You can specify which GEOS-Chem Classic diagnostic outputs you would like to archive with the :file:`HISTORY.rc` configuration file.
A simplified :file:`HISTORY.rc` file is shown below.
#============================================================================
# EXPID allows you to specify the beginning of the file path corresponding
# to each diagnostic collection. For example:
#
# EXPID: ./GEOSChem
# Will create netCDF files whose names begin "GEOSChem",
# in this run directory.
#
# EXPID: ./OutputDir/GEOSChem
# Will create netCDF files whose names begin with "GEOSChem"
# in the OutputDir sub-folder of this run directory.
#
#============================================================================
EXPID: ./OutputDir/GEOSChem
#==============================================================================
# %%%%% COLLECTION NAME DECLARATIONS %%%%%
#
# To disable a collection, place a "#" character in front of its name
#
# NOTE: These are the "default" collections for GEOS-Chem.
# But you can create your own custom diagnostic collections as well.
#==============================================================================
COLLECTIONS: 'SpeciesConc' ,
'SpeciesConcSubset' ,
'ConcAfterChem' ,
::
#==============================================================================
# %%%%% THE SpeciesConc COLLECTION %%%%%
#
# GEOS-Chem species concentrations (default = advected species)
#
# Available for all simulations
#==============================================================================
SpeciesConc.template: '%y4%m2%d2_%h2%n2z.nc4' ,
SpeciesConc.frequency: 00000000 060000 ,
SpeciesConc.duration: 00000001 000000 ,
SpeciesConc mode: 'instantaneous' ,
SpeciesConc.fields: 'SpeciesConcVV_?ADV?'
'SpeciesConcMND_?ADV?'
::
#==============================================================================
# %%%%% THE SpeciesConcSubset COLLECTION %%%%%
#
# Same as the SpeciesConc collection, but will subset data in the horizontal
# and vertical dimensions so that the netCDF diagnostic files will cover
# a smaller region of the globe. This can save disk space and memory.
#
# NOTE: This capability will be available in GEOS-Chem "Classic" 12.5.0
# and later versions.
#
# Available for all simulations
#==============================================================================
SpeciesConcSubset.template: '%y4%m2%d2_%h2%n2z.nc4',
SpeciesConcSubset.frequency: 060000,
SpeciesConcSubset.duration: 00000001 000000,
SpeciesConcSubset.mode: 'instantaneous',
SpeciesConcSubset.LON_RANGE: -40.0 60.0,
SpeciesConcSubset.LAT_RANGE: -10.0 50.0,
SpeciesConcSubset.levels: 1 2 3 4 5,
SpeciesConcSubset.fields: 'SpeciesConcVV_?ADV?',
'SpeciesConcMND_?ADV?',
::
#==============================================================================
# %%%%% THE ConcAfterChem COLLECTION %%%%%
#
# Concentrations of OH, HO2, O1D, O3P immediately after exiting the KPP solver
# or OH after the CH4 specialty-simulation chemistry routine.
#
# OH: Available for all full-chemistry simulations and CH4 specialty sim
# HO2: Available for all full-chemistry simulations
# O1D, O3P: Availalbe for full-chemistry simulations using UCX mechanism
#==============================================================================
ConcAfterChem.template: '%y4%m2%d2_%h2%n2z.nc4',
ConcAfterChem.frequency: 00000100 000000,
ConcAfterChem.duration: 00000100 000000,
ConcAfterChem.mode: 'time-averaged',
ConcAfterChem.fields: 'OHconcAfterChem',
'HO2concAfterChem',
'O1DconcAfterChem',
'O3PconcAfterChem',
::
In this :file:`HISTORY.rc` file, we are requesting three collections
(SpeciesConc, SpeciesConcSubset, and
ConcAfterChem). Each collection represents a set of netCDF
files that will contain the same diagnostic fields.
.. option:: COLLECTIONS:
List of **diagnostic collections** in the :file:`HISTORY.rc` file.
To turn off a collection, place a comment character (:literal:`#`)
before its name. For example:
.. code-block:: kconfig
COLLECTIONS: #'SpeciesConc',
'SpeciesConcSubset',
'ConcAfterChem',
turns off the :literal:`SpeciesConc` collection.
.. option:: <collection-name>.template
Determines the date and time format of the netCDF file names that
will be created for diagnostic collection :literal:`<collection-name>`.
The string :literal:`%y4%m2%d2_%h2%n2z.nc4` will print
:literal:`YYYYMMDD_hhmmz.nc4` to the end of each netCDF filename,
where:
- :literal:`YYYYMMDD` is the date in year/month/day format
- :literal:`hhmm` is the time in hour:minutes format.
