Merge pull request #22 from polyluxus/devel_0.3.0

Upgrade to 0.3.0

Author: polyluxus

README.md

@@ -91,8 +91,10 @@ The following script options are available:
               This also requires setting a queueing system with `-Q` (see below).
               (configuration option `run_interactive=sub`).
  * `-Q <ARG>` Set a queueing system for which the submitscript should be prepared.
-              Currently supported are `pbs-gen`, `bsub-gen`, and `bsub-rwth` 
+              Currently supported are `pbs-gen`, `slurm-gen`, `slurm-rwth`, `bsub-gen`, and `bsub-rwth` 
               (configuration option `request_qsys=<ARG>`).
+              The `*rwth` suffix will test a few more options and will set some constraints according to
+              the recommendations of the RWTH IT centre.
  * `-P <ARG>` Account to project `<ARG>`, which will also (currently) trigger
               `-Q bsub-rwth` to be set. It will not trigger `-s`/`-S`.
  * `-M`       Use preinstalled modules instead of paths. 
@@ -118,7 +120,8 @@ The following script options are available:
               If specified twice, it will also suppress warnings,
               if specified more than twice, it will suppress also errors.
  * `-h`       Prints a small help text and current configuration.
- * `-H`       Opens the `HOWTO` (manual) of the original distribution.
+ * `-H`       Retrieve the man page of xtb of the original distribution.
+ * `-X`       Retrieve the man page of xcontrol of the original distribution.
 
 ## Included files
 
@@ -128,16 +131,21 @@ The following files come with this script:
  * `runxtb.rc` An example set-up file.
  * `xtb.dummy` A tiny bash script only for testing. 
    This will only echo `<coord_file> [options]` verbatim.
+ * `crest.prepare.sh` A small script that creates a new directory 
+   with a suitable `coord` file to start a `crest` run.
  * `README.md` This file.
  * `configure` A directury containing a script to configure the wrapper.
 
 ## Exit status
 
-The script carries over the exit statusses of its dependencies.
+The script `runxtb` carries over the exit statusses of its dependencies.
 In interactive mode that is the exit status of `xtb`.
-In submission mode it is the exit status of `qsub` or `bsub`.
+In submission mode it is the exit status of `qsub`, `bsub`, or `sbatch`.
 In all other cases it will be `0` if everything went according to plan,
 or `1` if there was a problem.  
+The script `crest.prepare.sh` will exit with `0` if nothing went wrong 
+and a crest run can be started. If files are not present, or I/O operations
+fail it will exit with `1`.  
 The dummy script `xtb.dummy` always exits with `2`.
 
 ## Debug
@@ -154,4 +162,4 @@ please include the debug output when submitting a bug report to the
 [GitHub issue tracker](https://github.com/polyluxus/runxtb.bash/issues).
 
 
-(Martin; 2019-02-14; wrapper version 0.2.1)
+(Martin; 2019-03-18; wrapper version 0.3.0)

configure/configure.sh

@@ -17,6 +17,12 @@ warning ()
     return 1
 }
 
+fatal ()
+{
+    echo    "ERROR  :  $*" >&2
+    exit 1
+}
+
 debug ()
 {
     echo    "DEBUG   : $*" >&4
@@ -224,6 +230,13 @@ recover_rc ()
     if read_boolean ; then ask_installation_path ; fi
   fi
   debug "use_xtbhome=$use_xtbhome; use_xtbname=$use_xtbname"
+  if [[ -z $use_xtbname ]] ; then 
+    ask_callname
+  else
+    message "recovered setting 'xtb_callname=$use_xtbname'."
+    ask "Would you like to change these settings?"
+    if read_boolean ; then ask_callname ; fi
+  fi
 
   use_chatty="$stay_quiet"
   if [[ -z $use_chatty ]] ; then
@@ -256,20 +269,21 @@ recover_rc ()
   debug "use_interactivity=$use_interactivity"
 
