- bash scripts in /tools/ now generate random file names to avoid conflict with possibly existing files, e.g. when the same script is executed several times simultaneously.

Author: pierrehirel

tools/dat_mulvec.sh

@@ -24,8 +24,10 @@ else
   do
     printf ">>> Multiplying vectors by $factor in $f ..."
     if [ -e $f ]; then
-      awk -v fac=$factor '{print $1 " " $2 " " $3 " " fac*$4 " " fac*$5 " " fac*$6}' $f >>/tmp/temp.dat
-      mv -f /tmp/temp.dat $f
+      # Generate random file name
+      of="$(mktemp ./XXXXXXXX.tmp)"
+      awk -v fac=$factor '{print $1 " " $2 " " $3 " " fac*$4 " " fac*$5 " " fac*$6}' $f >> ${of}
+      mv -f ${of} $f
       printf " Done.\n"
     else
       printf " File doesn't exist, skipping.\n"

tools/dat_rm0.sh

@@ -17,8 +17,10 @@ else
   do
     printf ">>> Removing lines with zero vectors in $f ..."
     if [ -e $f ]; then
-      awk '{if($4!=0.0 && $5!=0.0 && $6!=0.0) print $0 }' $f >>/tmp/temp.dat
-      mv -f /tmp/temp.dat $f
+      # Generate random file name
+      of="$(mktemp ./XXXXXXXX.tmp)"
+      awk '{if($4!=0.0 && $5!=0.0 && $6!=0.0) print $0 }' $f >> ${of}
+      mv -f ${of} $f
       printf " Done.\n"
     else
       printf " File doesn't exist, skipping.\n"

tools/lmp_atom2charge.sh

@@ -23,18 +23,21 @@ else
       #Check that it is a LAMMPS file
       islmp=$(grep "atom types" $f | wc -l)
       if [ $islmp = 1 ]; then
+        # Generate random file name
+        of="$(mktemp ./XXXXXXXX.tmp)"
         # If the keyword "Atoms" is not followed by "# charge", add it
         atomic=$(grep "Atoms" $f | grep "charge" | wc -l)
         if [ $atomic = 0 ]; then
           sed -i '/Atoms/ c\Atoms  # charge' $f
         fi
-        # Add a column of zero after column 2
-        awk '{if(NR>9 && NF>4 && $1>0 && $2>0)
+        nrAtom=$(awk '/^Atom/{print NR}' $f)
+        # Add a column of zero after keyword "Atom"
+        awk -v n="${nrAtom}" '{if(NR>n && NF>4 && $1>0 && $2>0)
                 {print $1 "\t" $2 "\t0.0\t" $(NF-2) "\t" $(NF-1) "\t" $NF}
               else
                 {print}
-             }' $f >/tmp/temp.lmp
-        mv -f /tmp/temp.lmp $f
+             }' $f > ${of}
+        mv -f ${of} $f
         printf " Done.\n"
       else
         printf " Not a LAMMPS data file, skipping.\n"

tools/lmp_charge2atom.sh

@@ -22,6 +22,8 @@ else
       #Check that it is a LAMMPS file
       islmp=$(grep "atom types" $f | wc -l)
       if [ $islmp = 1 ]; then
+        # Generate random file name
+        of="$(mktemp ./XXXXXXXX.tmp)"
         # If the keyword "Atoms" is not followed by "# atomic" add it
         charge=$(grep "Atoms" $f | grep "atomic" | wc -l)
         if [ $charge = 0 ]; then
@@ -32,8 +34,8 @@ else
                 {print $1 "\t" $2 "\t" $(NF-2) "\t" $(NF-1) "\t" $NF}
               else
                 {print}
-             }' $f >/tmp/temp.lmp
-        mv -f /tmp/temp.lmp $f
+             }' $f > ${of}
+        mv -f ${of} $f
         printf " Done.\n"
       else
         printf " Not a LAMMPS data file, skipping.\n"