--- MITgcm_contrib/jmc_script/extract_StD	2006/04/10 20:10:46	1.2
+++ MITgcm_contrib/jmc_script/extract_StD	2020/02/11 22:17:43	1.4
@@ -1,10 +1,10 @@
-#!/bin/sh
+#! /usr/bin/env bash
 
-# $Header: /home/ubuntu/mnt/e9_copy/MITgcm_contrib/jmc_script/extract_StD,v 1.2 2006/04/10 20:10:46 jmc Exp $
+# $Header: /home/ubuntu/mnt/e9_copy/MITgcm_contrib/jmc_script/extract_StD,v 1.4 2020/02/11 22:17:43 jmc Exp $
 # $Name:  $
 
 add=0 ; mut=0 ;
-if [ $# -ge 3 ] 
+if [ $# -ge 3 ]
 then
  if test $1 = '-a' ; then add=1; shift; fi
  if test $1 = '-s' ; then mut=1; shift; fi
@@ -36,7 +36,7 @@
 else
  shift; shift; shift; listV=$*
 fi
-if test $mut = 0 ; then 
+if test $mut = 0 ; then
  grep '^# Fields ' $inpFil
  echo 'selected var:' $listV
 #echo 'sufx, tmpFil:' $sufx $tmpFil
@@ -47,9 +47,7 @@
 do
  case $vv in
    'Eta') var='ETAN'     ; vfl=$vv ;;
-              'ETAN'     ) var=$vv ; vfl='Eta' ;;
-   'Et2') var='ETANSQ'   ; vfl=$vv ;;
-              'ETANSQ'   ) var=$vv ; vfl='Et2' ;;
+              'ETAN'     ) var=$vv ; vfl='Eta';;
      'T') var='THETA'    ; vfl=$vv ;;
               'THETA'    ) var=$vv ; vfl='T' ;;
      'S') var='SALT'     ; vfl=$vv  ;;
@@ -61,11 +59,19 @@
      'W') var='WVEL'     ; vfl=$vv  ;;
               'WVEL'     ) var=$vv ; vfl='W' ;;
    'Phi') var='PHIHYD'   ; vfl=$vv  ;;
-              'PHIHYD'   ) var=$vv ; vfl='Phi' ;;
+              'PHIHYD'   ) var=$vv ; vfl='Phi';;
+   'Et2') var='ETANSQ'   ; vfl=$vv ;;
+              'ETANSQ'   ) var=$vv ; vfl='Et2';;
+    'T2') var='THETASQ'  ; vfl=$vv ;;
+              'THETASQ'  ) var=$vv ; vfl='T2' ;;
+    'S2') var='SALTSQ'   ; vfl=$vv  ;;
+              'SALTSQ'   ) var=$vv ; vfl='S2' ;;
     'U2') var='UVELSQ'   ; vfl=$vv  ;;
               'UVELSQ'   ) var=$vv ; vfl='U2' ;;
     'V2') var='VVELSQ'   ; vfl=$vv  ;;
               'VVELSQ'   ) var=$vv ; vfl='V2' ;;
+    'W2') var='WVELSQ'   ; vfl=$vv  ;;
+              'WVELSQ'   ) var=$vv ; vfl='W2' ;;
        *)  var=$vv ; vfl=$vv ;;
  esac
 #echo 'grep -m 1' "^ field : ${var} " $inpFil
@@ -81,7 +87,7 @@
   then flag=0
     outFil=${prfx}'_head'.$sufx
     nLin=`sed -n "/^# end of header/=" $inpFil`
-    head -$nLin $inpFil > $tmpFil 
+    head -$nLin $inpFil > $tmpFil
     if test -f $outFil -a $add = 0 ; then rm -f $outFil ; fi
     if test -f $outFil
     then
@@ -115,7 +121,7 @@
   echo "/^ field : $var /{" > $sedFil
   if test $nLev = 1 ; then k=0 ; else k=-1 ; fi
   while [ $k -le $nLev ]
-  do 
+  do
    echo "N" >> $sedFil
    k=`expr $k + 1`
   done
@@ -126,7 +132,7 @@
   if test $mut = 0 ; then head -1 $tmpFil ; fi
   if test -f $outFil -a $add = 0 ; then rm -f $outFil ; fi
   touch $outFil
-  sed '/^ k /d' $tmpFil | sed '/^ field /d' >> $outFil 
+  sed '/^ k /d' $tmpFil | sed '/^ field /d' >> $outFil
   rm -f $sedFil $tmpFil
  fi
 done