   use_queue="$request_qsys"
-  use_bsub_project="$bsub_project"
+  # Try to recover old vrsion where it was bsub_project
+  use_qsys_project="${qsys_project:-$bsub_project}"
   if [[ -z $use_queue ]] ; then
     ask_qsys_details
   else
     message "Recovered queueing system setting 'request_qsys=$use_queue'."
-    if [[ ! -z $use_bsub_project ]] ; then 
-      message "Recovered project setting 'bsub_project=$bsub_project'."
+    if [[ -n $use_qsys_project ]] ; then 
+      message "Recovered project setting 'qsys_project=$use_qsys_project'."
       ask "Would you like to change these settings?"
     else
       ask "Would you like to change this setting?"
     fi
     if read_boolean ; then ask_qsys_details ; fi
   fi
-  debug "use_queue=$use_queue; use_bsub_project=$use_bsub_project"
+  debug "use_queue=$use_queue; use_qsys_project=$use_qsys_project"
 
   use_module_system="$use_modules"
   use_module_items=( "${load_modules[@]}" )
@@ -329,7 +343,7 @@ read_boolean ()
   pattern_true_false="[Tt]([Rr]([Uu][Ee]?)?)?|[Ff]([Aa]([Ll]([Ss][Ee]?)?)?)?"
   pattern_yes_no="[Yy]([Ee][Ss]?)?|[Nn][Oo]?"
   pattern="($pattern_true_false|$pattern_yes_no|0|1)"
-  until [[ $readvar =~ ^[[:space:]]*$pattern[[:space:]]*$ ]] ; do
+  until [[ $readvar =~ ^[[:space:]]*${pattern}[[:space:]]*$ ]] ; do
     message "Please enter t(rue)/y(es)/1 or f(alse)/n(o)/0."
     echo -n "Answer  : " >&3
     read -r readvar
@@ -397,6 +411,13 @@ ask_installation_path ()
   debug "use_xtbname=$use_xtbname"
 }
 
+ask_callname ()
+{
+  ask "What is the name of the xtb binary?"
+  use_xtbname="$(read_human_input)"
+  debug "use_xtbname=$use_xtbname"
+}
+
 ask_modules ()
 {
   ask "If a modular cluster management is available, do you want to use it?"
@@ -453,7 +474,7 @@ ask_interactivity ()
 
 ask_qsys_details ()
 {
-  message "Currently supported: pbs-gen, bsub-gen, bsub-rwth"
+  message "Currently supported: pbs-gen, bsub-gen, slurm-gen, bsub-rwth, slurm-rwth"
   local test_queue
   test_queue=$(read_human_input)
   debug "test_queue=$test_queue"
@@ -464,11 +485,17 @@ ask_qsys_details ()
     [Bb][Ss][Uu][Bb]* )
       use_queue="bsub-gen"
       ask "What project would you like to specify?"
-      use_bsub_project=$(read_human_input)
-      debug "use_bsub_project=$use_bsub_project"
+      use_qsys_project=$(read_human_input)
+      debug "use_qsys_project=$use_qsys_project"
+      ;;&
+    [Ss][Ll][Uu][Rr][Mm]* )
+      use_queue="slurm-gen"
+      ask "What project would you like to specify?"
+      use_qsys_project=$(read_human_input)
+      debug "use_qsys_project=$use_qsys_project"
       ;;&
     *[Rr][Ww][Tt][Hh] )
-      use_queue="bsub-rwth"
+      use_queue="${use_queue%-*}-rwth"
       ;;
     '' )
       : ;;
@@ -635,7 +662,7 @@ print_settings ()
   echo     "###"
 
   echo     "## Set default queueing system for which the script should be written"
-  echo     "## (pbs-gen, bsub-gen, or bsub-rwth [special case, see source])"
+  echo     "## (pbs-gen, bsub-gen, slurm-gen, or *-rwth [special cases, see source])"
   echo     "#  "
   if [[ -z $use_queue ]] ; then
     echo   "#  request_qsys=\"bsub-rwth\""
@@ -645,14 +672,14 @@ print_settings ()
   echo     "#  "
   echo     "###"
 
