Large diffs are not rendered by default.

@@ -0,0 +1,35 @@
#PBS -l walltime=9999:0:00
#PBS -l nodes=118:ppn=48
#PBS -N glyions1o
#PBS -S /bin/bash
#PBS -j oe
#PBS -m ae
#PBS -M ngirmang.1@osu.edu


PBSBASE=glyions1o
#source $HOME/.bashrc

#This outputs the name of the root node
#to the directory where you submitted this PBS job
echo $HOSTNAME > $PBS_O_WORKDIR/hostname.txt
cat $PBS_NODEFILE | uniq > $PBS_O_WORKDIR/nodesfile.txt

module load openmpi-1.4.3-gnu-rpm


cd "$PBS_O_WORKDIR"
#zipper
./loopscript zipper &> $PBS_O_WORKDIR/zipper.log&
zipper_PID=$!
#movne
./loopscript movne &> $PBS_O_WORKDIR/movne.log&
movne_PID=$!


mpirun -np 5632 -hostfile $PBS_NODEFILE ./lsp-10-3d $PBSBASE.lsp >$PBS_O_WORKDIR/$PBSBASE.o.txt

kill $zipper_PID
./zipper -a >$PBS_O_WORKDIR
kill $movne_PID
./movne
@@ -0,0 +1,25 @@
#PBS -l walltime=168:0:00
#PBS -l select=235:ncpus=24:mpiprocs=24
#PBS -N glyions1o
#PBS -S /bin/bash
#PBS -j oe
#PBS -m ae
#PBS -M ngirmang.1@osu.edu
#PBS -A __projectid__
#PBS -q standard


PBSBASE=glyions1o
#source $HOME/.bashrc

#This outputs the name of the root node
#to the directory where you submitted this PBS job
echo $HOSTNAME > $PBS_O_WORKDIR/hostname.txt
cat $PBS_NODEFILE | uniq > $PBS_O_WORKDIR/nodesfile.txt


cd "$PBS_O_WORKDIR"


aprun -n 5632 ./lsp-10-3d $PBSBASE.lsp >$PBS_O_WORKDIR/$PBSBASE.o.txt

@@ -0,0 +1,25 @@
#PBS -l walltime=14:0:00
#PBS -l select=235:ncpus=24:mpiprocs=24
#PBS -N glyions1o
#PBS -S /bin/bash
#PBS -j oe
#PBS -m ae
#PBS -M ngirmang.1@osu.edu
#PBS -A __projectid__
#PBS -q standard


PBSBASE=glyions1o
#source $HOME/.bashrc

#This outputs the name of the root node
#to the directory where you submitted this PBS job
echo $HOSTNAME > $PBS_O_WORKDIR/hostname.txt
cat $PBS_NODEFILE | uniq > $PBS_O_WORKDIR/nodesfile.txt


cd "$PBS_O_WORKDIR"


aprun -n 5632 ./lsp-10-3d $PBSBASE.lsp >$PBS_O_WORKDIR/$PBSBASE.o.txt

@@ -0,0 +1,25 @@
#PBS -l walltime=48:0:00
#PBS -l select=235:ncpus=24:mpiprocs=24
#PBS -N glyions1o
#PBS -S /bin/bash
#PBS -j oe
#PBS -m ae
#PBS -M ngirmang.1@osu.edu
#PBS -A __projectid__
#PBS -q standard


PBSBASE=glyions1o
#source $HOME/.bashrc

#This outputs the name of the root node
#to the directory where you submitted this PBS job
echo $HOSTNAME > $PBS_O_WORKDIR/hostname.txt
cat $PBS_NODEFILE | uniq > $PBS_O_WORKDIR/nodesfile.txt


cd "$PBS_O_WORKDIR"


aprun -n 5632 ./lsp-10-3d $PBSBASE.lsp >$PBS_O_WORKDIR/$PBSBASE.o.txt

@@ -0,0 +1,25 @@
#PBS -l walltime=24:0:00
#PBS -l select=235:ncpus=24:mpiprocs=24
#PBS -N glyions1o
#PBS -S /bin/bash
#PBS -j oe
#PBS -m ae
#PBS -M ngirmang.1@osu.edu
#PBS -A __projectid__
#PBS -q bigmem


PBSBASE=glyions1o
#source $HOME/.bashrc

#This outputs the name of the root node
#to the directory where you submitted this PBS job
echo $HOSTNAME > $PBS_O_WORKDIR/hostname.txt
cat $PBS_NODEFILE | uniq > $PBS_O_WORKDIR/nodesfile.txt


cd "$PBS_O_WORKDIR"


aprun -n 5632 ./lsp-10-3d $PBSBASE.lsp >$PBS_O_WORKDIR/$PBSBASE.o.txt

@@ -0,0 +1,25 @@
#PBS -l walltime=0:30:00
#PBS -l select=235:ncpus=24:mpiprocs=24
#PBS -N glyions1o
#PBS -S /bin/bash
#PBS -j oe
#PBS -m ae
#PBS -M ngirmang.1@osu.edu
#PBS -A __projectid__
#PBS -q debug


PBSBASE=glyions1o
#source $HOME/.bashrc

#This outputs the name of the root node
#to the directory where you submitted this PBS job
echo $HOSTNAME > $PBS_O_WORKDIR/hostname.txt
cat $PBS_NODEFILE | uniq > $PBS_O_WORKDIR/nodesfile.txt


cd "$PBS_O_WORKDIR"


aprun -n 5632 ./lsp-10-3d $PBSBASE.lsp >$PBS_O_WORKDIR/$PBSBASE.o.txt

@@ -0,0 +1,25 @@
#PBS -l walltime=168:0:00
#PBS -l select=176:ncpus=32:mpiprocs=32
#PBS -N glyions1o
#PBS -S /bin/bash
#PBS -j oe
#PBS -m ae
#PBS -M ngirmang.1@osu.edu
#PBS -A __projectid__
#PBS -q standard_lw


