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

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(The JValues collection)
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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:35, 18 July 2019 (UTC)
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:35, 18 July 2019 (UTC)
 +
 +
== The KppDiags collection ==
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 +
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.
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*If this collection is not already present in the <tt>HISTORY.rc</tt> file in [[Creating GEOS-Chem run directories|the GEOS-Chem run directory for your selected simulation]], you can copy and paste this into your <tt>HISTORY.rc</tt> file and edit accordingly. 
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*To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> in front of the field name.
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*Please see our ''[[Legend for History diagnostics]]'' page for more information about each of the collection tags.
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  KppDiags.template:          '%y4%m2%d2_%h2%n2z.nc4',
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  KppDiags.format:            'CFIO',
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  KppDiags.frequency:        010000
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  KppDiags.duration:          010000
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  KppDiags.mode:              'time-averaged'
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  KppDiags.fields:            'KppIntCounts                  ', 'GIGCchem',
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                              'KppJacCounts                  ', 'GIGCchem',
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                              'KppTotSteps                  ', 'GIGCchem',
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                              'KppAccSteps                  ', 'GIGCchem',
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                              'KppRejSteps                  ', 'GIGCchem',
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                              'KppLuDecomps                  ', 'GIGCchem',
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                              'KppSubsts                    ', 'GIGCchem',
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                              'KppSmDecomps                  ', 'GIGCchem',
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::
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This table describes the diagnostic quantities belonging to the JValues collection:
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*''NOTE: '''All fullchem''' refers to all simulations that use [[GEOS-Chem_chemistry_mechanisms#Mechanisms_for_GEOS-Chem_v11-02|a full-chemistry mechanism]] (i.e. benchmark, complexSOA*, standard, tropchem. aciduptake, marinePOA, RRTMG, TOMAS).''
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{| border=1 cellspacing=0 cellpadding=5
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|-valign="top" bgcolor="#CCCCCC"
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!width="225px"|Diagnostic name
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!width="225px"|Description
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!width="125px"|Units
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!width="80px"|Wildcards
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!width="150px"|Simulations
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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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|-valign="top"
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|KppIntCounts
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|Number of times the KPP integrator was called
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|count
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|
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|
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*all fullchem
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|
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*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
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|
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|-valign="top"
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|KppJacCounts
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|Number of times the Jacobian matrix was constructed
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|count
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|
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|
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*all fullchem
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|
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*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
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|
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|-valign="top"
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|KppTotSteps
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|Total number of integration timesteps
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|count
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|
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|
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*all fullchem
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|
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*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
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|
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|-valign="top"
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|KppAccSteps
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|Number of accepted integration timesteps
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|count
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|
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|
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*all fullchem
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|
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*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
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|
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|-valign="top"
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|KppRejSteps
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|Number of rejected integration timesteps
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|count
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|
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|
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*all fullchem
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|
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*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
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|
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|-valign="top"
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|KppLuDecomps
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|Number of LU decompositions performed
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|count
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|
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|
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*all fullchem
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|
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*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
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|
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|-valign="top"
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|KppSubsts
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|Number of matrix substitutions performed.  Includes forward and backward substitutions.
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|count
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|
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|
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*all fullchem
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|
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*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
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|
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|-valign="top"
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|KppSmDecomps
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|Number of singular matrix decopositions performed.
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* NOTE: For Rosenbrock solvers, this will be zero everywhere, because the Rosenbrock method utilizes LU decomposition.
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|count
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|
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|
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*all fullchem
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|
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*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
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|
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|}
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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:59, 13 December 2019 (UTC)
  
 
== The ProdLoss Collection ==
 
== The ProdLoss Collection ==

Revision as of 15:59, 13 December 2019

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 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.
OHconcAfterChem OH concentration immediately after exiting the FlexChem solver molec/cm3
  • all fullchem
  • CH4
HO2concAfterChem HO2 concentration immediately after exiting the FlexChem solver molec/cm3
  • all fullchem
O1DconcAfterChem O1D concentration immediately after exiting the FlexChem solver molec/cm3
  • UCX fullchem
O3PconcAfterChem O3P concentration immediately after exiting the FlexChem solver molec/cm3
  • UCX fullchem

--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.
Jval_<spcname> Photolysis rates 1/s
  • ?PHO?
  • all fullchem

