Difference between revisions of "History collections for chemistry and photolysis"
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+ | '''''[[History collections for budgets|Previous]] | [[History collections for convection and wet deposition|Next]] | [[Guide to GEOS-Chem History diagnostics]]''''' | ||
+ | #[[Overview of History diagnostics]] | ||
+ | #[[Legend for History diagnostics]] | ||
+ | #[[Collections for History diagnostics]] | ||
+ | #[[History collections for advection and mixing]] | ||
+ | #[[History collections for aerosols]] | ||
+ | #[[History collections for budgets]] | ||
+ | #<span style="color:blue">'''History collections for chemistry and photolysis'''</span> | ||
+ | #[[History collections for convection and wet deposition]] | ||
+ | #[[History collections for dry deposition]] | ||
+ | #[[History collections for mercury and POPs]] | ||
+ | #[[History collections for met fields and related quantities]] | ||
+ | #[[History collections for methane]] | ||
+ | #[[History collections for species concentrations]] | ||
+ | #[[History collections for TransportTracers]] | ||
+ | #[[Replicating the behavior of the prior timeseries diagnostics]] | ||
+ | #[[Adding new History diagnostics]] | ||
− | |||
− | + | == The ConcAfterChem collection == | |
+ | |||
+ | The '''ConcAfterChem''' collection contains diagnostics for OH, HO2, etc. species immediately upon exiting the [[FlexChem]] solver. | ||
− | To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> in front of the field name. | + | Here is a sample definition section for the ConcAfterChem collection. |
+ | *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. | ||
+ | *To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> 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.template: '%y4%m2%d2_%h2%n2z.nc4', | ||
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This table describes the diagnostic quantities belonging to the ConcAfterChem collection: | This table describes the diagnostic quantities belonging to the ConcAfterChem collection: | ||
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− | |||
− | |||
{| border=1 cellspacing=0 cellpadding=5 | {| border=1 cellspacing=0 cellpadding=5 | ||
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!width="80px"|Wildcards | !width="80px"|Wildcards | ||
!width="150px"|Simulations | !width="150px"|Simulations | ||
+ | !width="175px"|Notes | ||
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]] | !width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]] | ||
− | |||
|-valign="top" | |-valign="top" | ||
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− | * | + | *fullchem |
+ | *CH4 | ||
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− | |||
| | | | ||
+ | *[[List of diagnostics archived to bpch format|ND43]], #1 | ||
|-valign="top" | |-valign="top" | ||
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− | * | + | *fullchem |
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− | |||
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+ | *[[List of diagnostics archived to bpch format|ND43]], #3 | ||
|-valign="top" | |-valign="top" | ||
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− | * | + | *fullchem |
+ | | | ||
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*[[List of diagnostics archived to bpch format|ND43]], #4 | *[[List of diagnostics archived to bpch format|ND43]], #4 | ||
− | |||
|-valign="top" | |-valign="top" | ||
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− | * | + | *fullchem |
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− | |||
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+ | *[[List of diagnostics archived to bpch format|ND43]], #5 | ||
|} | |} | ||
− | |||
− | + | == The JValues collection == | |
The '''JValues''' collection contains diagnostics for photolysis rates for various chemical species, obtained from the FAST-JX photolysis mechanism. | 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. | + | Here is a sample definition section for the JValues collection. |
− | + | *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. | |
− | To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> in front of the field name. | + | *To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> 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.template: '%y4%m2%d2_%h2%n2z.nc4', | ||
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This table describes the diagnostic quantities belonging to the JValues collection: | This table describes the diagnostic quantities belonging to the JValues collection: | ||
− | |||
− | |||
{| border=1 cellspacing=0 cellpadding=5 | {| border=1 cellspacing=0 cellpadding=5 | ||
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!width="80px"|Wildcards | !width="80px"|Wildcards | ||
!width="150px"|Simulations | !width="150px"|Simulations | ||
+ | !width="175px"|Notes | ||
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]] | !width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]] | ||
