merge master into master_in_yosemite

.gitignore

 FP_ecmwf_gfortran*
 *.o
-*_mod.mod
+*.mod
 .DS_Store
 output
+src/FLEXPART_*
+fort.*
+CONVERT2
 FLEXPART_laptop

tests/NILU/run_test

@@ -5,9 +5,20 @@ test_dir=$1  # name of dir with pathname and options to be used
 FP_exec=$2   # path to executable to be run
 base_dir=$3  # base for the output
 options_default=$4
+
+echo run test '>' input
+echo $1
+echo $2
+echo $3
+echo $4
+
+#  echo name= $name
+#  echo working dir= $path_tests/test_$name
+#  echo executable= $FP_exec 
+#  echo default options from $options_default 
  
 #echo FP_exec=$FP_exec
-echo $FLEXOUT_TMP
+echo env var FLEXOUT_TMP=$FLEXOUT_TP
 
 #suffix=$(date "+%y-%m-%d_%H%M%S")
 test_tmp=${FLEXOUT_TMP}${base_dir}${test_dir}
@@ -17,15 +28,24 @@ current_dir=$(pwd)
 #echo test_tmp=$test_tmp
 mkdir $test_tmp
 
-echo copy default options $options_default  to temp dir $test_tmp/options
+echo run test '>' copy default options to temp dir
+echo from  $options_default  to $test_tmp/options
 cp -r $options_default $test_tmp/options
 #override default options
-echo copy this test option files to temp dir
-cp  ${test_dir}/options/* $test_tmp/options/
-echo copy SPECIES from ${test_dir}/options/SPECIES/* to $test_tmp/options/SPECIES/
-cp  ${test_dir}/options/SPECIES/* $test_tmp/options/SPECIES/
+echo copy test options files to temp dir
+echo ${test_dir}/options/* $test_tmp/options/
+cp   ${test_dir}/options/* $test_tmp/options/
+echo copy test options/SPECIES to temp dir if needed
+
+if [ -d "${test_dir}/options/SPECIES" ]; then
+echo from ${test_dir}/options/SPECIES/* to $test_tmp/options/SPECIES/
+cp        ${test_dir}/options/SPECIES/*    $test_tmp/options/SPECIES/
+fi
+
 # copy paths form repo source exec tmp dir 
+echo copy test pathnames to temp dir
 cp ${test_dir}/pathnames $test_tmp
+echo create output dir ${test_tmp}/output
 mkdir ${test_tmp}/output
 
 #cp test_1/run $test_tmp
@@ -36,7 +56,9 @@ cd $test_tmp
 #  '&>' o is bash for both out and err
 #echo run $FP_exec   to  out.log #&
 #$FP_exec   &> out.log #&
+echo execute test
 $FP_exec > stdout.log 2> stderr.log #&
+echo flexpart terminated
 
 
 

tests/NILU/run_tests

@@ -36,14 +36,13 @@ mkdir $path_tests
 #declare -a test_names=('2' 'Volc')
 #declare -a test_names=('1' 'HelloWorld' 'Fwd1' 'Fwd2' 'Bwd1' 'Volc' '2')
 
-#blabla
 #Print the Whole Bash Array
 s_test_names=${test_names[@]}
 # Length of the Bash Array
 n_tests=${#test_names[@]}
 #echo n_tests=$n_tests
-echo run $n_tests  tests:  $s_test_names
-
+echo run $s_test_names
+echo total $n_tests tests
 #test
 #tests_dir='tests_15-08-19_113139/'
 #path_tests=${path_flextest}/$tests_dir
@@ -56,10 +55,13 @@ while [ $i -lt $i_end ] ;
 do
   let j=i+1
   name=${test_names[i]};
-  echo test no. $j name= $name
-  echo in $path_tests/test_$name
+  echo run test no. $j  
+#  echo name= $name
+#  echo working dir= $path_tests/test_$name
+#  echo executable= $FP_exec 
+#  echo default options from $options_default 
   ./run_test test_$name  $FP_exec $path_tests $options_default
-  echo terminated
+  echo test $name terminated
   success="$(cat $path_tests/test_$name/$outlog  | grep CONGRATULATIONS  | wc -l)"
   echo success=$success
 let i=i+1;