Merge pull request #5 from polyluxus/bugfix_and_test_3.5.0

small bugfixes, display manual, ready for Multiwfn 3.5

CHANGES.txt

@@ -1,10 +1,15 @@
 VERSIONLOG
 
+0.5.1 2018-04-13
+  minor bugfixes
+  initial tests with Multiwfn 3.5
+  added option to display manual (if installed)
+
 0.5.0 2018-04-11
   Rewrite installation routines
   Added rc handling
   Removed legacy mode 
-  (To Do) Rework remote mode, i.e. implement another scheduler
+  Reworked remote mode, i.e. implement another scheduler (BSUB)
 
 0.4.4 2018-01-11
   Warns about local settings.ini
@@ -53,4 +58,4 @@ VERSIONLOG
   The first working draft of the script.
   Version 3.3.8 of Multiwfn.
 
-(Martin; 0.4.4; 2018-01-11)
+(Martin; 0.5.1; 2018-04-13)

INSTALL.txt

@@ -105,8 +105,18 @@ working on it further, but until then see the following.
 
 (e) What else?
 
-  Make sure the script is executeable.
+  If you want to access the manual with the -H switch, you need to download 
+  it and put it with the executable. The script searches for a pdf file,
+  and will display the first it finds.
+
+  There are a couple of options implemented to look for a pdf viewer,
+  the safest is to set 'use_pdfviewer=' to your preferred one in the rc.
+  Tested are in that order: "use_pdfviewer" xdg-open gvfs-open evince okular less.
+
+  Also please make sure the script is executeable.
    (chmod +x <scriptname>)
+  Occasionally the Multiwfn distribution itself was not marked executable;
+  therefore better check that one, too.
 
   Now everything should be done.
 
@@ -119,4 +129,4 @@ working on it further, but until then see the following.
   Alternatively you can add an alias, or add the multiwfn
   directory to your PATH.
 
-(Martin; 0.5.0; 2018-04-11)
+(Martin; 0.5.1; 2018-04-13)

README.md

@@ -1,6 +1,7 @@
 # runMultiwfn.bash
 
 A wrapper for Multiwfn 3.4.1 (Linux) written in bash.
+Initial tests with Multiwfn 3.5 have been successful, too.
 
 It does probably work without any modification for any newer
 version; as long as the definitions of the environment variables 
@@ -152,9 +153,15 @@ The following option switches are available:
        Suppress logging messages of the script.
        (May be specified multiple times.)
 
-  - `h`
+  - `-h`
        Prints a short version of the options.
 
+  - `-H`
+       Displays the manual (if installed, see INSTALL.txt).
+       This requires a pdfviewer installed, which can be set in the rc.
+       The script will test a few commands before giving up (see the
+       example `runMultiwfn.rc` for details). 
+
 ---
 
 ## Examples
@@ -178,4 +185,4 @@ or via github (polyluxus), or any other way you can think of.
 I have a blog (that has not been updated in a while): 
 https://thedailystamp.wordpress.com/
 
-(Martin; 0.5.0; 2018-04-11)
+(Martin; 0.5.1; 2018-04-13)

runMultiwfn.rc

@@ -39,3 +39,8 @@ bsub_rwth_project="default"
 # By default clean up the temporary setting.ini
 settingsini_nocleanup="false"
 
+# Set a default pdfviewer (needs to be an executable command found through PATH)
+# Tested in that order are: "$use_pdfviewer" xdg-open gvfs-open evince okular less 
+use_pdfviewer="xpdf"
+
+# (Martin; 0.5.1; 2018-04-13)

runMultiwfn.sh

@@ -2,14 +2,18 @@
 
 #Multiwfn initialization script
 # See CHANGES.txt
-version="0.5.0"
-versiondate="2018-04-11"
+version="0.5.1"
+versiondate="2018-04-13"
 
 # The following two lines give the location of the installation.
 # They can be set in the rc file, too.
 installpath_Multiwfn_gui="/path/is/not/set"
 installpath_Multiwfn_nogui="/path/is/not/set"
 
+# Set a default pdfviewer (needs to be an executable command found through PATH)
+# Tested in that order are: "$use_pdfviewer" xdg-open gvfs-open evince okular less 
+use_pdfviewer="xpdf"
+
 # See the readme file for more details. 
 
