Cleanup create_trajectories.sh with shellcheck

utils/create_trajectories.sh

@@ -3,7 +3,7 @@
 # ---------------------------------------------------------------------------------
 # create_trajectories.sh - Generate and execute a set ABIN simulations
 #
-# Initial geometries (and optionally velocities) are taken sequentially from XYZ movie files.
+# Initial geometries (and optionally velocities) are taken sequentially from a XYZ trajectory file.
 
 # The trajectories are executed and stored in $folder.
 
@@ -12,47 +12,72 @@
 # 	abin-randomint PRNG program for generating random seeds, should be in your $PATH.
 #---------------------------------------------------------------------------------
 
-#######-----SETUP---#############
-irandom0=156863189  # random seed, set negative for random seed based on time
-movie=coords.xyz    # PATH TO a XYZ movie with initial geometries
-veloc=vels.xyz      # PATH to XYZ initial velocities (optional)
-isample=1	    # initial number of traj
-nsample=100	    # number of trajectories
-folder=MP2-NH4      # Name of the folder with trajectories
-inputdir=TEMPLATE-$folder   # Directory with input files for ABIN
-abin_input=$inputdir/input.in   # main input file for ABIN
-launch_script=$inputdir/r.abin	# this is the file that is submitted by qsub
-submit="qsub -q nq -cwd  " # comment this line if you don't want to submit to queue yet
-rewrite=0            # if =1 -> rewrite trajectories that already exist
-jobs=20              # number of batch jobs to submit. Trajectories will be distributed accordingly.
-
-molname=$folder      # Name of the job in the queue
+# Exit if undefined variable is used
+set -u
+
+#### SETUP ####
+# Path to a XYZ file with initial geometries
+movie=coords.xyz
+# Path to XYZ file with initial velocities (optional)
+# veloc=vels.xyz
+
+# Starting index for the initial geometries
+isample=1
+# End index
+nsample=100
+
+# Folder name where the trajectories will be created
+folder=MY_MOLECULE_TRAJS
+
+# Directory with the input files for ABIN (input.in et al)
+inputdir=TEMPLATE-$folder
+
+# File with ABIN input parameters, we need this path
+# so we can inject random number seed into it.
+abin_input=$inputdir/input.in
+
+# Random seed to generate random seeds for individual trajectories
+# Set to a negative number for a time-based random seed.
+irandom0=156863189
+
+# Specify path to launch script that is normally submitted to the queuing system.
+# Comment out this line if you're running locally.
+launch_script=$inputdir/r.abin
+# If you don't provide a launch script,
+# we need a (preferably absolute) path to abin executable
+# abin_exe=/path/to/abin
+
+# Comment out this line if you don't want to run calculations yet
+# submit_command="qsub -cwd -V -q nq -cwd "
+# If you don't use queing system (like SLURM), use the following line
+# submit_command=bash
+
+# Number of batch jobs to submit to queue
+# set only if you have more trajectories than jobs
+# jobs=20
 ########## END OF SETUP ##########
 
 
 function files_exist {
-  for f in $*;do
-    if [[ ! -f $f ]];then
+  for f in "$@";do
+    if [[ -n ${f-} && ! -f $f ]]; then
       echo "ERROR: File '$f' does not exist!"
       exit 1
     fi
   done
 }
 
 function folders_exist {
-  for d in $*;do
-    if [[ ! -d $d ]];then
+  for d in "$@";do
+    if [[ -n ${f-} && ! -d $d ]]; then
       echo "ERROR: Directory '$d' does not exist!"
       exit 1
     fi
   done
 }
 
 folders_exist "$inputdir"
-files_exist "$movie" "$abin_input" "$launch_script"
-if [[ -n "$veloc" ]];then
-  files_exist "$veloc"
-fi
+files_exist "$movie" "${veloc-}" "$abin_input" "${launch_script-}"
 
 natom=$(head -1 $movie)
 if [[ $natom -lt 1 ]];then
@@ -62,145 +87,139 @@ fi
 echo "Number of atoms = $natom"
 
