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 The GCHP documentation on http://wiki.seas.harvard.edu/ will stay online for several months, but it is outdated and no longer active!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:_Configuration|Previous]] | [[Developing_GCHP|Next]] | [[Getting Started with GCHP]] | [[GCHP Main Page]]''''' | '''''[[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]] | ||
| + | #[[Setting_Up_the_GCHP_Environment|Setting Up the GCHP Environment]] | ||
#[[Downloading_GCHP|Downloading Source Code and Data Directories]] | #[[Downloading_GCHP|Downloading Source Code and Data Directories]] | ||
| + | #[[Compiling_GCHP|Compiling]] | ||
#[[Obtaining_a_GCHP_Run_Directory|Obtaining a Run Directory]] | #[[Obtaining_a_GCHP_Run_Directory|Obtaining a Run Directory]] | ||
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#[[Running_GCHP:_Basics|Running GCHP: Basics]] | #[[Running_GCHP:_Basics|Running GCHP: Basics]] | ||
#[[Running_GCHP:_Configuration|Running GCHP: Configuration]] | #[[Running_GCHP:_Configuration|Running GCHP: Configuration]] | ||
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#[[GCHP_Run_Configuration_Files|Run Configuration Files]] | #[[GCHP_Run_Configuration_Files|Run Configuration Files]] | ||
<br> | <br> | ||
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==GCHP Output== | ==GCHP Output== | ||
===List of Output Files=== | ===List of Output Files=== | ||
| − | + | 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=" | + | !width="400px"|Description |
| − | !width=" | + | !width="300px"|Notes |
|-valign="top" | |-valign="top" | ||
|<tt>OutputDir/GCHP.{collection}.YYYYMMDD_HHmmz.nc4</tt> | |<tt>OutputDir/GCHP.{collection}.YYYYMMDD_HHmmz.nc4</tt> | ||
| − | |Diagnostic output data | + | |Diagnostic output data |
| − | + | |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> | ||
| − | | | + | |If adapting an example run script, this file is the primary GCHP log file. |
| − | + | |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" | |-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. | |
|-valign="top" | |-valign="top" | ||
|<tt>cap_restart</tt> | |<tt>cap_restart</tt> | ||
| − | |MAPL output text file containing GCHP run end time | + | |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 <tt>CAP.rc</tt> is used instead. | |
|-valign="top" | |-valign="top" | ||
|<tt>*.rcx</tt> | |<tt>*.rcx</tt> | ||
| − | | | + | |History collection information. |
| − | | | + | |One file per collection. |
|-valign="top" | |-valign="top" | ||
|<tt>EGRESS</tt> | |<tt>EGRESS</tt> | ||
| + | |Empty file produced by MAPL. | ||
|Can be ignored. | |Can be ignored. | ||
| − | |||
|-valign="top" | |-valign="top" | ||
|<tt>logfile.000000.out</tt> | |<tt>logfile.000000.out</tt> | ||
| − | | | + | |Log file for advection settings. |
| | | | ||
|-valign="top" | |-valign="top" | ||
| − | |<tt> | + | |<tt>warnings_and_errors.log</tt> |
| − | |Can be ignored | + | |MAPL logging layer output. |
| − | + | |Can be ignored since GCHP does not currently use GMAO library pFlogger. | |
| + | |||
|} | |} | ||
| − | If you run GCHP using | + | If you run GCHP using a job scheduler then you will also have a system output file. |
===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). However, if is renamed to include 'restart' and the timestamp automatically by the sample run scripts | + | 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.''' | 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.''' | ||
| Line 81: | Line 80: | ||
===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>. 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). | |
| − | + | ||
| − | 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> | + | |
| − | + | 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== | ||
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
- Hardware and Software Requirements
- Setting Up the GCHP Environment
- Downloading Source Code and Data Directories
- Compiling
- Obtaining a Run Directory
- Running GCHP: Basics
- Running GCHP: Configuration
- Output Data
- Developing GCHP
- Run Configuration Files
Contents
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
