Difference between revisions of "History collections for species concentrations"
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+ | '''''[[History collections for methane|Previous]] | [[History collections for TransportTracers|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]] | ||
+ | #<span style="color:blue">'''History collections for species concentrations'''</span> | ||
+ | #[[History collections for TransportTracers]] | ||
+ | #[[History collections for CO2]] | ||
+ | #[[Replicating the behavior of the prior timeseries diagnostics]] | ||
+ | #[[Adding new History diagnostics]] | ||
+ | |||
+ | |||
+ | == The BoundaryConditions collection == | ||
+ | |||
+ | ''NOTE: If you are not setting up for a nested-grid simulation, then you can disable this collection.'' | ||
+ | |||
+ | The '''BoundaryConditions''' diagnostic collection contains advected species concentrations (archived from a global simulation) that will be used by nested-grid simulations as transport boundary conditions. Like SpeciesConc, it archives data with units of mol/mol dry air. | ||
+ | |||
+ | Here is a sample definition section for the SpeciesConc 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. | ||
+ | |||
+ | BoundaryConditions.template: '%y4%m2%d2_%h2%n2z.nc4', | ||
+ | BoundaryConditions.format: 'CFIO', | ||
+ | BoundaryConditions.frequency: 00000000 030000 | ||
+ | BoundaryConditions.duration: 00000100 000000 | ||
+ | BoundaryConditions.mode: 'instantaneous' | ||
+ | BoundaryConditions.fields: 'SpeciesBC_?ADV? ', 'GIGCchem', | ||
+ | :: | ||
+ | |||
+ | This table describes the diagnostic quantities belonging to the BoundaryConditions collection: | ||
+ | |||
+ | {| border=1 cellspacing=0 cellpadding=5 | ||
+ | |-valign="top" bgcolor="#CCCCCC" | ||
+ | !width="225px"|Diagnostic name | ||
+ | !width="225px"|Description | ||
+ | !width="125px"|Units | ||
+ | !width="100px"|Wildcards | ||
+ | !width="150px"|Simulations | ||
+ | !width="175px"|Notes | ||
+ | |||
+ | |-valign="top" | ||
+ | |SpeciesBC_<spcname> | ||
+ | |Advected species concentrations used as boundary conditions for nested-grid simulations | ||
+ | |mol/mol dry air | ||
+ | | | ||
+ | *?ADV? | ||
+ | | | ||
+ | *all simulations | ||
+ | | | ||
+ | *<span style="color:darkgreen">'''Added in 12.4.0'''</span> | ||
+ | |} | ||
+ | |||
+ | == The ConcAboveSfc collection == | ||
+ | |||
+ | The ConcAboveSfc collection is [[History collections for dry deposition#The ConcAboveSfc collection|listed on our ''History collections for dry deposition'' page]]. | ||
+ | |||
+ | == The ConcAfterChem collection == | ||
+ | |||
+ | The ConcAfterChem collection is [[History collections for chemistry and photolysis#The ConcAfterChem collection|listed on our ''History collections for chemistry and photolysis'' page]]. | ||
+ | |||
+ | --[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 14:21, 19 July 2019 (UTC) | ||
+ | |||
== The Restart collection == | == The Restart collection == | ||
The '''Restart''' diagnostic collection contains fields for saving out to the GEOS-Chem restart file. This type of diagnostic output is used in all GEOS-Chem simulations; therefore, we have listed Restart first in the <tt>HISTORY.rc</tt> files that ship with each [[Creating_GEOS-Chem_run_directories|GEOS-Chem run directory]]. | The '''Restart''' diagnostic collection contains fields for saving out to the GEOS-Chem restart file. This type of diagnostic output is used in all GEOS-Chem simulations; therefore, we have listed Restart first in the <tt>HISTORY.rc</tt> files that ship with each [[Creating_GEOS-Chem_run_directories|GEOS-Chem run directory]]. | ||
− | Here is a sample definition section for the | + | Here is a sample definition section for the Restart 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: The restart file will be created in the GEOS_Chem run directory, not in the <tt>OutputDir</tt> sub-folder.'' | ||
− | Restart. | + | Restart.filename: './GEOSChem.Restart.%y4%m2%d2_%h2%n2z.nc4', |
Restart.format: 'CFIO', | Restart.format: 'CFIO', | ||
Restart.frequency: 'End', | Restart.frequency: 'End', | ||
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!width="225px"|Description | !width="225px"|Description | ||
!width="125px"|Units | !width="125px"|Units | ||
− | !width=" | + | !width="100px"|Wildcards |
!width="150px"|Simulations | !width="150px"|Simulations | ||
− | !width=" | + | !width="175px"|Notes |
− | + | ||
|-valign="top" | |-valign="top" | ||
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|mol/mol dry air | |mol/mol dry air | ||
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− | * | + | *?ALL? |
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*all simulations | *all simulations | ||
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− | + | *Use <tt>?ALL?</tt> to make sure all species get archived | |
*Variables renamed from <tt>SPC_</tt> to <tt>SpeciesRst_</tt> in [[GEOS-Chem 12#12.1.0|12.1.0]] | *Variables renamed from <tt>SPC_</tt> to <tt>SpeciesRst_</tt> in [[GEOS-Chem 12#12.1.0|12.1.0]] | ||
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*tropchem | *tropchem | ||
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− | + | *<span style="color:darkgreen">'''Added in 12.1.0'''</span> | |
− | * | + | |