− | |||
|-valign="top" | |-valign="top" | ||
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*?PHO? | *?PHO? | ||
| | | | ||
− | * | + | *fullchem |
+ | | | ||
| | | | ||
*[[List_of_diagnostics_archived_to_bpch_format#ND22:_Photolysis_diagnostics|ND22]] | *[[List_of_diagnostics_archived_to_bpch_format#ND22:_Photolysis_diagnostics|ND22]] | ||
+ | |||
+ | |-valign="top" | ||
+ | |JvalO3O1D | ||
+ | |Photolysis rate of O3 -> O1D | ||
+ | |1/s | ||
| | | | ||
− | * | + | | |
+ | *fullchem | ||
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 13.0.0'''</span> | ||
+ | | | ||
+ | |||
+ | |-valign="top" | ||
+ | |JvalO3O3P | ||
+ | |Photolysis rate of O3 -> O3P | ||
+ | |1/s | ||
+ | | | ||
+ | | | ||
+ | *fullchem | ||
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 13.0.0'''</span> | ||
+ | | | ||
+ | |||
|} | |} | ||
− | + | == 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 <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. | ||
+ | *To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> 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', | ||
+ | :: | ||
− | To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> in front of the field name. | + | This table describes the diagnostic quantities belonging to the JValues collection: |
+ | *''NOTE: '''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).'' | ||
+ | |||
+ | {| border=1 cellspacing=0 cellpadding=5 | ||
+ | |-valign="top" bgcolor="#CCCCCC" | ||
+ | !width="225px"|Diagnostic name | ||
+ | !width="225px"|Description | ||
+ | !width="125px"|Units | ||
+ | !width="80px"|Wildcards | ||
+ | !width="150px"|Simulations | ||
+ | !width="175px"|Notes | ||
+ | !width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]] | ||
+ | |||
+ | |-valign="top" | ||
+ | |KppIntCounts | ||
+ | |Number of times the KPP integrator was called | ||
+ | |count | ||
+ | | | ||
+ | | | ||
+ | *fullchem | ||
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 12.7.0'''</span> | ||
+ | | | ||
+ | |||
+ | |-valign="top" | ||
+ | |KppJacCounts | ||
+ | |Number of times the Jacobian matrix was constructed | ||
+ | |count | ||
+ | | | ||
+ | | | ||
+ | *fullchem | ||
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 12.7.0'''</span> | ||
+ | | | ||
+ | |||
+ | |-valign="top" | ||
+ | |KppTotSteps | ||
+ | |Total number of integration timesteps | ||
+ | |count | ||
+ | | | ||
+ | | | ||
+ | *fullchem | ||
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 12.7.0'''</span> | ||
+ | | | ||
+ | |||
+ | |-valign="top" | ||
+ | |KppAccSteps | ||
+ | |Number of accepted integration timesteps | ||
+ | |count | ||
+ | | | ||
+ | | | ||
+ | *fullchem | ||
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 12.7.0'''</span> | ||
+ | | | ||
+ | |||
+ | |-valign="top" | ||
+ | |KppRejSteps | ||
+ | |Number of rejected integration timesteps | ||
+ | |count | ||
+ | | | ||
+ | | | ||
+ | *fullchem | ||
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 12.7.0'''</span> | ||
+ | | | ||
+ | |||
+ | |-valign="top" | ||
+ | |KppLuDecomps | ||
+ | |Number of LU decompositions performed | ||
+ | |count | ||
+ | | | ||
+ | | | ||
+ | *fullchem | ||
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 12.7.0'''</span> | ||
+ | | | ||
+ | |||
+ | |-valign="top" | ||
+ | |KppSubsts | ||
+ | |Number of matrix substitutions performed. Includes forward and backward substitutions. | ||
+ | |count | ||
+ | | | ||
+ | | | ||
+ | *fullchem | ||
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 12.7.0'''</span> | ||
+ | | | ||
+ | |||
+ | |-valign="top" | ||
+ | |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 | ||
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 12.7.0'''</span> | ||
+ | | | ||
+ | |||
+ | |} | ||
+ | |||
+ | == 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 <tt>metrics.py</tt> 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 <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. | ||
+ | *To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> 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. | ||
+ | |||
+ | {| border=1 cellspacing=0 cellpadding=5 | ||
+ | |-valign="top" bgcolor="#CCCCCC" | ||
+ | !width="225px"|Diagnostic name | ||
+ | !width="225px"|Description | ||
+ | !width="125px"|Units | ||
+ | !width="80px"|Wildcards | ||
+ | !width="150px"|Simulations | ||
+ | !width="175px"|Notes | ||
+ | !width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]] | ||
+ | |||
+ | |-valign="top" | ||
+ | |AirMassColumnFull | ||
+ | |Air mass, full atmosphere column sums | ||
+ | |kg | ||
+ | | | ||
+ | | | ||
+ | *fullchem | ||
+ | *CH4 | ||
+ | *tagCH4 | ||
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 13.0.0'''</span> | ||
+ | | | ||
+ | |||
+ | |-valign="top" | ||
+ | |LossOHbyCH4columnTrop | ||
+ | |Loss rate of CH4 by OH, tropospheric column sums | ||
+ | |molec cm-3 | ||
+ | | | ||
+ | | | ||
+ | *fullchem | ||
+ | *CH4 | ||
+ | *tagCH4 | ||
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 13.0.0'''</span> | ||
