Difference between revisions of "GCHP Output Data"

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<span style="color:crimson;font-size:120%">'''The GCHP documentation has moved to https://gchp.readthedocs.io/.''' The GCHP documentation on http://wiki.seas.harvard.edu/ will stay online for several months, but it is outdated and no longer active!</span>
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__FORCETOC__
 
__FORCETOC__
'''''[[Running_GCHP|Previous]] | [[Developing_GCHP|Next]] | [[Getting_Started_With_GCHP|Getting Started with GCHP]]'''''
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'''''[[Running_GCHP:_Configuration|Previous]] | [[Developing_GCHP|Next]] | [[Getting Started with GCHP]] | [[GCHP Main Page]]'''''
 
#[[GCHP_Hardware_and_Software_Requirements|Hardware and Software Requirements]]
 
#[[GCHP_Hardware_and_Software_Requirements|Hardware and Software Requirements]]
#[[Downloading_GCHP|Downloading Source Code]]
 
#[[Obtaining_a_GCHP_Run_Directory|Obtaining a Run Directory]]
 
 
#[[Setting_Up_the_GCHP_Environment|Setting Up the GCHP Environment]]
 
#[[Setting_Up_the_GCHP_Environment|Setting Up the GCHP Environment]]
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#[[Downloading_GCHP|Downloading Source Code and Data Directories]]
 
#[[Compiling_GCHP|Compiling]]
 
#[[Compiling_GCHP|Compiling]]
#[[GCHP_Basic_Example_Run|Basic Example Run]]
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#[[Obtaining_a_GCHP_Run_Directory|Obtaining a Run Directory]]
#[[GCHP_Run_Configuration_Files|Run Configuration Files]]
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#[[Running_GCHP:_Basics|Running GCHP: Basics]]
#[[Running_GCHP|Advanced Run Examples]]
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#[[Running_GCHP:_Configuration|Running GCHP: Configuration]]
 
#<span style="color:blue">'''Output Data'''</span>
 
#<span style="color:blue">'''Output Data'''</span>
 
#[[Developing_GCHP|Developing GCHP]]
 
#[[Developing_GCHP|Developing GCHP]]
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#[[GCHP_Run_Configuration_Files|Run Configuration Files]]
 
<br>
 
<br>
  
==Output Files==
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==GCHP Output==
  
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 <tt>make cleanup_output</tt> within the run directory.
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===List of Output Files===
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GCHP produces the following output data and log files:
  
 
{| border=1 cellspacing=0 cellpadding=5
 
{| border=1 cellspacing=0 cellpadding=5
|- bgcolor="#CCCCCC" valign="top"
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|-valign="top" bgcolor="#CCCCCC" valign="top"
! Filename
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!width="400px"|Filename
!|Description
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!width="400px"|Description
|-
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!width="300px"|Notes
| <tt>OutputDir/GCHP.center.YYYYMMDD.nc4</tt>
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| Cubed sphere output data
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|-valign="top"
|-
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|<tt>OutputDir/GCHP.{collection}.YYYYMMDD_HHmmz.nc4</tt>
| <tt>GCHP.log</tt>
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|Diagnostic output data
| Log file containing GCHP standard output such as is generated by files in MAPL source code in directory <tt>GCHP/Shared</tt>. Note that you can change this log file's name when you run GCHP. <tt>GCHP.log</tt> is the default name used in the sample run scripts and in examples in this user guide.
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|You may customize the filename format for any collection within config file <tt>HISTORY.rc</tt>
|-
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| <tt>PET00000.EOSCHEMchem.log</tt>
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|-valign="top"
| Log file containing GEOS-Chem standard output such as is generated by files in source code directory <tt>GeosCore</tt>. This file does not contain output generated by code in the <tt>GCHP</tt> source code directory.
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|<tt>gchp.log</tt>
|-
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|If adapting an example run script, this file is the primary GCHP log file.
| <tt>HEMCO.log</tt>
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|Includes all model standard output as well output from sourcing <tt>gchp.env</tt> and <tt>runConfig.sh</tt>. If using the multi-run option then this file is not produced; standard output is sent to the job log file instead per job.
| Log file generated by HEMCO. This file is also output when running GEOS-Chem classic.
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|-
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|-valign="top"
| <tt>cap_restart</tt>
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|<tt>HEMCO.log</tt>
| 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 <tt>input.geos</tt>. 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 <tt>CAP.rc</tt>. If an old <tt>cap_restart</tt> is present, simulation time information in that file will be used even if different from <tt>CAP.rc</tt>.
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|Log file generated by HEMCO.  
|-
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|This file is also output when running GEOS-Chem Classic.
| <tt>regrid.rcx</tt>, <tt>center.rcx</tt>
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| Can be ignored.
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|-valign="top"
|-  
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|<tt>cap_restart</tt>
| <tt>EGRESS</tt>
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|MAPL output text file containing GCHP run end time.
| Can be ignored.
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|This file may 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.
|-  
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| <tt>trac_avg.gchp_c24_standard.YYYYMMDDHHmm</tt>
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|-valign="top"
| This file is a vestige of GEOS-Chem classic code. It can be ignored. All GCHP data output is in the <tt>OutputDir</tt> subdirectory. Diagnostics are not currently output.
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|<tt>*.rcx</tt>
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|History collection information.
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|One file per collection.
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|-valign="top"
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|<tt>EGRESS</tt>
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|Empty file produced by MAPL.
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|Can be ignored.
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|-valign="top"
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|<tt>logfile.000000.out</tt>
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|Log file for advection settings.
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|
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|-valign="top"
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|<tt>warnings_and_errors.log</tt>
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|MAPL logging layer output.
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|Can be ignored since GCHP does not currently use GMAO library pFlogger.
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|}
 
|}
  
==Data Visualization and Post-Processing==
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If you run GCHP using a job scheduler then you will also have a system output file.
  
