runmd

   1 if [ -z "$1" ]; then
   2         echo "specify a directory for logging and save files"
   3         exit
   4 fi
   5
   6 if [ ! -f ./config ]; then
   7         echo "no config file found"
   8         exit
   9 fi
  10
  11 [ ! -d $1 ] && mkdir -p $1
  12
  13 ./clean $1
  14
  15 cp -v config $1/config
  16
  17 mkdir -p logs
  18 logfile=logs/run_`basename $1`.log
  19 time ./mdrun -c ./config -s $1 | tee $logfile
  20
  21 if [ "$?" == "0" ]; then
  22         #./perms
  23         if [ "$1" ] ; then
  24                 # whole simulation cell
  25                 #./visualize -w 640 -h 480 -d $1
  26
  27                 # crt
  28                 mkdir -p $1/crt
  29                 check=`grep crt\ init $logfile`
  30                 if [ "$check" = "  crt init" ]; then
  31                         grep crt\ energy $logfile | \
  32                                 awk -F: '{ print $2 }' | \
  33                                 awk -F\ -\  '{ print $1 " " $2 }' > \
  34                                 $1/crt/energy
  35                         for i in $1/s-crt_*.save; do
  36                                 nr=`basename $i | awk -F_ '{ print $2 }' | \
  37                                         awk -F. '{ print $1 }'`
  38                                 ./s2xyz $i > $1/crt/atomic_conf_${nr}.xyz
  39                         done
  40                         ./visualize -w 640 -h 480 -d $1/crt \
  41                                     -nll -0.56 -0.56 -0.76 -fur 0.56 0.56 0.56 \
  42                                     -b -0.5 -0.5 -0.5 0.5 0.5 0.5 \
  43                                     -c -0.2 -2.0 0.6 -L 0 0 -0.1 \
  44                                     -r 0.6 -B 0.1
  45                 fi
  46
  47                 ./visualize -w 640 -h 480 -d $1 \
  48                             -nll -0.56 -0.56 -0.76 -fur 0.56 0.56 0.56 \
  49                             -b -0.5 -0.5 -0.5 0.5 0.5 0.5 \
  50                             -c -0.2 -2.0 0.6 -L 0 0 -0.1 \
  51                             -r 0.6 -B 0.1
  52
  53                 # old rasmol
  54                 #rasmol -32 -nodisplay < $1/visualize.scr > /dev/null 2>&1
  55                 ./ppm2avi $1
  56
  57         fi
  58 fi
  59