Get jbdiagnose working in a user-friendly manner

 * Add script to call jbdiagnose.x
 * Add vertical level definitions in share/levdef
 * Update CMake infrastructure

CMakeLists.txt

@@ -24,6 +24,9 @@ file(GLOB_RECURSE sources  src/*.F90 src/*.h)
 add_executable(jbdiagnose.x ${sources})
 
 # install executables and scripts
-install (TARGETS ${EXECUTABLES} 
+install (TARGETS jbdiagnose.x
          PERMISSIONS OWNER_EXECUTE OWNER_WRITE OWNER_READ GROUP_EXECUTE GROUP_READ
-         DESTINATION bin)
+         DESTINATION libexec)
+
+add_subdirectory (scripts)
+add_subdirectory (share)

README.md

@@ -1,2 +1,29 @@
 # HarmonieDaTools
 Collection of Harmonie DA tools
+
+## Installation
+```
+cd HarmonieDaTools
+mkdir build
+cd build
+cmake .. -DCMAKE_INSTALL_PREFIX=/path/to/da_tools 
+make 
+make install
+```
+Add DA Tools to your PATH:
+```
+export PATH=/path/to/da_tools:$PATH
+```
+
+## Tools
+### Jb diagnose
+ Help/usage:
+```
+jbdiagnose -h
+```
+
+ Example:
+```
+jbdiagnose -b jb_data/stabfiltn_IRELAND75L65_jbconv.bal -c jb_data/stabfiltn_IRELAND75L65_jbconv.cv -g 15000 -l harmL65
+```
+

scripts/CMakeLists.txt

@@ -0,0 +1,15 @@
+function (install_scripts)
+  foreach (file ${ARGV})
+    get_filename_component (name_without_extension ${file} NAME_WE)
+    install (FILES ${file}
+             PERMISSIONS OWNER_EXECUTE OWNER_WRITE OWNER_READ GROUP_EXECUTE GROUP_READ
+             DESTINATION bin
+             RENAME ${name_without_extension})
+  endforeach ()
+endfunction()
+
+install_scripts (jbdiagnose.sh)
+#install (FILES python_script.py
+#         PERMISSIONS OWNER_EXECUTE OWNER_WRITE OWNER_READ GROUP_EXECUTE GROUP_READ
+#         DESTINATION bin)
+#

