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

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(The ProdLoss Collection)
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=== The ConcAfterChem collection ===
+
__FORCETOC__
 +
'''''[[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.
 
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 <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.
+
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.
+
*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',
Line 19: Line 40:
  
 
This table describes the diagnostic quantities belonging to the ConcAfterChem collection:
 
This table describes the diagnostic quantities belonging to the ConcAfterChem collection:
 
+
*''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).''
''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).''
+
*''NOTE: '''UCX fullchem''' refers to all full-chemistry simulations that use [[UCX chemistry mechanism|UCX]] (i.e. benchmark, standard, aciduptake, marinePOA).''
 
+
''NOTE: '''UCX fullchem''' refers to all full-chemistry simulations that use [[UCX chemistry mechanism|UCX]] (i.e. benchmark, standard, aciduptake, marinePOA).''
+
  
 
{| border=1 cellspacing=0 cellpadding=5  
 
{| border=1 cellspacing=0 cellpadding=5  
Line 41: Line 60:
 
|
 
|
 
*all fullchem
 
*all fullchem
 +
*CH4
 
|
 
|
 
|
 
|
Line 82: Line 102:
 
--[[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 JValues collection ===
+
== 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. 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.   
+
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',
Line 99: Line 120:
  
 
This table describes the diagnostic quantities belonging to the JValues collection:
 
This table describes the diagnostic quantities belonging to the JValues collection:
 
+
*''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).''
''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).''
+
  
 
{| border=1 cellspacing=0 cellpadding=5  
 
{| border=1 cellspacing=0 cellpadding=5  
Line 123: Line 143:
 
|
 
|
 
*[[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
 +
|
 +
|
 +
*all fullchem
 +
|To be added in 13.0.0
 +
|
 +
 +
|-valign="top"
 +
|JvalO3O3P
 +
|Photolysis rate of O3 -> O3P
 +
|1/s
 +
|
 +
|
 +
*all fullchem
 +
|To be added in 13.0.0
 +
|
 +
 
|}
 
|}
  
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:35, 18 July 2019 (UTC)
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:01, 3 June 2020 (UTC)
  
=== The ProdLoss Collection ===
+
== The KppDiags collection ==
  
The '''ProdLoss''' collection contains chemical production and loss rates.
+
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 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.   
+
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.
  
To prevent an individual field from being included in the diagnostic output, place a comment character <tt>#</tt> in front of the field name.
+
  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',
 +
::
  
''NOTE: This example is for the '''benchmark''' simulation.  Some quantities in this collection are not applicable to certain simulations.''
+
This table describes the diagnostic quantities belonging to the JValues collection:
 +
*''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).''
 +
 
 +
{| 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="150px"|Notes
 +
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
 +
 
 +
|-valign="top"
 +
|KppIntCounts
 +
|Number of times the KPP integrator was called
 +
|count
 +
|
 +
|
 +
*all fullchem
 +
|
 +
*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
 +
|
 +
 
 +
|-valign="top"
 +
|KppJacCounts
 +
|Number of times the Jacobian matrix was constructed
 +
|count
 +
|
 +
|
 +
*all fullchem
 +
|
 +
*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
 +
|
 +
 
 +
|-valign="top"
 +
|KppTotSteps
 +
|Total number of integration timesteps
 +
|count
 +
|
 +
|
 +
*all fullchem
 +
|
 +
*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
 +
|
 +
 
 +
|-valign="top"
 +
|KppAccSteps
 +
|Number of accepted integration timesteps
 +
|count
 +
|
 +
|
 +
*all fullchem
 +
|
 +
*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
 +
|
 +
 
 +
|-valign="top"
 +
|KppRejSteps
 +
|Number of rejected integration timesteps
 +
|count
 +
|
 +
|
 +
*all fullchem
 +
|
 +
*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
 +
|
 +
 
 +
|-valign="top"
 +
|KppLuDecomps
 +
|Number of LU decompositions performed
 +
|count
 +
|
 +
|
 +
*all fullchem
 +
|
 +
*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
 +
|
 +
 
 +
|-valign="top"
 +
|KppSubsts
 +
|Number of matrix substitutions performed.  Includes forward and backward substitutions.
 +
|count
 +
|
 +
|
 +
*all fullchem
 +
|
 +
*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
 +
|
 +
 
 +
|-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
 +
|
 +
|
 +
*all fullchem
 +
|
 +
*Added in [[GEOS-Chem 12#12.7.0|12.7.0]]
 +
|
 +
 
 +
|}
 +
 
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|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 <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',
Line 155: Line 326:
 
                               '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: '''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).''
''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).''
+
  
 
{| border=1 cellspacing=0 cellpadding=5  
 
{| border=1 cellspacing=0 cellpadding=5  
Line 168: Line 341:
 
!width="80px"|Wildcards
 
!width="80px"|Wildcards
 
!width="150px"|Simulations
 
!width="150px"|Simulations
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
 
 
!width="150px"|Notes
 
!width="150px"|Notes
 +
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
  
 
|-valign=top"  
 
|-valign=top"  
Line 182: Line 355:
 
