modified runmd scripts + added pressure debug line (commented) to moldyn

diff --git a/moldyn.c b/moldyn.c
index dd8a527..b79dea6 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -1698,6 +1698,7 @@ printf("\rsched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)",
        sched->count,i,moldyn->total_steps,
        moldyn->t,moldyn->t_avg,
        moldyn->p/BAR,moldyn->p_avg/BAR,
+       //moldyn->p/BAR,(moldyn->p-2.0*moldyn->ekin/(3.0*moldyn->volume))/BAR,
        moldyn->volume,
        (int)(t2.tv_sec-t1.tv_sec));
 

diff --git a/runmd b/runmd
index 5db09fd..d50d9ae 100755 (executable)
--- a/runmd
+++ b/runmd
@@ -14,7 +14,7 @@ fi
 
 cp -v config $1/config
 
-./mdrun -c ./config -s $1
+time ./mdrun -c ./config -s $1
 
 if [ "$?" == "0" ]; then
        #./perms

diff --git a/runmd_rx200 b/runmd_rx200
index 9368141..4e4966e 100755 (executable)
--- a/runmd_rx200
+++ b/runmd_rx200
@@ -23,22 +23,5 @@ cat > run_$rf <<-EOF
 EOF
 
 # submit job
-qsub run_$rf
-
-if [ "$?" == "0" ]; then
-       #./perms
-       if [ "$1" ] ; then
-               # whole simulation cell
-               #./visualize -w 640 -h 480 -d $1
-
-               # center unit cell
-               #./visualize -w 640 -h 480 -d $1 \
-               #            -nll -2.4 -2.4 -2.4 -fur 3.8 3.8 3.8 \
-               #           -b -2.03 -2.03 -2.03 3.39 3.39 3.39 \
-               #           -r 0.6 -c 0.5 -11.0 2.5 -B 0.1
-
-               # old rasmol
-               #rasmol -32 -nodisplay < $1/visualize.scr > /dev/null 2>&1
-               #./ppm2avi $1
-       fi
-fi
+qsub -q all.q run_$rf
+