--Bob Yantosca (talk) 21:35, 18 July 2019 (UTC)

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

--Bob Yantosca (talk) 15:59, 13 December 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.
Diagnostics applicable only to the aciduptake simulation
ProdSO4fromOxidationOnDust Production of SO4 from oxidation on dust aerosols kg S/s
  • aciduptake
ProdNITfromHNO3uptakeOnDust Production of NIT from HNO3 uptake on dust aerosols kg N/s
  • aciduptake
ProdSO4fromUptakeOfH2SO4g Production of SO4 from uptake of H2SO4(g) kg S/s
  • aciduptake
Diagnostics applicable only to the aerosol-only simulation
ProdSO2fromDMSandOH Production of SO2 from DMS + OH (in sulfate_mod.F) kg S/s
  • aerosol
ProdSO2fromDMSandNO3 Production of SO2 from DMS + NO3R kg S/s
  • aerosol
ProdSO2fromDMS Total P(SO2) from DMS kg S/s
  • aerosol
ProdMSAfromDMS Production of MSA from DMS kg S/s
  • aerosol
ProdSO4fromGasPhase Production of SO4 in the gas phase kg S/s
  • aerosol
Diagnostics applicable only to the aerosol-only and all fullchem simulations
ProdBCPIfromBCPO Production of hydrophilic BC from hydrophobic BCs kg
  • aerosol
  • all fullchem
ProdOCPIfromOCPO Production of hydrophilic BC from hydrophobic BCs kg
  • aerosol
  • all fullchem
ProdSO4fromH2O2inCloud Production of SO4 from aqueous oxidation of H2O2 in clouds kg S/s
  • aerosol
  • all fullchem
ProdSO4fromO2inCloudMetal Production of SO4 from aqueous oxidation of O2 from metals in cloud kg S/s
  • aerosol
  • all fullchem
ProdSO4fromO3inCloud Production of SO4 from aqueous oxidation of O3 in clouds kg S/s
  • aerosol
  • all fullchem
ProdSO4fromO3inSeaSalt Production of SO4 from O3 in sea salt kg S/s
  • aerosol
  • all fullchem
ProdSO4fromO3s Production of SO4 from aqueous phase SO3-- loss by OH kg S/s
  • aerosol
  • all fullchem
ProdSO4fromSRO3 Production of SO4 from sulfur production rate of O3 kg S/s
  • aerosol
  • all fullchem
LossHNO3onSeaSalt Loss of HNO3 on sea salt aerosols kg S/s
  • aerosol
  • all fullchem
Diagnostics applicable only to full-chemistry simulations
ProdSO4fromHOBrinCloud Production of SO4 from aqueous oxidation of HOBr in clouds kg S/s
  • all fullchem
ProdSO4fromSRHOBr Production of SO4 from sulfur production rate of HOBr+O3 kg S/s
  • all fullchem
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?
  • all fullchem
  • tagCO
  • tagO3
Loss_<spcname> Chemical loss for a given species or family molec/cm3/s
  • ?LOS?
  • all fullchem
  • tagCO
  • tagO3

--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.
Chem_phSav ISORROPIA aerosol pH 1
  • all fullchem
Chem_HplusSav ISORROPIA H+ concentration M
  • all fullchem
Chem_WaterSav ISORROPIA aerosol water μg/m3
  • all fullchem
Chem_SulRatSav ISORROPIA sulfate concentration M
  • all fullchem
Chem_NaRatSav ISORROPIA Na+ concentration M
  • all fullchem
Chem_AcidPurSav ISORROPIA acidpur ?? concentration M
  • all fullchem
Chem_BiSulSav ISORROPIA bisulfate (general acid) concentration M
  • all fullchem
Chem_phCloud Cloud PH 1
  • all fullchem
Chem_SSAlk Sea salt alkalinity 1
  • all fullchem
Chem_HSO3AQ Cloud bisulfite concentration mol/L
  • all fullchem
Chem_SO3AQ Cloud sulfite concentration mol/L
  • all fullchem
Chem_fupdateHOBr Correction factor for HOBr removal by SO2 mol/L
  • all fullchem

--Bob Yantosca (talk) 19:55, 17 May 2018 (UTC)



Previous | Next | Guide to GEOS-Chem History diagnostics