*aciduptake
 
*aciduptake
 
|
 
|
*[[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"  
Line 193: Line 366:
 
*aciduptake
 
*aciduptake
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #13]]
 
 
|
 
|
 +
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #13]]
  
 
|-valign="top"
 
|-valign="top"
Line 204: Line 377:
 
*aciduptake
 
*aciduptake
 
|
 
|
*[[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"  
Line 218: Line 391:
 
*aerosol
 
*aerosol
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #1]]
 
 
|
 
|
 +
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #1]]
  
 
|-valign="top"  
 
|-valign="top"  
Line 229: Line 402:
 
*aerosol
 
*aerosol
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #2]]
 
 
|
 
|
 +
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #2]]
  
 
|-valign="top"
 
|-valign="top"
Line 240: Line 413:
 
*aerosol
 
*aerosol
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #3]]
 
 
|
 
|
 +
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #3]]
  
 
|-valign="top"
 
|-valign="top"
Line 251: Line 424:
 
*aerosol
 
*aerosol
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #4]]
 
 
|
 
|
 +
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #4]]
  
 
|-valign="top"
 
|-valign="top"
Line 262: Line 435:
 
*aerosol
 
*aerosol
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #5]]
 
 
|
 
|
 +
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #5]]
  
 
|-valign=top"  
 
|-valign=top"  
Line 277: Line 450:
 
*all fullchem
 
*all fullchem
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND07:_BC_and_OC_sources|ND07 #4]]
 
 
|
 
|
 +
*[[List_of_diagnostics_archived_to_bpch_format#ND07:_BC_and_OC_sources|ND07 #4]]
  
 
|-valign="top"
 
|-valign="top"
Line 289: Line 462:
 
*all fullchem
 
*all fullchem
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND07:_BC_and_OC_sources|ND07 #9]]
 
 
|
 
|
 +
*[[List_of_diagnostics_archived_to_bpch_format#ND07:_BC_and_OC_sources|ND07 #9]]
  
 
|-valign="top"
 
|-valign="top"
Line 301: Line 474:
 
*all fullchem
 
*all fullchem
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #6]]
 
 
|
 
|
 +
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #6]]
  
 
|-valign="top"
 
|-valign="top"
Line 313: Line 486:
 
*all fullchem
 
*all fullchem
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #8]]
+
*New in [[GEOS-Chem 12#12.0.0|12.0.0]]
 
|
 
|
*New in v11-02
+
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #8]]
  
 
|-valign="top"
 
|-valign="top"
Line 326: Line 499:
 
*all fullchem
 
*all fullchem
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #7]]
 
 
|
 
|
 +
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #7]]
  
 
|-valign="top"  
 
|-valign="top"  
Line 338: Line 511:
 
*all fullchem
 
*all fullchem
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #9]]
 
 
|
 
|
 +
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #9]]
  
 
|-valign="top"
 
|-valign="top"
Line 350: Line 523:
 
*all fullchem
 
*all fullchem
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #19]]
+
*New in [[GEOS-Chem 12#12.0.0|12.0.0]]
 
|
 
|
*New in v11-02
+
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #19]]
  
 
|-valign="top"
 
|-valign="top"
Line 363: Line 536:
 
*all fullchem
 
*all fullchem
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #17]]
+
*New in [[GEOS-Chem 12#12.0.0|12.0.0]]
 
|
 
|
*New in v11-02
+
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #17]]
  
 
|-valign="top"  
 
|-valign="top"  
Line 376: Line 549:
 
*all fullchem
 
*all fullchem
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND07:_BC_and_OC_sources|ND07 #15]]
 
 
|
 
|
 +
*[[List_of_diagnostics_archived_to_bpch_format#ND07:_BC_and_OC_sources|ND07 #15]]
  
 
|-valign=top"  
 
|-valign=top"  
Line 390: Line 563:
 
*all fullchem
 
*all fullchem
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #16]]
+
*New in [[GEOS-Chem 12#12.0.0|12.0.0]]
 
|
 
|
*New in v11-02
+
*[[List_of_diagnostics_archived_to_bpch_format#ND05:_P.2FL_for_sulfate_aerosols|ND05 #16]]
  
 
|-valign="top"
 
|-valign="top"
Line 401: Line 574:
 
|
 
|
 
*all fullchem
 
*all fullchem
 +
|
 +
*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 #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
 
|
 
|
*New in v11-02
+
|
 +
*all fullchem
 +
|
 +
*New in [[GEOS-Chem 12#12.0.0|12.0.0]]
 +
|
 +
 
 +
|-valign="top"
 +
|ProdCOfromNMVOC
 +
|Production of CO from NMVOCs
 +
|molec cm-3 s-1
 +
|
 +
|
 +
*all fullchem
 +
|
 +
*New in [[GEOS-Chem 12#12.0.0|12.0.0]]
 +
|
 +
 
  
 
|-valign=top"  
 
|-valign=top"  
Line 420: Line 616:
 