-  echo     "## If project options are enabled (e.g. for bsub-rwth), "
-  echo     "## set to which it should be accounted."
+  echo     "## If project/ account options are enabled (e.g. for bsub-rwth), "
+  echo     "## set the name to which it should be accounted to."
   echo     "## This can be overwritten with -P0 or -P default."
   echo     "#"
-  if [[ -z $use_bsub_project ]] ; then
-    echo   "#  bsub_project=\"default\""
+  if [[ -z $use_qsys_project ]] ; then
+    echo   "#  qsys_project=\"default\""
   else
-    echo   "   bsub_project=\"$use_bsub_project\""
+    echo   "   qsys_project=\"$use_qsys_project\""
   fi
   echo     "#  "
   echo     "###"
@@ -702,21 +729,25 @@ print_settings ()
 
 create_bin_link ()
 {
-    local link_target_path="$HOME/bin"
-    local link_target_name="runxtb"
-    local link_target="$link_target_path/$link_target_name"
+  local link_target_path="$HOME/bin"
+  local link_target_name link_target link_source
 
+  for link_target_name in "runxtb" "crest.prepare" ; do
+    link_target="$link_target_path/$link_target_name"
+    link_source="$runxtbrc_path/${link_target_name}.sh"
     if [[ -e "$link_target" ]] ; then
       debug "Link '$link_target' does already exist."
+      continue
     else
       ask "Would you like to create a symbolic link '$link_target'?"
       if read_boolean ; then
         [[ -r "$link_target_path" ]] || fatal "Cannot read '$link_target_path'."
         [[ -w "$link_target_path" ]] || fatal "Cannot write to '$link_target_path'."
-        [[ -x "$runxtbrc_path/runxtb.sh" ]] || fatal "Not executable: '$runxtbrc_path/runxtb.sh'."
-        message "$(ln -vs "$runxtbrc_path/runxtb.sh" "$link_target")"
+        [[ -x "$link_source" ]] || fatal "Not executable: '$link_source'."
+        message "$( ln -vs "$link_source" "$link_target" )"
       fi
     fi
+  done
 }
 
