Difference between revisions of "GCHP Output Data"

From Geos-chem
Jump to: navigation, search
(Data Visualization and Post-Processing)
(List of Output Files)
Line 25: Line 25:
  
 
|-valign="top"
 
|-valign="top"
| <tt>OutputDir/GCHP.{collection}.YYYYMMDD_HHmmz.nc4</tt>
+
|<tt>OutputDir/GCHP.{collection}.YYYYMMDD_HHmmz.nc4</tt>
| Cubed sphere output data. Note that you can change the filename format for any collection within HISTORY.rc.
+
|Diagnostic output data. Note that you can change the filename format for any collection within HISTORY.rc.
 
|
 
|
  
 
|-valign="top"
 
|-valign="top"
 
|<tt>gchp.log</tt>
 
|<tt>gchp.log</tt>
|Sample run script <tt>gchp.run</tt> 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.  
+
|Primary GCHP log file. Sample run scripts <tt>gchp.run</tt> and <tt>gchp.loca.run</tt> are configured to send all stdout to this file by default.  
 
|Please include this file when [[Submitting GEOS-Chem support requests|submitting a support request]].
 
|Please include this file when [[Submitting GEOS-Chem support requests|submitting a support request]].
  
Line 40: Line 40:
 
|-valign="top"
 
|-valign="top"
 
|<tt>HEMCO.log</tt>
 
|<tt>HEMCO.log</tt>
|Log file generated by HEMCO. This file is also output when running GEOS-Chem classic.
+
|Log file generated by HEMCO. This file is also output when running GEOS-Chem Classic.
 
|Please include this file when [[Submitting GEOS-Chem support requests|submitting a support request]].
 
|Please include this file when [[Submitting GEOS-Chem support requests|submitting a support request]].
  
Line 46: Line 46:
 
|<tt>cap_restart</tt>
 
|<tt>cap_restart</tt>
 
|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 <tt>CAP.rc</tt> is used instead.
 
|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 <tt>CAP.rc</tt> is used instead.
|Please include this file when [[Submitting GEOS-Chem support requests|submitting a support request]].
+
|
  
 
|-valign="top"
 
|-valign="top"
 
|<tt>*.rcx</tt>
 
|<tt>*.rcx</tt>
|Contains basic information about each diagnostic collection.
+
|Can be ignored.
 
|
 
|
  
 
|-valign="top"  
 
|-valign="top"  
 
|<tt>EGRESS</tt>
 
|<tt>EGRESS</tt>
 +
|Can be ignored.
 +
|
 +
 +
|-valign="top"
 +
|<tt>logfile.000000.out</tt>
 
|Can be ignored.
 
|Can be ignored.
 
|
 
|

Revision as of 18:09, 26 April 2019

Previous | Next | User Manual Home | GCHP Home

  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

placeholder

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 for comparing datasets

placeholder

Previous | Next | User Manual Home | GCHP Home