+ | | | ||
+ | |||
+ | |-valign="top" | ||
+ | |LossOHbyMCFcolumnTrop | ||
+ | |Loss rate of CH3CCl3 (aka MCF) by OH, tropospheric column sums | ||
+ | |molec cm-3 | ||
+ | | | ||
+ | | | ||
+ | *fullchem | ||
+ | *CH4 | ||
+ | *tagCH4 | ||
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 13.0.0'''</span> | ||
+ | | | ||
+ | |||
+ | |-valign="top" | ||
+ | |OHwgtByAirMassColumnFull | ||
+ | |Airmass-weighted mean OH concentration, full-atmosphere column sums | ||
+ | |kg air kg OH m-3 | ||
+ | | | ||
+ | | | ||
+ | *fullchem | ||
+ | *CH4 | ||
+ | *tagCH4 | ||
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 13.0.0'''</span> | ||
+ | | | ||
+ | |||
+ | |-valign=top" | ||
+ | !colspan="7" bgcolor="#CCFFFF"|Diagnostics applicable only to the CH4 or tagCH4 simulations | ||
+ | |||
+ | |-valign="top" | ||
+ | |CH4emission | ||
+ | |CH4 emission, used for computing OH metrics | ||
+ | |kg s-1 | ||
+ | | | ||
+ | | | ||
+ | *CH4 | ||
+ | *tagCH4 | ||
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 13.0.0'''</span> | ||
+ | | | ||
+ | |||
+ | |-valign="top" | ||
+ | |CH4massColumnFull | ||
+ | |Airmass-weighted CH4 concentration, full-atmosphere column sums | ||
+ | |kg air kg CH4 m-3 | ||
+ | | | ||
+ | | | ||
+ | *CH4 | ||
+ | *tagCH4 | ||
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 13.0.0'''</span> | ||
+ | | | ||
+ | |||
+ | |-valign="top" | ||
+ | |CH4massColumnTrop | ||
+ | |Airmass-weighted CH4 concentration, troposphere-only column sums | ||
+ | |kg air kg CH4 m-3 | ||
+ | | | ||
+ | | | ||
+ | *CH4 | ||
+ | *tagCH4 | ||
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 13.0.0'''</span> | ||
+ | | | ||
+ | |||
+ | |} | ||
+ | |||
+ | == The ProdLoss Collection == | ||
+ | |||
+ | The '''ProdLoss''' collection contains chemical production and loss rates. | ||
− | ''NOTE: This example is for the '''benchmark''' simulation. Some quantities in this collection are not applicable to certain simulations.'' | + | Here is a sample definition section for the ProdLoss collection. |
+ | *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. | ||
+ | *To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> 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.template: '%y4%m2%d2_%h2%n2z.nc4', | ||
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'Loss_?LOS? ', 'GIGCchem', | 'Loss_?LOS? ', 'GIGCchem', | ||
'LossHNO3onSeaSalt ', 'GIGCchem', | 'LossHNO3onSeaSalt ', 'GIGCchem', | ||
+ | 'ProdCOfromCH4 ', 'GIGCchem', | ||
+ | 'ProdCOfromNMVOC ', 'GIGCchem', | ||
:: | :: | ||
The table below describes diagnostic quantities belonging to the ProdLoss collection. | The table below describes diagnostic quantities belonging to the ProdLoss collection. | ||
− | + | *''NOTE: '''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).'' | |
− | ''NOTE: ''' | + | |
{| border=1 cellspacing=0 cellpadding=5 | {| border=1 cellspacing=0 cellpadding=5 | ||
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!width="80px"|Wildcards | !width="80px"|Wildcards | ||
!width="150px"|Simulations | !width="150px"|Simulations | ||
+ | !width="175px"|Notes | ||
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]] | !width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]] | ||
− | |||
|-valign=top" | |-valign=top" | ||
− | !colspan="7" bgcolor="#CCFFFF"|Diagnostics applicable only to the | + | !colspan="7" bgcolor="#CCFFFF"|Diagnostics applicable only to the fullchem simulation with the aciduptake option |
|-valign="top" | |-valign="top" | ||
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− | *aciduptake | + | *fullchem w/ aciduptake |
+ | | | ||
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*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #12]] | *[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #12]] | ||
− | |||
|-valign="top" | |-valign="top" | ||
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− | *aciduptake | + | *fullchem w/ aciduptake |
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− | |||
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+ | *[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #13]] | ||
|-valign="top" | |-valign="top" | ||
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− | *aciduptake | + | *fullchem w/ aciduptake |
+ | | | ||
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*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #14]] | *[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #14]] | ||
− | |||
|-valign=top" | |-valign=top" | ||
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− | *aerosol | + | *aerosol-only |
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− | |||
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+ | *[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #1]] | ||
|-valign="top" | |-valign="top" | ||
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− | *aerosol | + | *aerosol-only |
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− | |||
