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Interpretation of Sections 15 and 16. - - If the disclaimer of warranty and limitation of liability provided - above cannot be given local legal effect according to their terms, - reviewing courts shall apply local law that most closely approximates - an absolute waiver of all civil liability in connection with the - Program, unless a warranty or assumption of liability accompanies a - copy of the Program in return for a fee. - - END OF TERMS AND CONDITIONS - - How to Apply These Terms to Your New Programs - - If you develop a new program, and you want it to be of the greatest - possible use to the public, the best way to achieve this is to make it - free software which everyone can redistribute and change under these terms. - - To do so, attach the following notices to the program. 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If not, see . - - Also add information on how to contact you by electronic and paper mail. - - If the program does terminal interaction, make it output a short - notice like this when it starts in an interactive mode: - - Copyright (C) - This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. - This is free software, and you are welcome to redistribute it - under certain conditions; type `show c' for details. - - The hypothetical commands `show w' and `show c' should show the appropriate - parts of the General Public License. Of course, your program's commands - might be different; for a GUI interface, you would use an "about box". - - You should also get your employer (if you work as a programmer) or school, - if any, to sign a "copyright disclaimer" for the program, if necessary. - For more information on this, and how to apply and follow the GNU GPL, see - . - - The GNU General Public License does not permit incorporating your program - into proprietary programs. 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Accepting Warranty or Additional Liability. - - While redistributing the Work or Derivative Works thereof, You may choose to - offer, and charge a fee for, acceptance of support, warranty, indemnity, or - other liability obligations and/or rights consistent with this License. - However, in accepting such obligations, You may act only on Your own behalf - and on Your sole responsibility, not on behalf of any other Contributor, and - only if You agree to indemnify, defend, and hold each Contributor harmless - for any liability incurred by, or claims asserted against, such Contributor - by reason of your accepting any such warranty or additional liability. - - END OF TERMS AND CONDITIONS - - APPENDIX: How to apply the Apache License to your work - - To apply the Apache License to your work, attach the following boilerplate - notice with the fields enclosed by brackets "[]" replaced with your own - identifying information. (Don't include the brackets!) The text should be - enclosed in the appropriate comment syntax for the file format. We also - recommend that a file or class name and description of purpose be included on - the same "printed page" as the copyright notice for easier identification within - third-party archives. - - NASA Docket No. GSC-15,354-1, and identified as "GEOS-5 GCM Modeling Software” - - “Copyright © 2008 United States Government as represented by the Administrator - of the National Aeronautics and Space Administration. All Rights Reserved.” - - Licensed under the Apache License, Version 2.0 (the "License"); you may not use - this file except in compliance with the License. You may obtain a copy of the - License at - - http://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software distributed - under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR - CONDITIONS OF ANY KIND, either express or implied. See the License for the - specific language governing permissions and limitations under - the License. - - - NASA