- :literal:`z` denotes "Zulu", which is an abbreviation for UTC
time.
- :literal:`.nc4` denotes that the data file is in the netCDF-4
format.
.. option:: <collection-name>.frequency
Determines how often the diagnostic fields belonging to collection
:literal:`<collection-name>` collection will be written to a netCDF
file. For example:
- :literal:`010000` schedules diagnostic archival each hour.
- :literal:`00000100 000000` schedules diagnostic output each month.
- :literal:`00000001 000000` (or :literal:`240000`) schedules
diagnostic output each day.
- ... etc. ...
.. option:: <collection-name>.duration
Determines how often a new netCDF file will be created for collection
:literal:`<collection-name>`. For example:
- :literal:`010000` creates a new netCDF each hour.
- :literal:`00000100 000000` creates a new netCDF file each month.
month.
- :literal:`00000001 000000` (or :literal:`240000`) creates a new
netCDF file each day.
.. option:: <collection-name>.mode
Determines the averaging method for collection
:literal:`<collection-name>`. Accepted values are:
.. option:: instantaneous
Data will be archived as instantaneous "snapshots" at the
frequency specified in :option:`<collection-name>.frequency`.
.. option:: time-averaged
Data will be time-averaged with the frequency specified in
:option:`<collection-name>.frequency`.
.. option:: <collection-name>.fields
A list of the diagnostic fields that will be included in collection
:literal:`<collection-name>`.
A single underscore :literal:`_` denotes a **species-based diagnostic
field**. To request output for a single species, list the species
name immediately after the underscore, such as:
.. code-block:: kconfig
SpeciesConc.fields: 'SpeciesConcVV_NO'
'SpeciesConcVV_O3'
'SpeciesConcVV_CO'
... etc ...
::
You may also use a **wildcard** such as :literal:`?ADV?`, which requests
all advected species:
.. code-block:: kconfig
SpeciesConc.fields: 'SpeciesConcVV_?ADV?'
... etc ...
::
The complete wildcard list is shown below. Wildcards are case-insensitive.
- :literal:`?ADV?`: Only the advected species
- :literal:`?AER?`: Only the aerosol species
- :literal:`?ALL?`: All GEOS-Chem species
- :literal:`?DRYALT?`: Only the dry-deposited species whose
concentrations we wish to archive at a given altitude above the
surface. (In practice these are only O3 and HNO3.)
- :literal:`?DRY?`: Only the dry-deposited species
- :literal:`?FIX?`: Only the inactive (aka "fixed") species in the
KPP chemical mechanism
- :literal:`?GAS?`: Only the gas-phase species
- :literal:`?HYG?`: Only aerosols that undergo hygroscopic growth
(sulfate, BC, OC, SALA, SALC)
- :literal:`?LOS?`: Only chemical loss species or families
- :literal:`?KPP?`: Only the KPP species
- :literal:`?PHO?`: Only the photolyzed species
- :literal:`?VAR?`: Only the active (aka "variable") species in the
KPP chemical mechanism
- :literal:`?WET?`: Only the wet-deposited species
- :literal:`?PRD?`: Only chemical production species or families
- :literal:`?DUSTBIN?`: Only the dust bin number
- :literal:`?PHOTOBIN?` Number of a given wavelength bin for photolysis
To include fields from the :code:`State_Chm` object in collection
:literal:`<collection-name>`, precede the field name with
:literal:`Chem_`:
.. code-block:: kconfig
'Chem_phCloud',
... etc ...
To include fields from the :code:`State_Met` object in collection
:literal:`<collection-name>`, precede the field name with
:literal:`Met_`:
.. code-block:: kconfig
'Met_T'.
'Met_PS',
'Met_SPHU',
... etc ...
Both :literal:`Chem_` and :literal:`Met_` specifiers are case-insensitive.
.. option:: <collection-name>.LON_RANGE **Optional**. Restrict data fields of collection :literal:`<collection-name>` to the range :literal:`min_lon, max_lon`.
.. option:: <collection-name>.LAT_RANGE **Optional**. Restrict data fields of collection :literal:`<collection-name>` to the range :literal:`min_lat, max_lat`.
.. option:: <collection-name>.levels **Optional**. Restrict data fields of collection :literal:`<collection-name>` to the specified levels (e.g., :literal:`1,2,3,4,5` or :literal:`1-5`).
.. option:: :: Signifies the end of the definition section for collection :literal:`<collection-name>`.