*Replaced local array <tt>H2O2s</tt> in wetscav_mod.F | *Replaced local array <tt>H2O2s</tt> in wetscav_mod.F | ||
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*tropchem | *tropchem | ||
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− | + | *<span style="color:darkgreen">'''Added in 12.1.0'''</span> | |
− | * | + | |
*Replaced local array <tt>SO2s</tt> in wetscav_mod.F | *Replaced local array <tt>SO2s</tt> in wetscav_mod.F | ||
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*tropchem | *tropchem | ||
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− | + | *<span style="color:darkgreen">'''Added in 12.1.0'''</span> | |
− | * | + | |
*Replaced local array <tt>DRY_TOTN</tt> in get_ndep_mod.F | *Replaced local array <tt>DRY_TOTN</tt> in get_ndep_mod.F | ||
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*tropchem | *tropchem | ||
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− | + | *<span style="color:darkgreen">'''Added in 12.1.0'''</span> | |
− | * | + | |
*Replaced local array <tt>WET_TOTN</tt> in get_ndep_mod.F | *Replaced local array <tt>WET_TOTN</tt> in get_ndep_mod.F | ||
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*tropchem | *tropchem | ||
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− | + | *<span style="color:darkgreen">'''Added in 12.1.0'''</span> | |
− | * | + | |
*Replaced local array <tt>HSAVE_KPP</tt> in flexchem_mod.F90 | *Replaced local array <tt>HSAVE_KPP</tt> in flexchem_mod.F90 | ||
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*benchmark | *benchmark | ||
*standard | *standard | ||
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*Moved to Restart collection from HEMCO restart file in [[GEOS-Chem 12#12.1.0|12.1.0]] | *Moved to Restart collection from HEMCO restart file in [[GEOS-Chem 12#12.1.0|12.1.0]] | ||
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*all simulations | *all simulations | ||
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− | + | *<span style="color:darkgreen">'''Added in 12.1.0'''</span> | |
− | * | + | |
|-valign="top" | |-valign="top" | ||
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*all simulations | *all simulations | ||
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− | + | *<span style="color:darkgreen">'''Added in 12.1.0'''</span> | |
− | * | + | |
|-valign="top" | |-valign="top" | ||
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*all simulations | *all simulations | ||
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− | + | *<span style="color:darkgreen">'''Added in 12.1.0'''</span> | |
− | * | + | |
|-valign="top" | |-valign="top" | ||
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*all simulations | *all simulations | ||
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− | + | *<span style="color:darkgreen">'''Added in 12.1.0'''</span> | |
− | * | + | |
|-valign="top" | |-valign="top" | ||
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*all simulations | *all simulations | ||
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− | + | *<span style="color:darkgreen">'''Added in 12.1.0'''</span> | |
− | * | + | |
|} | |} | ||
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== The SpeciesConc collection == | == The SpeciesConc collection == | ||
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The '''SpeciesConc''' diagnostic collection contains advected species concentrations. This type of diagnostic output is used in all GEOS-Chem simulations. | The '''SpeciesConc''' diagnostic collection contains advected species concentrations. This type of diagnostic output is used in all GEOS-Chem simulations. | ||
− | Here is a sample definition section for the SpeciesConc collection. 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 SpeciesConc 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. | ||
SpeciesConc.template: '%y4%m2%d2_%h2%n2z.nc4', | SpeciesConc.template: '%y4%m2%d2_%h2%n2z.nc4', | ||
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!width="100px"|Wildcards | !width="100px"|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.]] | ||
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|-valign="top" | |-valign="top" | ||
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*all simulations | *all simulations | ||
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*[[List of diagnostics archived to bpch format|ND45]] | *[[List of diagnostics archived to bpch format|ND45]] | ||
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*[[List of diagnostics archived to bpch format|ND50]] | *[[List of diagnostics archived to bpch format|ND50]] | ||
*[[List of diagnostics archived to bpch format|ND51]] | *[[List of diagnostics archived to bpch format|ND51]] | ||
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− | --[[ | + | ---- |
+ | '''''[[History collections for methane|Previous]] | [[History collections for TransportTracers|Next]] | [[Guide to GEOS-Chem History diagnostics]]''''' |
Latest revision as of 16:46, 22 April 2021
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
- History collections for CO2
- Replicating the behavior of the prior timeseries diagnostics
- Adding new History diagnostics
Contents
The BoundaryConditions collection
NOTE: If you are not setting up for a nested-grid simulation, then you can disable this collection.
