Difference between revisions of "GCHP Run Configuration Files"

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=== input.geos ===
 
=== input.geos ===
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Other parts of the GEOS-Chem Classic <tt>input.geos</tt> file that are not relevant to GCHP are simply not included in the file that is copied to the GCHP run directory.
 
Other parts of the GEOS-Chem Classic <tt>input.geos</tt> file that are not relevant to GCHP are simply not included in the file that is copied to the GCHP run directory.
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=== HEMCO_Config.rc ===
 
=== HEMCO_Config.rc ===
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Like <tt>input.geos</tt>, information about the <tt>HEMCO_Config.rc</tt> file is the same as for GEOS-Chem Classic with a few exceptions. See the [[The_HEMCO_Config.rc_file
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|HEMCO_Config.rc file wiki page]] for an overview of the file.
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Some content of the <tt>HEMCO_Config.rc</tt> file is ignored by GCHP. This is because MAPL ExtData handles file input rather than HEMCO in GCHP.
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Items at the top of the file that are ignored include:
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*ROOT data directory path
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*METDIR path
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*DiagnPrefix
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*DiagnFreq
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*Wildcard
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In the BASE EMISSIONS section and beyond, columns that are ignored include:
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*sourceFile
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*sourceVar
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*sourceTime
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*C/R/E
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*SrcDim
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*SrcUnit
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All of the above information is specified in file <tt>ExtData.rc</tt> instead with the exception of diagnostic prefix and frequency. Diagnostic filename and frequency information is specified in <tt>HISTORY.rc</tt>.
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=== HEMCO_Diagn.rc ===
 
=== HEMCO_Diagn.rc ===
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Like in GEOS-Chem Classic, the <tt>HEMCO_Diagn.rc</tt> file is used to map between HEMCO containers and output file diagnostic names. However, while all uncommented diagnostics listed in <tt>HEMCO_Diagn.rc</tt> are output as HEMCO diagnostics in GEOS-Chem Classic, only the subset also listed in <tt>HISTORY.rc</tt> are output in GCHP. See the [[The_HEMCO_Diagn.rc_file|HEMCO_Diagn.rc file wiki page]] for an overview of the file.
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=== input.nml ===
 
=== input.nml ===

Revision as of 00:22, 17 November 2020

Previous | Getting Started with GCHP | GCHP Main Page

  1. Hardware and Software Requirements
  2. Setting Up the GCHP Environment
  3. Downloading Source Code and Data Directories
  4. Compiling
  5. Obtaining a Run Directory
  6. Running GCHP: Basics
  7. Running GCHP: Configuration
  8. Output Data
  9. Developing GCHP
  10. Run Configuration Files


Overview

GCHP is controlled using a set of resource configuration files that are included in the GCHP run directory, most of which are denoted by suffix .rc. These files contain information required by GCHP including hardware allocation, initialization and runtime parameters, locations of necessary files, and where, what and how to read and write data to and from GCHP. Files include:

  1. CAP.rc
  2. ExtData.rc
  3. GCHP.rc
  4. input.geos
  5. HEMCO_Config.rc
  6. HEMCO_Diagn.rc
  7. input.nml
  8. HISTORY.rc

Updating configuration files

Several run-time settings must be set consistently across multiple files. Inconsistencies may result in your program crashing or yielding unexpected results. To avoid mistakes and make run configuration easier, we therefore include bash shell script runConfig.sh in run directories to update the most commonly used settings in the configuration files. Sourcing this script will update other config files to use values specified in runConfig.sh. This is done automatically at run start if using any of the example run scripts provided with GCHP. The updated settings will be printed to the GCHP log file by default.

Using runConfig.sh to configure common settings makes run configure much simpler, but also comes with peril. If you manually edit a config file setting that is also set in runConfig.sh then the setting in runConfig.sh will be used. For example, most frequency and duration settings for diagnostics in HISTORY.rc are set in runConfig.sh. File runConfig.sh must be edited rather than HISTORY.rc to change frequency and duration of output files. Please get very familiar with the options in runConfig.sh and be conscientious about not updating the same setting elsewhere.

While much of the labor of updating the various configuration files has been eliminated by runConfig.sh, it is still worth understanding what is happening under the hood with the other files. This page details the settings within those other configuration files and what they are used for.

