apply autoformatting; update to latest develop for dev/ufs-weather-model branch; fix wave_elevation export for coupling with CICE6

.github/workflows/gnu.yml

@@ -25,7 +25,7 @@ jobs:
       - name: checkout-ww3
         if: steps.cache-env.outputs.cache-hit != 'true'
         uses: actions/checkout@v2
-        with: 
+        with:
             path: ww3
       # Cache spack, OASIS, and compiler
       # No way to flush Action cache, so key may have # appended

.github/workflows/intel.yml

@@ -34,7 +34,7 @@ jobs:
       - name: checkout-ww3
         if: steps.cache-env.outputs.cache-hit != 'true'
         uses: actions/checkout@v2
-        with: 
+        with:
             path: ww3
 
       # Cache spack, OASIS, and compiler

cmake/FindMETIS.cmake

@@ -14,5 +14,5 @@ find_package_handle_standard_args(
     ${CMAKE_FIND_PACKAGE_NAME}
     REQUIRED_VARS metis_lib
     metis_inc)
-  
+
 message(STATUS "Found METIS: ${metis_lib}")

model/bin/ad3.tmpl

@@ -89,7 +89,7 @@
   compress=0               # source code compression par in w3adc
                            # if not 0, documentaion removed from .f90 file
 
-# 1.d Get data from setup file - - - - - - - - - - - - - - - - - - - - - - - - 
+# 1.d Get data from setup file - - - - - - - - - - - - - - - - - - - - - - - -
 
   source $(dirname $0)/w3_setenv
   main_dir=$WWATCH3_DIR
@@ -201,14 +201,14 @@
   if [ "$w3adc" = 'yes' ]
   then
 
-# 2.b Run CPP preprocessor  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
+# 2.b Run CPP preprocessor  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 
     #Generate list of CPP Flags based on switches:
     CPPFLAGS=()
-    for sw in $sw_str 
-    do 
+    for sw in $sw_str
+    do
        CPPFLAGS+=("-DW3_$sw")
-    done 
+    done
 
     CPPFLAGS+=("-D__WW3_SWITCHES__='$sw_str'")
 
@@ -259,14 +259,14 @@
 #  rm -f *.mod ## too indiscriminate
 
   ## Using find -iname most succinct, but maybe not all version of find have
-  ## the -iname option? 
+  ## the -iname option?
 #  find . -iname "${name}.mod" -delete  # not all versions of find have -iname?
 
-  # Fall back on grep -i 
+  # Fall back on grep -i
   mods=`ls *.mod 2> /dev/null | grep -i "${name}.mod"`
   if [ -n ${mods} ]; then
     rm -f ${mods}
-  fi 
+  fi
 
 # --------------------------------------------------------------------------- #
 # 3. Compile source code f / f90                                              #
@@ -346,13 +346,13 @@ then
       ## ChrisB: Don't move all module files...could break parallel make.
       ## Just target specific module file (could be mixed case filename
       ## depending on compiler - use case insensitive find):
-#      mods=`ls *.mod 2> /dev/null` 
+#      mods=`ls *.mod 2> /dev/null`
 
       ## Using find -iname most succinct, but maybe not all version of find have
-      ## the -iname option? 
+      ## the -iname option?
 #      mods=`find . -iname "${name}.mod"` # not all versions of find have -iname?
 
-      # Fall back on grep -i 
+      # Fall back on grep -i
       mods=`ls *.mod 2> /dev/null | grep -i "${name}.mod"`
       if [ -n "$mods" ]
       then

model/bin/all_switches

@@ -26,7 +26,7 @@
   echo 'Find all switches in WAVEWATCH III'
   echo '----------------------------------'
 
-# 1.b Get data from setup file - - - - - - - - - - - - - - - - - - - - - - - - 
+# 1.b Get data from setup file - - - - - - - - - - - - - - - - - - - - - - - -
 
   source $(dirname $0)/w3_setenv
   main_dir=$WWATCH3_DIR

model/bin/cmplr.env

@@ -21,7 +21,7 @@
 # remarks :                                                                   #
 #                                                                             #
 #  - template files comp.tmpl and link.tmpl will be used to create the        #
-#    comp and link file based on the following environment variables :        # 
+#    comp and link file based on the following environment variables :        #
 #    $optc, $optl, $comp_seq, $comp_mpi, $optomp, $err_pattern, $warn_pattern #
 #                                                                             #
 #                                                                             #
@@ -61,8 +61,8 @@ if [ "$cmplr" == "mpt" ] || [ "$cmplr" == "mpt_debug" ] || [ "$cmplr" == "mpt_pr
     comp_seq='ftn'
     comp_mpi='ftn'
   fi
-    
- 
+
+
   # OPTIONS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 
   # common options
@@ -104,7 +104,7 @@ if [ "$cmplr" == "mpt" ] || [ "$cmplr" == "mpt_debug" ] || [ "$cmplr" == "mpt_pr
     optl="$optl -xhost"
   fi
 
