GCHP Output Data

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Revision as of 21:31, 2 August 2018 by Lizzie Lundgren (Talk | contribs) (Data Visualization and Post-Processing)

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

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
OutputDir/GCHP.center.YYYYMMDD.nc4 Cubed sphere output data
GCHP.log Log file containing GCHP standard output such as is generated by files in MAPL source code in directory GCHP/Shared. Note that you can change this log file's name when you run GCHP. GCHP.log is the default name used in the sample run scripts and in examples in this user guide.
PET00000.EOSCHEMchem.log Log file containing GEOS-Chem standard output such as is generated by files in source code directory GeosCore. This file does not contain output generated by code in the GCHP source code directory.
HEMCO.log Log file generated by HEMCO. This file is also output when running GEOS-Chem classic.
cap_restart Text file either generated on the fly by MAPL if one does not already exist or is output by a previous GCHP run. Its contents replace the simulation start and end time information in input.geos. Unless doing multi-segmneted runs, this file should be deleted before starting a new run so that MAPL creates a new file with the start and duration information stored in CAP.rc. If an old cap_restart is present, simulation time information in that file will be used even if different from CAP.rc.
regrid.rcx, center.rcx Can be ignored.
EGRESS Can be ignored.
trac_avg.gchp_c24_standard.YYYYMMDDHHmm This file is a vestige of GEOS-Chem classic code. It can be ignored. All GCHP data output is in the OutputDir subdirectory. Diagnostics are not currently output.

Data Visualization and Post-Processing

GCHP output 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.

Each collection output file contains data on the cubed sphere grid at the resolution of your run. You can conservatively regrid to lat-lon for post-run analysis using one of the tools described below.

  1. Python package xESMF developed by Jiawei Zhuang (Harvard). This package is a wrapper for the ESMF python regridding interface.
  2. Jupyter Notebook developed by Lizzie Lundgren. This notebook contains example python code to regrid and compare GCHP and GEOS-Chem netcdf diagnostics using Jiawei Zhuang's xESMF package.
  3. FORTRAN tool CSRegridTool developed by Sebastian Eastham (MIT). This tool regrids cubed sphere and lat-lon netcdf files.
  4. Matlab package CSGrid developed by Sebastian Eastham (MIT). This package is a data analysis and visualization suite for both cubed sphere and lat-lon GEOS-Chem data.

Please note that we also have a [python tutorial] available on the GEOS-Chem GitHub site. We are also in the process of migrating GAMAP IDL benchmarking code to python in the [[1]] package currently in development. We will no longer maintain IDL code for post-processing of GEOS-Chem output once we completely replace binary diagnostics with netcdf diagnostics in GEOS-Chem Classic.

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