Difference between revisions of "GCHP Output Data"

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(Data Visualization and Post-Processing)
(Data Visualization and Post-Processing)
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==Data Visualization and Post-Processing==
 
==Data Visualization and Post-Processing==
  
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.  
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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.
  
 
#[https://github.com/lizziel/geoschem_data_visualization 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 [https://github.com/JiaweiZhuang/xESMF <tt>xESMF</tt>] and [https://github.com/JiaweiZhuang/cubedsphere cubedsphere] packages developed by Jiawei Zhuang (Harvard).
 
#[https://github.com/lizziel/geoschem_data_visualization 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 [https://github.com/JiaweiZhuang/xESMF <tt>xESMF</tt>] and [https://github.com/JiaweiZhuang/cubedsphere cubedsphere] packages developed by Jiawei Zhuang (Harvard).
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#[https://github.com/geoschem/GEOSChem-python-tutorial GEOS-Chem python tutorial] written by Jiawei Zhuang for handling GEOS-Chem lat-lon data in both NetCDF and binary formats.
 
#FORTRAN tool [https://bitbucket.org/sdeastham/csregridtool <tt>CSRegridTool</tt>] developed by Sebastian Eastham (MIT) to regrid cubed sphere and lat-lon netcdf files.
 
#FORTRAN tool [https://bitbucket.org/sdeastham/csregridtool <tt>CSRegridTool</tt>] developed by Sebastian Eastham (MIT) to regrid cubed sphere and lat-lon netcdf files.
 
#Matlab package [https://bitbucket.org/gcst/csgrid <tt>CSGrid</tt>] developed by Sebastian Eastham (MIT) to provide a data analysis and visualization suite for both cubed sphere and lat-lon GEOS-Chem data.
 
#Matlab package [https://bitbucket.org/gcst/csgrid <tt>CSGrid</tt>] developed by Sebastian Eastham (MIT) to provide a data analysis and visualization suite for both cubed sphere and lat-lon GEOS-Chem data.
 
Please note that we also have a [https://github.com/geoschem/GEOSChem-python-tutorial GEOS-Chem Classic python tutorial] written by Jiawei Zhuang available on the GEOS-Chem GitHub site. We are also in the process of migrating GAMAP IDL benchmarking code to python in the [https://github.com/geoschem/gcpy gcpy] 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.
 
  
 
'''''[[Running_GCHP|Previous]] | [[Developing_GCHP|Next]] | [[Getting_Started_With_GCHP|User Manual Home]] | [[GEOS-Chem_HP|GCHP Home]]'''''
 
'''''[[Running_GCHP|Previous]] | [[Developing_GCHP|Next]] | [[Getting_Started_With_GCHP|User Manual Home]] | [[GEOS-Chem_HP|GCHP Home]]'''''

Revision as of 17:00, 31 August 2018

Previous | Next | User Manual Home | GCHP Home

  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. Configuring a Run
  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
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 Log file containing GCHP standard output including what would typically go to a GEOS-Chem Classic log file. Note that you can change this log file's name when you run GCHP by editing it in your run script.
PET00000.GEOSCHEMchem.log Can be ignored.
HEMCO.log Log file generated by HEMCO. This file is also output when running GEOS-Chem classic.
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 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.

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.

Restart Files

To be added

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. 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).
  2. GEOS-Chem python tutorial written by Jiawei Zhuang for handling GEOS-Chem lat-lon data in both NetCDF and binary formats.
  3. FORTRAN tool CSRegridTool developed by Sebastian Eastham (MIT) to regrid cubed sphere and lat-lon netcdf files.
  4. 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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