*tagO3
 
*tagO3
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND65:_Chemical_production_and_loss_diagnostics|ND65]]
 
 
|
 
|
 +
*[[List_of_diagnostics_archived_to_bpch_format#ND65:_Chemical_production_and_loss_diagnostics|ND65]]
  
 
|-valign="top"
 
|-valign="top"
Line 434: Line 630:
 
*tagO3
 
*tagO3
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND65:_Chemical_production_and_loss_diagnostics|ND65]]
 
 
|
 
|
 +
*[[List_of_diagnostics_archived_to_bpch_format#ND65:_Chemical_production_and_loss_diagnostics|ND65]]
 +
 
|}
 
|}
  
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:25, 17 May 2018 (UTC)
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:25, 17 May 2018 (UTC)
  
=== The StateChm Collection ===
+
== 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. 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.   
+
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',
Line 470: Line 667:
  
 
The table below describes diagnostic quantities belonging to the StateChm collection.
 
The table below describes diagnostic quantities belonging to the StateChm collection.
 
+
*''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).''
''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).''
+
  
 
{| border=1 cellspacing=0 cellpadding=5  
 
{| border=1 cellspacing=0 cellpadding=5  
Line 480: Line 676:
 
!width="80px"|Wildcards
 
!width="80px"|Wildcards
 
!width="150px"|Simulations
 
!width="150px"|Simulations
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
 
 
!width="150px"|Notes
 
!width="150px"|Notes
 +
!width="100px"|[[List of diagnostics archived to bpch format|Bpch equiv.]]
  
 
|-valign="top"
 
|-valign="top"
Line 491: Line 687:
 
*all fullchem
 
*all fullchem
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND73:_ISORROPIA_diagnostics|ND73 #1]]
 
 
|
 
|
 +
*[[List_of_diagnostics_archived_to_bpch_format#ND73:_ISORROPIA_diagnostics|ND73 #1]]
  
 
|-valign="top"
 
|-valign="top"
Line 502: Line 698:
 
*all fullchem
 
*all fullchem
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND73:_ISORROPIA_diagnostics|ND73 #2]]
 
 
|
 
|
 +
*[[List_of_diagnostics_archived_to_bpch_format#ND73:_ISORROPIA_diagnostics|ND73 #2]]
  
 
|-valign="top"
 
|-valign="top"
Line 513: Line 709:
 
*all fullchem
 
*all fullchem
 
|
 
|
*[[List_of_diagnostics_archived_to_bpch_format#ND73:_ISORROPIA_diagnostics|ND73 #3]]
 
 
|
 
|
 +
*[[List_of_diagnostics_archived_to_bpch_format#ND73:_ISORROPIA_diagnostics|ND73 #3]]
  
 
|-valign="top"  
 
|-valign="top"  
Line 564: Line 760:
 
*all fullchem
 
*all fullchem
 
|
 
|
 +
*New in [[GEOS-Chem 12#12.0.0|12.0.0]]
 
|
 
|
*New in v11-02
 
  
 
|-valign="top"
 
|-valign="top"
Line 575: Line 771:
 
*all fullchem
 
*all fullchem
 
|
 
|
 +
*New in [[GEOS-Chem 12#12.0.0|12.0.0]]
 
|
 
|
*New in v11-02
 
  
 
|-valign="top"
 
|-valign="top"
Line 586: Line 782:
 
*all fullchem
 
*all fullchem
 
|
 
|
 +
*New in [[GEOS-Chem 12#12.0.0|12.0.0]]
 
|
 
|
*New in v11-02
 
  
 
|-valign="top"
 
|-valign="top"
Line 597: Line 793:
 
*all fullchem
 
*all fullchem
 
|
 
|
 +
*New in [[GEOS-Chem 12#12.0.0|12.0.0]]
 
|
 
|
*New in v11-02
 
  
 
|-valign="top"
 
|-valign="top"
Line 608: Line 804:
 
*all fullchem
 
*all fullchem
 
|
 
|
 +
*New in [[GEOS-Chem 12#12.0.0|12.0.0]]
 
|
 
|
*New in v11-02
 
  
 
|}
 
|}
  
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:55, 17 May 2018 (UTC)
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:55, 17 May 2018 (UTC)
 +
 +
 +
----
 +
'''''[[History collections for budgets|Previous]] | [[History collections for convection and wet deposition|Next]] | [[Guide to GEOS-Chem History diagnostics]]'''''

Revision as of 15:41, 11 June 2020

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
JvalO3O1D Photolysis rate of O3 -> O1D 1/s
  • all fullchem
To be added in 13.0.0
JvalO3O3P Photolysis rate of O3 -> O3P 1/s
  • all fullchem
To be added in 13.0.0

--Bob Yantosca (talk) 21:01, 3 June 2020 (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',
                              'ProdCOfromCH4                 ', 'GIGCchem',
                              'ProdCOfromNMVOC               ', '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
ProdCOfromCH4 Production of CO from CH4 molec cm-3 s-1
  • all fullchem
ProdCOfromNMVOC Production of CO from NMVOCs molec cm-3 s-1
  • 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