OPEN SOURCE SOFTWARE AGREEMENT - - NASA OPEN SOURCE AGREEMENT VERSION 1.3 - - THIS OPEN SOURCE AGREEMENT ("AGREEMENT") DEFINES THE RIGHTS OF USE, - REPRODUCTION, DISTRIBUTION, MODIFICATION AND REDISTRIBUTION OF CERTAIN - COMPUTER SOFTWARE ORIGINALLY RELEASED BY THE UNITED STATES GOVERNMENT AS - REPRESENTED BY THE GOVERNMENT AGENCY LISTED BELOW ("GOVERNMENT AGENCY"). - THE UNITED STATES GOVERNMENT, AS REPRESENTED BY GOVERNMENT AGENCY, IS AN - INTENDED THIRD-PARTY BENEFICIARY OF ALL SUBSEQUENT DISTRIBUTIONS OR - REDISTRIBUTIONS OF THE SUBJECT SOFTWARE. ANYONE WHO USES, REPRODUCES, - DISTRIBUTES, MODIFIES OR REDISTRIBUTES THE SUBJECT SOFTWARE, AS DEFINED - HEREIN, OR ANY PART THEREOF, IS, BY THAT ACTION, ACCEPTING IN FULL THE - RESPONSIBILITIES AND OBLIGATIONS CONTAINED IN THIS AGREEMENT. - - Government Agency: National Aeronautics and Space Administration - Government Agency Original Software Designation: GSC-15354-1 - Government Agency Original Software Title: GEOS-5 GCM Modeling Software - User Registration Requested. Please Visit http://opensource.gsfc.nasa.gov - Government Agency Point of Contact for Original Software: - Dale Hithon, SRA Assistant, (301) 286-2691 - - 1. DEFINITIONS - - A. "Contributor" means Government Agency, as the developer of the - Original Software, and any entity that makes a Modification. - - B. "Covered Patents" mean patent claims licensable by a Contributor - that are necessarily infringed by the use or sale of its Modification - alone or when combined with the Subject Software. - - C. 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"Original Software" means the computer software first released under - this Agreement by Government Agency with Government Agency designation - GSC-15354-1 and entitled GEOS-5 GCM Modeling Software, including source - code, object code and accompanying documentation, if any. - - H. "Recipient" means anyone who acquires the Subject Software under - this Agreement, including all Contributors. - - I. "Redistribution" means Distribution of the Subject Software after a - Modification has been made. - - J. "Reproduction" means the making of a counterpart, image or copy of - the Subject Software. - - K. "Sale" means the exchange of the Subject Software for money or - equivalent value. - - L. "Subject Software" means the Original Software, Modifications, or - any respective parts thereof. - - M. "Use" means the application or employment of the Subject Software - for any purpose. - - - - 2. GRANT OF RIGHTS - - A. 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Point of Contact: Any Recipient contact with Government Agency is to - be directed to the designated representative as follows: Dale Hithon, - SRA Assistant, (301) 286-2691. - - -SMVGEAR chemical solver (used in GEOS-Chem v10-01 and prior versions): ------------------------------------------------------------------------------ - - ********************************************************************* - ************ WRITTEN BY MARK JACOBSON (1993) ************ - *** (C) COPYRIGHT, 1993 BY MARK Z. JACOBSON *** - *** U.S. COPYRIGHT OFFICE REGISTRATION NO. TXu 670-279 *** - *** (650) 723-6836 *** - ********************************************************************* diff --git a/README.md b/README.md index 9f0d7c8..cc5b472 100644 --- a/README.md +++ b/README.md @@ -33,13 +33,24 @@ $ conda deactivate # Deactivate the environment $ ls make_102L.ncl make_40L.ncl make_74L.ncl PS.2005-2014.nc4 ``` - + 3. Run the script corresponding to the desired output grid: ```console - $ ncl make_40L.ncl + $ ncl make_102L.ncl # Regrids to 102 vertical levels, or + $ ncl make_74L.ncl # Regrids to 74 vertical levels, or + $ ncl make_40L.ncl # Regrids to 40 vertical levels ``` - + 4. Copy the regridded data files to the proper GCAP2 data folder in the `ExtData` directory structure. 