 # TODO: Verify number of atoms and lines in the velocity file
-let natom2=natom+2
-lines=$(cat $movie | wc -l)
-geoms=$(expr $lines / $natom2)
+(( natom2=natom+2 ))
+lines=$(wc -l < $movie)
+(( geoms=lines/natom2 ))
 if [[ $nsample -gt $geoms ]];then
    echo "ERROR: Number of geometries ($geoms) is smaller than number of samples($nsample)."
    echo "Change parameter \"nsample\"."
    exit 1
 fi
 
 # determine number of ABIN simulations per job
-let nsimul=nsample-isample+1
+(( nsimul=nsample-isample+1 ))
+if [[ -z ${jobs-} ]]; then
+   jobs=$nsimul
+fi
+
 if [[ $nsimul -le $jobs ]];then
    remainder=0
    injob=1
    jobs=$nsimul
 else
-   let injob=nsimul/jobs  #number of simulations per job
+   (( injob=nsimul/jobs ))  #number of simulations per job
    # determine the remainder and distribute it evenly between jobs
-   let remainder=nsimul-injob*jobs
+   (( remainder=nsimul-injob*jobs ))
 fi
 
-
 j=1
 i=$isample
 w=0 #current number of simulations in current j-th job
 
-#--------------------generation of random numbers--------------------------------
+# Generate random number generator seeds for individual trajectories
 echo "Generating $nsample random integers for random seeds"
 echo "abin-randomint --seed $irandom0 --num $nsample > iran.dat"
-abin-randomint --seed $irandom0 --num $nsample > iran.dat
-if [[ $? -ne "0" ]];then
+if ! abin-randomint --seed $irandom0 --num $nsample > iran.dat
+then
   echo "ERROR: Could not generate random numbers"
   exit 1
 fi
 
 mkdir -p $folder
 cp iseed0 "$abin_input" $folder
 
-let offset=natom2*isample-natom2
-
-if [[ "$rewrite" -eq "1" ]];then
-    rm -f $folder/$molname.$isample.*.sh
-fi
-
+(( offset=natom2*isample-natom2 ))
 
 while [[ $i -le "$nsample" ]];do
 
-   let offset=offset+natom2     
+   (( offset=offset+natom2 ))
 
    if [[ -d "$folder/TRAJ.$i" ]];then
-      if [[ "$rewrite" -eq "1" ]];then
-
-         rm -r $folder/TRAJ.$i ; mkdir $folder/TRAJ.$i
-
-      else
 
          echo "Trajectory number $i already exists!"
-         echo "Exiting..."
+         echo "If you want to overwrite it, first remove it:"
+         echo "'rm -r $folder/TRAJ.$i'"
          exit 1
 
-      fi
-
    else
 
       mkdir $folder/TRAJ.$i
 
    fi
 
+   # Copy all the files from the template directory
    cp -r $inputdir/* $folder/TRAJ.$i
 
-
    # Prepare input geometry and velocities
-
-   head -$offset $movie | tail -$natom2 > geom
-   if [[ ! -z "$veloc" ]];then
-      head -$offset $veloc | tail -$natom2 > veloc.in
-   fi
-
-   mv geom $folder/TRAJ.$i/mini.dat
-
-   if [[ ! -z "$veloc" ]];then
-      mv veloc.in $folder/TRAJ.$i/
+   head -$offset $movie | tail -$natom2 > $folder/TRAJ.$i/initial.xyz
+   if [[ -n "${veloc-}" ]];then
+      head -$offset "$veloc" | tail -$natom2 > $folder/TRAJ.$i/veloc.in
    fi
 
-
-## Now prepare input.in and r.abin
-   irandom=`head -$i iran.dat |tail -1`
+   ## Now prepare input.in and r.abin
+   irandom=$(head -$i iran.dat |tail -1)
 