Configuration file descriptions

The following table lists the core functions of each of the configuration files in the GCHP run directory. See the individual subsections on each file for additional information.

File Primary function in GCHP
CAP.rc Controls parameters used by the highest level gridded component (CAP). This includes simulation run time information, name of the Root gridded component (GCHP), config filenames for Root and History, and toggles for certain MAPL logging utilities (timers, memory, and import/export name printing).
ExtData.rc Config file for the MAPL ExtData component. Specifies input variable information, including name, regridding method, read frequency, offset, scaling, and file path. All GCHP imports must be specified in this file. Toggles at the top of the file enable MAPL ExtData debug prints and using most recent year if current year of data is unavailable. Default values may be used by specifying file path /dev/null.
GCHP.rc Controls high-level aspects of the simulation, including grid type and resolution, core distribution, stretched-grid parameters, timesteps, and restart file configuration.
input.geos Primary config file for GEOS-Chem. Same function as in GEOS-Chem Classic except grid, simulation start/end, met field source, timers, and data directory information are ignored.
HEMCO_Config.rc Contains emissions information used by HEMCO. Same function as in GEOS-Chem Classic except only HEMCO name, species, scale IDs, category, and hierarchy are used. Diagnostic frequency, file path, read frequency, and units are ignored, and are instead stored in GCHP config file ExtData.rc. All HEMCO variables listed in HEMCO_Config.rc for enabled emissions must also have an entry in ExtData.rc.
HEMCO_Diagn.rc Contains information mapping HISTORY.rc diagnostic names to HEMCO containers. Same function as in GEOS-Chem Classic except that not all items in HEMCO_Diagn.rc will be output; only emissions listed in HISTORY.rc will be included in diagnostics. All GCHPctm diagnostics listed in HISTORY.rc that start with Emis, Hco, or Inv must have a corresponding entry in HEMCO_Diagn.rc.
input.nml Namelist used in advection for domain stack size and stretched grid parameters.
HISTORY.rc Config file for the MAPL History component. Configures diagnostic output from GCHP.


CAP.rc

CAP.rc is the configuration file for the top-level gridded component called CAP. This gridded component can be thought of as the primary driver of GCHP. Its config file handles general runtime settings for GCHP including time parameters, performance profiling routines, and system-wide timestep (hearbeat). Combined with output file cap_restart, CAP.rc configures the exact dates for the next GCHP run.

Parameter Description
ROOT_NAME Sets the name MAPL uses to initialize the ROOT child gridded component component within CAP. CAP uses this name in all operations when querying and interacting with ROOT. It is set to GCHP.
ROOT_CF Resource configuration file for the ROOT component. It is set to GCHP.rc.
HIST_CF Resource configuration file for the MAPL HISTORY gridded component (another child gridded component of CAP). It is set to HISTORY.rc.
BEG_DATE Simulation begin date in format YYYYMMDD hhmmss. This parameter is overrided in the presence of output file cap_restart containing a different start date.
END_DATE Simulation end date in format YYYYMMDD hhmmss. If BEG_DATE plus duration (JOB_SGMT) is before END_DATE then simulation will end at BEG_DATE + JOB_SGMT. If it is after then simulation will end at END_DATE.
JOB_SGMT Simulation duration in format YYYYMMDD hhmmss. The duration must be less than or equal to the difference between start and end date or the model will crash.
HEARTBEAT_DT The timestep of the ESMF/MAPL internal clock, in seconds. All other timesteps in GCHP must be a multiple of HEARTBEAT_DT. ESMF queries all components at each heartbeat to determine if computation is needed. The result is based upon individual component timesteps defined in GCHP.rc.
MAPL_ENABLE_TIMERS Toggles printed output of runtime MAPL timing profilers. This is set to YES. Timing profiles are output at the end of every GCHP run.
MAPL_ENABLE_MEMUTILS Enables runtime output of the programs' memory usage. This is set to YES.
PRINTSPEC Allows an abbreviated model run limited to initializat and print of Import and Export state variable names. Options include: 0 (default): Off; 1: Imports and Exports only; 2: Imports only; and 3: Exports only.
USE_SHMEM This setting is deprecated but still has an entry in the file.
REVERSE_TIME Enables running time backwards in CAP. Default is 0 (off).