5. Deactivate the Python environment (as described above). + +6. In some cases, the scripts may not have added the regridded `lev` dimension. You can then use one of the scripts in the `fixlev` folder to update the file: + + ```console + $ cd fixlev + $ ./fixlev_gcap2_102.sh /path/to/102/level/file + $ ./fixlev_gcap2_74.sh /path/to/74/level/file + $ ./fixlev_gcap2_40.sh /path/to/40/level/file + ``` diff --git a/fixlev/fixlev_gcap2_104.sh b/fixlev/fixlev_gcap2_104.sh new file mode 100755 index 0000000..107fa98 --- /dev/null +++ b/fixlev/fixlev_gcap2_104.sh @@ -0,0 +1,10 @@ +#!/bin/bash + +# Add the lev dimension back into the file +ncap2 -O -h -s 'lev[lev]={1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104}; lev@long_name="GEOS-Chem level"; lev@units="level"; lev@positive="up";lev@axis="Z"' "${1}" "tmp.nc" +mv "tmp.nc" "${1}" + +# Compress and chunk the file +./nc_chunk.pl "${1}" 1 + +exit 0 diff --git a/fixlev/fixlev_gcap2_40.sh b/fixlev/fixlev_gcap2_40.sh new file mode 100755 index 0000000..85b169d --- /dev/null +++ b/fixlev/fixlev_gcap2_40.sh @@ -0,0 +1,10 @@ +#!/bin/bash + +# Add the lev dimension back into the file +ncap2 -O -h -s 'lev[lev]={1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40}; lev@long_name="GEOS-Chem level"; lev@units="level"; lev@positive="up";lev@axis="Z"' "${1}" "tmp.nc" +mv "tmp.nc" "${1}" + +# Compress and chunk the file +./nc_chunk.pl "${1}" 1 + +exit 0 diff --git a/fixlev/fixlev_gcap2_74.sh b/fixlev/fixlev_gcap2_74.sh new file mode 100755 index 0000000..441433c --- /dev/null +++ b/fixlev/fixlev_gcap2_74.sh @@ -0,0 +1,10 @@ +#!/bin/bash + +# Add the lev dimension back into the file +ncap2 -O -h -s 'lev[lev]={1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74}; lev@long_name="GEOS-Chem level"; lev@units="level"; lev@positive="up";lev@axis="Z"' "${1}" "tmp.nc" +mv "tmp.nc" "${1}" + +# Compress and chunk the file +./nc_chunk.pl "${1}" 1 + +exit 0 diff --git a/fixlev/nc_chunk.pl b/fixlev/nc_chunk.pl new file mode 100755 index 0000000..b14937a --- /dev/null +++ b/fixlev/nc_chunk.pl @@ -0,0 +1,229 @@ +#!/usr/bin/perl -w + +#------------------------------------------------------------------------------ +# GEOS-Chem Global Chemical Transport Model ! +#------------------------------------------------------------------------------ +#BOP +# +# !MODULE: nc_chunk.pl +# +# !DESCRIPTION: This perl script can be used to chunk and/or deflate a +# netCDF file. It will first do a ncdump command to find out the dimensions +# of the file, and then chunk the file along lon and lat. This is optimal +# for GEOS-Chem and GCHP. +#\\ +#\\ +# !USES: +# +require 5.003; # Need this version of Perl or newer +use English; # Use English language +use Carp; # Get detailed error messages +use strict; + +# !CALLING SEQUENCE: +# nc_chunk.pl NETCDF-FILE-NAME [DEFLATION-LEVEL] +# +# !REMARKS: +# Must have the NetCDF Operators (NCO) installed. +# +# !REVISION HISTORY: +# 12 Apr 2018 - R. Yantosca - Initial version +#EOP +#------------------------------------------------------------------------------ +# GEOS-Chem Global Chemical Transport Model ! +#------------------------------------------------------------------------------ +#BOP +# +# !IROUTINE: chunkTheFile +# +# !DESCRIPTION: Calls nccopy to chunk a netCDF file along lon and lat +# dimensions. If the deflation factor is greater than zero, it will also +# tell nccopy to compress the netCDF file with that deflation level. +#\\ +#\\ +# !INTERFACE: +# +sub chunkTheFile($$) { +# +# !INPUT PARAMETERS: +# + my ( $ncFile, $deflate ) = @_; # NetCDF file name to be chunked + # and the deflation factor +# +# !REVISION HISTORY: +# 12 Apr 2018 - R. Yantosca - Initial version +#EOP +#------------------------------------------------------------------------------ +#BOC +# +# !LOCAL VARIABLES: +# + # Scalars + my $isDims = 0; + + # Strings + my $cmd = ""; + my $latCmd = ""; + my $latSize = ""; + my $lonCmd = ""; + my $lonSize = ""; + my $levCmd = ""; + my $timeCmd = ""; + my $nfCmd = ""; + my $line = ""; + my $result = ""; + + # Arrays + my @ncDumpTxt = (); + my @subStrs = (); + + # Exit if the file does not exist + if ( !