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.. _histguide: ########################################### Archive output with the History diagnostics ########################################### ============ Introduction ============ GEOS-Chem Classic and GCHP allow you to save various diagnostic fields to netCDF files via the **History** component. In the following sections you will learn how to schedule diagnostics for output using History. .. note:: HEMCO has its own diagnostic archiving capability. Please see the `HEMCO diagnostics `_ chapter of `The HEMCO User's Guide `_ more information. Note that HEMCO diagnostics are configured from configuration file :file:`HEMCO_Diagn.rc` for both GCHP and GEOS-Chem Classic but diagnostics are also specified in :file:`HISTORY.rc` for GCHP only. .. _histguide-configfile: The HISTORY.rc configuration file --------------------------------- You can request GEOS-Chem diagnostics by editing the :file:`HISTORY.rc` configuration file. This file lists the groups of diagnostic outputs (called **collections**), and the parameters for each collection (frequency of archival, mode of archiving, fields per collection, etc.). GEOS-Chem Classic will write netCDF files for each collection at the output intervals that you specify in :file:`HISTORY.rc`. If using GCHP this is done by the MAPL History component also using configuration file :file:`HISTORY.rc`. .. _histguide-configfile-sample: Sample HISTORY.rc file ~~~~~~~~~~~~~~~~~~~~~~~ The following is a stripped-down :file:`HISTORY.rc` file example for illustration purposes. The :file:`HISTORY.rc` file that you will find in your GEOS-Chem run directory will contain more collections than what is shown below. This example is for GEOS-Chem Classic. .. code-block:: kconfig #============================================================================ # 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. #============================================================================== 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.format: 'CFIO', SpeciesConc.mode: 'instantaneous', SpeciesConc.fields: 'SpeciesConcVV_?ADV?', 'SpeciesConcMND_?ALL?', :: #============================================================================== # %%%%% 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: 00000000 060000 SpeciesConcSubset.duration: 00000001 000000 SpeciesConcSubset.format: 'CFIO', 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?', :: #============================================================================== # %%%%% 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.format: 'CFIO', 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, or types of netCDF file output. The table below explains in more detail parameters shown in the :file:`HISTORY.rc` file above. .. _histguide-configfile-sample-expid: EXPID ^^^^^ Thi :literal:`EXPID` parameter controls the filename prefix, which is set to :file:`./OutputDir/GEOSChem` by default. This means that diagnostic files will be written to the :file:`./OutputDir` directory of the GEOS-Chem run directory, and will start with the prefix :file:`GEOSChem`. .. note:: Restart files are placed in the :file:`./Restarts` subdirectory of the run directory instead of :file:`./OutputDir`, which only contains diagnostic files. .. _histguide-configfile-sample-coll: COLLECTIONS ^^^^^^^^^^^ The :literal:`COLLECTIONS:` tag specifies all of the diagnostic **collections** that you wish to activate during a GEOS-Chem simulation. Each collection represents a group of diagnostic quantities that will be written to disk in netCDF file format. The collection name will be automatically added to the netCDF file name along with the date/or time. Each GEOS-Chem run directory will ship with its own customized :file:`HISTORY.rc` configuration file. Only the diagnostic collections pertaining to a particular GEOS-Chem simulation will be included in the corresponding :file:`HISTORY.rc` file. Each collection name must be bracketed by single quotes, and be followed by a comma. To disable an entire diagnostic collection, simply put a :literal:`#` comment character in front of the collection name in the :literal:`COLLECTIONS:` section. GEOS-Chem will expect to find a collection definition section for each of the activated collections listed under the :literal:`COLLECTIONS:` section. In other words, if you have :option:`SpeciesConc` listed under :literal:`COLLECTIONS:`, but there is no further information provided about the :option:`SpeciesConc` collection, then GEOS-Chem will halt with an error message. .. note:: You are not limited to the collections that are pre-defined in the :file:`HISTORY.rc` configuration file. You may create additional diagnostic collections to suit your research purposes. .. _histguide-configfile-sample-sc: SpeciesConc ^^^^^^^^^^^ Name of the first collection in this :file:`HISTORY.rc` file. .. _histguide-configfile-sample-sc-tmpl: SpeciesConc.template ^^^^^^^^^^^^^^^^^^^^ Determines the date and time format for the :ref:`histguide-configfile-sample-sc` collection filename suffix, as described below: - :literal:`%y4%m2%d2_%h2%n2z.nc4` prints :literal:`YYYYMMDD_hhmmz.nc4` to the end of each netCDF filename. - :literal:`YYYYMMDD` is the date in year/month/day format; - :literal:`hhmm` is the time in :literal:`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. .. note:: For example, the complete file path for the :ref:`histguide-configfile-sample-sc` collection at 00:00 UTC on 2020/01/01 will be :file:`./OutputDir/GEOSChem.SpeciesConc.20200101_0000z.nc4`, where: - :ref:`histguide-configfile-sample-expid` specifies the filename prefix (:file:`./OutputDir/GEOSChem`). - :ref:`histguide-configfile-sample-sc-tmpl` specifies the format of the filename suffix (:file:`.20200101_0000z.nc4`). .. _histguide-configfile-sample-sc-freq: SpeciesConc.frequency ^^^^^^^^^^^^^^^^^^^^^ Determines how often the diagnostic quantities belonging to the :ref:`histguide-configfile-sample-sc` collection will be saved to a netCDF file. This can be specified as either :literal:`hhmmss` or :literal:`YYYYMMDD hhmmss`. In the above example, data belonging to the collection will be written to the file every 6 hours. Because :option:`SpeciesConc` is an instantaneous collection, no time-averaging will be performed. SpeciesConc.format ^^^^^^^^^^^^^^^^^^ **For GCHP simulations only.** This tag indicates the I/O library that will be used. SpeciesConc.duration ^^^^^^^^^^^^^^^^^^^^ Determines how often a new :option:`SpeciesConc` netCDF file will be created. Uses the same format as :ref:`histguide-configfile-sample-sc-freq:`. SpeciesConc.mode ^^^^^^^^^^^^^^^^ Determines the averaging method for the :option:`SpeciesConc` collection. Allowable values are: - :literal:`instantaneous`: Archives instantaneous values at the interval specified by :ref:`histguide-configfile-sample-sc-freq:`. - :literal:`time-averaged`: Archives values averaged over the interval specified by :ref:`histguide-configfile-sample-sc-freq:`. SpeciesConc.fields ^^^^^^^^^^^^^^^^^^ Lists the diagnostic quantities to be archived in the :ref:`histguide-configfile-sample-sc` collection. Some diagnostic quantities (e.g. concentrations, fluxes, masses) may also have an extra dimension, which represents species, size bins, reaction numbers, etc. For example, to request the ozone species concentration (in mixing ratio units) you may use the field name :literal:`SpeciesConcVV_O3`. The species name is separated from the quantity name by a single underscore. .. note:: For GCHP, each diagnostic field must be followed by the name of the ESMF gridded component that it is associated with. For arrays in GEOS-Chem objects State_Met, State_Chm, and State_Diag this is :literal:`'GCHPchem',`. A few diagnostics may also be output from the advection component of GCHP which has ESMF gridded component name :literal:`DYNAMICS`. If you are using GEOS-Chem Classic,you may also use a :ref:`wildcard ` to specify a given category of species. In the above example :literal:`SpeciesConcVV_?ADV?` refers to all advected species and :literal:`SpeciesConcVV_?ALL?` refers to all species (both advected and non-advected). .. note:: GCHP does not allow the use of wildcards. Each diagnostic quantity must be listed individually. :literal:`::` separator ^^^^^^^^^^^^^^^^^^^^^^^ Signifies the end of the :ref:`histguide-configfile-sample-sc` definition section. The :literal:`::` may be placed at any column. SpeciesConc.subset ^^^^^^^^^^^^^^^^^^ Name of the second diagnostic collection specified in this sample :file:`HISTORY.rc` configuration file. In this collection we will request output to be restricted to a subset of the horizontal grid. The :literal:`.template`, :literal:`.frequency`, :literal:`.duration`, :literal:`:mode`, and :literal:`.fields` are described for the :ref:`histguide-configfile-sample-sc` collection above, so we will not repeat them here. SpeciesConcSubset.LON_RANGE ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Defines the longitude range (:literal:`min max`) where diagnostic data will be archived. Data outside of this range will be ignored. If this option is omitted, values at all longitudes (:literal:`-180 180`) will be included. SpeciesConcSubset.LAT_RANGE ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Defines the latitude range (:literal:`min max`) where diagnostic data will be archived. Data outside of this range will be ignored. If this option is omitted, values at all latitudes (:literal:`-90 90`) will be included. SpeciesConcSubset.levels ^^^^^^^^^^^^^^^^^^^^^^^^ Specifies the levels that you wish to be included in the diagnostic archiving. If omitted, data at all levels will be included. .. note:: In GEOS-Chem Classic, all levels between the minimum and maximum level specified will be included in the diagnostic archival. This differs from the behavior in GCHP, which archives only the specified levels. ConcAfterChem ^^^^^^^^^^^^^ Name of the third collection specified in this sample :file:`HISTORY.rc` configuration file. The :literal:`.template`, :literal:`.frequency`, :literal:`.duration`, :literal:`:mode`, and :literal:`.fields` are described for the :ref:`histguide-configfile-sample-sc` collection above, so we will not repeat them here. ConcAftercChem.mode In this example, the :literal:`ConcAfterChem.mode` setting indicates that the :literal:`ConcAfterChem` collection will contain ime-averaged data. The averaging interval is set in the :literal:`frequency` field. .. _histguide-wildcards: Wildcards (GEOS-Chem Classic only) ---------------------------------- For GEOS-Chem Classic diagnostic output, you can use the following wildcards with diagnostic quantities that have a species/bin/reaction dimension: .. list-table:: :header-rows: 1 * - Wildcard - Description - Example * - :literal:`?ADV?` - Advected species - :literal:`SpeciesConcVV_?ADV?` * - :literal:`?AER?` - Aerosol species - :literal:`SpeciesConcVV_?AER?` * - :literal:`?ALL?` - All species - :literal:`SpeciesConcVV_?ALL?` * - :literal:`?DRY?` - Dry-deposited species - :literal:`SpeciesConcVV_?DRY?` * - :literal:`?DRYALT?` - Species for the :ref:`histguide-concabovechem` collection - :literal:`SpeciesConcVV_?DRYALT` * - :literal:`?DUSTBIN?` - Dust bin number - :literal:`AODdust550nm_?DUSTBIN?` * - :literal:`?FIX?` - Fixed species in the KPP chemistry mechanism - :literal:`SpeciesConcVV_?FIX?` * - :literal:`?GAS?` - Gas-phase species - :literal:`SpeciesConcVV_?GAS?` * - :literal:`?HYG?` - Aerosol species that undergo hygroscopic growth - (e.g. black carbon) - :literal:`AODhyg550nm_?HYG?` * - :literal:`?KPP?` - All species (fixed variable) in the KPP chemistry mechanism - `SpeciesConcVV_?KPP?` * - :literal:`?LOS?` - Chemical loss species or familes - `SpeciesConcVV_?LOS?` * - :literal:`?PHO?` - Photolyzed species - `SpeciesConcVV_?PHO?` * - :literal:`?PRD?` - Chemical production species or families - :literal:`SpeciesConcVV_?PRD?` * - :literal:`?RRTMG?` - RRTMG-computed fluxes - :literal:`RadAllSkywSurf_?RRTMG?` * - :literal:`?RXN?` - KPP reaction rates - :literal:`RxnRate_?RXN?` * - :literal:`?TOMASBIN?` - TOMAS size bins - :literal:`TomasH2SO4Mass_?TOMASBIN?` * - :literal:`?UVFLX?` - UV flux bins - :literal:`UVFluxDiffuse_?UVFLX?` * - :literal:`?VAR?` - Variable (i.e. active) species in the KPP mechanism - :literal:`SpeciesConcVV_?VAR?` * - :literal:`?WET?` - Wet-deposited species - :literal:`SpeciesConcVV_?WET` .. _histguide-prefixes: Prefixes -------- You may add any field from the :code:`State_Met` and :code:`State_Chm` objects to any diagnostic collection as well. These fields must be prefixed as described below: .. list-table:: :header-rows: 1 * - Wildcard - Description - Example * - :literal:`Chem_` - Request diagnostic output from the :literal:`State_Chm` object - :literal:`Chem_pHCloud` * - :literal:`Met_` - Request diagnostic output from the :literal:`State_Met` object - :literal:`Met_SPHU` .. _histguide-filename: File naming convention ---------------------- As mentioned above, :option:`SpeciesConc.template`, GEOS-Chem History files adhere to the following naming convention: .. code-block:: none EXPID.collection-name.collection-template e.g. .. code-block:: none ../OutputDir/GEOSChem.SpeciesConc.20200101_0000z.nc4 The duration tag of each collection in :file:`HISTORY.rc` controls how often a new file will be written to disk, as we saw :ref:`above `: .. code-block:: none SpeciesConc.duration: 00000001 000000 # Write a new file each day SpeciesConcSubset.duration: 00000001 000000 # Write a new file each day ConcAfterChem.duration: 00000100 000000 # Write a new file each month Therefore, based on all of these settings in our example :file:`HISTORY.rc` file, GEOS-Chem will write the following netCDF files to disk in the current run directory: .. code-block:: console GEOSChem.SpeciesConc.20160101_0000z.nc4 GEOSChem.SpeciesConcSubset.20160101_0000z.nc4 GEOSChem.SpeciesConc.20160102_0000z.nc4 GEOSChem.SpeciesConcSubset.20160102_0000z.nc4 GEOSChem.SpeciesConc.20160103_0000z.nc4 GEOSChem.SpeciesConcSubset.20160102_0000z.nc4 GEOSChem.SpeciesConc.20160104_0000z.nc4 GEOSChem.SpeciesConcSubset.20160104_0000z.nc4 ... etc ... GEOSChem.ConcAfterChem.20160101_0000z.nc4 GEOSChem.ConcAfterChem.20160201_0000z.nc4 GEOSChem.ConcAfterChem.20160301_0000z.nc4 GEOSChem.ConcAfterChem.20160401_0000z.nc4 ... etc ... .. _histgude-vertcoords: Vertical coordinates in netCDF files ------------------------------------ All netCDF files produced by GEOS-Chem (i.e. diagnostic files and restart files) adhere to the :ref:`the COARDS netCDF convention `. for the lon, lat, and time dimensions. For the vertical dimension, we have chosen to use the following coordinate variables to include in GEOS-Chem Classic output files, emulating the file format of the NCAR Community Earth System Model (CESM): .. code-block:: console variables: double lev(lev) ; lev:long_name = "hybrid level at midpoints (1000*(A+B))" ; lev:units = "level" ; lev:positive = "down" ;\ lev:standard_name = "atmosphere_hybrid_sigma_pressure_coordinate" ; lev:formula_terms = "a: hyam b: hybm p0: P0 ps: PS" ; double hyam(lev) ; hyam:long_name = "hybrid A coefficient at layer midpoints" ; double hybm(lev) ; hybm:long_name = "hybrid B coefficient at layer midpoints" ; double ilev(ilev) ; ilev:long_name = "hybrid level at interfaces (1000*(A+B))" ; ilev:units = "level" ; ilev:positive = "down" ; ilev:standard_name = "atmosphere_hybrid_sigma_pressure_coordinate" ; ilev:formula_terms = "a: hyai b: hybi p0: P0 ps: PS" ; double hyai(ilev) ; hyai:long_name = "hybrid A coefficient at layer interfaces" ; double hybi(ilev) ; hybi:long_name = "hybrid B coefficient at layer interfaces" ; double P0 ; P0:long_name = "reference pressure" ; The lev variable is used for data that is placed on the midpoints between vertical levels. This is an "approximate" eta coordinate, which is close to 1 at the surface and close to zero at the atmosphere top. .. code-block:: console lev = 0.99250002413, 0.97749990013, 0.962499776, 0.947499955, 0.93250006, 0.91749991, 0.90249991, 0.88749996, 0.87249996, 0.85750006, 0.842500125, 0.82750016, 0.8100002, 0.78750002, 0.762499965, 0.737500105, 0.7125001, 0.6875001, 0.65625015, 0.6187502, 0.58125015, 