/s
  • aerosol-only
Diagnostics applicable only to the aerosol-only and fullchem simulations
ProdBCPIfromBCPO Production of hydrophilic BC from hydrophobic BCs kg
  • aerosol-only
  • fullchem
ProdOCPIfromOCPO Production of hydrophilic BC from hydrophobic BCs kg
  • aerosol-only
  • fullchem
ProdSO4fromH2O2inCloud Production of SO4 from aqueous oxidation of H2O2 in clouds kg S/s
  • aerosol-only
  • fullchem
ProdSO4fromO2inCloudMetal Production of SO4 from aqueous oxidation of O2 from metals in cloud kg S/s
  • aerosol-only
  • fullchem
ProdSO4fromO3inCloud Production of SO4 from aqueous oxidation of O3 in clouds kg S/s
  • aerosol-only
  • fullchem
ProdSO4fromO3inSeaSalt Production of SO4 from O3 in sea salt kg S/s
  • aerosol-only
  • fullchem
ProdSO4fromO3s Production of SO4 from aqueous phase SO3-- loss by OH kg S/s
  • aerosol-only
  • fullchem
ProdSO4fromSRO3 Production of SO4 from sulfur production rate of O3 kg S/s
  • aerosol-only
  • fullchem
LossHNO3onSeaSalt Loss of HNO3 on sea salt aerosols kg S/s
  • aerosol-only
  • fullchem
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
ProdSO4fromSRHOBr Production of SO4 from sulfur production rate of HOBr+O3 kg S/s
  • fullchem
  • Added in 12.0.0
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
Loss_<spcname> Chemical loss for a given species or family molec/cm3/s
  • ?LOS?
  • fullchem
  • tagCO
  • tagO3

The RxnRates Collection

The RxnRates collection contains reaction rates from the chemical mechanism (as computed by the KPP-generated solver code). For example, in the case of the NO + O3 → NO2 + O2 reaction the returned quantity is k[NO][O3] in molec/cm3/s.

Here is a sample definition section for the RxnRates 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.
 #
 # It is best to list individual reactions to avoid using too much memory.
 # Reactions should be listed as "RxnRate_EQnnn", where nnn is the reaction
 # index as listed in KPP/fullchem/gckpp_Monitor.F90 or KPP/Hg/gckpp_monitor.F90
 # (pad zeroes as needed)
 #
 RxnRates.template:   '%y4%m2%d2_%h2%n2z.nc4',
 RxnRates.frequency:  00000000 010000
 RxnRates.duration:   00000000 010000
 RxnRates.mode:       'time-averaged'
 RxnRates.fields:     'RxnRate_EQ001                           ',
                      'RxnRate_EQ002                           ',


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
RxnRate_EQnnn Rate for reaction nnn (see gckpp_Monitor.F90 for the reaction number. s-1
  • ?RXN?
  • fullchem
  • Hg (in 13.4.0 and later)
  • carboncycle (in 14.1.0 and later)

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 Wildcards Simulations Notes Bpch equiv.
Chem_phSav ISORROPIA aerosol pH 1
  • fullchem
Chem_HplusSav ISORROPIA H+ concentration M
  • fullchem
Chem_WaterSav ISORROPIA aerosol water μg/m3
  • fullchem
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


Previous | Next | Guide to GEOS-Chem History diagnostics

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