ExtData.rc

ExtData.rc contains input variable and file read information for GCHP. Explanatory information about the file is located at the top of the configuration file in all run directories. The file format is the same as that used in the GEOS model, and GMAO/NASA documentation for it can be found at the ExtData component page on the GEOS-5 wiki.

The following two parameters are set at the top of the file:

Parameter Name Description
Ext_AllowExtrat Logical toggle to use data from nearest year available. This is set to true for GCHP. Note that GEOS-Chem Classic accomplishes the same effect but with more flexibility in HEMCO_Config.rc. That functionality of HEMCO_Config.rc is ignored in GCHP.
DEBUG_LEVEL Turns MAPL ExtData debug prints on/off. This is set to 0 in GCHP (off), but may be set to 1 to enable. Beware that turning on ExtData debug prints greatly slows down the model, and prints are only done from the root thread. Use this when debugging problems with input files.

The rest of the file contains space-delimited lines, one for each variable imported to the model from an external file. Columns are as follows in order as they appear left to right in the file:

Name in Column Header Description
Export Name Name of imported met field (e.g. ALBD) or HEMCO emissions container name (e.g. GEIA_NH3_ANTH).
Units Unit string nested within single quotes. '1' indicates there is no unit conversion from the native units in the netCDF file.
Clim Enter Y if the file is a 12 month climatology, otherwise enter N. If you specify it is a climatology ExtData the data can be on either one file or 12 files if they are templated appropriately with one per month.
Conservative Enter Y the data should be regridded in a mass conserving fashion through a tile file. F;{VALUE} can also be used for fractional regridding. Otherwise enter N to use the non-conervative bilinear regridding.
Refresh Time Template Possible values include:
  • -: The field will only be updated once the first time ExtData runs
  • 0: Update the variable at every step. ExtData will do a linear interpolation to the current time using the available data.
  • %y4-%m2-%h2T%h2:%n2:00: Set the recurring time to update the file. The file will be updated when the evaluated template changes. For example, a template in the form %y4-%m2-%d2T12:00:00 will cause the variable to be updated at the start of a new day (i.e. when the clock hits 2007-08-02T00:00:00 it will update the variable but the time it will use for reading and interpolation is 2007-08-02T12:00:00).
Offset Factor Factor the variable will be shifted by. Use none for no shifting.
Scale Factor Factor the variable will be scaled by. Use none for no scaling.
External File Variable The name of the variable in the netCDF data file, e.g. ALBEDO in met fields.
External File Template Path to the netCDF data file. If not using the data, specify /dev/null to reduce processing time. If there are no tokens in the template name ExtData will assume that all the data is on one file. Note that if the data on file is at a different resolution that the application grid, the underlying I/O library ExtData uses will regrid the data to the application grid.


GCHP.rc

GCHP.rc is the resource configuration file for the ROOT component within GCHP. The ROOT gridded component includes three children gridded components, including one each for GEOS-Chem, FV3 advection, and the data utility environment needed to support them.