0.5437501, 0.5062501, 0.4687501, 0.4312501, 0.3937501, 0.3562501, 0.31279158, 0.26647905, 0.2265135325, 0.192541016587707, 0.163661504087706, 0.139115, 0.11825, 0.10051436, 0.085439015, 0.07255786, 0.06149566, 0.05201591, 0.04390966, 0.03699271, 0.03108891, 0.02604911, 0.021761005, 0.01812435, 0.01505025, 0.01246015, 0.010284921, 0.008456392, 0.0069183215, 0.005631801, 0.004561686, 0.003676501, 0.002948321, 0.0023525905, 0.00186788, 0.00147565, 0.001159975, 0.00090728705, 0.0007059566, 0.0005462926, 0.0004204236, 0.0003217836, 0.00024493755, 0.000185422, 0.000139599, 0.00010452401, 7.7672515e-05, 5.679251e-05, 4.0142505e-05, 2.635e-05, 1.5e-05 ; The lev variable may be used for quick plotting. To compute the actual pressure at the midpoint of the grid box (I,J,L), you will need to supply your own 2-D surface pressure field (e.g. saved from another diagnostic file): .. code-block:: console Pmid = ( hyam(L) * PS(I,J) ) + hybm(L) The ilev variable is used for data that is placed on vertical level edges or "interfaces" (hence the "i" in ilev). This is also an "approximate" eta coordinate. .. code-block:: console ilev = 1, 0.98500004826, 0.969999752, 0.9549998, 0.94000011, 0.92500001, 0.90999981, 0.89500001, 0.87999991, 0.86500001, 0.85000011, 0.83500014, 0.82000018, 0.80000022, 0.77499982, 0.75000011, 0.7250001, 0.7000001, 0.6750001, 0.6375002, 0.6000002, 0.5625001, 0.5250001, 0.4875001, 0.4500001, 0.4125001, 0.3750001, 0.3375001, 0.28808306, 0.24487504, 0.208152025, 0.176930008175413, 0.150393, 0.127837, 0.108663, 0.09236572, 0.07851231, 0.06660341, 0.05638791, 0.04764391, 0.04017541, 0.03381001, 0.02836781, 0.02373041, 0.0197916, 0.0164571, 0.0136434, 0.0112769, 0.009292942, 0.007619842, 0.006216801, 0.005046801, 0.004076571, 0.003276431, 0.002620211, 0.00208497, 0.00165079, 0.00130051, 0.00101944, 0.0007951341, 0.0006167791, 0.0004758061, 0.0003650411, 0.0002785261, 0.000211349, 0.000159495, 0.000119703, 8.934502e-05, 6.600001e-05, 4.758501e-05, 3.27e-05, 2e-05, 1e-05 ; To compute the actual pressure at the bottom and top edges of the grid box (I,J,L), you will need to supply your own 2-D surface pressure field (e.g. saved from another diagnostic file): .. code-block:: console Pbot = ( hyai(L ) * PS(I,J) ) + hybi(L ) Ptop = ( hyai(L+1) * PS(I,J) ) + hybi(L+1) GCHP history files contain simply the lev coordinate which is the level index of the model. Level 1 corresponds to surface for all diagnostics retrieved from GEOS-Chem arrays State_Met, State_Diag, and State_Chm. These include all diagnostics that have prefix :literal:`Met_` or :literal:`Chm_` as well as all other :literal:`GCHPchem` diagnostics that do not begin with :literal:`Emis`. Diagnostics that begin with :literal:`Emis` or that have gridded component name other than :literal:`GCHPchem` have Level 1 correspond to top-of-atmosphere. .. _histguide-collections: ====================== Diagnostic collections ====================== The diagnostic collections described in the sections below are used by default in GEOS-Chem simulations. You can create your own customized collections by modifying the :file:`HISTORY.rc` file. The only restriction is that you cannot mix data that is placed on grid box layer edges in the same collection as data placed on grid box layer centers. This violates the netCDF convention that all data variables have to be defined with the same vertical dimension. .. note:: For diagnostic quantities that have a species/bin/reaction dimension, we will use the abbreviation :literal:`` to indicate a species/bin/reaction name or wildcard. For example, :literal:`SpeciesConcVV_` means that the diagnostic quantity can be a single species (:literal:`SpeciesConcVV_O3`) or a wildcarded subset of species (:literal:`SpeciesConcVV_?ADV?`). .. _histguide-advfluxvert: AdvFluxVert ----------- The **AdvFluxVert** collection contains diagnostics for vertical transport in GEOS-Chem Classic advection. In practice, this collection is only used to obtain the vertical flux of O3 from GEOS-Chem Classic fullchem benchmark simulations. Most GEOS-Chem users will not need to activate this collection. **Sample definition section for HISTORY.rc** .. code-block:: kconfig AdvFluxVert.template: '%y4%m2%d2_%h2%n2z.nc4', AdvFluxVert.frequency: 00000100 000000 AdvFluxVert.duration: 00000100 000000 AdvFluxVert.mode: 'time-averaged' AdvFluxVert.fields: 'AdvFluxVert_O3', :: **List of diagnostic fields in the AdvFluxVert collection** +------------------------------+---------------------------+-------+-----------+ | Diagnostic field | Description | Units | Wildcards | +==============================+===========================+=======+===========+ | AdvFluxVert_ | Vertical flux of species | kg/s | ?ADV? | | | in advection | | | +------------------------------+---------------------------+-------+-----------+ .. _histguide-aerosolmass: AerosolMass ----------- The **AerosolMass** collection contains diagnostics for aerosol mass and particulate matter from full-chemistry simulations. **Sample definition section for HISTORY.rc** .. code-block:: kconfig AerosolMass.template: '%y4%m2%d2_%h2%n2z.nc4', AerosolMass.frequency: 00000100 000000 AerosolMass.duration: 00000100 000000 AerosolMass.mode: 'time-averaged' AerosolMass.fields: 'AerMassASOA ', 'AerMassBC ', 'AerMassINDIOL ', 'AerMassISN1OA ', 'AerMassISOA ', 'AerMassLVOCOA ', 'AerMassNH4 ', 'AerMassNIT ', 'AerMassOPOA ', 'AerMassPOA ', 'AerMassSAL ', 'AerMassSO4 ', 'AerMassSOAGX ', 'AerMassSOAIE ', 'AerMassSOAME ', 'AerMassSOAMG ', 'AerMassTSOA ', 'BetaNO ', 'PM25 ', 'TotalBiogenicOA', 'TotalOA ', 'TotalOC ', :: **List of diagnostic fields in the AerosolMass collection** +-----------------------+-------------------------------+--------------------+ | Diagnostic field | Description | Units | +=======================+===============================+====================+ | AerMassASOA\ [#B]_ | Aerosol products of light | :math:`{\mu}g/m^3` | | | aromatics + IVOC oxidation | | +-----------------------+-------------------------------+--------------------+ | AerMassBC | Aerosol products of light | :math:`{\mu}g/m^3` | | | aromatics + IVOC oxidation | | +-----------------------+-------------------------------+--------------------+ | AerMassINDIOL\ [#B]_ | Generic aerosol-phase | :math:`{\mu}g/m^3` | | | organonitrate hydrolysis | | | | product | | +-----------------------+-------------------------------+--------------------+ | AerMassISN10A\ [#B]_ | Aerosol phase 2nd generation | :math:`{\mu}g/m^3` | | | hydroxynitrates formed from | | | | ISOP + NO3 rxn pathway | | +-----------------------+-------------------------------+--------------------+ | AerMassISOA\ [#B]_ | Aerosol products of isoprene | :math:`{\mu}g/m^3` | | | oxidation | | +-----------------------+-------------------------------+--------------------+ | AerMassLVOCOA\ [#B]_ | Aerosol-phase low-volatility | :math:`{\mu}g/m^3` | | | non-IEPOX product of ISOPOOH | | | | (RIP) oxidation | | +-----------------------+-------------------------------+--------------------+ | AerMassNH4 | Ammonium | :math:`{\mu}g/m^3` | +-----------------------+-------------------------------+--------------------+ | AerMassNIT | Inorganic nitrate aerosol | :math:`{\mu}g/m^3` | +-----------------------+-------------------------------+--------------------+ | AerMassPOA\ [#B]_ | Aerosols from SVOCs | :math:`{\mu}g/m^3` | +-----------------------+-------------------------------+--------------------+ | AerMassOPOA\ [#B]_ | Aerosols products of POG | :math:`{\mu}g/m^3` | | | oxidation | | +-----------------------+-------------------------------+--------------------+ | AerMassSAL | Sea salt aerosol (SALA+SALC) | :math:`{\mu}g/m^3` | +-----------------------+-------------------------------+--------------------+ | AerMassSO4 | Sulfate | :math:`{\mu}g/m^3` | +-----------------------+-------------------------------+--------------------+ | AerMassSOAGX\ [#B]_ | Aerosol phase glyoxal | :math:`{\mu}g/m^3` | +-----------------------+-------------------------------+--------------------+ | AerMassSOAIE\ [#B]_ | Aerosol phase IEPOX | :math:`{\mu}g/m^3` | +-----------------------+-------------------------------+--------------------+ | AerMassSOAME\ [#B]_ | Aerosol phase IMAE | :math:`{\mu}g/m^3` | +-----------------------+-------------------------------+--------------------+ | AerMassSOAMG\ [#B]_ | Aerosol phase methylglyoxal | :math:`{\mu}g/m^3` | +-----------------------+-------------------------------+--------------------+ | AerMassTSOA\ [#B]_ | Aerosol products of terpene | :math:`{\mu}g/m^3` | | | oxidation | | +-----------------------+-------------------------------+--------------------+ | BetaNO\ [#B]_ | NO branching ratio | :math:`{\mu}g/m^3` | +-----------------------+-------------------------------+--------------------+ | PM25 | Particulate matter (d < 2.5 | :math:`{\mu}g/m^3` | | | :math:{\mu}m`) | | +-----------------------+-------------------------------+--------------------+ | TotalBiogenicOA\ | Sum of all organic aerosol | :math:`{\mu}g/m^3` | | [#C]_ | | | +-----------------------+-------------------------------+--------------------+ | TotalOA\ [#B]_ | Sum of all organic aerosol | :math:`{\mu}g/m^3` | +-----------------------+-------------------------------+--------------------+ | TotalOC | Sum of all organic carbon | :math:`{\mu}g/m^3` | +-----------------------+-------------------------------+--------------------+ .. rubric:: Notes for the AerosolMass collection .. [#B] Only defined for fullchem simulations with complex SOA species. .. [#C] Defined for aerosol-only simulations or fullchem simulations. .. _histguide-aerosols: Aerosols -------- The **Aerosols** collection contains diagnostics for aerosol optical depth and related quantities from full-chemistry simulations. .. note:: Some diagnostic fields in the Aerosols collection may be computed at up to 3 wavelengths (:literal:`WL1`, :literal:`WL2`, :literal:`WL3`) as specified in this menu of the :file:`geoschem_config.yml` file: .. code-block:: yaml rrtmg_rad_transfer_model: ... etc ... aod_wavelengths_in_nm: - 550 For GEOS-Chem simulations that do not use the RRTMG radiative transfer model, you may specify only one wavelength :literal:`WL1`, which is set to a default value of 550 nm. For GEOS-Chem simulations using RRTMG, you may specify up to 2 more additional wavelengths (:literal:`WL2` and :literal:`WL3`). GEOS-Chem will replace the tokens :literal:`WL1`, :literal:`WL2`, :literal:`WL3` in diagnostic field names with the corresponding wavelength. For example, these diagnostic fields: .. code-block:: AODHygWL1_BCPI AODDustWL1_DST1 AODStratLiquidAerWL1 AODPolarStratCloudWL1 AODSOAfromAqIsopreneWL1 AODStratLiquidAerWL1 AODPolarStratCloudWL1 will be saved to the :file:`GEOSChem.Aerosols.YYYYMMDD_hhmmz.nc4` file(s) under these names: .. code-block:: AODHyg550nm_BCPI AODDust550nm_DST1 AODStratLiquidAer550nm AODPolarStratCloud550nm AODSOAfromAqIsoprene550nm AODStratLiquidAer550nm AODPolarStratCloud550nm **Sample definition section for HISTORY.rc** .. code-block:: kconfig Aerosols.template: '%y4%m2%d2_%h2%n2z.nc4', Aerosols.frequency: 00000100 000000 Aerosols.duration: 00000100 000000 Aerosols.mode: 'time-averaged' Aerosols.fields: 'AODDust ', 'AODDustWL1_?DUSTBIN? ', 'AODHygWL1_?HYG? ', 'AODSOAfromAqIsopreneWL1 ', 'AODStratLiquidAerWL1 ', 'AODPolarStratCloudWL1 ', 'AerHygroscopicGrowth_?HYG? ', 'AerNumDensityStratLiquid ', 'AerNumDensityStratParticulate', 'AerAqueousVolume ', 'AerSurfAreaDust ', 'AerSurfAreaHyg_?HYG? ', 'AerSurfAreaStratLiquid ', 'AerSurfAreaPolarStratCloud ', 'Chem_AeroAreaMDUST1 ', 'Chem_AeroAreaMDUST2 ', 'Chem_AeroAreaMDUST3 ', 'Chem_AeroAreaMDUST4 ', 'Chem_AeroAreaMDUST5 ', 'Chem_AeroAreaMDUST6 ', 'Chem_AeroAreaMDUST7 ', 'Chem_AeroAreaSULF ', 'Chem_AeroAreaBC ', 'Chem_AeroAreaOC ', 'Chem_AeroAreaSSA ', 'Chem_AeroAreaSSC ', 'Chem_AeroAreaBGSULF ', 'Chem_AeroAreaICEI ', 'Chem_AeroRadiMDUST1 ', 'Chem_AeroRadiMDUST2 ', 'Chem_AeroRadiMDUST3 ', 'Chem_AeroRadiMDUST4 ', 'Chem_AeroRadiMDUST5 ', 'Chem_AeroRadiMDUST6 ', 'Chem_AeroRadiMDUST7 ', 'Chem_AeroRadiSULF ', 'Chem_AeroRadiBC ', 'Chem_AeroRadiOC ', 'Chem_AeroRadiSSA ', 'Chem_AeroRadiSSC ', 'Chem_AeroRadiBGSULF ', 'Chem_AeroRadiICEI ', 'Chem_WetAeroAreaMDUST1 ', 'Chem_WetAeroAreaMDUST2 ', 'Chem_WetAeroAreaMDUST3 ', 'Chem_WetAeroAreaMDUST4 ', 'Chem_WetAeroAreaMDUST5 ', 'Chem_WetAeroAreaMDUST6 ', 'Chem_WetAeroAreaMDUST7 ', 'Chem_WetAeroAreaSULF ', 'Chem_WetAeroAreaBC ', 'Chem_WetAeroAreaOC ', 'Chem_WetAeroAreaSSA ', 'Chem_WetAeroAreaSSC ', 'Chem_WetAeroAreaBGSULF ', 'Chem_WetAeroAreaICEI ', 'Chem_WetAeroRadiMDUST1 ', 'Chem_WetAeroRadiMDUST2 ', 'Chem_WetAeroRadiMDUST3 ', 'Chem_WetAeroRadiMDUST4 ', 'Chem_WetAeroRadiMDUST5 ', 'Chem_WetAeroRadiMDUST6 ', 'Chem_WetAeroRadiMDUST7 ', 'Chem_WetAeroRadiSULF ', 'Chem_WetAeroRadiBC ', 'Chem_WetAeroRadiOC ', 'Chem_WetAeroRadiSSA ', 'Chem_WetAeroRadiSSC ', 'Chem_WetAeroRadiBGSULF ', 'Chem_WetAeroRadiICEI ', 'Chem_StatePSC ', 'Chem_KhetiSLAN2O5H2O ', 'Chem_KhetiSLAN2O5HCl ', 'Chem_KhetiSLAClNO3H2O ', 'Chem_KhetiSLAClNO3HCl ', 'Chem_KhetiSLAClNO3HBr ', 'Chem_KhetiSLABrNO3H2O ', 'Chem_KhetiSLABrNO3HCl ', 'Chem_KhetiSLAHOClHCl ', 'Chem_KhetiSLAHOClHBr ', 'Chem_KhetiSLAHOBrHCl ', 'Chem_KhetiSLAHOBrHBr ', :: **List of diagnostic fields in the Aerosols collection** +----------------------------------+-------------------------+---------+-----------+ | Diagnostic field | Description | Units | Wildcard | +==================================+=========================+=========+===========+ | AODDust\ [#X]_ | Mineral dust optical | 1 | | | | depth @ WL1 | | | +----------------------------------+-------------------------+---------+-----------+ | AODDustWL1\_\ [#X]_ | AOD for each dust bin | 1 | ?DUSTBIN? | | | @ WL1 | | | +----------------------------------+-------------------------+---------+-----------+ | AODHygWL1\_\ [#X]_ | AOD @ WL1 for aerosol | 1 | ?HYG? | | | species | | | +----------------------------------+-------------------------+---------+-----------+ | AODSOAfromAqIsopreneWL1\ [#Y]_ | Optical depth of SOA | 1 | | | | from aqueous isoprene | | | | | @ WL1 | | | +----------------------------------+-------------------------+---------+-----------+ | AODStratLiquidAerWL1 | Stratospheric liquid | 1 | | | | optical depth @ WL1 | | | | | | | | +----------------------------------+-------------------------+---------+-----------+ | AODPolarStratCloudWL1 | Polar stratospheric | 1 | | | | cloud type 1a/2 optical | | | | | depth @ WL1 | | | +----------------------------------+-------------------------+---------+-----------+ | AerHygroscopicGrowth\_\ | Hygroscopic growth | 1 | ?HYG? | | [#X]_ | of aerosol species | | | +----------------------------------+-------------------------+---------+-----------+ | AerNumDensityStratLiquid | Stratospheric liquid | 1/cm3 | | | | aerosol number density | | | +----------------------------------+-------------------------+---------+-----------+ | AerNumDensityStratParticulate | Stratospheric | 1/cm3 | | | | particulate aerosol | | | | | number density | | | +----------------------------------+-------------------------+---------+-----------+ | AerAqueousVolume | Aqueous aerosol volume | cm2/cm3 | | +----------------------------------+-------------------------+---------+-----------+ | AerSurfAreaDust | Surface area of | cm2/cm3 | | | | mineral dust | | | +----------------------------------+-------------------------+---------+-----------+ | AerSurfAreaHyg\_ | Surface area of | cm2/cm3 | ?HYG? | | | aerosol species | | | +----------------------------------+-------------------------+---------+-----------+ | AerSurfAreaStratLiquid | Stratospheric liquid | cm2/cm3 | | | | surface area | | | | | | | | +----------------------------------+-------------------------+---------+-----------+ | AerSurfaceAreaPolarStratCloud | Polar stratospheric | cm2/cm3 | | | | cloud type 1a/2 | | | | | surface area | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroAreaMDUST1\ [#X]_ | Dry aerosol area for | cm2/cm3 | | | | mineral dust | | | | | (0.15 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroAreaMDUST2\ [#X]_ | Dry aerosol area for | cm2/cm3 | | | | mineral dust | | | | | (0.25 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroAreaMDUST3\ [#X]_ | Dry aerosol area for | cm2/cm3 | | | | mineral dust | | | | | (0.4 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroAreaMDUST4\ [#X]_ | Dry aerosol area for | cm2/cm3 | | | | mineral dust | | | | | (0.8 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroAreaMDUST5\ [#X]_ | Dry aerosol area for | cm2/cm3 | | | | mineral dust | | | | | (1.5 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroAreaMDUST6\ [#X]_ | Dry aerosol area for | cm2/cm3 | | | | mineral dust | | | | | (2.5 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroAreaMDUST7\ [#X]_ | Dry aerosol area for | cm2/cm3 | | | | mineral dust | | | | | (4.0 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroAreaSULF\ [#X]_ | Dry aerosol area for | cm2/cm3 | | | | sulfate aerosol | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroAreaBC\ [#X]_ | Dry aerosol area for | cm2/cm3 | | | | black carbon | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroAreaOC\ [#X]_ | Dry aerosol area for | cm2/cm3 | | | | organic carbon | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroAreaSSA\ [#X]_ | Dry aerosol area for | cm2/cm3 | | | | sea salt aerosol, | | | | | accumulation mode | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroAreaSSC\ [#X]_ | Dry aerosol area for | cm2/cm3 | | | | sea salt aerosol, | | | | | coarse mode | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroAreaBGSULF | Dry aerosol area for | cm2/cm3 | | | | background | | | | | stratospheric sulfate | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroAreaICEI | Dry aerosol area for | cm2/cm3 | | | | irregular ice cloud | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroRadiMDUST1\ [#X]_ | Dry aerosol radius for | cm | | | | mineral dust | | | | | (0.15 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroRadiMDUST2\ [#X]_ | Dry aerosol radius for | cm | | | | mineral dust | | | | | (0.25 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroRadiMDUST3\ [#X]_ | Dry aerosol radius for | cm | | | | mineral dust | | | | | (0.4 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroRadiMDUST4\ [#X]_ | Dry aerosol radius for | cm | | | | mineral dust | | | | | (0.8 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroRadiMDUST5\ [#X]_ | Dry aerosol radius for | cm | | | | mineral dust | | | | | (1.5 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroRAdiMDUST6\ [#X]_ | Dry aerosol radius for | cm | | | | mineral dust | | | | | (2.5 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroRadiMDUST7\ [#X]_ | Dry aerosol radius for | cm | | | | mineral dust | | | | | (4.0 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroRadiSULF\ [#X]_ | Dry aerosol radius for | cm | | | | sulfate aerosol | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroRadiBC\ [#X]_ | Dry aerosol radius for | cm | | | | black carbon | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroRadiOC\ [#X]_ | Dry aerosol radius for | cm | | | | organic carbon | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroRadiSSA\ [#X]_ | Dry aerosol radius for | cm | | | | sea salt aerosol, | | | | | accumulation mode | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroRadiSSC\ [#X]_ | Dry aerosol radius for | cm | | | | sea salt aerosol, | | | | | coarse mode | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroRadiBGSULF | Dry aerosol radius for | cm | | | | background | | | | | stratospheric sulfate | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroRadiICEI | Dry aerosol Radius for | cm | | | | irregular ice cloud | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroAreaMDUST1\ [#X]_ | Wet aerosol area for | cm2/cm3 | | | | mineral dust | | | | | (0.15 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroAreaMDUST2\ [#X]_ | Wet aerosol area for | cm2/cm3 | | | | mineral dust | | | | | (0.25 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroAreaMDUST3\ [#X]_ | Wet aerosol area for | cm2/cm3 | | | | mineral dust | | | | | (0.4 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroAreaMDUST4\ [#X]_ | Wet aerosol area for | cm2/cm3 | | | | mineral dust | | | | | (0.8 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroAreaMDUST5\ [#X]_ | Wet aerosol area for | cm2/cm3 | | | | mineral dust | | | | | (1.5 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroAreaMDUST6\ [#X]_ | Wet aerosol area for | cm2/cm3 | | | | mineral dust | | | | | (2.5 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_AeroAreaMDUST7\ [#X]_ | Dry aerosol area for | cm2/cm3 | | | | mineral dust | | | | | (4.0 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroAreaSULF\ [#X]_ | Wet aerosol area for | cm2/cm3 | | | | sulfate aerosol | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroAreaBC\ [#X]_ | Wet aerosol area for | cm2/cm3 | | | | black carbon | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroAreaOC\ [#X]_ | Wet aerosol area for | cm2/cm3 | | | | organic carbon | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroAreaSSA\ [#X]_ | Wet aerosol area for | cm2/cm3 | | | | sea salt aerosol, | | | | | accumulation mode | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroAreaSSC\ [#X]_ | Wet aerosol area for | cm2/cm3 | | | | sea salt aerosol, | | | | | coarse mode | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroAreaBGSULF | Wet aerosol area for | cm2/cm3 | | | | background | | | | | stratospheric sulfate | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroAreaICEI | Wet aerosol area for | cm2/cm3 | | | | irregular ice cloud | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroRadiMDUST1\ [#X]_ | Wet aerosol radius for | cm | | | | mineral dust | | | | | (0.15 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroRadiMDUST2\ [#X]_ | Wet aerosol radius for | cm | | | | mineral dust | | | | | (0.25 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroRadiMDUST3\ [#X]_ | Wet aerosol radius for | cm | | | | mineral dust | | | | | (0.4 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroRadiMDUST4\ [#X]_ | Wet aerosol radius for | cm | | | | mineral dust | | | | | (0.8 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroRadiMDUST5 \ [#X]_ | Wet aerosol radius for | cm | | | | mineral dust | | | | | (1.5 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroRAdiMDUST6\ [#X]_ | Wet aerosol radius for | cm | | | | mineral dust | | | | | (2.5 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroRadiMDUST7\ [#X]_ | Wet aerosol radius for | cm | | | | mineral dust | | | | | (4.0 :math:`{\mu}m`) | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroRadiSULF\ [#X]_ | Wet aerosol radius for | cm | | | | sulfate aerosol | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroRadiBC\ [#X]_ | Wet aerosol radius for | cm | | | | black carbon | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroRadiOC\ [#X]_ | Wet aerosol radius for | cm | | | | organic carbon | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroRadiSSA\ [#X]_ | Wet aerosol radius for | cm | | | | sea salt aerosol, | | | | | accumulation mode | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroRadiSSC\ [#X]_ | Wet aerosol radius for | cm | | | | sea salt aerosol, | | | | | coarse mode | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroRadiBGSULF | Wet aerosol radius for | cm | | | | background | | | | | stratospheric sulfate | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_WetAeroRadiICEI | Wet aerosol Radius for | cm | | | | irregular ice cloud | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_KhetiSLAN2O5H2O | Sticking coefficient | 1 | | | | for N2O5 + H2O rxn | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_KhetiSLAN2O5HCl | Sticking coefficient | 1 | | | | for N2O5 + HCl rxn | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_KhetiSLACLNO3H2O | Sticking coefficient | 1 | | | | for ClNO3 + H2O rxn | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_KhetiSLACLNO3HCL | Sticking coefficient | 1 | | | | for ClNO3 + HCl rxn | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_KhetiSLACLNO3HBR | Sticking coefficient | 1 | | | | for ClNO3 + HBr rxn | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_KhetiSLABRNO3H2O | Sticking coefficient | 1 | | | | for BrNO3 + H2O rxn | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_KhetiSLABRNO3HCL | Sticking coefficient | 1 | | | | for BrNO3 + HCl rxn | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_KhetiSLAHOCLHCL | Sticking coefficient | 1 | | | | for HOCl + HCl rxn | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_KhetiSLAHOCLHBR | Sticking coefficient | 1 | | | | for HOCl + HBr rxn | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_KhetiSLAHOBRHCL | Sticking coefficient | 1 | | | | for HOBr + HCl rxn | | | +----------------------------------+-------------------------+---------+-----------+ | Chem_KhetiSLAHOBRHBR | Sticking coefficient | 1 | | | | for HOBr + HBr rxn | | | +----------------------------------+-------------------------+---------+-----------+ .. rubric:: Notes for the Aerosols colletion .. [#X] Defined for aerosol-only and fullchem simulations. .. [#Y] Only defined for fullchem simulation with complex SOA species. .. _histguide-boundaryconditions: BoundaryConditions ------------------ The **BoundaryConditions** diagnostic collection contains advected species concentrations (archived from a global simulation) that will be used by GEOS-Chen Classic nested-grid simulations as transport boundary conditions. **Sample definition section for HISTORY.rc** .. code-block:: kconfig BoundaryConditions.template: '%y4%m2%d2_%h2%n2z.nc4', BoundaryConditions.frequency: 00000000 030000 BoundaryConditions.duration: 00000100 000000 BoundaryConditions.mode: 'instantaneous' BoundaryConditions.fields: 'SpeciesBC_?ADV?', :: **List of diagnostic fields in the BoundaryConditions collection** +-----------------------+-------------------------+-------------+-----------+ | Diagnostic field | Description | Units | Wildcard | +=======================+=========================+=============+===========+ | SpeciesBC_\ | Advected species | mol/mol dry | ?ADV? | | [#D]_ | concentrations used | air | | | | as boundary conditions | | | | | GEOS-Chem Classic | | | | | nested-grid simulations | | | +-----------------------+-------------------------+-------------+-----------+ .. rubric:: Footnotes .. [#D] This diagnostic is only for use with GEOS-Chem Classic. .. _histguide-budget: Budget ------ The **Budget** diagnostic collection is a 2D diagnostic containing the mass tendencies per grid cell, in kg/s, for each species within a region of the column and across each GEOS-Chem component. The diagnostic is calculated by taking the difference in vertically summed column mass before and after major GEOS-Chem components. There are three pre-defined column regions defined for this diagnostic: troposphere-only, PBL-only, and full column, as well as a user-defined column region. By post-processing this diagnostic you can calculate global mass change or mass change across regions by summing the diagnostic values for the relevant grid cells. You can also retrieve the mass change across a longer chunk of time by multiplying the time-averaged output by the number of seconds in the averaging period. While there are seven major components in GEOS-Chem, there are only six implemented for the budget diagnostics: chemistry, mixing, convection, transport (GEOS-Chem Classic only), wet deposition, and combined emissions and dry deposition. .. attention:: Emissions and dry deposition components are combined together for this diagnostic because of the way they are applied at the same time. Furthermore, if using non-local PBL mixing then the emissions and dry deposition budget diagnostic will not capture all fluxes from these sources and sinks. This is because emissions and dry deposition tendencies below the PBL are applied within mixing instead. When using full mixing, however, mixing and emissions/dry deposition budget diagnostics are fully separated. **Sample definition section for HISTORY.rc** .. code-block:: kconfig Budget.template: '%y4%m2%d2_%h2%n2z.nc4', Budget.frequency: 00000100 000000 Budget.duration: 00000100 000000 Budget.mode: 'time-averaged' Budget.fields: 'BudgetChemistryFull_?ADV? ', 'BudgetChemistryPBL_?ADV? ', 'BudgetChemistryTrop_?ADV? ', 'BudgetEmisDepFull_?ADV? ', 'BudgetEmisDepTrop_?ADV? ', 'BudgetEmisDepPBL_?ADV? ', 'BudgetTransportFull_?ADV? ', 'BudgetTransportTrop_?ADV? ', 'BudgetTransportPBL_?ADV? ', 'BudgetMixingFull_?ADV? ', 'BudgetMixingTrop_?ADV? ', 'BudgetMixingPBL_?ADV? ', 'BudgetConvectionFull_?ADV?', 'BudgetConvectionTrop_?ADV?', 'BudgetConvectionPBL_?ADV? ', 'BudgetWetDepFull_?WET? ', 'BudgetWetDepTrop_?WET? ', 'BudgetWetDepPBL_?WET? ', :: **List of diagnostic fields in the Budget collection** +---------------------------------------+---------------------------------+----------+ | Diagnostic field | Mass tendency (kg/s) across ... | Wildcard | +=======================================+=================================+==========+ | BudgetChemistryFull_ | Chemistry (full atmosphere) | ?ADV? | +---------------------------------------+---------------------------------+----------+ | BudgetChemistryLevs1to35_\ | Chemistry (fixed level range) | ?ADV? | | [#E]_ | | | +---------------------------------------+---------------------------------+----------+ | BudgetChemistryPBL_ | Chemistry (PBL only) | ?ADV? | +---------------------------------------+---------------------------------+----------+ | BudgetChemistryTrop_ | Chemistry (troposphere only) | ?ADV? | +---------------------------------------+---------------------------------+----------+ | BudgetConvectionFull_ | Convection (full atmosphere) | ?ADV? | +---------------------------------------+---------------------------------+----------+ | BudgetConvectionLevs1to35_ | Convection (fixed level range) | ?ADV? | | [#E]_ | | | +---------------------------------------+---------------------------------+----------+ | BudgetConvectionPBL_ | Convection (PBL only) | ?ADV? | +---------------------------------------+---------------------------------+----------+ | BudgetConvectionTrop_ | Convection (troposphere only) | ?ADV? | +---------------------------------------+---------------------------------+----------+ | BudgetEmisDepFull_\ [#F]_ | Emissions & dry deposition | ?ADV? | | | (full atmosphere) | | +---------------------------------------+---------------------------------+----------+ | BudgetEmisDepLevs1to35_\ | Emissions & dry deposition | ?ADV? | | [#E]_ [#F]_ | (fixed level range) | | +---------------------------------------+---------------------------------+----------+ | BudgetEmisDepPBL_\ [#F]_ | Emissions & dry deposition | ?ADV? | | | (PBL only) | | +---------------------------------------+---------------------------------+----------+ | BudgetEmisDepTrop_\ [#F]_ | Emissions & dry deposition | ?ADV? | | | (troposphere only) | | +---------------------------------------+---------------------------------+----------+ | BudgetMixingFull_ [#G]_ | PBL mixing (full atmosphere) | ?ADV? | +---------------------------------------+---------------------------------+----------+ | BudgetMixingLevs1to35_\ | PBL mixing (full atmosphere) | ?ADV? | | [#E]_ [#G]_ | (fixed level range) | | +---------------------------------------+---------------------------------+----------+ | BudgetMixingPBL_\ [#G]_ | PBL mixing (PBL only) | ?ADV? | +---------------------------------------+---------------------------------+----------+ | BudgetMixingTrop_\ [#G]_ | PBL mixing (troposphere only) | ?ADV? | +---------------------------------------+---------------------------------+----------+ | BudgetTransportFull_\ [#H]_ | Transport (full attmosphere) | ?ADV? | +---------------------------------------+---------------------------------+----------+ | BudgetTransportLevs1to35_\ | Transport (fixed level range) | ?ADV? | | [#E]_ [#H]_ | | | +---------------------------------------+---------------------------------+----------+ | BudgetTransportPBL_\ [#H]_ | Transport (PBL only) | ?ADV? | +---------------------------------------+---------------------------------+----------+ | BudgetTransportTrop_\ [#H]_ | Transport (troposphere only) | ?ADV? | +---------------------------------------+---------------------------------+----------+ | BudgetWetDepFull_ | Wet deposition | ?WET? | | | (full atmosphere) | | +---------------------------------------+---------------------------------+----------+ | BudgetWetDepLevs1to35_\ | Wet deposition (fixed level | ?WET? | | [#E]_ | range) | | +---------------------------------------+---------------------------------+----------+ | BudgetWetDepPBL_ | Wet deposition (PBL only) | ?WET | +---------------------------------------+---------------------------------+----------+ .. rubric:: Notes for the Budget collection .. [#E] These diagnostic quantities allow you to compute mass tendencies in a fixed level range. The lower level and upper level of the range is specified in the diagnostic name (:literal:`LevsXtoY`). Levels 1 to 35 (surface to approximately the tropopause) are the default settings. .. [#F] The emissions and dry deposition budget diagnostics will not capture all fluxes if using the non-local PBL mixing scheme since these tendencies are applied within mixing in :file:`vdiff_mod.F90` below the PBL. When using full mixing, however, mixing and emissions/dry deposition are fully separated. .. [#G] The mixing budget diagnostics includes the application of emissions and dry deposition below the PBL if using the non-local PBL mixing scheme (vdiff). .. [#H] GEOS-Chem Classic only .. _histguide-carbon: Carbon ------ The **Carbon** collection contains diagnostic fields specific to the GEOS-Chem carbon gases simulation. **Sample definition section for HISTORY.rc** .. code-block:: kconfig Carbon.template: '%y4%m2%d2_%h2%n2z.nc4', Carbon.frequency: 00000100 000000 Carbon.duration: 00000100 000000 Carbon.mode: 'time-averaged' Carbon.fields: 'OHconcAfterChem', 'ProdCOfromCH4 ', 'ProdCOfromNMVOC', 'ProdCO2fromCO ', :: **List of diagnostic fields in the Carbon collection** +--------------------+----------------------------------------------+-----------+ | Diagnostic field | Description | Units | +====================+==============================================+===========+ | OHconcAfterChem | OH concentration immediately after chemistry | molec/cm3 | +--------------------+----------------------------------------------+-----------+ | ProdCOfromCH4 | Production of CO from CH4 | molec/cm3 | +--------------------+----------------------------------------------+-----------+ | ProdCOfromNMVOC | Production of CO from non-methane VOCs | molec/cm3 | +--------------------+----------------------------------------------+-----------+ | ProdCO2fromCO | Production of CO2 from CO oxidation | molec/cm3 | +--------------------+----------------------------------------------+-----------+ .. _histguide-ch4: CH4 --- The **CH4** collection contains diagnostics for loss of CH4 and OH concentration for the CH4 simulation. .. attention:: This simulation is slated to be replaced by the GEOS-Chem carbon gases simulation. when this happens, the CH4 collection will be replaced by the :ref:`histguide-carbon` collection. **Sample definition section for HISTORY.rc** .. code-block:: kconfig CH4.template: '%y4%m2%d2_%h2%n2z.nc4', CH4.frequency: 00000100 000000 CH4.duration: 00000100 000000 CH4.mode: 'time-averaged' CH4.fields: 'OHconcAfterChem ', 'LossCH4byClinTrop ', 'LossCH4byOHinTrop ', 'LossCH4inStrat ', :: **List of diagnostic fields in the CH4 collection** +--------------------+------------------------------------------+--------+ | Diagnostic field | Description | Units | +====================+==========================================+========+ | LossCH4byClinTrop | Loss of CH4 by raction with Cl in the | kg/s | | | troposphere | | +--------------------+------------------------------------------+--------+ | LossCH4byOHinTrop | Loss of CH4 by raction with OH in the | kg/s | | | troposphere | | +--------------------+------------------------------------------+--------+ | LossCH4inStrat | Loss of CH4 in the stratosphere | kg/s | +--------------------+------------------------------------------+--------+ | OHconcAfterChem | OH concentration after chemistry | kg/s | +--------------------+------------------------------------------+--------+ .. _histguide-cloudconvflux: CloudConvFlux ------------- The **CloudConvFlux** collection contains diagnostics for mass fluxes in cloud convection. **Sample definition section for HISTORY.rc** .. code-block:: kconfig CloudConvFlux.template: '%y4%m2%d2_%h2%n2z.nc4', CloudConvFlux.frequency: 00000100 000000 CloudConvFlux.duration: 00000100 000000 CloudConvFlux.mode: 'time-averaged' CloudConvFlux.fields: 'CloudConvFlux_?ADV?', :: **List of diagnostic fields in the CloudConvFlux collection** +-------------------------+--------------------+----------+------------+ | Diagnostic field | Description | Units | Wildcards | +=========================+====================+==========+============+ | CloudConvFlux_ | Mass change due to | kg/s | ?ADV? |br| | | | cloud convection | | ?GAS? |br| | | | | | ?WET? | +-------------------------+--------------------+----------+------------+ .. _histguide-co: CO --- The **CO** collection contains diagnostic fields for the GEOS-Chem tagged CO simulation. .. attention:: The tagged CO simulation is slated to be replaced by the GEOS-Chem carbon gases simulation. When this happens, the CO collection will be replaced with the :ref:`histguide-carbon` collection. .. code-block:: CO.template: '%y4%m2%d2_%h2%n2z.nc4', CO.frequency: 00000100 000000 CO.duration: 00000100 000000 CO.mode: 'time-averaged' CO.fields: 'ProdCOfromCH4 ', 'ProdCOfromNMVOC', :: **List of diagnostic fields in the CO collection** +-------------------+----------------------------------------+-------+ | Diagnostic field | Description | Units | +===================+========================================+=======+ | ProdCOfromCH4 | Production of CO from CH4 | kg/s | +-------------------+----------------------------------------+-------+ | ProdCOfromNMVOC | Production of CO from non-methane VOCs | kg/s | +-------------------+----------------------------------------+-------+ .. _histguide-co2: CO2 --- The **CO2** collection contains diagnostic outputs from the GEOS-Chem CO2 simulation. .. attention:: The CO2 simulation is slated to be replaced by the new GEOS-Chem carbon gases simulation. When this happens, the CO2 collection will be replaced with the :ref:`histguide-carbon` collection. .. note:: Several other diagnostics for the CO2 simulation are archived via `HEMCO diagnostics `_. **Sample definition section for HISTORY.rc** .. code-block:: kconfig CO2.template: '%y4%m2%d2_%h2%n2z.nc4', CO2.frequency: 00000100 000000 CO2.duration: 00000100 000000 CO2.mode: 'time-averaged' CO2.fields: 'ProdCO2fromCO', :: **List of diagnostic fields in the CO2 collection** +------------------+-------------------------------+---------+ | Diagnostic field | Description | Units | +==================+===============================+=========+ | ProdCO2fromCO | Chemical production of CO2 | kg/m2/s | | | from CO oxidation | | +------------------+-------------------------------+---------+ .. _histguide-concabovesfc: ConcAboveSfc ------------ The **ConcAboveSfc** diagnostic collection uses dry deposition quantities (surface resistance, dry deposition velocity) to compute the species concentration of O3 and HNO3 at a given altitude (such as 10 m) above the surface. This will facilitate comparison between GEOS-Chem and observational networks (e.g. CASTNET), which often place instruments above the canopy at approx. 10m height. .. attention:: If dry deposition is turned off in your simulation, then you must disable this collection, or else your run will stop with an error. **Sample definition section for HISTORY.rc** .. code-block:: kconfig ConcAboveSfc.template: '%y4%m2%d2_%h2%n2z.nc4', ConcAboveSfc.mode: 'instantaneous' ConcAboveSfc.fields: 'DryDepRaALT1 ', 'DryDepVelForALT1_?DRYALT?', 'SpeciesConcALT1_?DRYALT? ', :: **List of diagnostic fields in the ConcAboveSfc collection** +-----------------------------+----------------------------+---------+----------+ | Diagnostic field | Description | Units | Wildcard | +=============================+============================+=========+==========+ | DryDepRaALT1\ | Dry deposition aerodynamic | s/cm | | | [#Z]_ | resistance at ALT1 meters | | | | | above the surface | | | +-----------------------------+----------------------------+---------+----------+ | DryDepVelForALT1_\ | Dry deposition velocity of | cm/s | ?DRYALT? | | [#Z]_ [#I]_ | species tagged with the | | | | | ?DRYALT?\wildcard | | | +-----------------------------+----------------------------+---------+----------+ | SpeciesConcALT1_\ | Concentration of species | mol/mol | ?DRYALT? | | [#Z]_ [#I]_ | tagged with the ?DRYALT? | dry air | | | | wildcard | | | +-----------------------------+----------------------------+---------+----------+ .. rubric:: Notes about the ConcAboveSfc collection .. [#Z] Replace :literal:`ALT1` with the altitude in meters above the surface at which you would like these quantities computed. For example: :literal:`DryDepVelFor10m_?DRYALT?`, etc. .. [#I] Currently the :literal:`?DRYALT?` species are O3 and HNO3. .. _histguide-concafterchem: ConcAfterChem ------------- The **ConcAfterChem** collection contains diagnostics for OH, HO2, etc. species immediately upon exiting the chemical solver. **Sample definition section for HISTORY.rc** .. code-block:: kconfig 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', 'O3concAfterChem ', 'RO2concAfterChem', :: **List of diagnostic fields in the ConcAfterChem collection** +-------------------+-------------------------------+-----------+ | Diagnostic field | Description | Units | +===================+===============================+===========+ | HO2concAfterChem | HO2 immediately after exiting | mol/mol | | | the chemical solver | | +-------------------+-------------------------------+-----------+ | O1DconcAfterChem | O1D immediately after exiting | molec/cm3 | | | the chemical solver | | +-------------------+-------------------------------+-----------+ | O3concAfterChem | O3 immediately after exiting | molec/cm3 | | | the chemical solver | | +-------------------+-------------------------------+-----------+ | O3PconcAfterChem | O3P immediately after exiting | molec/cm3 | | | the chemical solver | | +-------------------+-------------------------------+-----------+ | OHconcAfterChem | OH immediately after exiting | molec/cm3 | | | the chemical solver | | +-------------------+-------------------------------+-----------+ | RO2concAfterChem | RO2 immediately after exiting | molec/cm3 | | | the chemical solver | | +-------------------+-------------------------------+-----------+ .. _histguide-drydep: DryDep ------ The **DryDep** collection contains diagnostics for the flux and velocity of each species lost to dry-deposition. **Sample definition section for HISTORY.rc** .. code-block:: kconfig DryDep.template: '%y4%m2%d2_%h2%n2z.nc4', DryDep.frequency: 00000100 000000 DryDep.duration: 00000100 000000 DryDep.mode: 'time-averaged' DryDep.fields: 'DryDepVel_?DRY?', 'DryDepMix_?DRY?', 'DryDepChm_?DRY?', 'DryDep_?DRY? ', :: **List of diagnostic fields in the DryDep collection** +-----------------------+-------------------------------+---------------+----------+ | Diagnostic field | Description | Units | Wildcard | +=======================+===============================+===============+==========+ | DryDep_ | Total dry deposition flux | molec/cm2/s | ?DRY? | +-----------------------+-------------------------------+---------------+----------+ | DryDepChm_ | Dry deposition flux (computed | molec/cm2/s | ?DRY? | | | in chemistry) | | | +-----------------------+-------------------------------+---------------+----------+ | DryDepMix_ | Dry deposition flux (computed | molec/cm2/s | ?DRY? | | | in the PBL) | | | +-----------------------+-------------------------------+---------------+----------+ | DryDepVel_ | Dry deposition velocity | cm/s | ?DRY? | +-----------------------+-------------------------------+---------------+----------+ .. _histguide-jvalues: JValues ------- The **JValues** collection contains diagnostics for photolysis rates for various chemical species, obtained from the photolysis mechanism. **Sample definition section for HISTORY.rc** .. code-block:: kconfig JValues.template: '%y4%m2%d2_%h2%n2z.nc4', JValues.frequency: 00000100 000000 JValues.duration: 00000100 000000 JValues.mode: 'time-averaged' JValues.fields: 'Jval_?PHO?', 'JvalO3O1D ', 'JvalO3O3P ', :: **List of diagnostic fields in the JValues collection** +--------------------+-------------------------------+--------+----------+ | Diagnostic field | Description | Units | Wildcard | +====================+===============================+========+==========+ | Jval_ | Photolysis rates | 1/s | ?PHO? | +--------------------+-------------------------------+--------+----------+ | JvalO3O1D | Photolysis rate of O3 | 1/s | | | | :math:`\rightarrow` O1D | | | +--------------------+-------------------------------+--------+----------+ | JvalO3O3P | Photolysis rate of O3 | 1/s | | | | :math:`\rightarrow` O3P | | | +--------------------+-------------------------------+--------+----------+ .. _histguide-kppardiags: KppARDiags ---------- The **KppARDiags** collection contains diagnostics for the KPP Rosenbrock solver with mechanism auto-reduction. You may leave this collection disabled unless you are interested in assessing the solver's performance. **Sample definition section for HISTORY.rc** .. code-block:: kconfig KppARDiags.template: '%y4%m2%d2_%h2%n2z.nc4', KppARDiags.frequency: 00000100 000000 KppARDiags.duration: 00000100 000000 KppARDiags.mode: 'time-averaged' KppARDiags.fields: 'KppAutoReducerNVAR', 'KppAutoReduceThres', 'KppcNONZERO ', :: **List of diagnostic fields in the KppARDiags collection** +--------------------+-------------------------------------+-------------+ | Diagnostic field | Description | Units | +====================+=====================================+=============+ | KppAutoReducerNVAR | Number of species (``rNVAR``) in | count | | | the auto-reduced mechanism | | +--------------------+-------------------------------------+-------------+ | KppAutoReduceThres | Auto-reduction threshold | molec/cm3/s | +--------------------+-------------------------------------+-------------+ | KppcNONZERO | Number of nonzero elements | count | | | (``cNONZERO``) in LU decomposition | | | | in the auto-reduced mechanism | | +--------------------+-------------------------------------+-------------+ .. _histguide-kppdiags: KppDiags -------- The **KppDiags** collection contains KPP solver diagnostics. You may leave this collection disabled unless you are interested in assessing the solver's performance. **Sample definition section for HISTORY.rc** .. code-block:: kconfig KppDiags.template: '%y4%m2%d2_%h2%n2z.nc4', KppDiags.frequency: 00000100 000000 KppDiags.duration: 00000100 000000 KppDiags.mode: 'time-averaged' KppDiags.fields: 'KppIntCounts', 'KppJacCounts', 'KppTotSteps ', 'KppAccSteps ', 'KppRejSteps ', 'KppLuDecomps', 'KppSubsts ', 'KppSmDecomps', :: **List of diagnostic fields in the KppDiags collection** .. list-table:: :header-rows: 1 * - Diagnostic field - Description - Units * - KppAccSteps - Number of accepted integration timesteps - count * - KppIntCounts - Number of times the function to be evaluated was called from within the integrator - count * - KppJacCounts - Number of times the Jacobian matrix was constructed - count * - KppLuDecomps - Number of LU decompositions performed - count * - KppNegatives - Number of negative values - count * - KppNegatives0 - Number of negative values except on the first timestep - count * - KppSmDecomps [#J]_ - Number of singular matrix decompositions performed - count * - KppSubsts - Number of matrix substitutions performed (both forward & backward substitutions) - count * - KppRejSteps - Number of rejected integration timesteps - count * - KppTime [#JJ]_ - Time spent within the integrator - s * - KppTotSteps - Total number of integration timesteps - count .. rubric:: Footnotes .. [#J] For Rosenbrock solvers, KppSmDecomps will be zero everywhere, because the Rosenbrock method utilizes LU decomposition instead of singular matrix decomposition. .. [#JJ] KppTime will likely not be identical between two successive simulations, as the time spent in the integrator