( -f $ncFile ) ) { print "Could not find $ncFile!\n"; exit(-1); } + + # Save the contents of ncdump to an array + @ncDumpTxt = qx/ncdump -cts $ncFile/; + + # Parse the ncdump line + foreach $line ( @ncDumpTxt ) { + + # Remove newlines + chomp( $line ); + + # We have entered the dimensions section + if ( $line =~ m/dimensions:/ ) { $isDims = 1; } + + # Look for the lon and lat dimensions + if ( $isDims > 0 ) { + + # Create chunking command for lon dimension + if ( $line =~ m/[Ll][0o][Nn]/ || $line =~ m/[Xx][Dd][Ii][Mm]/ ) { + $lonCmd = $line; + $lonCmd =~ s/ = /\//g; + $lonCmd =~ s/ ;//g; + $lonCmd =~ s/^\s+|\s+$//g + } + + # Create chunking command for lat dimension + if ( $line =~ m/[Ll][Aa][Tt]/ || $line =~ m/[Yy][Dd][Ii][Mm]/) { + $latCmd = $line; + $latCmd =~ s/ = /\//g; + $latCmd =~ s/ ;//g; + $latCmd =~ s/^\s+|\s+$//g + } + + # Create chunking command for level midpoints dimension + if ( $line =~ m/[Ll][Ee][Vv]/ ) { + @subStrs = split( ' = ', $line ); + $levCmd = "$subStrs[0]/1"; + $levCmd =~ s/^\s+|\s+$//g + } + + # Create chunking command for level interfaces dimension + if ( $line =~ m/[Ii][Ll][Ee][Vv]/ ) { + @subStrs = split( ' = ', $line ); + $levCmd = "$subStrs[0]/1"; + $levCmd =~ s/^\s+|\s+$//g + } + + # Create chunking command for time dimension + if ( $line =~ m/[Tt][Ii][Mm][Ee]/ ) { + @subStrs = split( ' = ', $line ); + $timeCmd = "$subStrs[0]/1"; + $timeCmd =~ s/^\s+|\s+$//g + } + + # Create chunking command for Xdim dimension + if ( $line =~ m/[Nn][Ff]/ ) { + $nfCmd = $line; + $nfCmd =~ s/ = /\//g; + $nfCmd =~ s/ ;//g; + $nfCmd =~ s/^\s+|\s+$//g + } + + } + + # We have exited the dimensions section + if ( $line =~ m/variables:/ ) { goto quit; } + } + +quit: + + # Chunking command + if ( $nfCmd ne "" ) { + + # Cubed-sphere options + if ( $levCmd eq "" && $timeCmd eq "" ) + { $cmd = "nccopy -c $lonCmd,$latCmd,$nfCmd"; } + elsif ( $levCmd eq "" ) + { $cmd = "nccopy -c $lonCmd,$latCmd,$nfCmd,$timeCmd"; } + else + { $cmd = "nccopy -c $lonCmd,$latCmd,$nfCmd,$levCmd,$timeCmd"; } + + } else { + + # Lat-lon options + if ( $levCmd eq "" && $timeCmd eq "" ) + { $cmd = "nccopy -c $lonCmd,$latCmd"; } + elsif ( $levCmd eq "" ) + { $cmd = "nccopy -c $lonCmd,$latCmd,$timeCmd"; } + else + { $cmd = "nccopy -c $lonCmd,$latCmd,$levCmd,$timeCmd"; } + } + + # Deflation command + if ( $deflate > 0 ) { $cmd .= " -d$deflate" } + + # Add file name to the command + $cmd .= " $ncFile tmp.$ncFile; mv tmp.$ncFile $ncFile"; + print "$cmd\n"; + + # Execute the command + $result = qx/$cmd/; + chomp( $result ); + if ( $result ne "" ) { print "$result\n"; } + + # Exit and pass status code back + return( $? ); +} +#EOP +#------------------------------------------------------------------------------ +# GEOS-Chem Global Chemical Transport Model ! +#------------------------------------------------------------------------------ +#BOP +# +# !IROUTINE: main +# +# !DESCRIPTION: Driver program for the nc_chunk.pl script. +#\\ +#\\ +# !INTERFACE: +# +sub main(@) { +# +# !REVISION HISTORY: +# 12 Apr 2018 - R. Yantosca - Initial version +#EOP +#------------------------------------------------------------------------------ +#BOC + + # Error message + my $errMsg = "Usage: nc_chunk.pl NETCDF-FILE-NAME"; + + # If the user passes a filename from the command line, use it + # Otherwise, default to "UnitTest.input" + if ( scalar( @ARGV ) == 2 ) { &chunkTheFile( @ARGV, ); } + elsif ( scalar( @ARGV ) == 1 ) { &chunkTheFile( @ARGV, 0 ); } + else { print "$errMsg\n"; exit( -1 ); } + + # Exit and pass status code backq + return( $? ); +} +#EOC + +#------------------------------------------------------------------------------ + +# Call main program +main(); + +# Exit and pass status code back to Unix shell +exit( $? );