Parameter Description
NX, NY Number of grid cells in the two MPI sub-domain dimensions. NX * NY must equal the number of CPUs. NY must be a multiple of 6.
GCHP.GRID_TYPE Type of grid GCHP will be run at. Should always be Cubed-Sphere.
GCHP.GRIDNAME Descriptive grid label for the simulation. The default grid name is PE24x144-CF. The grid name includes how the pole is treated, the face side length, the face side length times six, and whether it is a Cubed Sphere Grid or Lat/Lon. The name PE24x144-CF indicates polar edge (PE), 24 cells along one face side, 144 for 24*6, and a cubed-sphere grid (CF). Many options here are defined in MAPL_Generic.
Must be consistent with IM and JM.'
GCHP.NF Number of cubed-sphere faces. This is set to 6.
GCHP.IM_WORLD Number of grid cells on the side of a single cubed sphere face.
Get a rough idea of equivalent lat/lon resolution by dividing 90 by IM. Choose your timestep settings accordingly (see RUN_DT below).
GCHP.IM Number of grid cells on the side of a single cubed sphere face.
Get a rough idea of equivalent lat/lon resolution by dividing 90 by IM. Choose your timestep settings accordingly (see RUN_DT below).
GCHP.JM Number of grid cells times 6, essentially defining the second dimension if all six faces are stacked in a 2-dimensional array.
Must be to equal to IM*6.
GCHP.LM Number of vertical grid cells. The default value is 72.
Must be equal to the vertical resolution of the offline meteorological fields since MAPL cannot regrid vertically
GCHP.STRETCH_FACTOR
GCHP.TARGET_LON
GCHP.TARGET_LAT
IM
JM
LM
GEOChem_CTM A toggle that tells FVDycore that it is operating as a transport model rather than a prognostic model if set to 1.
AdvCore_Advection Default is 1.
DYCORE Should either be set to OFF (default) or ON. This value does nothing, but MAPL will crash if it is not declared.
HEARTBEAT_DT The timestep in seconds that the DYCORE Component should be called. Default is 600.
Must be a multiple of HEARTBEAT_DT in CAP.rc.
SOLAR_DT The timestep in seconds that the SOLAR Component should be called. Default is 600.
Must be a multiple of HEARTBEAT_DT in CAP.rc.
IRRAD_DT The timestep in seconds that the IRRAD Component should be called. ESMF checks this value during its timestep check. Default is 600.
Must be a multiple of HEARTBEAT_DT in CAP.rc.
RUN_DT The timestep in seconds that the RUN Component should be called. ESMF checks this value during its timestep check. The recommended timestep [s] per grid resolution (see IM) are: 1800 (4x5); 900 (2x2.5); 600 (1x1.25); 600 (1/2 degree); 300 (1/4 degree).
Must be a multiple of HEARTBEAT_DT in CAP.rc.
GCHPchem_DT The timestep in seconds that the GIGCchem Component should be called. ESMF checks this value during its timestep check. Default is 1200.
Must be a multiple of HEARTBEAT_DT in CAP.rc.
RRTMG_DT The timestep in seconds that the GIGCchem Component should be called. ESMF checks this value during its timestep check. Default is 1200.
Must be a multiple of HEARTBEAT_DT in CAP.rc.
DYNAMICS_DT The timestep in seconds that the DYNAMICS Component should be called. ESMF checks this value during its timestep check. Default is 600.
Must be a multiple of HEARTBEAT_DT in CAP.rc.
SOLARAvrg, IRRADAvrg Default is 0.
GCHPchem_REFERENCE_TIME
PRINTRC Specifies which resource values to print. Options include 0: Non-Default Values, and 1: All Values. Default setting is 0.
PARALLEL_READFORCING Enables or disables parallel I/O processes when writing the restart files. Default value is 0 (disabled).
NUM_READERS, NUM_WRITERS Number of simultaneous readers. Should divide evenly unto NY. Default value is 1.
BKG_FREQUENCY Active observer when desired. Default value is 0.
RECORD_FREQUENCY
RECORD_REF_DATE
RECORD_REF_TIME
GCHOchem_INTERNAL_RESTART_FILE The filename of the internal restart file to be written.
GCHPchem_INTERNAL_RESTART_TYPE The format of the internal restart file. Valid types include pbinary and pnc4.
GCHPchem_INTERNAL_CHECKPOINT_FILE The filename of the internal checkpoint file to be written.
GCHPchem_INTERNAL_CHECKPOINT_TYPE The format of the internal checkstart file. Valid types include pbinary and pnc4.
GCHPchem_INTERNAL_HEADER Only needed when the file type is set to pbinary. Specifies if a binary file is self-describing.
DYN_INTERNAL_RESTART_FILE The filename of the DYNAMICS internal restart file to be written.
DYN_INTERNAL_RESTART_TYPE The format of the DYNAMICS internal restart file. Valid types include pbinary and pnc4.
DYN_INTERNAL_CHECKPOINT_FILE The filename of the DYNAMICS internal checkpoint file to be written.
DYN_INTERNAL_CHECKPOINT_TYPE The format of the DYNAMICS internal checkpoint file. Valid types include pbinary and pnc4.
DYN_INTERNAL_HEADER Only needed when the file type is set to pbinary. Specifies if a binary file is self-describing.
RUN_PHASES This is 1 in GCHP.
HEMCO_CONFIG Name of the HEMCO configuration file. Default is HEMCO_Config.rc.
STDOUT_LOGFILE Log filename template. Default is PET%%%%%.GEOSCHEMchem.log.
STDOUT_LOGLUN Logical unit number for stdout. Default value is 700.
MEMORY_DEBUG_LEVEL Default is 0 (off).
WRITE_RESTART_BY_OSERVER


input.geos

Information about the input.geos file is the same as for GEOS-Chem Classic with a few exceptions. See the input.geos file wiki page for an overview of the file.