The BoundaryConditions diagnostic collection contains advected species concentrations (archived from a global simulation) that will be used by nested-grid simulations as transport boundary conditions. Like SpeciesConc, it archives data with units of mol/mol dry air.
Here is a sample definition section for the SpeciesConc 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.
BoundaryConditions.template: '%y4%m2%d2_%h2%n2z.nc4', BoundaryConditions.format: 'CFIO', BoundaryConditions.frequency: 00000000 030000 BoundaryConditions.duration: 00000100 000000 BoundaryConditions.mode: 'instantaneous' BoundaryConditions.fields: 'SpeciesBC_?ADV? ', 'GIGCchem', ::
This table describes the diagnostic quantities belonging to the BoundaryConditions collection:
Diagnostic name | Description | Units | Wildcards | Simulations | Notes |
---|---|---|---|---|---|
SpeciesBC_<spcname> | Advected species concentrations used as boundary conditions for nested-grid simulations | mol/mol dry air |
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The ConcAboveSfc collection
The ConcAboveSfc collection is listed on our History collections for dry deposition page.
The ConcAfterChem collection
The ConcAfterChem collection is listed on our History collections for chemistry and photolysis page.
--Bob Yantosca (talk) 14:21, 19 July 2019 (UTC)
The Restart collection
The Restart diagnostic collection contains fields for saving out to the GEOS-Chem restart file. This type of diagnostic output is used in all GEOS-Chem simulations; therefore, we have listed Restart first in the HISTORY.rc files that ship with each GEOS-Chem run directory.
Here is a sample definition section for the Restart 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: The restart file will be created in the GEOS_Chem run directory, not in the OutputDir sub-folder.
Restart.filename: './GEOSChem.Restart.%y4%m2%d2_%h2%n2z.nc4', Restart.format: 'CFIO', Restart.frequency: 'End', Restart.duration: 'End', Restart.mode: 'instantaneous' Restart.fields: 'SpeciesRst_?ALL? ', 'GIGCchem', 'Chem_H2O2AfterChem ', 'GIGCchem', 'Chem_SO2AfterChem ', 'GIGCchem', 'Chem_DryDepNitrogen ', 'GIGCchem', 'Chem_WetDepNitrogen ', 'GIGCchem', 'Chem_KPPHvalue ', 'GIGCchem', 'Met_DELPDRY ', 'GIGCchem', 'Met_PS1WET ', 'GIGCchem', 'Met_PS1DRY ', 'GIGCchem', 'Met_SPHU1 ', 'GIGCchem', 'Met_TMPU1 ', 'GIGCchem', ::
This table describes the diagnostic quantities belonging to the SpeciesConc collection:
Diagnostic name | Description | Units | Wildcards | Simulations | Notes |
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SpeciesRst_<spcname> | Instantaneous chemical species concentrations for use in starting subsequent GEOS-Chem simulations | mol/mol dry air |
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Chm_H2O2AfterChem | Concentration of H2O2 after sulfate chemistry | v/v |
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Chm_SO2AfterChem | Concentration of SO2 after sulfate chemistry | v/v |
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Chm_DryDepNitrogen | Dry deposited nitrogen | molec/cm2/s |
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Chm_WetDepNitrogen | Wet deposited nitrogen | molec/cm2/s |
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Chm_KPPHvalue | H-value for Rosenbrock solver | unitless |
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Chm_StatePSC | Polar stratospheric cloud type | count |
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Met_DELPDRY | Delta-pressure across grid box (dry air) | hPa |
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Met_PS1WET | Wet surface pressure at dt start | hPa |
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Met_PS1DRY | Dry surface pressure at dt start | hPa |
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Met_SPHU1 | Instantaneous specific humidity at time=T | g kg-1 |
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Met_TMPU1 | Instantaneous temperature at time=T | K |
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The SpeciesConc collection
The SpeciesConc diagnostic collection contains advected species concentrations. This type of diagnostic output is used in all GEOS-Chem simulations.
Here is a sample definition section for the SpeciesConc 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.
SpeciesConc.template: '%y4%m2%d2_%h2%n2z.nc4', SpeciesConc.format: 'CFIO', SpeciesConc.frequency: 00000100 000000 SpeciesConc.duration: 00000100 000000 SpeciesConc.mode: 'time-averaged' SpeciesConc.fields: 'SpeciesConc_?ADV? ', 'GIGCchem', ::
This table describes the diagnostic quantities belonging to the SpeciesConc collection:
Diagnostic name | Description | Units | Wildcards | Simulations | Notes | Bpch equiv. |
---|---|---|---|---|---|---|
SpeciesConc_<spcname> | Chemical species concentrations | mol/mol dry air |
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