scripts/jbdiagnose.sh

@@ -0,0 +1,154 @@
+#!/usr/bin/env bash
+
+# This script will write stats from Jb files in ASCII 
+# suitable for plotting ...
+
+bold=$(tput bold)
+normal=$(tput sgr0)
+unline=$(tput smul)
+
+PROGNAME=`basename $0`
+
+# Define a usage function
+usage() {
+
+cat << USAGE
+
+${bold}NAME${normal}
+        ${PROGNAME} - write Jb statistics
+
+${bold}USAGE${normal}
+        ${PROGNAME} -b <bal-file> -c <cv-file> -g <grid-spacing>
+                    -l <level-definition> [-L] [ -h ]
+
+${bold}DESCRIPTION${normal}
+        Script to start new LBC processing suite
+
+${bold}OPTIONS${normal}
+        -b ${unline}bal-file${normal}
+           bal file
+
+        -c ${unline}cv-file${normal}
+           cv file
+
+        -g ${unline}grid-spacing${normal}
+           Grid-spacing in metres
+        
+        -l ${unline}level-definition${normal}
+           Level definition (A's and B's) 
+        
+        -L List available level definitions
+        
+        -h Help! Print usage information.
+
+USAGE
+}
+
+BALFILE=DUMMY
+CVILE=DUMMY
+GRIDSIZE=DUMMY
+LEVELDEF=DUMMY
+
+#
+# Where am I?
+#
+this_script_loc="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
+appdir=$(dirname ${this_script_loc})
+bindir=${appdir}/bin
+libdir=${appdir}/lib
+exedir=${appdir}/libexec
+levdir=${appdir}/share/levdef
+
+if [ ${#} -eq 0 ]; then
+  echo "No command line arguments provided"
+  echo "Try '${PROGNAME} -h' for more information"
+  exit 1
+fi
+
+while getopts b:c:g:l:Lh option
+do
+  case $option in
+    b)
+       BALFILE=$OPTARG
+       ;;
+    c)
+       CVFILE=$OPTARG
+       ;;
+    g)
+       GRIDSIZE=$OPTARG
+       ;;
+    l)
+       LEVELDEF=$OPTARG
+       ;;
+    L)
+       echo "Will list level defs here ..."
+       ;;
+    h)
+       usage
+       exit 0
+       ;;
+    *)
+       echo
+       echo "Try '${PROGNAME} -h' for more information"
+       ;;
+  esac
+done
+
+if [ ${BALFILE} == "DUMMY" ]; then
+  echo "Please define bal-file using -b"
+  echo "Try '${PROGNAME} -h' for more information"
+  exit 1
+fi
+
+if [ ${CVFILE} == "DUMMY" ]; then
+  echo "Please define cv-file using -c"
+  echo "Try '${PROGNAME} -h' for more information"
+  exit 1
+fi
+
+if [ ${GRIDSIZE} == "DUMMY" ]; then
+  echo "Please define grid-size using -g"
+  echo "Try '${PROGNAME} -h' for more information"
+  exit 1
+fi
+
+if [ ${LEVELDEF} == "DUMMY" ]; then
+  echo "Please define level-definition using -l"
+  echo "Try '${PROGNAME} -h' for more information"
+  exit 1
+fi
+
+echo
+echo "BALFILE=${BALFILE}"
+echo "CVILE=${CVFILE}"
+echo "GRIDSIZE=${GRIDSIZE}"
+echo "LEVELDEF=${LEVELDEF}"
+echo
+
+#
+# Construct namjbconv namelist
+#
+if [ ! -s ${levdir}/${LEVELDEF}.def ]; then
+  echo "${levdir}/${LEVELDEF}.def not found"
+  echo "Try $PROGNAME -L to list available level definitions"
+  exit 1
+fi
+
+echo "&namjbconv" > jbconv.nam
+echo "gsize_in  =  ${GRIDSIZE}," >> jbconv.nam
+cat ${levdir}/${LEVELDEF}.def >> jbconv.nam
+echo "/" >> jbconv.nam
+
+#
+# Create soft links for jbdiagnose.x
+#
+ln ${BALFILE} stabal96.bal
+ln ${CVFILE}  stabal96.cv
+
+${exedir}/jbdiagnose.x < jbconv.nam
+
+rm -f stabal96.cv
+rm -f stabal96.bal
+rm -f jbconv.nam
+
+exit 0

share/CMakeLists.txt

@@ -0,0 +1,2 @@
+install( DIRECTORY levdef DESTINATION share PATTERN "CMakeLists.txt" EXCLUDE )
+