 #

crest.prepare.sh

@@ -0,0 +1,180 @@
+#!/bin/bash
+#hlp ===== Not Part of xTB =====
+#hlp DESCRIPTION:
+#hlp   This is a little helper script to set up a crest (via xTB) calculation.
+#hlp   
+#hlp   It basically creates a directory (optional) with a molecular 
+#hlp   structure in turbomole format called 'coord'.
+#hlp   Script requires Open Babel.
+#hlp  
+#hlp USAGE:
+#hlp   ${0##*} [script options] 
+#hlp 
+
+#
+# Print logging information and warnings nicely.
+# If there is an unrecoverable error: display a message and exit.
+#
+
+message ()
+{
+    if (( stay_quiet <= 0 )) ; then
+      echo "INFO   : " "$*" >&3
+    else
+      debug "(info   ) " "$*"
+    fi
+}
+
+warning ()
+{
+    if (( stay_quiet <= 1 )) ; then
+      echo "WARNING: " "$*" >&2
+    else
+      debug "(warning) " "$*"
+    fi
+    return 1
+}
+
+fatal ()
+{
+    exit_status=1
+    if (( stay_quiet <= 2 )) ; then 
+      echo "ERROR  : " "$*" >&2
+    else
+      debug "(error  ) " "$*"
+    fi
+    exit "$exit_status"
+}
+
+debug ()
+{
+  echo "DEBUG  : (${FUNCNAME[1]})" "$*" >&4
+}    
+
+#
+# Print some helping commands
+# The lines are distributed throughout the script and grepped for
+#
+
+helpme ()
+{
+    local line
+    local pattern="^[[:space:]]*#hlp[[:space:]]?(.*)?$"
+    while read -r line; do
+      [[ "$line" =~ $pattern ]] && eval "echo \"${BASH_REMATCH[1]}\""
+    done < <(grep "#hlp" "$0")
+    exit 0
+}
+
+backup_if_exists ()
+{
+  local move_source="$1"
+  # File does not exist, then everithing is fine, return with status 0
+  [[ -f "$move_source" ]] || return 0
+  # File exists, print a warning 
+  warning "File '$move_source' already exists."
+  # make a backup 
+  # (test default name first, if that exists, relegate to tool)
+  local move_target="${move_source}.bak"
+  [[ -f "$move_target" ]] && move_target=$( mktemp "${move_target}.XXXX" ) 
+  # if moving failed for whatever reason, return with status 1
+  message "Create backup: $( mv -v -- "$move_source" "$move_target" 2>&1 )" || return 1
+}
+
+###
+#
+# MAIN
+#
+###
+
+exec 3>&1
+
+if [[ "$1" == "debug" ]] ; then
+  # Secret debugging switch
+  exec 4>&1
+  shift 
+else
+  exec 4> /dev/null
+fi
+
+
+# Initialise Variables
+stay_quiet="0"
+OPTIND=1
+
+while getopts :d:qh options ; do
+  case $options in
+    #hlp OPTIONS:
+    #hlp 
+    #hlp   -d <ARG> Use <ARG> as directory name to set up. [Default: crest]
+    #hlp            If <ARG> is '.', then skip creating a directory, 
+    #hlp            instead convert a found '*.xyz' to 'coord', or
+    #hlp            rename existing 'xtbopt.coord' to 'coord'.
+    d) 
+      crest_dir="$OPTARG"
+      ;;
+    #hlp   -q       Stay quiet! (Only this startup script)
+    #hlp            May be specified multiple times to be more forceful.
+    q) 
+      (( stay_quiet++ )) 
+      ;;
+    #hlp   -h       Prints this help text
+    h) 
+      helpme 
+      ;;
+    \?) 
+      fatal "Invalid option: -$OPTARG." 
+      ;;
+    :) 
+      fatal "Option -$OPTARG requires an argument." 
+      ;;
+
+  esac
+done
+
+crest_dir="${crest_dir:-crest}"
+if [[  "$crest_dir" != '.' ]] ; then
+  [[ -d "$crest_dir" ]] && fatal "Directory exists: $crest_dir"
+  message "$( mkdir -v -- "$crest_dir" )" || fatal "Failed to create '$crest_dir'."
+else
+  debug "Target directory is '$crest_dir'."
+fi
+
+if [[ -r "xtbopt.xyz" ]] ; then
+  obabel_cmd="$( command -v obabel )" || fatal "Command not found: obabel"
+  backup_if_exists "$crest_dir/coord"
+  message "$( "$obabel_cmd" -ixyz "xtbopt.xyz" -oTmol -O"$crest_dir/coord" 2>&1 )" || fatal "Failure in Open Babel."
+elif [[ -r "xtbopt.coord" ]] ; then
+  message "Found optimised molecular structure in turbomole format."
+  backup_if_exists "$crest_dir/coord"
+  message "$( cp -v -- "xtbopt.coord" "$crest_dir/coord" )"
+else
+  warning "No optimised molecular structure found in current directory."
+  for structure_file in "coord" *.xyz ; do
+    if [[ -r "$structure_file" ]] ; then
+      message "Will use molecular structure in '$structure_file' instead."
+      if [[ "$structure_file" == "coord" ]] ; then
+        [[ "$crest_dir" == '.' ]] && fatal "'$structure_file' and '$crest_dir/coord' are the same file."
+        message "$( cp -v -- "$structure_file" "$crest_dir/coord" )"
+        break
+      else
+        obabel_cmd="$( command -v obabel )" || fatal "Command not found: obabel"
+        backup_if_exists "$crest_dir/coord"
+        message "$( "$obabel_cmd" -ixyz "$structure_file" -oTmol -O"$crest_dir/coord" 2>&1 )" || fatal "Failure in Open Babel."
+        break
+      fi
+    fi
+  done
+fi
+
+if [[ -r ".UHF" ]] ; then
+  message "$( cp -v -- ".UHF" "$crest_dir/.UHF" )"
+fi
+
+if [[ -r ".CHRG" ]] ; then
+  message "$( cp -v -- ".CHRG" "$crest_dir/.CHRG" )"
+fi
+
+debug "Content of created directory: $( ls -lah "$crest_dir" )"
+message "All Done: ${0##*/}."
+