-  #Flags for CPP: 
+  #Flags for CPP:
   cppad3procflag='-E'
   cppad3flag2=' '
   cppad3flag3='-o'
@@ -140,7 +140,7 @@ if [ "$cmplr" == "intel" ]          || [ "$cmplr" == "intel_debug" ]    || [ "$c
     comp_seq='ftn'
     comp_mpi='ftn'
   fi
-  
+
   if [ ! -z "$(echo $cmplr | grep cheyenne)" ] ; then
     comp_seq='ifort'
     comp_mpi='mpif90'
@@ -162,7 +162,7 @@ if [ "$cmplr" == "intel" ]          || [ "$cmplr" == "intel_debug" ]    || [ "$c
   if [ ! -z "$(echo $cmplr | grep datarmor)" ] || [ "$cmplr" == "hera.intel" ] || [ "$cmplr" == "orion.intel" ] || \
      [ "$cmplr" == "wcoss_cray" ] || [ "$cmplr" == "wcoss_dell_p3" ] || [ "$cmplr" == "cheyenne.intel" ] || \
      [ "$cmplr" == "gaea.intel" ] || [ "$cmplr" == "jet.intel" ] || [ "$cmplr" == "wcoss2" ] || \
-     [ "$cmplr" == "stampede.intel" ] || [ "$cmplr" == "s4.intel" ] || [ "$cmplr" == "expanse.intel" ] ; then 
+     [ "$cmplr" == "stampede.intel" ] || [ "$cmplr" == "s4.intel" ] || [ "$cmplr" == "expanse.intel" ] ; then
      optomp="-qopenmp"
   else
      optomp="-openmp"
@@ -219,7 +219,7 @@ if [ "$cmplr" == "intel" ]          || [ "$cmplr" == "intel_debug" ]    || [ "$c
   fi
 
 
-  #Flags for CPP: 
+  #Flags for CPP:
   cppad3procflag='-E'
   cppad3flag2=' '
   cppad3flag3='>'
@@ -301,7 +301,7 @@ if [ "$cmplr" == "gnu" ] || [ "$cmplr" == "gnu_debug" ] || [ "$cmplr" == "gnu_pr
     optc="$optc -fPIC"
   fi
 
-  #Flags for CPP: 
+  #Flags for CPP:
   cppad3procflag='-E'
   cppad3flag2=' '
   cppad3flag3='-o'
@@ -361,7 +361,7 @@ if [ "$cmplr" == "pgi" ] || [ "$cmplr" == "pgi_debug" ] || [ "$cmplr" == "pgi_pr
     optl="$optl"
   fi
 
-  #Flags for CPP: 
+  #Flags for CPP:
   cppad3procflag='-E'
   cppad3flag2=' '
   cppad3flag3='>'
@@ -419,7 +419,7 @@ if [ "$cmplr" == "ukmo_cray" ] || [ "$cmplr" == "ukmo_cray_debug" ] || \
 
   # system-dependant options
   # N/A
-  #Flags for CPP: 
+  #Flags for CPP:
   cppad3procflag='-eP'
   cppad3flag2=' '
   cppad3flag3='#'

model/bin/comp.tmpl

@@ -46,7 +46,7 @@
   name="$1"
   echo "      Compiling $name"
 
-# 1.b Initial clean-up - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
+# 1.b Initial clean-up - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 
   rm -f $name.l
   rm -f $name.o
@@ -120,7 +120,7 @@
     fi
   fi
 
-# 3.b Make file comp.stat  - - - - - - - - - - - - - - - - - - - - - - - - - - 
+# 3.b Make file comp.stat  - - - - - - - - - - - - - - - - - - - - - - - - - -
 
   echo "ERROR    $nr_err"   > comp.stat.$name
   echo "WARNING  $nr_war"  >> comp.stat.$name
@@ -131,12 +131,12 @@
 #     comment lines are to be numbered.
 
   # listing done by the compiler
-  if [ -s $name.lst ] 
+  if [ -s $name.lst ]
   then
     mv $name.lst $name.l
   fi
   # add comp options, warnings and error to listing
-  if [ -s $name.l ] 
+  if [ -s $name.l ]
   then
     echo '------------' >> $name.l
     echo "$comp $opt"   >> $name.l

model/bin/find_switch

@@ -26,7 +26,7 @@
   echo 'Find switches in WAVEWATCH III'
   echo '------------------------------'
 
-# 1.b Process/save input - - - - - - - - - - - - - - - - - - - - - - - - - - - 
+# 1.b Process/save input - - - - - - - - - - - - - - - - - - - - - - - - - - -
 
   if test "$#" != '0'
   then
@@ -38,21 +38,21 @@
 
   echo ' ' ; echo "Files including $switch :" ; echo ' '
 
-# 1.c Get data from setup file - - - - - - - - - - - - - - - - - - - - - - - - 
+# 1.c Get data from setup file - - - - - - - - - - - - - - - - - - - - - - - -
 
   source $(dirname $0)/w3_setenv
   main_dir=$WWATCH3_DIR
   temp_dir=$WWATCH3_TMP
   source=$WWATCH3_SOURCE
   list=$WWATCH3_LIST
 