share/levdef/harmL65.def

@@ -0,0 +1,45 @@
+nlev_nl   =      65,
+ahalf_nl  = 0.00000000,      2000.00000000,      4000.21287319,
+         6002.09662113,      7911.25838577,      9633.01049417,
+        11169.37146237,     12522.57753978,     13695.00149653,
+        14689.11546998,     15507.49052823,     16154.69697732,
+        16632.12471208,     16940.14949960,     17082.34869816,
+        17065.28164099,     16898.18367797,     16592.58939571,
+        16161.90395878,     15620.94340550,     14985.46502362,
+        14271.70773051,     13495.95994372,     12674.16909910,
+        11821.60314859,     10952.57042620,     10080.20053763,
+         9216.28565403,      8371.17893039,      7553.74479607,
+         6771.35457397,      6029.92021691,      5333.95880836,
+         4686.68074804,      4090.09511346,      3545.12645110,
+         3051.73811264,      2609.05813936,      2215.50455766,
+         1868.90774223,      1566.62821060,      1305.66882073,
+         1081.85503306,       890.47596795,       727.74548529,
+          590.17748096,       474.58767980,       378.08857614,
+          298.07947335,       232.23312781,       178.48015386,
+          134.99207440,       100.16369201,        72.59529482,
+           51.07508967,        34.56216490,        22.17022046,
+           13.15225964,         6.88641310,         2.86306141,
+            0.67344356,         0.00000000,         0.00000000,
+            0.00000000,         0.00000000,         0.00000000, 
+bhalf_nl  = 0.00000000,         0.00000000,         0.00000000,
+            0.00000000,         0.00095468,         0.00382570,
+            0.00862327,         0.01535782,         0.02404046,
+            0.03468314,         0.04729839,         0.06195102,
+            0.07868187,         0.09744325,         0.11815586,
+            0.14071098,         0.16497348,         0.19078554,
+            0.21797086,         0.24633925,         0.27569119,
+            0.30582244,         0.33652825,         0.36760726,
+            0.39886479,         0.43011564,         0.46118624,
+            0.49191624,         0.52215946,         0.55178443,
+            0.58067442,         0.60872709,         0.63585388,
+            0.66197911,         0.68703898,         0.71098036,
+            0.73375964,         0.75534143,         0.77569737,
+            0.79480486,         0.81264598,         0.82920633,
+            0.84454000,         0.85875505,         0.87191802,
+            0.88409276,         0.89534045,         0.90571965,
+            0.91528643,         0.92409452,         0.93219549,
+            0.93963895,         0.94647277,         0.95274328,
+            0.95849551,         0.96377340,         0.96862008,
+            0.97307803,         0.97718944,         0.98099640,
+            0.98454132,         0.98786727,         0.99102462,
+            0.99406510,         0.99703923,         1.00000000,

share/levdef/hirlL60.def

@@ -0,0 +1,43 @@
+nlev_nl   =      60,
+ahalf_nl  = 0.00000000,      2000.05135426,      4033.40907891,
+         6074.40328124,      8099.63670588,     10087.89367010,
+        12020.06658606,     13879.06676239,     15649.75041085,
+        17318.83964105,     18874.85209658,     20308.02335589,
+        21610.23752964,     22774.95349175,     23797.14016962,
+        24673.19673574,     25400.90458140,     25979.33203475,
+        26408.79136269,     26690.74701491,     26827.77478534,
+        26823.47214753,     26682.39550616,     26409.99528681,
+        26012.54977341,     25497.08526683,     24871.31302372,
+        24143.55208429,     23322.66080848,     22417.97990382,
+        21439.22595692,     20396.44798444,     19299.92669234,
+        18160.12861384,     16987.58390227,     15792.86806530,
+        14586.45478044,     13378.69029188,     12179.68413384,
+        10999.25363904,      9846.77794029,      8731.20481400,
+         7660.88648378,      6643.53270367,      5686.12140321,
+         4794.80922574,      3974.84219208,      3230.45458673,
+         2564.80865572,      1979.88863358,      1476.41314284,
+         1053.75138659,       709.81576221,       441.03262309,
+          242.16324537,       106.30163568,        24.73731477,
+            0.00000000,         0.00000000,         0.00000000,
+            0.00000000,
+bhalf_nl  = 0.00000000,         0.00000000,         0.00000000,
+            0.00023670,         0.00092292,         0.00224844,
+            0.00438079,         0.00746615,         0.01163013,
+            0.01697863,         0.02359864,         0.03155913,
+            0.04091181,         0.05169201,         0.06391953,
+            0.07759939,         0.09272279,         0.10926775,
+            0.12720022,         0.14647459,         0.16703484,
+            0.18881506,         0.21174059,         0.23572858,
+            0.26068905,         0.28652551,         0.31313601,
+            0.34041375,         0.36824815,         0.39652539,
+            0.42512962,         0.45394336,         0.48284882,
+            0.51172809,         0.54046468,         0.56894389,
+            0.59705391,         0.62468618,         0.65173687,
+            0.67810731,         0.70370500,         0.72844406,
+            0.75224667,         0.77504346,         0.79677456,
+            0.81739014,         0.83685163,         0.85513240,
+            0.87221834,         0.88810912,         0.90281875,
+            0.91637651,         0.92882764,         0.94023440,
+            0.95067674,         0.96025322,         0.96908170,
+            0.97730036,         0.98506843,         0.99256705,
+            1.00000000,