Difference between revisions of "GCHP Output Data"

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Revision as of 23:06, 6 March 2019

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  1. Hardware and Software Requirements
  2. Downloading Source Code and Data Directories
  3. Obtaining a Run Directory
  4. Setting Up the GCHP Environment
  5. Compiling
  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 Cubed sphere output data. Note that you can change the filename format for any collection within HISTORY.rc.
gchp.log Sample run script gchp.run is configured to send all stdout to this file by default. This is optional and you can configure stdout to go to a different file by editing your run script. For example, if using SLURM then you can include #SBATCH -o slurm.%j.out to send stdout to your slurm file instead. 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. Please include this file when submitting a support request.
*.rcx Contains basic information about each diagnostic collection.
EGRESS 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.

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. Any 2D or 3D arrays stored in State_Met, State_Chm, or State_Diag can be included in a History collection.

Data Visualization and Post-Processing

GEOS-Chem Classic users typically use IDL GAMAP for GEOS-Chem data visualization and analysis. However, this software is only compatible with lat-lon data. It therefore is not possible to use it directly with GCHP output data which is on a cubed sphere grid. Other tools have therefore been developed to use specifically with GCHP data. Functionalities include regridding between cubed sphere and lat-lon, plotting on either a cubed sphere or lat-lon grid, and direct comparison of GEOS-Chem Classic and GCHP output data via regridding. See the following resources to get started. Please note that all of these resources can also be used with GEOS-Chem Classic netcdf output data.

  1. gcpy python package for GEOS-Chem ***Recommended***
  2. Jupyter notebooks developed by Lizzie Lundgren (Harvard) with example python code to explore, plot, regrid, and compare GCHP and GEOS-Chem netcdf diagnostics using the xESMF and cubedsphere packages developed by Jiawei Zhuang (Harvard).
  3. GEOS-Chem python tutorial written by Jiawei Zhuang for handling GEOS-Chem lat-lon data in both NetCDF and binary formats.
  4. FORTRAN tool CSRegridTool developed by Sebastian Eastham (MIT) to regrid cubed sphere and lat-lon netcdf files.
  5. Matlab package CSGrid developed by Sebastian Eastham (MIT) to provide a data analysis and visualization suite for both cubed sphere and lat-lon GEOS-Chem data.

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