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+ | *[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #2]] | ||
|-valign="top" | |-valign="top" | ||
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− | *aerosol | + | *aerosol-only |
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− | |||
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+ | *[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #3]] | ||
|-valign="top" | |-valign="top" | ||
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− | *aerosol | + | *aerosol-only |
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− | |||
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+ | *[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #4]] | ||
|-valign="top" | |-valign="top" | ||
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− | *aerosol | + | *aerosol-only |
| | | | ||
− | |||
| | | | ||
+ | *[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #5]] | ||
|-valign=top" | |-valign=top" | ||
− | !colspan="7" bgcolor="#CCFFFF"|Diagnostics applicable only to the aerosol-only and | + | !colspan="7" bgcolor="#CCFFFF"|Diagnostics applicable only to the aerosol-only and fullchem simulations |
|-valign="top" | |-valign="top" | ||
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| | | | ||
| | | | ||
− | *aerosol | + | *aerosol-only |
− | * | + | *fullchem |
| | | | ||
− | |||
| | | | ||
+ | *[[List_of_diagnostics_archived_to_bpch_format#ND07:_BC_and_OC_sources|ND07 #4]] | ||
|-valign="top" | |-valign="top" | ||
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− | *aerosol | + | *aerosol-only |
− | * | + | *fullchem |
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− | |||
| | | | ||
+ | *[[List_of_diagnostics_archived_to_bpch_format#ND07:_BC_and_OC_sources|ND07 #9]] | ||
|-valign="top" | |-valign="top" | ||
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− | *aerosol | + | *aerosol-only |
− | * | + | *fullchem |
| | | | ||
− | |||
| | | | ||
+ | *[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #6]] | ||
|-valign="top" | |-valign="top" | ||
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− | *aerosol | + | *aerosol-only |
− | * | + | *fullchem |
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− | *[[ | + | *New in [[GEOS-Chem 12#12.0.0|12.0.0]] |
| | | | ||
− | * | + | *[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #8]] |
|-valign="top" | |-valign="top" | ||
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| | | | ||
| | | | ||
− | *aerosol | + | *aerosol-only |
− | * | + | *fullchem |
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− | |||
| | | | ||
+ | *[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #7]] | ||
|-valign="top" | |-valign="top" | ||
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| | | | ||
− | *aerosol | + | *aerosol-only |
− | * | + | *fullchem |
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− | |||
| | | | ||
+ | *[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #9]] | ||
|-valign="top" | |-valign="top" | ||
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− | *aerosol | + | *aerosol-only |
− | * | + | *fullchem |
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− | *[[ | + | *New in [[GEOS-Chem 12#12.0.0|12.0.0]] |
| | | | ||
− | * | + | *[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #19]] |
|-valign="top" | |-valign="top" | ||
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− | *aerosol | + | *aerosol-only |
− | * | + | *fullchem |
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− | *[[ | + | *New in [[GEOS-Chem 12#12.0.0|12.0.0]] |
| | | | ||
− | * | + | *[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #17]] |
|-valign="top" | |-valign="top" | ||
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− | *aerosol | + | *aerosol-only |
− | * | + | *fullchem |
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− | |||
| | | | ||
+ | *[[List_of_diagnostics_archived_to_bpch_format#ND07:_BC_and_OC_sources|ND07 #15]] | ||
|-valign=top" | |-valign=top" | ||
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− | * | + | *fullchem |
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− | * | + | *<span style="color:darkgreen">'''Added in 12.0.0'''</span> |
| | | | ||
− | * | + | *[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #16]] |
|-valign="top" | |-valign="top" | ||
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− | * | + | *fullchem |
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 12.0.0'''</span> | ||
| | | | ||
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #18]] | *[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #18]] | ||
+ | |||
+ | |-valign="top" | ||
+ | |ProdCOfromCH4 | ||
+ | |Production of CO from CH4 | ||
+ | |molec cm-3 s-1 | ||
+ | | | ||
+ | | | ||
+ | *fullchem | ||
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 12.0.0'''</span> | ||
+ | | | ||
+ | |||
+ | |-valign="top" | ||
+ | |ProdCOfromNMVOC | ||
+ | |Production of CO from NMVOCs | ||
+ | |molec cm-3 s-1 | ||
+ | | | ||