will depend on local cluster conditions. .. _histguide-leveledgediags: LevelEdgeDiags -------------- The **LevelEdgeDiags** collection contains diagnostics for quantities (mostly met fields) that are defined on the vertical edges of each grid box. According to the COARDS convention, all of the data variables in a netCDF file must be defined with the same vertical dimension. **Sample definition section for HISTORY.rc** .. code-block:: kconfig LevelEdgeDiags.template: '%y4%m2%d2_%h2%n2z.nc4', LevelEdgeDiags.frequency: 00000100 000000 LevelEdgeDiags.duration: 00000100 000000 LevelEdgeDiags.mode: 'time-averaged' LevelEdgeDiags.fields: 'Met_CMFMC ', 'Met_PEDGE ', 'Met_PEDGEDRY', 'Met_PFICU ', 'Met_PFILSAN ', 'Met_PFLCU ', 'Met_PFLLSAN ', :: **List of diagnostic fields in the LevelEdgeDiags collection** +------------------+----------------------------------------+---------+ | Diagnostic field | Description | Units | +==================+========================================+=========+ | Met_CMFMC | Upward moist convective mass flux | kg/m2/s | +------------------+----------------------------------------+---------+ | Met_PEDGE | Surface pressure at level edges (based | hPa | | | on moist air) | | +------------------+----------------------------------------+---------+ | Met_PEDGEDRY | Surface pressure at level edges (based | hPa | | | on dry air) | | +------------------+----------------------------------------+---------+ | Met_PFICU | 3d flux of ice convective | kg/m2/s | | | precipitation | | +------------------+----------------------------------------+---------+ | Met_PFILSAN | 3d flux of ice non-convective | kg/m2/s | | | precipitation | | +------------------+----------------------------------------+---------+ | Met_PFLCU | 3d flux of liquid convective | kg/m2/s | | | precipitation | | +------------------+----------------------------------------+---------+ | Met_PFLLSAN | 3d flux of liquid non-convective | kg/m2/s | | | precipitation | | +------------------+----------------------------------------+---------+ .. _histguide-mercurychem: MercuryChem ----------- The **MercuryChem** collection contains concentrations and prod/loss diagnostic outputs for the GEOS-Chem mercury simulation. **Sample definition section for HISTORY.rc** .. code-block:: kconfig MercuryChem.template: '%y4%m2%d2_%h2%n2z.nc4', MercuryChem.frequency: ${RUNDIR_HIST_TIME_AVG_FREQ} MercuryChem.duration: ${RUNDIR_HIST_TIME_AVG_DUR} MercuryChem.mode: 'time-averaged' MercuryChem.fields: 'HgBrAfterChem ', 'HgClAfterChem ', 'HgOHAfterChem ', 'HgBrOAfterChem ', 'HgClOAfterChem ', 'HgOHOAfterChem ', 'Hg2GToHg2P ', 'Hg2PToHg2G ', 'Hg2GasToHg2StrP', 'Hg2GasToSSA ', :: **List of diagnostic fields in the MercuryChem collection** +------------------+---------------------------------+-------------+ | Diagnostic field | Description | Units | +==================+=================================+=============+ | Hg2GToHg2P | Hg2 gas transferred to Hg2P | molec/cm3/s | +------------------+---------------------------------+-------------+ | Hg2GasToHg2StrP | Hg2 gas transferred to Hg2StrP | molec/cm3/s | +------------------+---------------------------------+-------------+ | Hg2GasToSSA | Hg2 gas transferred to sea | molec/cm3/s | | | salt aerosol | | +------------------+---------------------------------+-------------+ | Hg2PToHg2G | Hg2P transferred to Hg2 gas | molec/cm3/s | +------------------+---------------------------------+-------------+ | HgBrAfterChem | HgBr concentration | mol/mol | | | immediately after chemistry | | +------------------+---------------------------------+-------------+ | HgBrOAfterChem | HgBrO concentration | mol/mol | | | immediately after chemistry | | +------------------+---------------------------------+-------------+ | HgClAfterChem | HgCl concentration | mol/mol | | | immediately after chemistry | | +------------------+---------------------------------+-------------+ | HgClOAfterChem | HgClO concentration | mol/mol | | | immediately after chemistry | | +------------------+---------------------------------+-------------+ | HgOHAfterChem | HgOH concentration | mol/mol | | | immediately after chemistry | | +------------------+---------------------------------+-------------+ | HgOHOAfterChem | HgOHO concentration | mol/mol | | | immediately after chemistry | | +------------------+---------------------------------+-------------+ .. _histguide-mercuryemis: MercuryEmis ----------- The **MercuryEmis** collection contains emission diagnostics for the GEOS-Chem mercury simulation. .. note:: Several other mercury emission diagnostics are archived via `HEMCO diagnostics `_. **Sample definition section for HISTORY.rc** .. code-block:: kconfig MercuryEmis.template: '%y4%m2%d2_%h2%n2z.nc4', MercuryEmis.frequency: 00000100 000000 MercuryEmis.duration: 00000100 000000 MercuryEmis.mode: 'time-averaged' MercuryEmis.fields: 'EmisHg0land ', 'EmisHg0ocean', 'EmisHg0soil ', 'EmisHg0snow ', :: **List of diagnostic fields in the MercuryEmis collection** +------------------+-------------------------------+-------+ | Diagnostic field | Description | Units | +==================+===============================+=======+ | EmisHg0land | Re-emission of Hg0 from land | kg/s | +------------------+-------------------------------+-------+ | EmisHg0ocean | Emissions of Hg0 from oceans | kg/s | +------------------+-------------------------------+-------+ | EmisHg0snow | Emission of Hg0 from snowpack | kg/s | +------------------+-------------------------------+-------+ | EmisHg0soil | Emissions of Hg0 from soils | kg/s | +------------------+-------------------------------+-------+ .. _histguide-mercuryocean: MercuryOcean ------------ The **MercuryOcean** collection contains diagnostics from the mercury ocean model, used in the GEOS-Chem mercury simulation. **Sample definition section for HISTORY.rc** .. code-block:: kconfig MercuryOcean.template: '%y4%m2%d2_%h2%n2z.nc4', MercuryOcean.frequency: 00000000 040000 MercuryOcean.duration: 00000000 040000 MercuryOcean.mode: 'time-averaged' MercuryOcean.fields: 'FluxHg0fromAirToOcean ', 'FluxHg0fromOceanToAir ', 'FluxHg2HgPfromAirToOcean', 'FluxHg2toDeepOcean ', 'FluxOCtoDeepOcean ', 'MassHg0inOcean ', 'MassHg2inOcean ', 'MassHgPinOcean ', 'MassHgTotalInOcean ', :: **List of diagnostic fields in the MercuryOcean collection** +--------------------------+-----------------------------+-------+ | Diagnostic field | Description | Units | +==========================+=============================+=======+ | FluxHg0fromAirToOcean | Deposition flux of Hg0 from | kg/s | | | the atmosphere to the ocean | | +--------------------------+-----------------------------+-------+ | FluxHg0fromOceanToAir | Volatization flux of Hg0 | kg/s | | | from the ocean to the | | | | atmosphere | | +--------------------------+-----------------------------+-------+ | FluxHg2HgPfromAirToOcean | Deposition flux of Hg2 + | kg/s | | | HgP from atmosphere to | | | | ocean | | +--------------------------+-----------------------------+-------+ | FluxHg2toDeepOcean | Flux of Hg2 sunk to the | kg/s | | | deep ocean | | +--------------------------+-----------------------------+-------+ | MassHg0inOcean | Total mass of oceanic Hg0 | kg | +--------------------------+-----------------------------+-------+ | MassHg2inOcean | Total mass of oceanic Hg2 | kg | +--------------------------+-----------------------------+-------+ | MassHgPinOcean | Total mass of oceanic HgP | kg | +--------------------------+-----------------------------+-------+ | MassHgTotalInOcean | Total mass of all organic | kg | | | mercury | | +--------------------------+-----------------------------+-------+ .. _histguide-metrics: Metrics ------- The **Metrics** collection contains diagnostics for computing OH metrics from a GEOS-Chem full chemistry simulation (needed for benchmarking). To compute the OH metrics, you must run the Python script :file:`metrics.py` that ships with each fullchem or CH4 run directory. **Sample definition section for HISTORY.rc** .. code-block:: kconfig Metrics.template: '%y4%m2%d2_%h2%n2z.nc4', Metrics.frequency: 'End', Metrics.duration: 'End', Metrics.mode: 'time-averaged' Metrics.fields: 'AirMassColumnFull ', 'LossOHbyCH4columnTrop ', 'LossOHbyMCFcolumnTrop ', 'OHwgtByAirMassColumnFull', :: **List of diagnostic fields in the Metrics collection** +--------------------------+--------------------------------------+-----------+ | Diagnostic field | Description | Units | +==========================+======================================+===========+ | AirMassColumnFull | Air mass column (full atmosphere) | kg | +--------------------------+--------------------------------------+-----------+ | LossOHbyCH4columnTrop | Loss rate of CH4 by OH (tropospheric | molec/cm3 | | | column sums) | | +--------------------------+--------------------------------------+-----------+ | LossOHbyMCFcolumnTrop | Loss rate of CH4 by CH3CCl3 aka MCF | molec/cm3 | | | (tropospheric column sums) | | +--------------------------+--------------------------------------+-----------+ | OHwgtByAirMassColumnFull | Airmass-weighted OH concentration | kg air/\ | | | (full atmosphere column sums) | kg OH/m3 | +--------------------------+--------------------------------------+-----------+ .. _histguide-prodloss: ProdLoss -------- The **ProdLoss** collection contains chemical production and loss rates. **Sample definition section for HISTORY.rc** .. code-block:: kconfig ProdLoss.template: '%y4%m2%d2_%h2%n2z.nc4', ProdLoss.frequency: 00000100 000000 ProdLoss.duration: 00000100 000000 ProdLoss.mode: 'time-averaged' ProdLoss.fields: 'Prod_?PRD? ', 'ProdBCPIfromBCPO ', 'ProdOCPIfromOCPO ', 'ProdHMSfromSO2andHCHOinCloud', 'ProdSO2andHCHOfromHMSinCloud', 'ProdSO4fromHMSinCloud ', 'ProdSO4fromH2O2inCloud ', 'ProdSO4fromO2inCloudMetal ', 'ProdSO4fromO3inCloud ', 'ProdSO4fromO3inSeaSalt ', 'ProdSO4fromHOBrInCloud ', 'ProdSO4fromSRO3 ', 'ProdSO4fromSRHObr ', 'ProdSO4fromO3s ', 'Loss_?LOS? ', 'LossHNO3onSeaSalt ', 'ProdCOfromCH4 ', 'ProdCOfromNMVOC ', :: **List of diagnostic fields in the ProdLoss collection** +------------------------------+-----------------------------+---------+----------+ | Diagnostic field | Description | Units | Wildcard | +==============================+=============================+=========+==========+ | Loss_ | Chemical loss for a | molec/\ | ?LOS? | | | given species or family | cm3 | | +------------------------------+-----------------------------+---------+----------+ | LossHNO3onSeaSalt\ | L(HNO3) on sea salt | kg S/s | | | [#M]_ | aerosols | | | +------------------------------+-----------------------------+---------+----------+ | Prod_ | Chemical production for a | molec/\ | ?PRD? | | | given species or family | cm3 | | +------------------------------+-----------------------------+---------+----------+ | ProdBCPIfromBCPO\ | Production of hydrophilic | kg | | | [#M]_ | BC from hydrophobic BC | | | +------------------------------+-----------------------------+---------+----------+ | ProdCOfromCH4\ | P(CO) from CH4 | molec/\ | | | [#N]_ | | cm3 | | +------------------------------+-----------------------------+---------+----------+ | ProdCOfromNMVOC\ | P(CO) from NMVOCs | molec/\ | | | [#N]_ | SO3-- loss by OH | cm3 | | +------------------------------+-----------------------------+---------+----------+ | ProdOCPIfromOCPO\ | Production of hydrophilic | kg | | | [#M]_ | OC from hydrophobic OC | | | +------------------------------+-----------------------------+---------+----------+ | ProdMSAfromDMS\ | P(MSA) from DMS | kg S/s | | | [#L]_ | | | | +------------------------------+-----------------------------+---------+----------+ | ProdNITfromHNO3uptakeOnDust\ | P(NIT) from HNO3 uptake | kg N/s | | | [#K]_ | on dust aerosols | | | +------------------------------+-----------------------------+---------+----------+ | ProdSO2fromDMS\ [#L]_ | Total P(SO2) from DMS | kg S/s | | +------------------------------+-----------------------------+---------+----------+ | ProdSO2fromDMSandNO3\ | P(SO2) from DMS + NO3 | kg S/s | | | [#L]_ | | | | +------------------------------+-----------------------------+---------+----------+ | ProdSO2fromDMSandOH\ | P(SO2) from DMS + OH | kg S/s | | | [#L]_ | | | | +------------------------------+-----------------------------+---------+----------+ | ProdSO2fromOxidationOnDust\ | P(SO2) from DMS+OH | kg S/s | | | [#K]_ | on dust aerosols | | | +------------------------------+-----------------------------+---------+----------+ | ProdSO4fromGasPhase\ | P(SO4) in gas phase | kg S/s | | | [#L]_ | | | | +------------------------------+-----------------------------+---------+----------+ | ProdSO4fromH2O2inCloud\ | P(SO4) from aqueous | kg S/s | | | [#M]_ | oxidation of H2O2 | | | | | in clouds | | | +------------------------------+-----------------------------+---------+----------+ | ProdSO4fromHOBrinCloud\ | P(SO4) from aqueous | kg S/s | | | [#N]_ | oxidation of HOBr in clouds | | | +------------------------------+-----------------------------+---------+----------+ | ProdSO4fromO2inCloudMetal\ | P(SO4) from aqueous | kg S/s | | | [#M]_ | oxidation of O2 from | | | | | metals in cloud | | | +------------------------------+-----------------------------+---------+----------+ | ProdSO4fromO3inCloud\ | P(SO4) from aqueous | kg S/s | | | [#M]_ | oxidation of O3 in clouds | | | +------------------------------+-----------------------------+---------+----------+ | ProdSO4fromO3inSeaSalt\ | P(SO4) from O3 in sea salt | kg S/s | | | [#M]_ | | | | +------------------------------+-----------------------------+---------+----------+ | ProdSO4fromO3s\ [#M]_ | P(SO4) from aqueous phase | kg S/s | | | | SO3-- loss by OH | | | +------------------------------+-----------------------------+---------+----------+ | ProdSO4fromSRHOBR\ [#N]_ | P(SO4) from sulfur | kg S/s | | | | production rate of | | | | | HOBr + O3 | | | +------------------------------+-----------------------------+---------+----------+ | ProdSO4fromSRO3\ [#M]_ | P(SO4) from sulfur | kg S/s | | | | production rate of O3 | | | +------------------------------+-----------------------------+---------+----------+ | ProdSO4fromUptakeOfH2SO4g\ | P(SO4) from H2SO4 uptake | kg S/s | | | [#K]_ | on dust aerosols | | | +------------------------------+-----------------------------+---------+----------+ .. rubric:: Notes for the ProdLoss collection .. [#K] Only defined for fullchem simulation with aciduptake on dust. .. [#L] Only defined for the aerosol-only simulation. .. [#M] Defined for aerosol-only and fullchem simulations. .. [#N] Only defined for fullchem simulations. .. _histguide-radionuclide: RadioNuclide ------------ The **RadioNuclide** collection contains diagnostic outputs for radionuclide species in the GEOS-Chem TransportTracers simulation. .. note:: Emissions of Rn222, Be7, and Be10 species are archived to diagnostic output by `HEMCO diagnostics `_, and are thus not contained in this collection. **Sample definition section for HISTORY.rc** .. code-block:: kconfig RadioNuclide.template: '%y4%m2%d2_%h2%n2z.nc4', RadioNuclide.format: 'CFIO', RadioNuclide.frequency: 00000100 000000 RadioNuclide.duration: 00000100 000000 RadioNuclide.mode: 'time-averaged' RadioNuclide.fields: 'PbFromRnDecay ', 'RadDecay_Rn222 ', 'RadDecay_Pb210 ', 'RadDecay_Pb210s', 'RadDecay_Be7 ', 'RadDecay_Be7s ', 'RadDecay_Be10 ', 'RadDecay_Be10s ', :: **List of diagnostic fields in the RadioNuclide collection** +------------------+------------------------------------------+-------+ | Diagnostic field | Description | Units | +==================+==========================================+=======+ | PbFromRnDecay | Pb\ :sup:`210` created from | kg/s | | | radioactive decay | | +------------------+------------------------------------------+-------+ | RadDecay_Be7 | Loss of Be\ :sup:`7` | kg/s | | | due to radioactive decay | | +------------------+------------------------------------------+-------+ | RadDecay_Be7s | Loss of Be\ :sup:`7` (produced in the | kg/s | | | stratosphere) due to radioactive decay | | +------------------+------------------------------------------+-------+ | RadDecay_Be10 | Loss of Be\ :sup:`10` | kg/s | | | due to radioactive decay | | +------------------+------------------------------------------+-------+ | RadDecay_Be10s | Loss of Be\ :sup:`10` (produced in the | kg/s | | | stratosphere) due to radioactive decay | | +------------------+------------------------------------------+-------+ | RadDecay_Pb210 | Loss of Pb\ :sup:`210` | kg/s | | | due to radioactive decay | | +------------------+------------------------------------------+-------+ | RadDecay_Pb210s | Loss of Pb\ :sup:`210` (produced in the | kg/s | | | stratosphere) due to radioactive decay | | +------------------+------------------------------------------+-------+ | RadDecay_Rn222 | Loss of Rn\ :sup:`222` | kg/s | | | due to readioactive decay | | +------------------+------------------------------------------+-------+ .. _histguide-restart: Restart ------- The **Restart** diagnostic collection contains fields for saving out to the GEOS-Chem Classic restart file. This type of diagnostic output is used in all GEOS-Chem Classic simulations; therefore, we have listed Restart first in the :file:`HISTORY.rc` files that ship with each GEOS-Chem run directory. Note that GCHP restart files are not handled by the MAPL History component and therefore do not appear in :file:`HISTORY.rc`. .. note:: The restart file will be created in the :file:`Restarts/` subdirectory of the run directory, not in :file:`OutputDir/`. **Sample definition section for HISTORY.rc** .. code-block:: kconfig Restart.filename: './GEOSChem.Restart.