-# 1.d Raw data file  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
+# 1.d Raw data file  - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 
-### TO DO: This needs to be improved for CPP transition 
+### TO DO: This needs to be improved for CPP transition
   cd $main_dir/src
   grep "$switch" * | sed 's/\:/ /' | awk '{ print $1}' > ../.switch.files
 
-# 1.e Output - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
+# 1.e Output - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 
   last=$NULL
   for file in `cat ../.switch.files`

model/bin/link.tmpl

@@ -33,7 +33,7 @@
   echo "      Linking $prog"
   input="$*"
 
-# 1.b Get data from setup file - - - - - - - - - - - - - - - - - - - - - - - - 
+# 1.b Get data from setup file - - - - - - - - - - - - - - - - - - - - - - - -
 
   source $(dirname $0)/w3_setenv
   main_dir=$WWATCH3_DIR
@@ -42,7 +42,7 @@
   list=$WWATCH3_LIST
 
 
-# 1.c Initial clean-up - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
+# 1.c Initial clean-up - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 
   rm -f $main_dir/exe/$prog
 
@@ -117,15 +117,15 @@
     libs="$libs `$NETCDF_CONFIG --flibs` `$NETCDF_CONFIG --libs`"
   fi
 
-  # parmetis library 
+  # parmetis library
   if [ "$prog" = 'ww3_shel' ] || [ "$prog" = 'ww3_multi' ] || [ "$prog" = 'ww3_sbs1' ] ; then
     if [ "$pdlib_mod" = 'yes' ] ; then
       if [ -z "$(env | grep METIS_PATH)" ] ; then
         echo ''
         echo "[ERROR] METIS_PATH is not defined"
         exit 1
       fi
-      echo "link with parmetis" 
+      echo "link with parmetis"
       libs="$libs $METIS_PATH/lib/libparmetis.a $METIS_PATH/lib/libmetis.a"
     fi
   fi

model/bin/make_makefile.sh

@@ -126,7 +126,7 @@
     # Get file - the list of files to be compiled
     # and filel - list of files for linking a particular prog
     create_file_list
- 
+
     case $prog in
       ww3_grid) IDstring='Grid preprocessor' ;;
       ww3_strt) IDstring='Initial conditions program' ;;

model/bin/sort_all_switches

@@ -45,7 +45,7 @@ Options:
                      otherwise this gives an error exit
 EOF
 }
- 
+
 # 1.a.3 Process input (part 1)
 
   args=`getopt $optstr $*`
@@ -75,7 +75,7 @@ EOF
     exit 1
   fi
 
-# 1.a.4 Get data from setup file - - - - - - - - - - - - - - - - - - - - - - - - 
+# 1.a.4 Get data from setup file - - - - - - - - - - - - - - - - - - - - - - - -
 
   source $(dirname $0)/w3_setenv
   main_dir=$WWATCH3_DIR

model/bin/sort_switch

@@ -60,7 +60,7 @@ Options:
   -v               : verbose, show program output
 EOF
 }
- 
+
 # 1.a.3 Process input (part 1)
 
   args=`getopt $optstr $*`
@@ -112,14 +112,14 @@ EOF
     exit 2
   fi
 
-# 1.a.4 Get data from setup file - - - - - - - - - - - - - - - - - - - - - - - - 
+# 1.a.4 Get data from setup file - - - - - - - - - - - - - - - - - - - - - - - -
 
   source $(dirname $0)/w3_setenv
   main_dir=$WWATCH3_DIR
   temp_dir=$WWATCH3_TMP
   source=$WWATCH3_SOURCE
   list=$WWATCH3_LIST
- 
+
 # 1.a.5 Process input (part 2)
 
   bin_dir="$main_dir/exe"
@@ -133,7 +133,7 @@ EOF
 
   if [ ! -f $script ] ; then
     echo " *** cannot find $script ***" ; exit 5 ; fi
- 
+
 # 1.a.6 Additional setups
 
   outs="O0 O1 O2 O2a O2b O2c O3 O4 O5 O6 O7 O7a O7b O8 O9 O10 O11 O12 O13 O14 O15 O16"
@@ -162,7 +162,7 @@ EOF
     echo ' '
   fi
 
-# 1.d Set up work space  - - - - - - - - - - - - - - - - - - - - - - - - - - - 
+# 1.d Set up work space  - - - - - - - - - - - - - - - - - - - - - - - - - - -
 
   cd $temp_dir
 
@@ -300,7 +300,7 @@ EOF
           fi
         fi
       done
-   
+
     done
 
    if [ "$verbose" ]
@@ -433,7 +433,7 @@ EOF
 # --------------------------------------------------------------------------- #
 # 4. Dealing with left over switches                                          #
 # --------------------------------------------------------------------------- #
-# 4.a Loop over additional types 
+# 4.a Loop over additional types
 
   for type in out strace test
   do
@@ -457,7 +457,7 @@ EOF
 
 # 4.c Loop over switchs
 
-    for sw in $switches 
+    for sw in $switches
     do
       i_fnd='0'
       found=