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 The GCHP documentation on http://wiki.seas.harvard.edu/ will stay online for several months, but it is outdated and no longer active!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|User Manual Home]] | [[GEOS-Chem_HP|GCHP Home]]'''''
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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]]
#[[Running_GCHP|Configuring a Run]]
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#[[Running_GCHP:_Basics|Running GCHP: Basics]]
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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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===List of Output Files===
 
===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 <tt>make cleanup_output</tt> within the run directory.
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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
 
|-valign="top" bgcolor="#CCCCCC" valign="top"
 
|-valign="top" bgcolor="#CCCCCC" valign="top"
 
!width="400px"|Filename
 
!width="400px"|Filename
!width="500px"|Description
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!width="400px"|Description
!width="200px"|Notes
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!width="300px"|Notes
  
 
|-valign="top"
 
|-valign="top"
| <tt>OutputDir/GCHP.{collection}.YYYYMMDD_HHmmz.nc4</tt>
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|<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.
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|Diagnostic output data
|
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|You may customize the filename format for any collection within config file <tt>HISTORY.rc</tt>
  
 
|-valign="top"
 
|-valign="top"
 
|<tt>gchp.log</tt>
 
|<tt>gchp.log</tt>
|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.  
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|If adapting an example run script, this file is the primary GCHP log file.
|Please include this file when [[Submitting GEOS-Chem support requests|submitting a support request]].
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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.
  
|-valign="top"
 
|<tt>PET00000.GEOSCHEMchem.log</tt>
 
|Can be ignored.
 
|
 
 
|-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.
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|Log file generated by HEMCO.  
|Please include this file when [[Submitting GEOS-Chem support requests|submitting a support request]].
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|This file is also output when running GEOS-Chem Classic.
  
 
|-valign="top"
 
|-valign="top"
 
|<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.
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|MAPL output text file containing GCHP run end time.
|Please include this file when [[Submitting GEOS-Chem support requests|submitting a support request]].
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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.
  
 
|-valign="top"
 
|-valign="top"
 
|<tt>*.rcx</tt>
 
|<tt>*.rcx</tt>
|Contains basic information about each diagnostic collection.
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|History collection information.
|
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|One file per collection.
  
 
|-valign="top"  
 
|-valign="top"  
 
|<tt>EGRESS</tt>
 
|<tt>EGRESS</tt>
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|Empty file produced by MAPL.
 
|Can be ignored.
 
|Can be ignored.
|
 
  
 
|-valign="top"  
 
|-valign="top"  
|<tt>trac_avg.gchp_c24_standard.YYYYMMDDHHmm</tt>
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|<tt>logfile.000000.out</tt>
|Can be ignored. All GCHP data output diagnostics data is stored in the <tt>OutputDir</tt> subdirectory.  
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|Log file for advection settings.
 
|
 
|
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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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|}
 
|}
  
If you run GCHP using SLURM then you will also have a slurm output file that will contain potentially valuable information about your run.
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If you run GCHP using a job scheduler then you will also have a system output file.
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===Restart Files===
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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.
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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===
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>. Any 2D or 3D arrays stored in <tt>State_Met</tt>, <tt>State_Chm</tt>, or <tt>State_Diag</tt> can be included in a History collection.
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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.
  
 
==Data Visualization and Post-Processing==
 
==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.
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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.
  
#[https://github.com/geoschem/gcpy gcpy] python package for GEOS-Chem '''***Recommended***'''
 
#[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/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.
 
#Matlab package [https://github.com/geoschem/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.
 
  
'''''[[Running_GCHP|Previous]] | [[Developing_GCHP|Next]] | [[Getting_Started_With_GCHP|User Manual Home]] | [[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