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

diff --git a/moldyn.c b/moldyn.c
index dd8a527ff77f91bc1ce214ddb4370526222b357f..b79dea66946edb6032132b4b85df486e290916e4 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,
        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));
 
        moldyn->volume,
        (int)(t2.tv_sec-t1.tv_sec));
 

diff --git a/runmd b/runmd
index 5db09fdbb12520d8d3a90b1eaf9d6d915fd2dec9..d50d9ae39867107745d1b1b24c5eb25928318c6f 100755 (executable)
--- a/runmd
+++ b/runmd
@@ -14,7 +14,7 @@ fi
 
 cp -v config $1/config
 
 
 cp -v config $1/config
 

-./mdrun -c ./config -s $1
+time ./mdrun -c ./config -s $1

 
 if [ "$?" == "0" ]; then
        #./perms
 
 if [ "$?" == "0" ]; then
        #./perms

diff --git a/runmd_rx200 b/runmd_rx200
index 9368141576abff90d993d7fb2fd821b37e46e250..4e4966eabf14fa7b556c043ca1e5b6d0ddea8c77 100755 (executable)
--- a/runmd_rx200
+++ b/runmd_rx200
@@ -23,22 +23,5 @@ cat > run_$rf <<-EOF
 EOF
 
 # submit job
 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
+