The input.geos file used in GCHP is different in the following ways:

  • Start/End datetimes are ignored. Set this information in CAP.rc instead.
  • Root data directory is ignored. All data paths are specified in ExtData.rc instead with the exception of the FAST-JX data directory which is still listed (and used) in input.geos.
  • Met field is ignored. Met field source is described in file paths in ExtData.rc.
  • GC classic timers setting is ineffectual. GEOS-Chem Classic timers code is not compiled when building GCHP.

Other parts of the GEOS-Chem Classic input.geos file that are not relevant to GCHP are simply not included in the file that is copied to the GCHP run directory.


HEMCO_Config.rc

Like input.geos, information about the HEMCO_Config.rc file is the same as for GEOS-Chem Classic with a few exceptions. See the [[The_HEMCO_Config.rc_file |HEMCO_Config.rc file wiki page]] for an overview of the file.

Some content of the HEMCO_Config.rc file is ignored by GCHP. This is because MAPL ExtData handles file input rather than HEMCO in GCHP.

Items at the top of the file that are ignored include:

  • ROOT data directory path
  • METDIR path
  • DiagnPrefix
  • DiagnFreq
  • Wildcard

In the BASE EMISSIONS section and beyond, columns that are ignored include:

  • sourceFile
  • sourceVar
  • sourceTime
  • C/R/E
  • SrcDim
  • SrcUnit

All of the above information is specified in file ExtData.rc instead with the exception of diagnostic prefix and frequency. Diagnostic filename and frequency information is specified in HISTORY.rc.


HEMCO_Diagn.rc

Like in GEOS-Chem Classic, the HEMCO_Diagn.rc file is used to map between HEMCO containers and output file diagnostic names. However, while all uncommented diagnostics listed in HEMCO_Diagn.rc are output as HEMCO diagnostics in GEOS-Chem Classic, only the subset also listed in HISTORY.rc are output in GCHP. See the HEMCO_Diagn.rc file wiki page for an overview of the file.



input.nml

input.nml controls specific aspects of the FV3 dynamical core used for advection. Entries in input.nml are described below.

Parameter Description
&fms_nml Header for the FMS namelist which includes all variables directly below the header.
print_memory_usage Toggles memory usage prints to log. However, in practice turning it on or off does not have any effect.
domain_stack_size Domain stack size in bytes. This is set to 20000000 in GCHP to be large enough to use very few cores in a high resolution run. If the domain size is too small then you will get an "mpp domain stack size overflow error" in advection. If this happens, try increasing the domain stack size in this file.
&fv_core_nml Header for the finite-volume dynamical core namelist. This is commented out by default unless running on a stretched grid. Due to the way the file is read, commenting out the header declaration requires an additional comment character within the string, e.g. #&fv#_core_nml.
do_schmidt Logical for whether to use Schmidt advection. Set to .true. if using stretched grid; otherwise this entry is commented out.
stretch_fac Stretched grid factor, equal to the ratio of grid resolution in targeted high resolution region to the configured run resolution. This is commented out if not using stretched grid.
target_lat Target latitude of high resolution region if using stretched grid. This is commented out if not using stretched grid.
target_lon Target longitude of high resolution region if using stretched grid. This is commented out if not using stretched grid.


HISTORY.rc

The HISTORY.rc configuration file controls the diagnostic files output by GCHP. Information is organized into several sections:

  1. Single parameters set at the top of the file
  2. Grid label declaration list
  3. Definition for each grid in grid label list
  4. Variable collection declaration list
  5. Definition for each collection in collection list.