+ | | | ||
+ | *fullchem | ||
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 12.0.0'''</span> | ||
| | | | ||
− | |||
|-valign=top" | |-valign=top" | ||
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*?PRD? | *?PRD? | ||
| | | | ||
− | * | + | *fullchem |
*tagCO | *tagCO | ||
*tagO3 | *tagO3 | ||
| | | | ||
− | |||
| | | | ||
+ | *[[List_of_diagnostics_archived_to_bpch_format#ND65:_Chemical_production_and_loss_diagnostics|ND65]] | ||
|-valign="top" | |-valign="top" | ||
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*?LOS? | *?LOS? | ||
| | | | ||
− | * | + | *fullchem |
*tagCO | *tagCO | ||
*tagO3 | *tagO3 | ||
| | | | ||
− | |||
| | | | ||
+ | *[[List_of_diagnostics_archived_to_bpch_format#ND65:_Chemical_production_and_loss_diagnostics|ND65]] | ||
+ | |||
|} | |} | ||
− | + | == The StateChm Collection == | |
− | + | ||
− | + | ||
The '''StateChm ''' collection contains quantities from <tt>State_Chm</tt>, the Chemistry state object (other than the species concentrations, which are stored in the SpeciesConc collection). | The '''StateChm ''' collection contains quantities from <tt>State_Chm</tt>, 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. | + | Here is a sample definition section for the StateChm collection. |
− | + | *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. | |
− | To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> in front of the field name. | + | *To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> in front of the field name. |
− | + | *Other fields of the <tt>State_Chm</tt> object can be added to this collection by prefixing the field name with <tt>Chem_</tt>. | |
− | Other fields of the <tt>State_Chm</tt> object can be added to this collection by prefixing the field name with <tt>Chem_</tt>. | + | *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.template: '%y4%m2%d2_%h2%n2z.nc4', | ||
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The table below describes diagnostic quantities belonging to the StateChm collection. | The table below describes diagnostic quantities belonging to the StateChm collection. | ||
− | + | *''NOTE: '''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).'' | |
− | ''NOTE: ''' | + | |
{| border=1 cellspacing=0 cellpadding=5 | {| border=1 cellspacing=0 cellpadding=5 | ||
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!width="80px"|Wildcards | !width="80px"|Wildcards | ||
!width="150px"|Simulations | !width="150px"|Simulations | ||
+ | !width="175px"|Notes | ||
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]] | !width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]] | ||
− | |||
|-valign="top" | |-valign="top" | ||
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| | | | ||
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− | * | + | *fullchem |
| | | | ||
− | |||
| | | | ||
+ | *[[List_of_diagnostics_archived_to_bpch_format#ND73:_ISORROPIA_diagnostics|ND73 #1]] | ||
|-valign="top" | |-valign="top" | ||
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| | | | ||
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− | * | + | *fullchem |
| | | | ||
− | |||
| | | | ||
+ | *[[List_of_diagnostics_archived_to_bpch_format#ND73:_ISORROPIA_diagnostics|ND73 #2]] | ||
|-valign="top" | |-valign="top" | ||
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− | * | + | *fullchem |
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− | |||
| | | | ||
+ | *[[List_of_diagnostics_archived_to_bpch_format#ND73:_ISORROPIA_diagnostics|ND73 #3]] | ||
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+ | *<span style="color:darkgreen">'''Added in 12.0.0'''</span> | ||
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− | |||
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+ | *<span style="color:darkgreen">'''Added in 12.0.0'''</span> | ||
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− | |||
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+ | *<span style="color:darkgreen">'''Added in 12.0.0'''</span> | ||
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− | |||
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− | * | + | *fullchem |
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+ | *<span style="color:darkgreen">'''Added in 12.0.0'''</span> | ||
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− | |||
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− | * | + | *fullchem |
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+ | *<span style="color:darkgreen">'''Added in 12.0.0'''</span> | ||
| | | | ||
− | |||
|} | |} | ||
− | --[[ | + | |
+ | ---- | ||
+ | '''''[[History collections for budgets|Previous]] | [[History collections for convection and wet deposition|Next]] | [[Guide to GEOS-Chem History diagnostics]]''''' |
Revision as of 22:30, 8 December 2020
Previous | Next | Guide to GEOS-Chem History diagnostics
- Overview of History diagnostics
- Legend for History diagnostics
- Collections for History diagnostics
- History collections for advection and mixing