    # TODO: Validate this step
    sed -r "s/irandom *= *[0-9]+/irandom=$irandom/" $abin_input > $folder/TRAJ.$i/input.in 
 
-   cat > $folder/TRAJ.$i/r.$molname.$i << EOF
+   cat > $folder/TRAJ.$i/r.$folder.$i << EOF
 #!/bin/bash
-JOBNAME=ABIN.$molname.${i}_$$_\${JOB_ID}
 INPUTPARAM=input.in
-INPUTGEOM=mini.dat
-OUTPUT=output
+INPUTGEOM=initial.xyz
 EOF
 
-   if [[ ! -z $veloc ]];then
-      echo "INPUTVELOC=veloc.in" >> $folder/TRAJ.$i/r.$molname.$i
+   if [[ -n ${veloc-} ]];then
+      echo "INPUTVELOC=veloc.in" >> $folder/TRAJ.$i/r.$folder.$i
    fi
 
-   grep -v -e '/bin/bash' -e "JOBNAME=" -e "INPUTPARAM=" -e "INPUTGEOM=" -e "INPUTVELOC=" $launch_script >> $folder/TRAJ.$i/r.$molname.$i
-
-   chmod 755 $folder/TRAJ.$i/r.$molname.$i
-
+   if [[ -n ${launch_script-} ]];then
+      grep -v -e '/bin/bash' -e "INPUTPARAM=" -e "INPUTGEOM=" -e "INPUTVELOC=" $launch_script >> $folder/TRAJ.$i/r.$folder.$i
+   else
+      if [[ -n ${veloc-} ]]; then
+         echo "$abin_exe -i input.in -x initial.xyz -v veloc.in > abin.out 2>&1" > $folder/TRAJ.$i/r.$folder.$i
+      else
+         echo "$abin_exe -i input.in -x initial.xyz > abin.out 2>&1" > $folder/TRAJ.$i/r.$folder.$i
+      fi
+   fi
 
-   echo "cd TRAJ.$i" >> $folder/$molname.$isample.$j.sh
-   echo "./r.$molname.$i" >> $folder/$molname.$isample.$j.sh
-   echo "cd $PWD/$folder" >> $folder/$molname.$isample.$j.sh
+   echo "(cd TRAJ.$i && bash r.$folder.$i)" >> $folder/$folder.$isample.$j.sh
 
-#--Distribute calculations evenly between jobs for queue
+   # Distribute calculations evenly between jobs for queue
    if [[ $remainder -le 0 ]];then
-      let ncalc=injob
+      ncalc=injob
    else
-      let ncalc=injob+1 
+      (( ncalc=injob+1 ))
    fi
-   let w++
+   (( w++ ))
    if [[ $w -eq $ncalc ]] && [[ $j -lt $jobs ]]; then
-      let j++
-      let remainder--
-      let w=0
+      w=0
+      (( j++ ))
+      (( remainder-- ))
    fi
-#---------------------------------------------------------------------------
 
-   let i++
+   (( i++ ))
 
 done
 
 # Submit jobs
 k=1
-if [[ ! -z "$submit" ]];then
-   cd $folder
-   while [[ $k -le $j ]]
-   do
-      if [[ -f $molname.$isample.$k.sh ]];then
-         $submit -V -cwd $molname.$isample.$k.sh
-      fi
-      let k++
-   done
+if [[ -n "${submit_command-}" ]];then
+    cd $folder || exit 1
+    if [[ $submit_command = "bash" ]];then
+        echo "Launching $j calculations locally"
+        submit_command="nohup $submit_command"
+    else
+        echo "Submitting $j calculations with: $submit_command"
+    fi
+    while [[ $k -le $j ]]
+    do
+        if [[ -f $folder.$isample.$k.sh ]];then
+            $submit_command $folder.$isample.$k.sh &
+        fi
+        (( k++ ))
+    done
+    # Wait for submit commands to finish (they should be fast!)
+    if [[ $submit_command != "bash" ]]; then
+        wait
+    fi
 fi