Difference between revisions of "GCHP Output Data"

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#[[GCHP_Run_Configuration_Files|Run Configuration Files]]
 
#[[GCHP_Run_Configuration_Files|Run Configuration Files]]
 
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Please note that documentation on this page primarily reflects the latest GCHP public release which is currently the GCHP 12 series. The documentation will be updated for the GCHP 13.0.0 release over the coming months.
 
  
 
==GCHP Output==
 
==GCHP Output==

Revision as of 00:02, 10 November 2020

Previous | Next | 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


GCHP Output

List of Output Files

Running GCHP produces several output data and log files. The table belows lists what files to expect. All of these files are deleted if you run make cleanup_output within the run directory.

Filename Description Notes
OutputDir/GCHP.{collection}.YYYYMMDD_HHmmz.nc4 Diagnostic output data. Note that you can change the filename format for any collection within HISTORY.rc.
gchp.log Primary GCHP log file. Sample run scripts gchp.run and gchp.loca.run are configured to send all stdout to this file by default. Please include this file when submitting a support request.
PET00000.GEOSCHEMchem.log Can be ignored.
HEMCO.log Log file generated by HEMCO. This file is also output when running GEOS-Chem Classic. Please include this file when submitting a support request.
cap_restart MAPL output text file containing GCHP run end time to be used as the next run's start time if doing multi-segmented runs. If not doing multi-segmented runs then this file should be deleted prior to rerunning so that start information in CAP.rc is used instead.
*.rcx Can be ignored.
EGRESS Can be ignored.
logfile.000000.out Can be ignored.
trac_avg.gchp_c24_standard.YYYYMMDDHHmm Can be ignored. All GCHP data output diagnostics data is stored in the OutputDir subdirectory.

If you run GCHP using SLURM then you will also have a slurm output file that will contain potentially valuable information about your run.

Restart Files

GCHP restart files are called "checkpoint" files and are output to the main level of the run directory. The primary restart file is output at the end of the run and is named "gcchem_internal_checkpoint.nc" by default (see the previous chapter on configuring restart files). However, if is renamed to include 'restart' and the timestamp automatically by the sample run scripts. If you are outputting checkpoint files at regular intervals during your run then they will be output with format "gcchem_internal_checkpoint.nc.YYYYMMDD_HHmmz.bin". Despite the extension, these files are netcdf files. You may need to rename them to have the ".nc" extension for compatibility with your netcdf viewer or analysis software.

The GCHP checkpoint files contains all variables that are stored in the MAPL Internal state in GCHP and are analogous to the combined contents of the GEOS-Chem Classic and HEMCO restart files. There is one notable difference. All 3D variables in the GCHP restart file are vertically flipped. This is an important distinction to know about when comparing or preparing GCHP restart files.

Diagnostic Data

GCHP diagnostic data is in netCDF-4 format and is stored in the OutputDir directory within your run directory. The output filename format is GCHP.collection.YYYYMMDD_HHmmz.nc4 where one or more collection names are configured in the output configuration file HISTORY.rc. You are free to create as many additional collections with any names you choose by adding them to HISTORY.rc. You may include both 2D and 3D arrays in a single collection. However, all 3D arrays must have the same 3rd dimension size. In GCHP the 3rd dimension size is limited to # of level centers (72) and # of level edges (73).

Unlike in GEOS-Chem Classic, the contents of the HEMCO emissions diagnostic file are listed in HISTORY.rc and the output file has the same naming format as other diagnostic collections. Like the GCHP restart file, all 3D HEMCO diagnostics are flipped vertically relative to other outputs. This means the first element in the output array corresponds to top-of-atmosphere and the last element is surface. The GCPy python package includes being able to vertically flip the level dimension prior to plotting to make post-run analysis easier.

Data Visualization and Post-Processing

The GEOS-Chem python package GCPy is fully functional with GCHP output files. The same plotting functions are used for both GEOS-Chem Classic lat-lon data and GCHP cubed-sphere data, and contain the capability to automatically regrid between grid types and resolutions. Please see the GCPy GitHub page.



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