%y4%m2%d2_%h2%n2z.nc4', Restart.frequency: 'End', Restart.duration: 'End', Restart.mode: 'instantaneous' Restart.fields: 'SpeciesRst_?ALL? ', 'Chem_H2O2AfterChem ', 'Chem_SO2AfterChem ', 'Chem_DryDepNitrogen', 'Chem_WetDepNitrogen', 'Chem_KPPHvalue ', 'Met_DELPDRY ', 'Met_PS1WET ', 'Met_PS1DRY ', 'Met_SPHU1 ', 'Met_TMPU1 ', :: **List of diagnostic fields in the Restart collection** +--------------------+-----------------------------+-----------------+ | Diagnostic field | Description | Units | +====================+=============================+=================+ | Chm_DryDepNitrogen | Dry deposited nitrogen | molec/cm2/s | +--------------------+-----------------------------+-----------------+ | Chm_H2O2AfterChem | Concentration of H2O2 after | v/v | | | sulfate chemistry | | +--------------------+-----------------------------+-----------------+ | Chm_KPPHvalue | H-value for Rosenbrock | unitless | | | solver | | +--------------------+-----------------------------+-----------------+ | Chm_SO2AfterChem | Concentration of SO2 after | v/v | | | sulfate chemistry | | +--------------------+-----------------------------+-----------------+ | Chm_StatePSC | Polar stratospheric cloud | count | | | type | | +--------------------+-----------------------------+-----------------+ | Chm_WetDepNitrogen | Wet deposited nitrogen | molec/cm2/s | +--------------------+-----------------------------+-----------------+ | Met_DELPDRY | Delta-pressure across grid | hPa | | | box (dry air) | | +--------------------+-----------------------------+-----------------+ | Met_PS1WET | Wet surface pressure at dt | hPa | | | start | | +--------------------+-----------------------------+-----------------+ | Met_PS1DRY | Dry surface pressure at dt | hPa | | | start | | +--------------------+-----------------------------+-----------------+ | Met_SPHU1 | Instantaneous specific | g kg-1 | | | humidity at time=T | | +--------------------+-----------------------------+-----------------+ | Met_TMPU1 | Instantaneous temperature | K | | | at time=T | | +--------------------+-----------------------------+-----------------+ | SpeciesRst\_?ALL? | Instantaneous chemical | mol/mol dry air | | | species concentrations for | | | | use in starting subsequent | | | | GEOS-Chem simulations | | +--------------------+-----------------------------+-----------------+ .. _histguide-rrtmg: RRTMG ----- The **RRTMG** collection contains radiative flux diagnostics computed by the RRTMG radiative transfer model. You can leave this collection disabled unless your simulation uses RRTMG. .. note:: You may compute RRTMG diagnostic quantities at up to 3 wavelengths (:literal:`WL1`, :literal:`WL2`, :literal:`WL3`). Specify the wavelengths in this menu of the :file:`geoschem_config.yml` file: .. code-block:: yaml rrtmg_rad_transfer_model: activate: true aod_wavelengths_in_nm: - 550 700 1000 ... etc ... GEOS-Chem will replace the tokens :literal:`WL1`, :literal:`WL2`, :literal:`WL3` in diagnostic field names with the corresponding wavelength. For example: .. code-block:: RadAODWL1_SU RadAODWL2_SU RadAODWL3_SU will be saved to the :file:`GEOSChem.RRTMG.YYYYMMDD_hhmmz.nc4` file(s) under these names: .. code-block:: RadAOD550nm_SU RadAOD700nm_SU RadAOD1000nm_SU **Sample definition section for HISTORY.rc** .. code-block:: kconfig #============================================================================== # %%%%% THE RRTMG COLLECTION %%%%% # # Outputs for different species from the RRTMG radiative transfer model: # (See http://wiki.geos-chem.org/Coupling_GEOS-Chem_with_RRTMG) # # 0=BA (Baseline ) 1=O3 (Ozone ) 2=ME (Methane ) # 3=SU (Sulfate ) 4=NI (Nitrate ) 5=AM (Ammonium ) # 6=BC (Black carbon) 7=OA (Organic aerosol) 8=SS (Sea Salt ) # 9=DU (Mineral dust) 10=PM (All part. matter) 12=ST (Strat aer., UCX only) # # NOTES: # (1) Only request diagnostics you need to reduce the overall run time. # (2) The ?RRTMG? wildcard includes all output except ST (strat aerosols). # However, if ST is included explicitly for one diagnostic then it # will be included for all others that use the wildcard. # (3) Only enable ST if running with UCX. # (4) Optics diagnostics have a reduced set of output species (no BASE, O3, ME) #============================================================================== RRTMG.template: %y4%m2%d2_%h2%n2z.nc4', RRTMG.frequency: 00000100 000000 RRTMG.duration: 00000100 000000 RRTMG.mode: time-averaged' RRTMG.fields: 'RadClrSkyLWSurf_?RRTMG?', 'RadAllSkyLWSurf_?RRTMG?', 'RadClrSkySWSurf_?RRTMG?', 'RadAllSkySWSurf_?RRTMG?', 'RadClrSkyLWTOA_?RRTMG? ', 'RadAllSkyLWTOA_?RRTMG? ', 'RadClrSkySWTOA_?RRTMG? ', 'RadAllSkySWTOA_?RRTMG? ', 'RadAODWL1_?RRTMG? ', 'RadAsymWL1_?RRTMG? ', :: **List of diagnostic fields in the RRTMG collection** +---------------------------+--------------------------------+-------+----------+ | Diagnostic field | Description | Units | Wildcard | +===========================+================================+=======+==========+ | DynHeating | Dynamic heating rate in | K/day | ?RRTMG? | | | baseline simulation | | | +---------------------------+--------------------------------+-------+----------+ | DtRad | Temperature change due to | K | ?RRTMG? | | | radiative heating | | | +---------------------------+--------------------------------+-------+----------+ | RadAODWL1_ | Aerosol optical depth | 1 | ?RRTMG? | | | computed @ WL1 | | | +---------------------------+--------------------------------+-------+----------+ | RadAODWL2_ | Aerosol optical depth | 1 | ?RRTMG? | | | computed @ WL2 | | | +---------------------------+--------------------------------+-------+----------+ | RadAODWL3_ | Aerosol optical depth | 1 | ?RRTMG? | | | computed @ WL3 | | | +---------------------------+--------------------------------+-------+----------+ | RadAsymWL1_ | Asymmetry parameter | 1 | ?RRTMG? | | | computed @ WL1 | | | +---------------------------+--------------------------------+-------+----------+ | RadAsymWL2_ | Asymmetry parameter | 1 | ?RRTMG? | | | computed @ WL2 | | | +---------------------------+--------------------------------+-------+----------+ | RadAsymWL3_ | Asymmetry parameter | 1 | ?RRTMG? | | | computed @ WL3 | | | +---------------------------+--------------------------------+-------+----------+ | RadAllSkyLWSurf_ | All-sky longwave radiation | W/m2 | ?RRTMG? | | | at the surface | | | +---------------------------+--------------------------------+-------+----------+ | RadAllSkyLWTOA_ | All-sky longwave radiation | W/m2 | ?RRTMG? | | | at top-of-atmosphere | | | +---------------------------+--------------------------------+-------+----------+ | RadAllSkyLWTrop_ | All-sky longwave radiation | W/m2 | ?RRTMG? | | | at the tropopause | | | +---------------------------+--------------------------------+-------+----------+ | RadAllSkySWSurf_ | All-sky shortwave radiation | W/m2 | ?RRTMG? | | | at the surface | | | +---------------------------+--------------------------------+-------+----------+ | RadAllSkySWTOA_ | All-sky shortwave radiation | W/m2 | ?RRTMG? | | | at top-of-atmosphere | | | +---------------------------+--------------------------------+-------+----------+ | RadAllSkySWTrop_ | All-sky shortwave radiation | W/m2 | ?RRTMG? | | | at the tropopause | | | +---------------------------+--------------------------------+-------+----------+ | RadClrSkyLWSurf_ | Clear-sky longwave radiation | W/m2 | ?RRTMG? | | | at the surface | | | +---------------------------+--------------------------------+-------+----------+ | RadClrSkyLWTOA_ | Clear-sky longwave radiation | W/m2 | ?RRTMG? | | | at top-of-atmosphere | | | +---------------------------+--------------------------------+-------+----------+ | RadClrSkyLWTrop_ | Clear-sky longwave radiation | W/m2 | ?RRTMG? | | | at the tropopause | | | +---------------------------+--------------------------------+-------+----------+ | RadClrSkySWSurf_ | Clear-sky shortwave radiation | W/m2 | ?RRTMG? | | | at the surface | | | +---------------------------+--------------------------------+-------+----------+ | RadClrSkySWTOA_ | Clear-sky shortwave radiation | W/m2 | ?RRTMG? | | | at top-of-atmosphere | | | +---------------------------+--------------------------------+-------+----------+ | RadClrSkySWTrop_ | Clear-sky shortwave radiation | W/m2 | ?RRTMG? | | | at the tropopause | | | +---------------------------+--------------------------------+-------+----------+ | RadSSAWL1_ | Single-scattering albedo | 1 | ?RRTMG? | | | computed @ WL1 | | | +---------------------------+--------------------------------+-------+----------+ | RadSSAWL2_ | Single-scattering albedo | 1 | ?RRTMG? | | | computed @ WL2 | | | +---------------------------+--------------------------------+-------+----------+ | RadSSAWL3_ | Single-scattering albedo | 1 | ?RRTMG? | | | computed @ WL3 | | | +---------------------------+--------------------------------+-------+----------+ .. _histguide-rxnconst: RxnConst -------- The **RxnConst** collection contains reaction rate constants from the KPP solver. .. code-block:: kconfig # It is best to list individual reactions to avoid using too much memory. # Reactions should be listed as "RxnConst_EQnnn", where nnn is the reaction # index as listed in KPP/fullchem/gckpp_Monitor.F90 (pad zeroes as needed). # # The units of reaction rate constants vary according to the number of reactants # in the reaction. # # Available for the fullchem simulations. RxnConst.template: '%y4%m2%d2_%h2%n2z.nc4', RxnConst.frequency: ${RUNDIR_HIST_TIME_AVG_FREQ} RxnConst.duration: ${RUNDIR_HIST_TIME_AVG_DUR} RxnConst.mode: 'time-averaged' RxnConst.fields: 'RxnConst_EQ001 ', 'RxnConst_EQ002 ', :: **List of diagnostic fields in the RxnRate collection** Units are +------------------+-----------------------+-------+----------+ | Diagnostic field | Description | Units | Wildcard | +==================+=======================+=======+==========+ | RxnConst_EQnnn\ | Rate constant for KPP | [#P]_ | ?RXN? | | [#O]_ | reaction ``nnn`` | | | +------------------+-----------------------+-------+----------+ .. rubric:: Notes for the RxnRates collection .. [#O] See the :file:`gckpp_Monitor.F90` file to get a numbered list of reactions. .. [#P] Units are :literal:`{ (cm3/molec)**(nreactants-1) }/s` .. _histguide-rxnrates: RxnRates -------- The **RxnRates** collection contains reaction rates (aka equation rates) from the chemical mechanism (as computed by the KPP-generated solver code). For example, in the case of the NO + O\ :sub:`3` → NO\ :sub:`2` + O\ :sub:`2` reaction the returned quantity is k[NO][O\ :sub:`3`] in molec/cm\ :sup:`3`/s. Here is a sample definition section for the RxnRates collection. **Sample definition section for HISTORY.rc** .. code-block:: kconfig # # It is best to list individual reactions to avoid using too much memory. # Reactions should be listed as "RxnRate_EQnnn", where nnn is the reaction # index as listed in KPP/fullchem/gckpp_Monitor.F90, # KPP/carbon/gckpp_Monitor.F90, and KPP/Hg/gckpp_monitor.F90 # (pad zeroes as needed) # RxnRates.template: '%y4%m2%d2_%h2%n2z.nc4', RxnRates.frequency: 00000000 010000 RxnRates.duration: 00000000 010000 RxnRates.mode: 'time-averaged' RxnRates.fields: 'RxnRate_EQ001 ', 'RxnRate_EQ002 ', :: **List of diagnostic fields in the RxnRate collection** +-------------------+-------------------------------+-------------+----------+ | Diagnostic field | Description | Units | Wildcard | +===================+===============================+=============+==========+ | RxnRate_EQnnn\ | Rate for KPP reaction ``nnn`` | molec/cm3/s | ?RXN? | | [#Q]_ | | | | | | | | | +-------------------+-------------------------------+-------------+----------+ .. rubric:: Notes for the RxnRates collection .. [#Q] See the :file:`gckpp_Monitor.F90` file to get a numbered list of reactions. .. _histguide-satdiagn: SatDiagn -------- The **SatDiagn** collection contains diagnostic quantities that will be sampled within a specified local time range. This is to mimic the overpass sampling times of sun-synchronus satellite instruments. .. tip:: Set the the hours (local time) for the averaging interval with: .. code-block:: kconfig SatDiagn.hrrange: 11.98 15.02 **Sample definition section for HISTORY.rc** .. code-block:: kconfig SatDiagn.template: '%y4%m2%d2_%h2%n2z.nc4', SatDiagn.frequency: 00000001 000000 SatDiagn.duration: 00000100 000000 SatDiagn.hrrange: 11.98 15.02 SatDiagn.mode: 'time-averaged' SatDiagn.fields: 'SatDiagnConc_O3 ', 'SatDiagnOH ', 'SatDiagnRH ', 'SatDiagnAirDen ', 'SatDiagnBoxHeight ', 'SatDiagnPEdge ', 'SatDiagnTROPP ', 'SatDiagnPBLHeight ', 'SatDiagnPBLTop ', 'SatDiagnTAir ', 'SatDiagnGWETROOT ', 'SatDiagnGWETTOP ', 'SatDiagnPARDR ', 'SatDiagnPARDF ', 'SatDiagnPRECTOT ', 'SatDiagnSLP ', 'SatDiagnSPHU ', 'SatDiagnTS ', 'SatDiagnPBLTOPL ', 'SatDiagnMODISLAI ', 'SatDiagnWetLossLS_ ', 'SatDiagnWetLossConv_ ', 'SatDiagnJval_ ', 'SatDiagnJvalO3O1D ', 'SatDiagnJvalO3O3P ', 'SatDiagnDryDep_ ', 'SatDiagnDryDepVel_ ', 'SatDiagnOHreactivity ', 'SatDiagnColEmis_ ', 'SatDiagnSurfFlux_ ', 'SatDiagnProd_?PRD? ', 'SatDiagnLoss_?LOS? ', 'SatDiagnRxnRate_EQnnn', :: **List of diagnostic fields in the SatDiagn collection** +-------------------------------+-----------------------------+-----------+-----------+ | Diagnostic field | Description | Units | Wildcards | +===============================+=============================+===========+===========+ | SatDiagnAirDen | Air density | molec/cm3 | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnBoxHeight | Grid box height | m | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnColEmis_ | Column emissions | kg/m2/s | ?ADV? | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnConc_ | Dry mixing ratio of species | mol/mol | ?ADV? | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnDryDep_ | Dry deposition flux | molec/\ | ?DRY? | | | of species | cm2/s | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnDryDepVel_ | Dry deposition velocity | cm/s | ?DRY? | | | of species | | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnGWETROOT | Root zone soil moisture | 1 | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnGWETTOP | Topsoil moisture (or | 1 | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnJVal_ | Photolysis rate | 1/s | ?PHO? | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnJvalO3O1D | Photolysis rate for O3 | 1/s | | | | :math:`\rightarrow` O1D | | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnJvalO3O3P | Photolysis rate for O3 | 1/s | | | | :math:`\rightarrow` O1D | | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnLoss_ | Chemical loss of species | molec/\ | ?LOS? | | | or families | cm3/s | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnMODISLAI | MODIS daily LAI | m2/m2 | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnOH | OH number density | molec/cm3 | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnOHreactivity | OH reactivity | 1/s | | | | | | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnPARDF | Diffuse photosynthetically | W/m2 | | | | active radiation | | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnPARDR | Direct photosynthetically | W/m2 | | | | active radiation | | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnPBLHeight | PBL Height | m | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnPBLTop | PBL Top | m | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnPBLTOPL | PBL top height | level | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnPRECTOT | Total precipitation at | mm/day | | | | surface | | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnProd_ | Chemical production of | molec/\ | ?PRD? | | | species or families | cm3/s | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnRH | Relative humidity | % | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnRxnRate_EQnnn | Rate for chemical reaction | molec/\ | ?RXN? | | | ```nnn``` | cm3/s | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnSLP | Sea level pressure | hPa | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnSPHU | Specific humidity | g H2O/\ | | | | interpolated to current | kg air | | | | time | | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnSurfFlux_ | Total surface fluxes | kg/m2/s | ?ADV? | | | (emis - drydep) from | | | | | surface to top of PBL | | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnTAir | Air temperature | K | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnTROPP | Tropopause pressure | hPa | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnTS | Surface temperature at 2m | K | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnWetLossConv_ | Loss of soluble species in | kg/s | ?WET? | | | convective updrafts | | | +-------------------------------+-----------------------------+-----------+-----------+ | SatDiagnWetLossLS_ | Loss of soluble species in | kg/s | ?WET? | | | large-scale precipitation | | | +-------------------------------+-----------------------------+-----------+-----------+ .. _histguide-satdiagnedge: SatDiagnEdge ------------ The **SatDiagn** collection contains diagnostic quantities (placed on level edges) that will be sampled within a specified local time range. This is to mimic the overpass sampling times of sun-synchronus satellite instruments. .. tip:: Set the the hours (local time) for the averaging interval with: .. code-block:: kconfig SatDiagn.hrrange: 11.98 15.02 **Sample definition section for HISTORY.rc** .. code-block:: SatDiagnEdge.template: '%y4%m2%d2_%h2%n2z.nc4', SatDiagnEdge.frequency: 00000001 000000 SatDiagnEdge.duration: 00000100 000000 SatDiagnEdge.hrrange: 11.98 15.02 SatDiagnEdge.mode: 'time-averaged' SatDiagnEdge.fields: 'SatDiagnConc_PEDGE', :: **List of diagnostic fields in the SatDiagnEdge collection** +-------------------------------+-----------------------------+-----------+ | Diagnostic field | Description | Units | +===============================+=============================+===========+ | SatDiagnPEDGE | Pressure at grid box edges | hPa | +-------------------------------+-----------------------------+-----------+ .. _histguide-speciesconc: SpeciesConc ----------- The **SpeciesConc** diagnostic collection contains species concentrations. **Sample definition section for HISTORY.rc** .. code-block:: kconfig 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: 'SpeciesConcVV_?ALL?', 'SpeciesConcMND_?ALL?', :: **List of diagnostic fields in the SpeciesConc collection** +---------------------------+-----------------------+-----------+--------------+ | Diagnostic field | Description | Units | Wildcards | +===========================+=======================+===========+==============+ | SpeciesConcMND_ | Species concentration | molec/cm3 | can be used | | | | | with all | | | | | wildcards | +---------------------------+-----------------------+-----------+--------------+ | SpeciesConcVV_ | Species concentration | mol/mol | can be used | | | | dry air | with all | | | | | wildcards | +---------------------------+-----------------------+-----------+--------------+ .. _histguide-statechm: StateChm -------- The '''StateChm ''' collection contains quantities from State_Chm, the Chemistry State object (other than the species concentrations, which are stored in the SpeciesConc collection). **Sample definition section for HISTORY.rc** .. code-block:: kconfig StateChm.template: '%y4%m2%d2_%h2%n2z.nc4', 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', :: **List of diagnostic fields in the StateChm collection** +------------------+---------------------------------+---------------------+ | Diagnostic field | Description | Units | +==================+=================================+=====================+ | Chm_AcidPurSav | ISORROPIA acidpur concentration | M | +------------------+---------------------------------+---------------------+ | Chm_BiSulSav | ISORROPIA bisulfate general | M | | | acid concentration | | +------------------+---------------------------------+---------------------+ | Chm_fupdateHOBr | Correction factor for HOBr | mol/L | | | removal by SO2 | | | | grid box (wet air) | | +------------------+---------------------------------+---------------------+ | Chm_HplusSav | ISORROPIA H+ concentration | M | +------------------+---------------------------------+---------------------+ | Chm_HSO3AQ | Cloud bisulfite concentration | mol/L | +------------------+---------------------------------+---------------------+ | Chm_NaRatSav | ISORROPIA Na+ concentration | M | +------------------+---------------------------------+---------------------+ | Chm_phCloud | Cloud pH | 1 | +------------------+---------------------------------+---------------------+ | Chm_phSav | ISORROPIA aerosol pH | 1 | +------------------+---------------------------------+---------------------+ | Chm_SO3AQ | Cloud sulfite concentration | mol/L | +------------------+---------------------------------+---------------------+ | Chm_SulRatSav | ISORROPIA sulfate concentration | M | +------------------+---------------------------------+---------------------+ | Chm_SSalk | Sea salt alkalinity | | +------------------+---------------------------------+---------------------+ | Chm_WaterSav | ISORROPIA aerosol water | :math:`{\mu}g/m3` | +------------------+---------------------------------+---------------------+ .. _histguide-statemet: StateMet -------- The **StateMet** collection contains met fields and other derived quantities that are carried in the State_Met object. **Sample definition section for HISTORY.rc** .. code-block:: kconfig StateMet.template: '%y4%m2%d2_%h2%n2z.nc4', StateMet.frequency: 00000100 000000 StateMet.duration: 00000100 000000 StateMet.mode: 'time-averaged' StateMet.fields: 'Met_AD ', 'Met_AIRDEN ', 'Met_AIRVOL ', 'Met_ALBD ', 'Met_AREAM2 ', 'Met_AVGW ', 'Met_BXHEIGHT ', 'Met_ChemGridLev', 'Met_CLDF ', 'Met_CLDFRC ', 'Met_CLDTOPS ', 'Met_DELP ', 'Met_DQRCU ', 'Met_DQRLSAN ', 'Met_DTRAIN ', 'Met_EFLUX ', 'Met_FRCLND ', 'Met_FRLAKE ', 'Met_FRLAND ', 'Met_FRLANDIC ', 'Met_FROCEAN ', 'Met_FRSEAICE ', 'Met_FRSNO ', 'Met_GWETROOT ', 'Met_GWETTOP ', 'Met_HFLUX ', 'Met_LAI ', 'Met_LWI ', 'Met_PARDR ', 'Met_PARDF ', 'Met_PBLTOPL ', 'Met_PBLH ', 'Met_PHIS ', 'Met_PMID ', 'Met_PMIDDRY ', 'Met_PRECANV ', 'Met_PRECCON ', 'Met_PRECLSC ', 'Met_PRECTOT ', 'Met_PS1DRY ', 'Met_PS1WET ', 'Met_PS2DRY ', 'Met_PS2WET ', 'Met_PSC2WET ', 'Met_PSC2DRY ', 'Met_QI ', 'Met_QL ', 'Met_OMEGA ', 'Met_OPTD ', 'Met_REEVAPCN ', 'Met_REEVAPLS ', 'Met_SLP ', 'Met_SNODP ', 'Met_SNOMAS ', 'Met_SPHU ', 'Met_SPHU1 ', 'Met_SPHU2 ', 'Met_SUNCOS ', 'Met_SUNCOSmid ', 'Met_SWGDN ', 'Met_T ', 'Met_TAUCLI ', 'Met_TAUCLW ', 'Met_THETA ', 'Met_TMPU1 ', 'Met_TMPU2 ', 'Met_TO3 ', 'Met_TropHt ', 'Met_TropLev ', 'Met_TropP ', 'Met_TS ', 'Met_TSKIN ', 'Met_TV ', 'Met_U ', 'Met_U10M ', 'Met_USTAR ', 'Met_UVALBEDO ', 'Met_V ', 'Met_V10M ', 'Met_Z0 ', :: **List of diagnostic fields in the StateMet collection** +------------------+---------------------------+---------------------+ | Diagnostic field | Description | Units | +==================+===========================+=====================+ | Met_AD | Dry air mass | kg | +------------------+---------------------------+---------------------+ | Met_AIRDEN | Dry air density | kg/m3 | +------------------+---------------------------+---------------------+ | Met_AIRVOL | Grid box volume, dry air | m3 | +------------------+---------------------------+---------------------+ | Met_ALBD | Surface albedo | 1 | +------------------+---------------------------+---------------------+ | Met_AREAM2 | Grid box area | m2 | +------------------+---------------------------+---------------------+ | Met_AVGW | Water vapor volume mixing | vol H2O/vol dry air | | | ratio | | +------------------+---------------------------+---------------------+ | Met_BXHEIGHT | Grid box height | m | +------------------+---------------------------+---------------------+ | Met_ChemGridLev | Chemistry grid level | 1 | +------------------+---------------------------+---------------------+ | Met_CLDF | 3-D cloud fraction | | +------------------+---------------------------+---------------------+ | Met_CLDFRC | Column cloud fraction | 1 | +------------------+---------------------------+---------------------+ | Met_CLDTOPS | Maximum cloud top height | 1 | +------------------+---------------------------+---------------------+ | Met_DELP | Delta-pressure between | hPa | | | top and bottom edges of | | | | grid box (wet air) | | +------------------+---------------------------+---------------------+ | Met_DQRCU | Convective precipitation | kg/kg/s | | | production rate (dry air) | | +------------------+---------------------------+---------------------+ | Met_DTRAIN | Detrainment flux | kg/m2/s | +------------------+---------------------------+---------------------+ | Met_EFLUX | Latent heat flux | W/m2 | +------------------+---------------------------+---------------------+ | Met_FRCLND | Olson land fraction | 1 | +------------------+---------------------------+---------------------+ | Met_FRLAKE | Fraction of grid box | 1 | | | covered by lakes | | +------------------+---------------------------+---------------------+ | Met_FRLAND | Fraction of grid box | 1 | | | covered by land | | +------------------+---------------------------+---------------------+ | Met_FRLANDIC | Fraction of grid box | 1 | | | covered by land ice | | +------------------+---------------------------+---------------------+ | Met_FROCEAN | Fraction of grid box | 1 | | | covered by ocean | | +------------------+---------------------------+---------------------+ | Met_FRSEAICE | Fraction of grid box | 1 | | | covered by sea ice | | +------------------+---------------------------+---------------------+ | Met_FRSNO | Fraction of grid box | 1 | | | covered by snow | | +------------------+---------------------------+---------------------+ | Met_GWETROOT | Root soil moisture | 1 | +------------------+---------------------------+---------------------+ | Met_GWETTOP | Topsoil moisture | 1 | +------------------+---------------------------+---------------------+ | Met_HFLUX | Sensible heat flux | W/m2 | +------------------+---------------------------+---------------------+ | Met_LAI | Leaf area index from met | m2/m2 | | | field archive | | +------------------+---------------------------+---------------------+ | Met_LWI | Land-water-ice indices | 1 | +------------------+---------------------------+---------------------+ | Met_PARDF | Diffuse | W/m2 | | | photosynthetically active | | | | radiation | | +------------------+---------------------------+---------------------+ | Met_PARDR | Diffuse | W/m2 | | | photosynthetically active | | | | radiation | | +------------------+---------------------------+---------------------+ | Met_PBLTOPL | PBL top layer | 1 | +------------------+---------------------------+---------------------+ | Met_PBLH | PBL height | m | +------------------+---------------------------+---------------------+ | Met_PHIS | Surface geopotential | m | | | height | | +------------------+---------------------------+---------------------+ | Met_PMID | Pressure at midpoint of | hPa | | | model layers, defined as | | | | arithmetic average of | | | | edge pressures (wet air) | | +------------------+---------------------------+---------------------+ | Met_PMIDDRY | Pressure at midpoint of | hPa | | | model layers, defined as | | | | arithmetic average of | | | | edge pressures (dry air) | | +------------------+---------------------------+---------------------+ | Met_PRECANV | Anvil precipitation (at | mm/day | | | surface) | | +------------------+---------------------------+---------------------+ | Met_PRECCON | Convective precipitation | mm/day | | | (at surface) | | +------------------+---------------------------+---------------------+ | Met_PRECLSC | Large-scale precipitation | mm/day | | | (at surface) | | +------------------+---------------------------+---------------------+ | Met_PRECTOT | Total precipitation (at | mm/day | | | surface) | | +------------------+---------------------------+---------------------+ | Met_PS1DRY | Instantaneous surface | hPa | | | pressure at start of 3-hr | | | | met field interval (dry | | | | air) | | +------------------+---------------------------+---------------------+ | Met_PS2DRY | Instantaneous surface | hPa | | | pressure at end of 3-hr | | | | met field interval (dry | | | | air) | | +------------------+---------------------------+---------------------+ | Met_PSC2DRY | Surface pressure | hPa | | | interpolated to current | | | | time (dry air) | | +------------------+---------------------------+---------------------+ | Met_PS1WET | Instantaneous surface | hPa | | | pressure at start of 3-hr | | | | met field interval (wet | | | | air) | | +------------------+---------------------------+---------------------+ | Met_PS2WET | Instantaneous surface | hPa | | | pressure at end of 3-hr | | | | met field interval (wet | | | | air) | | +------------------+---------------------------+---------------------+ | Met_PSC2WET | Surface pressure | hPa | | | interpolated to current | | | | time (wet air) | | +------------------+---------------------------+---------------------+ | Met_QI | Ice mixing ratio (dry | kg/kg dry air | | | air) | | +------------------+---------------------------+---------------------+ | Met_QL | Liquid water mixing ratio | kg/kg dry air | | | (dry air) | | +------------------+---------------------------+---------------------+ | Met_OMEGA | Updraft velocity | Pa/s | +------------------+---------------------------+---------------------+ | Met_OPTD | Visible optical depth | 1 | +------------------+---------------------------+---------------------+ | Met_REEVAPCN | Evaporation of convective | kg/kg/s | | | precipitation (dry air) | | +------------------+---------------------------+---------------------+ | Met_REEVAPLS | Evaporation of | kg/kg/s | | | large-scale + anvil | | | | precipitation (dry air) | | +------------------+---------------------------+---------------------+ | Met_SLP | Sea level pressure | hPa | +------------------+---------------------------+---------------------+ | Met_SNODP | Snow depth | m | +------------------+---------------------------+---------------------+ | Met_SNOMAS | Snow mass | kg/m2 | +------------------+---------------------------+---------------------+ | Met_SPHU1 | Instantaneous specific | kg/kg | | | humidity at start of 3 hr | | | | met field interval (wet | | | | air) | | +------------------+---------------------------+---------------------+ | Met_SPHU2 | Instantaneous specific | kg/kg | | | humidity at end of 3-hr | | | | met field interval (wet | | | | air) | | +------------------+---------------------------+---------------------+ | Met_SPHU | Specific humidity | g H2O/kg air | | | interpolated to current | | | | time (wet air) | | +------------------+---------------------------+---------------------+ | Met_SUNCOS | Cosine of solar zenith | 1 | | | angle at current time | | +------------------+---------------------------+---------------------+ | Met_SUNCOSMID | Cosine of solar zenith | 1 | | | angle at midpoint of | | | | chemistry