 #####
@@ -57,6 +61,24 @@ helpme ()
     exit 0
 }
 
+display_manual ()
+{
+    local manual_location use_Multiwfnpath pdf_open pdf_open_command
+    use_Multiwfnpath=$(get_Multiwfnpath_or_exit "$installpath_Multiwfn_gui") || exit 1
+    if manual_location=$(find "$use_Multiwfnpath" -iname '*.pdf' -print -quit) ; then
+      debug "manual_location=$manual_location"
+      for pdf_open in "$use_pdfviewer" xdg-open gvfs-open evince okular less ; do
+        debug "Testing: $pdf_open"
+        pdf_open_command=$(command -v "$pdf_open") || continue
+        "$pdf_open_command" "$manual_location" && break
+        fatal "Could not find programm to open pdf; please check your settings."
+      done
+    else
+      fatal "Cannot find manual."
+    fi
+    exit 0
+}
+
 #
 # Print logging information and warnings nicely.
 # If there is an unrecoverable error: display a message and exit.
@@ -565,7 +587,7 @@ process_options ()
     #hlp    
     local OPTIND=1 
 
-    while getopts :m:p:w:gRl:i:o:c:qfkQ:P:sh options ; do
+    while getopts :m:p:w:gRl:i:o:c:qfkQ:P:shH options ; do
         case $options in
 
           #hlp     -m <ARG> Define memory to be used per thread in byte.
@@ -722,6 +744,10 @@ process_options ()
           #hlp
             h) helpme ;;
 
+          #hlp     -H       Display the manual. 
+          #hlp              Requires a pdfviewer and the manual to be installed.
+            H) display_manual ;;
+
            \?) fatal "Invalid option: -$OPTARG." ;;
 
             :) fatal "Option -$OPTARG requires an argument." ;;
@@ -749,7 +775,6 @@ process_options ()
 
 run_interactive ()
 {
-  exit 0
     export KMP_STACKSIZE=$requested_KMP_STACKSIZE
     message "Memory (KMP_STACKSIZE) is set to $KMP_STACKSIZE."
     Multiwfnpath="$use_Multiwfnpath"
@@ -810,6 +835,7 @@ runRemote ()
     echo "#!/bin/bash" >&9
     echo "# Submission script automatically created with $scriptname" >&9
 
+    local overhead_KMP_STACKSIZE
     overhead_KMP_STACKSIZE=$(( requested_KMP_STACKSIZE + 5000000 ))
 
     # Header is different for the queueing systems
@@ -831,8 +857,8 @@ runRemote ()
 			#BSUB -W ${requested_walltime%:*}
 			#BSUB -J ${submitscript%.*}
 			#BSUB -N 
-			#BSUB -o df-bp86svp.runMultiwfn.sh.o%J
-			#BSUB -e df-bp86svp.runMultiwfn.sh.e%J
+			#BSUB -o $submitscript.o%J
+			#BSUB -e $submitscript.e%J
 			EOF
       if [[ "$PWD" =~ [Hh][Pp][Cc] ]] ; then
         echo "#BSUB -R select[hpcwork]" >&9
@@ -853,7 +879,7 @@ runRemote ()
 		echo "Calculation $inputfile and $commandfile from $PWD."
 		echo "Working directry is $PWD"
 		
-		cd $PWD
+		cd "$PWD"
 		
 		export PATH="\$PATH:$use_Multiwfnpath"
 		export Multiwfnpath="$use_Multiwfnpath"
@@ -989,8 +1015,10 @@ fi
 write_temp_settingsini
 
 if [[ "$execmode" == "remote" ]] ; then
+  debug "Running remote."
   runRemote "$request_qsys"
 else
+  debug "Running interactive."
   run_interactive
 fi