Add scripts to restore the "lev" dimension

fixlev/fixlev_gcap2_104.sh fixlev/fixlev_gcap2_74.sh fixlev/fixlev_gcap2_40.sh - Script that uses the NCO "ncap2" function to restore the "lev" dimension to netCDF files created by NCL scripts. fixlev/nc_chunk.pl - Script for compressing and chunking README.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
geoschem · Aug 27, 2024 · 94eed21 · 94eed21
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diff --git a/LICENSE.txt.~1~ b/LICENSE.txt.~1~
diff --git 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
@@ -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 "${1}" 1
+
+exit 0
diff --git a/fixlev/fixlev_gcap2_40.sh b/fixlev/fixlev_gcap2_40.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+# Add the lev dimension back into the file
+ncap2 -O -h -s 'lev[lev]={1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40}; lev@long_name="GEOS-Chem level"; lev@units="level"; lev@positive="up";lev@axis="Z"' "${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
@@ -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
@@ -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( $? );