timestep | | +------------------+---------------------------+---------------------+ | Met_SWGDN | Incident shortwave | W/m2 | | | radiation at ground | | +------------------+---------------------------+---------------------+ | Met_TAUCLI | Visible optical depth of | 1 | | | ice clouds | | +------------------+---------------------------+---------------------+ | Met_TAUCLW | Visible optical depth of | 1 | | | water clouds | | +------------------+---------------------------+---------------------+ | Met_THETA | Potential temperature | K | +------------------+---------------------------+---------------------+ | Met_TMPU1 | Instantaneous temperature | K | | | at start of 3-hr met | | | | field interval | | +------------------+---------------------------+---------------------+ | Met_TMPU2 | Instantaneous temperature | K | | | at end of 3-hr met field | | | | interval | | +------------------+---------------------------+---------------------+ | Met_T | Temperature interpolated | K | | | to current time | | +------------------+---------------------------+---------------------+ | Met_TO3 | Total overhead ozone | Dobsons | | | column | | +------------------+---------------------------+---------------------+ | Met_TropHt | Tropopause height | u | +------------------+---------------------------+---------------------+ | Met_TropLev | Tropopause level | 1 | +------------------+---------------------------+---------------------+ | Met_TROPP | Tropopause pressure | hPa | +------------------+---------------------------+---------------------+ | Met_TS | Surface temperature | K | +------------------+---------------------------+---------------------+ | Met_TSKIN | Surface skin temperature | K | +------------------+---------------------------+---------------------+ | Met_U | East-west ccomponent of | m/s | | | wind | | +------------------+---------------------------+---------------------+ | Met_U10M | East-west component of | m/s | | | wind at 10 m height above | | | | surface | | +------------------+---------------------------+---------------------+ | Met_USTAR | Friction velocity | m/s | +------------------+---------------------------+---------------------+ | Met_UVALBEDO | Ultraviolet surface | 1 | | | albedo | | +------------------+---------------------------+---------------------+ | Met_V | North-south ccomponent of | m/s | | | wind | | +------------------+---------------------------+---------------------+ | Met_V10M | North-south component of | m/s | | | wind at 10 m height above | | | | surface | | +------------------+---------------------------+---------------------+ | Met_Z0 | Surface roughness height | m | +------------------+---------------------------+---------------------+ | FracOfTimeInTrop | Fraction of time spent in | 1 | | | the troposphere | | +------------------+---------------------------+---------------------+ .. _histguide-stratbm: StratBM ------- The **StratBM** collection contains diagnostic fields for GEOS-Chem 10-year stratospheric benchmark simulations. Unless you are involved with benchmarking GEOS-Chem, you may leave this collection deactivated. **Sample definition section for the StratBM collection** .. code-block:: kconfig StratBM.template: '%y4%m2%d2_%h2%n2z.nc4', StratBM.frequency: 00000000 010000 StratBM.duration: 00000001 000000 StratBM.mode: 'time-averaged' StratBM.fields: 'SpeciesConcVV_NO2 ', 'SpeciesConcVV_O3 ', 'SpeciesConcVV_ClO ', 'Met_PSC2WET ', 'Met_BXHEIGHT ', 'Met_AIRDEN ', 'Met_AD ', :: **List of diagnostic fields in the StateMet collection** +-------------------+---------------------------+-----------------+ | Diagnostic field | Description | Units | +===================+===========================+=================+ | Met_AD | Dry air mass | kg | +-------------------+---------------------------+-----------------+ | Met_AIRDEN | Dry air density | kg/m3 | +-------------------+---------------------------+-----------------+ | Met_BXHEIGHT | Grid box height | m | +-------------------+---------------------------+-----------------+ | Met_PSC2WET | Surface pressure | hPa | | | interpolated to current | | | | time (wet air) | | +-------------------+---------------------------+-----------------+ | SpeciesConcVV_ClO | ClO concentration | mol/mol dry air | +-------------------+---------------------------+-----------------+ | SpeciesConcVV_NO2 | NO2 concentration | mol/mol dry air | +-------------------+---------------------------+-----------------+ | SpeciesConcVV_O3 | O3 concentration | mol/mol dry air | +-------------------+---------------------------+-----------------+ .. _histguide-tomas: Tomas ----- The **TOMAS** collection contains diagnostic fields for fullchem simulations with TOMAS aerosol microphysics. .. code-block:: kconfig Tomas.template: '%y4%m2%d2_%h2%n2z.nc4', Tomas.format: 'CFIO', Tomas.timestampStart: .true. Tomas.monthly: 0 Tomas.frequency: 010000 Tomas.duration: 010000 Tomas.mode: 'time-averaged' Tomas.fields: 'TomasH2SO4mass_?TOMASBIN? ', #---------------------------------------------- # NOTE: for GEOS-Chem Classic you can use the # ?TOMASBIN? wildcard. For GCHP you will need # to list each diagnostic field individually # such as is shown below: #'TomasH2SO4mass_bin01 ', #'TomasH2SO4mass_bin02 ', #'TomasH2SO4mass_bin03 ', #'TomasH2SO4mass_bin04 ', #'TomasH2SO4mass_bin05 ', #'TomasH2SO4mass_bin06 ', #'TomasH2SO4mass_bin07 ', #'TomasH2SO4mass_bin08 ', #'TomasH2SO4mass_bin09 ', #'TomasH2SO4mass_bin10 ', #'TomasH2SO4mass_bin11 ', #'TomasH2SO4mass_bin12 ', #'TomasH2SO4mass_bin13 ', #'TomasH2SO4mass_bin14 ', #'TomasH2SO4mass_bin15 ', #---------------------------------------------- 'TomasH2SO4number_?TOMASBIN? ', 'TomasCOAGmass_?TOMASBIN ', 'TomasCOAGnumber_?TOMASBIN? ', 'TomasNUCRATEFN ', 'TomasNUCLmass_?TOMASBIN? ', 'TomasNUCLnumber_?TOMASBIN? ', 'TomasNUCRATEnumber_?TOMASBIN? ', 'TomasAQOXmass_?TOMASBIN? ', 'TomasAQOXnumber_?TOMASBIN? ', 'TomasMNFIXmass_?TOMASBIN? ', 'TomasMNFIXnumber_?TOMASBIN? ', 'TomasMNFIXh2so4mass_?TOMASBIN? ', 'TomasMNFIXh2so4number_?TOMASBIN? ', 'TomasMNFIXcoagmass_?TOMASBIN? ', 'TomasMNFIXcoagnumber_?TOMASBIN? ', 'TomasMNFIXaqoxmass_?TOMASBIN? ', 'TomasMNFIXaqoxnumber_?TOMASBIN? ', 'TomasMNFIXezwat1number_?TOMASBIN?', 'TomasMNFIXezwat2mass_?TOMASBIN? ', 'TomasMNFIXezwat2number_?TOMASBIN?', 'TomasMNFIXezwat3mass_?TOMASBIN? ', 'TomasMNFIXezwat3number_?TOMASBIN?', 'TomasMNFIXcheck1mass_?TOMASBIN? ', 'TomasMNFIXcheck1number_?TOMASBIN?', 'TomasMNFIXcheck2mass_?TOMASBIN? ', 'TomasMNFIXcheck2number_?TOMASBIN?', 'TomasMNFIXcheck3mass_?TOMASBIN? ', 'TomasMNFIXcheck3number_?TOMASBIN?', 'TomasSOAmass_?TOMASBIN? ', 'TomasSOAnumber_?TOMASBIN? ', :: **List of diagnostic fields for the Tomas collection** +----------------------------+-------------------------------+---------+----------+ | Diagnostic field | Description | Units | Wildcard | +============================+===============================+=========+==========+ | TomasAQOXmass\_\ | TomasAQOX mass rate | kg/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasAQOXnumber\_\ | TomasAQOX number rate | #/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasCOAGmass\_\ | TOMASCOAG mass rate | kg/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasCOAGnumber\_\ | TomasCOAG number rate | #/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasH2SO4mass\_\ | TomasH2SO4 mass rate | kg/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasH2SO4number\_\ | TomasH2SO4 number rate | #/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIX | Tomas error rate | 1 | [#R]_ | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIXmass\_\ | TomasMNFIX mass rate | kg/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIXnumber\_\ | TomasMNFIX number rate | #/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIXaqoxmass\_\ | TOMASMNFIXAQOX mass rate | kg/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIXaqoxnumber\_ | TOMASMNFIXAQOX number rate | #/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIXcoagmass\_\ | TomasMNFIXCOAG mass rate | kg/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIXcoagnumber\_\ | TomasMNFIXCOAG number rate | #/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIXcheck1mass\_\ | TOMASMNFIXCHECK1 mass rate | kg/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIXcheck1number\_\ | TOMASMNFIXCHECK1 number rate | #/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIXcheck2mass\_\ | TOMASMNFIXCHECK2 mass rate | kg/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIXcheck2number\_\ | TOMASMNFIXCHECK2 number rate | #/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIXcheck3mass\_\ | TOMASMNFIXCHECK3 mass rate | kg/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIXcheck3number\_\ | TOMASMNFIXCHECK3 number rate | #/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIXezwat1mass\_\ | TOMASMNFIXEZWAT1 mass rate | kg/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIXezwat1number\_\ | TOMASMNFIXEZWAT1 number rate | #/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIXezwat2mass\_\ | TOMASMNFIXEZWAT2 mass rate | kg/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIXezwat2number\_\ | TOMASMNFIXEZWAT2 number rate | #/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIXezwat3mass\_\ | TOMASMNFIXEZWAT3 mass rate | kg/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIXezwat3number\_\ | TOMASMNFIXEZWAT3 number rate | #/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIXh2so4mass\_\ | TomasMNFIXH2SO4 mass rate | kg/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasMNFIXh2so4number\_\ | TomasMNFIXH2SO4 number rate | #/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasNUCL | Tomas nucleation rate | 1 | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasNUCLmass\_\ | TomasNUCL mass rate | kg/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasNUCLnumber\_\ | TomasNUCL number rate | #/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasSOA | TomasSOA rate | 1 | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasSOAmass\_\ | TomasSOA mass rate | kg/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ | TomasSOAnumber\_\ | TomasSOA number rate | #/kg/s | [#R]_ | | | | | | +----------------------------+-------------------------------+---------+----------+ .. rubric:: Notes for the Tomas collection .. [#R] This diagnostic field can use the ?TOMASBIN? wildcard (for GEOS-Chem Classic only). .. _histguide-uvflux: UVFlux ------ The **UVFlux** diagnostic contains diffuse, direct, and net UV fluxes at each of the photolysis wavelength bins. **Sample definition section for HISTORY.rc** .. code-block:: kconfig UVFlux.template: '%y4%m2%d2_%h2%n2z.nc4', UVFlux.frequency: 00000100 000000 UVFlux.duration: 00000100 000000 UVFlux.mode: 'time-averaged' UVFlux.template: 'UVFluxDiffuse_?UVFLX?', 'UVFluxDirect_?UVFLX? ', 'UVFluxNet_?UVFLX? ', :: **List of diagnostic fields in the UvFlux collection** +--------------------------+-----------------------------------+-------+-----------+ | Diagnostic field | Description | Units | Wildcards | +==========================+===================================+=======+===========+ | UVFluxDiffuse_ | Diffuse UV flux in wavelength bin | W/m2 | ?UVFLX? | +--------------------------+-----------------------------------+-------+-----------+ | UVFluxDirect_ | Direct UV flux in wavelength bin | W/m2 | ?UVFLX? | +--------------------------+-----------------------------------+-------+-----------+ | UVFluxNet_ | Net UV flux in wavelength bin | W/m2 | ?UVFLX? | +--------------------------+-----------------------------------+-------+-----------+ .. _histguide-wetlossconv: WetLossConv ----------- The **WetLossConv** collection contains diagnostics fluxes of soluble species lost to wet scavenging in convective updrafts. **Sample definition section for HISTORY.rc** .. code-block:: kconfig WetLossConv.template: '%y4%m2%d2_%h2%n2z.nc4', WetLossConv.frequency: 00000100 000000 WetLossConv.duration: 00000100 000000 WetLossConv.mode: 'time-averaged' WetLossConv.fields: 'WetLossConv_?WET? ', 'WetLossConvFrac_?WET?', :: **List of diagnostic fields in the WetLossConv collection** +---------------------------+-------------------------------+--------+----------+ | Diagnostic field | Description | Units | Wildcard | +===========================+===============================+========+==========+ | WetLossConv_ | Loss of soluble species | kg/s | ?WET? | | | scavenged by cloud updrafts | | | | | in moist convection | | | +---------------------------+-------------------------------+--------+----------+ | WetLossConvFrac_ | Fraction of species scavenged | 1 | ?WET? | | | by cloud updrafts in moist | | | | | convection | | | +---------------------------+-------------------------------+--------+----------+ .. _histguide-wetlossls: WetLossLS --------- The **WetLossLS** collection contains diagnostics fluxes of soluble species lost to rainout and washout in large-scale wet deposition. **Sample definition section for HISTORY.rc** .. code-block:: kconfig WetLossLS.template: '%y4%m2%d2_%h2%n2z.nc4', WetLossLS.frequency: 00000100 000000 WetLossLS.duration: 00000100 000000 WetLossLS.mode: 'time-averaged' WetLossLS.fields: 'WetLossLS_?WET?', :: **List of diagnostic fields in the WetLossLS collection** +---------------------+------------------------------+--------+---------+ | Diagnostic field | Description | Units | Wildcard | +=====================+==============================+=======+==========+ | WetLossLS_ | Loss of soluble species | kg/s | ?WET? | | | in large-scale precipitation | | | +---------------------+------------------------------+-------+----------+ .. _histguide-add-new-diags: ============================== Adding new History diagnostics ============================== To add your own diagnostics we recommend that you find a similar existing diagnostic and use its implementation as a template. Most of the work is done in :file:`Headers/state_diag_mod.F90`. Briefly, the following updates to that file are essential for adding in your own netCDF diagnostics: #. Declare diagnostic array at top of module. |br| |br| #. Set diagnostic array pointer to null in :code:`Zero_State_Diag` subroutine. |br| |br| #. Create a section in :code:`Init_State_Diag` subroutine to allocate and register the array. |br| |br| #. Deallocate the diagnostic array in subroutine :code:`Cleanup_State_Diag`. |br| |br| #. Add an :code:`IF` block for the diagnostic within subroutine :code:`Get_Metadata_State_Diag` to define its metadata, making sure to list the diagnostic name with all capital letters. Good diagnostics to use as templates are :code:`SpeciesConcVV` for 3-dimensional arrays that are for all species and :code:`DryDepVel` for 2-dimensional arrays that are for a subset of species. If your diagnostic is not per species then :code:`AODDust` is a good diagnostic to look at. Search the file :code:`Headers/state_diag_mod.F90` for any of these strings to find all instances of code related to their implementation. Note that information about the dimensions and species collection the diagnostic will include must be specified when allocating the array in :code:`Init_State_Diag` and in :code:`Get_Metadata_State_Diag`. In the latter subroutine the :code:`Rank` is the integer number of dimensions of the diagnostic (not including species) and the :code:`TagID` string, if any, specifies the species collection to output the diagnostic per. Each :code:`TagID` is defined in subroutine Get_TagInfo. Each TagID string can also be used as a wildcard within :file:`HISTORY.rc` to simplify diagnostic name specification (for GEOS-Chem Classic only). Once you have implemented your diagnostic in :code:`Headers/state_diag_mod.F90`, try adding it to HISTORY.rc and running. You should get your diagnostic output in the netCDF output file as all zeros. The next step is to populate the array with whatever value you want to output. You should do this by passing the :code:`State_Diag` array to the location where you want to set the values. Then write code to fill the array. A simple test of your understanding is to initially set values to a constant other than zero and see if the output matches what you set the arrays to. For additional help implementing your own GEOS-Chem diagnostics please contact the GEOS-Chem Support Team.