Difference between revisions of "GCHP Output Data"

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===Restart Files===
 
===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). 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.
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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.
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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===
 
===Diagnostic Data===

Revision as of 23:05, 15 August 2019

Previous | Next | Getting Started With GCHP | GCHP Main Page

  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 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. Any 2D or 3D arrays stored in State_Met, State_Chm, or State_Diag can be included in a History collection. You may include both 2D and 3D arrays in a single collection, but be aware that 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).

The emissions diagnostics file is different from the netcdf emissions diagnostics file output by GEOS-Chem Classic. In GCHP the emissions to include in the file are listed in HISTORY.rc and the output file is sent to OutputDir with the same naming format as other diagnostic collections. All 3d data within the file are flipped vertically (surface is last element in the level dimension). Note that this is also true of the GCHP restart file due to the way MAPL stores the internal state.

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 and is generally used with binary diagnostics. Since we are phasing binary diagnostics out of GEOS-Chem we are no longer support IDL GAMAP.

Other tools have therefore been developed to use specifically with netcdf data, and including GCHP cubed-sphere 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 now for comparing datasets; further development is in progress***
  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.

Python package GCPy for comparing datasets

The GEOS-Chem benchmark code in GCPy is currently 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. GCPy is still in development but the benchmark plotting functions are ready for use by users. Please GCPy example materials posted on the Harvard ftp site to get started. If you encounter issues or have tips for other users, please report them on the GCPy GitHub issues page.



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