Single parameters set at the top of HISTORY.rc are as follows and apply to all collections:

Parameter Description
EXPID Filename prefix concatenated with each collection template string to define file path. It is set to OutputDir/GCHP so that all output diagnostic files are output to run subdirectory OutputDir and have filename begin with GCHP.
EXPDSC Export description included as attribute "Title" in output files
CoresPerNode Number of CPUs per node for your simulation.
VERSION Optional parameter included as attribute in output file.


The grid labels section of HISTORY.rc declares a list of descriptive grid strings followed by a definition for each declared grid label. Grids not in the grid label list may have definitions in the file; however, this will prevent them from being used in output collections. See the HISTORY.rc grid label section for syntax on declaring and defining grid labels.

Keywords that may be used for grid label definitions are in the table below. Note that this list is not exhaustive; MAPL may have additional keywords that may be used that have not yet been explored for use with GCHP.

Grid label keyword Description
GRID_TYPE Type of grid. May be Cubed-Sphere or LatLon.
IM_WORLD Side length of one cubed-sphere face, e.g. 24 if grid resolution is C24, or number of longitudinal grid boxes if lat-lon.
JM_WORLD Same as IM_WORLD but multiplied by 6 (number of faces), or number of latitudinal grid boxes if lat-lon.
POLE For lat-lon grids only. PC if latitudes are pole-centered and PE if latitudes are polar edge.
DATELINE For lat-lon grids only. DC if longitudes are dateline-centered and DE if longitudes are dateline-edge.
LAT_RANGE For lat-lon grids only. Regional grid latitudinal bounds.
LON_RANGE For lat-lon grids only. Regional grid longitudinal bounds.
LM Number of vertical levels.


The collections section of HISTORY.rc declares a list of descriptive strings that define unique collections of output variables and settings. As with grid labels, it is followed by a definition for each declared collection. Collections not in the collection list, or present but commented out, may have definitions in the file; however, this will prevent them from being output. See the HISTORY.rc collection section for syntax on declaring and defining output collections.

Keywords that may be used for collection definitions are in the table below. Note that this list is not exhaustive; MAPL may have additional keywords that may be used that have not yet been explored for use with GCHP.

Collection keyword Description
{COLLECTION}.template The output filename suffix that is appended to global parameter EXPID to define full output file path. Including a date string, such as '%y4%m2%d2, will insert the simulation start day following GrADS conventions. The default template for GCHP is set to %y4%m2%d2_%h2%n2z.nc4.
{COLLECTION}.format Character string defining the file format. Options include CFIO (default) for netCDF-4 or flat for binary files. Always output as CFIO when using GCHP.
{COLLECTION}.grid_label Declared grid label for output grid. If excluded the collection will be output on the cubed-sphere grid at native resolution, e.g. C24 if you run GCHP with grid resolution C24.
{COLLECTION}.conservative For lat-lon grids only. Set to 1 to conservatively regrid from cubed-sphere to lat-lon upon output. Exclude or set to 0 to use bilinear interpolation instead (not recommended).
{COLLECTION}.frequency The frequency at which output values are computed and archived, in format HHMMSS. For example, 010000 will calculate diagnostics every hour. The method of calculation is determined by the mode keyword. Unlike GEOS-Chem Classic, you cannot specify number of days, months, or years.
{COLLECTION}.duration The frequency at which files are written, in format HHMMSS. For example, 240000 will output daily files. The number of times in the file are determined by the frequency keyword. Unlike GEOS-Chem Classic, you cannot specify number of days, months, or years.
{COLLECTION}.mode Method of diagnostic calculation. Options are either instantaneous or time-averaged.
{COLLECTION}.fields List of character string pairs including diagnostic name and gridded component. All GCHP diagnostics belong to the GCHPchem gridded component.
Diagnostic names have prefixes that determine where MAPL History will look for them. Prefixes Emis, Inv, and Hco are HEMCO diagnostics and must have definitions in config file HEMCO_Diagn.rc. Prefixes Chem and Met are GEOS-Chem state variables stored in objects State_Chm and State_Met respectively. Prefix SPC corresponds to internal state species, meaning the same arrays that are output to the restart file. Prefix GEOS is reserved for use in the GEOS model. All other diagnostic name prefixes are interpreted as variables stored in the GEOS-Chem State_Diag object.



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