GCHP output data is in netCDF-4 format and is stored in the <tt>OutputDir</tt> directory within your run directory. The output filename format is <tt>GCHP.''collection''.YYYYMMDD_HHmmz.nc4</tt> where one or more collection names are configured in the output configuration file <tt>HISTORY.rc</tt>. The default collection is "center". You are free to create as many additional collections with any names you choose. Be aware that the vertical axis in GCHP output data is flipped relative to GEOS-Chem classic, with the lowest level index corresponding to the top of atmosphere.
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===Restart Files===
  
Each collection is 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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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.
  
We currently recommend that you the FORTRAN tool <tt>CSRegridTool</tt> developed by [[User:Sebastian_D._Eastham|Sebastian Eastham]] (MIT) for regridding GCHP output data to lat-lon. This package is available at https://bitbucket.org/sdeastham/csregridtool.
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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.'''
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===Diagnostic Data===
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GCHP diagnostic data is in netCDF-4 format and is stored in the <tt>OutputDir</tt> directory within your run directory. The output filename format is <tt>GCHP.''collection''.YYYYMMDD_HHmmz.nc4</tt> where one or more collection names are configured in the output configuration file <tt>HISTORY.rc</tt>. You are free to create as many additional collections with any names you choose by adding them to <tt>HISTORY.rc</tt>. You may include both 2D and 3D arrays in a single collection. However, 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).
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Unlike in GEOS-Chem Classic, the contents of the HEMCO emissions diagnostic file are listed in <tt>HISTORY.rc</tt> and the output file has the same naming format as other diagnostic collections. '''Like the GCHP restart file, all 3D HEMCO diagnostics are flipped vertically relative to other outputs.''' This means the first element in the output array corresponds to top-of-atmosphere and the last element is surface. The GCPy python package includes being able to vertically flip the level dimension prior to plotting to make post-run analysis easier.
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==Data Visualization and Post-Processing==
  
You may also use the <tt>CSGrid</tt> Matlab package, also developed by [[User:Sebastian_D._Eastham|Sebastian Eastham]] (MIT) and which contains an extensive library for post-processing and data visualization of both cubed sphere and lat-long grids. This package is available at https://bitbucket.org/gcst/csgrid.
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The GEOS-Chem python package GCPy is fully 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. Please see the [https://github.com/geoschem/gcpy GCPy] GitHub page.
  
Please note that the development of python tools for GCHP regridding and data analysis is currently in progress. This python suite will replace the IDL-based GAMAP software used with GEOS-Chem "classic". If you are interested in helping out with this project, please contact the GEOS-Chem Support Team.
 
  
'''''[[Running_GCHP|Previous]] | [[Developing_GCHP|Next]] | [[GEOS-Chem_HP|GCHP Home]]'''''
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----
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'''''[[Running_GCHP:_Configuration|Previous]] | [[Developing_GCHP|Next]] | [[Getting Started with GCHP]] | [[GCHP Main Page]]'''''

Latest revision as of 15:41, 8 December 2020


The GCHP documentation has moved to https://gchp.readthedocs.io/. The GCHP documentation on http://wiki.seas.harvard.edu/ will stay online for several months, but it is outdated and no longer active!



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

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


GCHP Output

List of Output Files

GCHP produces the following output data and log files:

Filename Description Notes
OutputDir/GCHP.{collection}.YYYYMMDD_HHmmz.nc4 Diagnostic output data You may customize the filename format for any collection within config file HISTORY.rc
gchp.log If adapting an example run script, this file is the primary GCHP log file. Includes all model standard output as well output from sourcing gchp.env and runConfig.sh. If using the multi-run option then this file is not produced; standard output is sent to the job log file instead per job.
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. This file may 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 History collection information. One file per collection.
EGRESS Empty file produced by MAPL. Can be ignored.
logfile.000000.out Log file for advection settings.
warnings_and_errors.log MAPL logging layer output. Can be ignored since GCHP does not currently use GMAO library pFlogger.

If you run GCHP using a job scheduler then you will also have a system output file.

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.

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. You may include both 2D and 3D arrays in a single collection. However, 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).

Unlike in GEOS-Chem Classic, the contents of the HEMCO emissions diagnostic file are listed in HISTORY.rc and the output file has the same naming format as other diagnostic collections. Like the GCHP restart file, all 3D HEMCO diagnostics are flipped vertically relative to other outputs. This means the first element in the output array corresponds to top-of-atmosphere and the last element is surface. The GCPy python package includes being able to vertically flip the level dimension prior to plotting to make post-run analysis easier.

Data Visualization and Post-Processing

The GEOS-Chem python package GCPy is fully 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. Please see the GCPy GitHub page.



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