- History collections for aerosols
- History collections for budgets
- History collections for chemistry and photolysis
- History collections for convection and wet deposition
- History collections for dry deposition
- History collections for mercury and POPs
- History collections for met fields and related quantities
- History collections for methane
- History collections for species concentrations
- History collections for TransportTracers
- Replicating the behavior of the prior timeseries diagnostics
- Adding new History diagnostics
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:
Diagnostic name | Description | Units | Wildcards | Simulations | Notes | Bpch equiv. |
---|---|---|---|---|---|---|
OHconcAfterChem | OH concentration immediately after exiting the FlexChem solver | molec/cm3 |
|
| ||
HO2concAfterChem | HO2 concentration immediately after exiting the FlexChem solver | molec/cm3 |
|
| ||
O1DconcAfterChem | O1D concentration immediately after exiting the FlexChem solver | molec/cm3 |
|
| ||
O3PconcAfterChem | O3P concentration immediately after exiting the FlexChem solver | molec/cm3 |
|
|
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 |
|
|
||
JvalO3O1D | Photolysis rate of O3 -> O1D | 1/s |
|
|
||
JvalO3O3P | Photolysis rate of O3 -> O3P | 1/s |
|
|
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 |
|
|
||
KppJacCounts | Number of times the Jacobian matrix was constructed | count |
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|
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KppTotSteps | Total number of integration timesteps | count |
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|
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KppAccSteps | Number of accepted integration timesteps | count |
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KppRejSteps | Number of rejected integration timesteps | count |
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|
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KppLuDecomps | Number of LU decompositions performed | count |
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|
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KppSubsts | Number of matrix substitutions performed. Includes forward and backward substitutions. | count |
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|
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KppSmDecomps | Number of singular matrix decopositions performed.
|
count |
|
|
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 |
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|
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LossOHbyCH4columnTrop | Loss rate of CH4 by OH, tropospheric column sums | molec cm-3 |
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LossOHbyMCFcolumnTrop | Loss rate of CH3CCl3 (aka MCF) by OH, tropospheric column sums | molec cm-3 |
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|
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OHwgtByAirMassColumnFull | Airmass-weighted mean OH concentration, full-atmosphere column sums | kg air kg OH m-3 |
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|
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Diagnostics applicable only to the CH4 or tagCH4 simulations | ||||||
CH4emission | CH4 emission, used for computing OH metrics | kg s-1 |
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|
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CH4massColumnFull | Airmass-weighted CH4 concentration, full-atmosphere column sums | kg air kg CH4 m-3 |
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CH4massColumnTrop | Airmass-weighted CH4 concentration, troposphere-only column sums | kg air kg CH4 m-3 |
|
|
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 |
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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 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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|
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ProdSO4fromSRO3 | Production of SO4 from sulfur production rate of O3 | kg S/s |
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|
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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 |
|
|
||
ProdSO4fromSRHOBr | Production of SO4 from sulfur production rate of HOBr+O3 | kg S/s |
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|
||
ProdCOfromCH4 | Production of CO from CH4 | molec cm-3 s-1 |
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|
||
ProdCOfromNMVOC | Production of CO from NMVOCs | molec cm-3 s-1 |
|
|
||
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 |
|
|
||
Loss_<spcname> | Chemical loss for a given species or family | molec/cm3/s |
|
|
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. |
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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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