PBSBASE=glyions1o
#source $HOME/.bashrc

#This outputs the name of the root node
#to the directory where you submitted this PBS job
echo $HOSTNAME > $PBS_O_WORKDIR/hostname.txt
cat $PBS_NODEFILE | uniq > $PBS_O_WORKDIR/nodesfile.txt


cd "$PBS_O_WORKDIR"


aprun -n 5632 ./lsp-10-3d $PBSBASE.lsp >$PBS_O_WORKDIR/$PBSBASE.o.txt

@@ -0,0 +1,25 @@
#PBS -l walltime=48:0:00
#PBS -l select=176:ncpus=32:mpiprocs=32
#PBS -N glyions1o
#PBS -S /bin/bash
#PBS -j oe
#PBS -m ae
#PBS -M ngirmang.1@osu.edu
#PBS -A __projectid__
#PBS -q standard_lw


PBSBASE=glyions1o
#source $HOME/.bashrc

#This outputs the name of the root node
#to the directory where you submitted this PBS job
echo $HOSTNAME > $PBS_O_WORKDIR/hostname.txt
cat $PBS_NODEFILE | uniq > $PBS_O_WORKDIR/nodesfile.txt


cd "$PBS_O_WORKDIR"


aprun -n 5632 ./lsp-10-3d $PBSBASE.lsp >$PBS_O_WORKDIR/$PBSBASE.o.txt

@@ -0,0 +1,25 @@
#PBS -l walltime=1:0:00
#PBS -l select=176:ncpus=32:mpiprocs=32
#PBS -N glyions1o
#PBS -S /bin/bash
#PBS -j oe
#PBS -m ae
#PBS -M ngirmang.1@osu.edu
#PBS -A __projectid__
#PBS -q debug


PBSBASE=glyions1o
#source $HOME/.bashrc

#This outputs the name of the root node
#to the directory where you submitted this PBS job
echo $HOSTNAME > $PBS_O_WORKDIR/hostname.txt
cat $PBS_NODEFILE | uniq > $PBS_O_WORKDIR/nodesfile.txt


cd "$PBS_O_WORKDIR"


aprun -n 5632 ./lsp-10-3d $PBSBASE.lsp >$PBS_O_WORKDIR/$PBSBASE.o.txt

@@ -0,0 +1,25 @@
#PBS -l walltime=24:0:00
#PBS -l select=176:ncpus=32:mpiprocs=32
#PBS -N glyions1o
#PBS -S /bin/bash
#PBS -j oe
#PBS -m ae
#PBS -M ngirmang.1@osu.edu
#PBS -A __projectid__
#PBS -q standard_sm


PBSBASE=glyions1o
#source $HOME/.bashrc

#This outputs the name of the root node
#to the directory where you submitted this PBS job
echo $HOSTNAME > $PBS_O_WORKDIR/hostname.txt
cat $PBS_NODEFILE | uniq > $PBS_O_WORKDIR/nodesfile.txt


cd "$PBS_O_WORKDIR"


aprun -n 5632 ./lsp-10-3d $PBSBASE.lsp >$PBS_O_WORKDIR/$PBSBASE.o.txt

@@ -0,0 +1,28 @@
#PBS -l walltime=96:0:00
#PBS -l nodes=470:ppn=12
#PBS -N glyions1o
#PBS -S /bin/bash
#PBS -j oe
#PBS -m ae
#PBS -M ngirmang.1@osu.edu


PBSBASE=glyions1o
#source $HOME/.bashrc

#This outputs the name of the root node
#to the directory where you submitted this PBS job
echo $HOSTNAME > $PBS_O_WORKDIR/hostname.txt
cat $PBS_NODEFILE | uniq > $PBS_O_WORKDIR/nodesfile.txt


cd "$PBS_O_WORKDIR"
#zipper
./loopscript zipper &> $PBS_O_WORKDIR/zipper.log&
zipper_PID=$!


mpiexec -n 5632 ./lsp-10-3d $PBSBASE.lsp >$PBS_O_WORKDIR/$PBSBASE.o.txt

kill $zipper_PID
./zipper -a >$PBS_O_WORKDIR
@@ -0,0 +1,33 @@
#PBS -l walltime=96:0:00
#PBS -l nodes=470:ppn=12
#PBS -N glyions1o
#PBS -S /bin/bash
#PBS -j oe
#PBS -m ae
#PBS -M ngirmang.1@osu.edu


PBSBASE=glyions1o
#source $HOME/.bashrc

#This outputs the name of the root node
#to the directory where you submitted this PBS job
echo $HOSTNAME > $PBS_O_WORKDIR/hostname.txt
cat $PBS_NODEFILE | uniq > $PBS_O_WORKDIR/nodesfile.txt


cd "$PBS_O_WORKDIR"
#zipper
./loopscript zipper &> $PBS_O_WORKDIR/zipper.log&
zipper_PID=$!
#movne
./loopscript movne &> $PBS_O_WORKDIR/movne.log&
movne_PID=$!


mpiexec -n 5632 ./lsp-10-3d $PBSBASE.lsp >$PBS_O_WORKDIR/$PBSBASE.o.txt

kill $zipper_PID
./zipper -a >$PBS_O_WORKDIR
kill $movne_PID
./movne
@@ -0,0 +1,25 @@
#PBS -l walltime=168:0:00
#PBS -l select=128:ncpus=44:mpiprocs=44
#PBS -N glyions1o
#PBS -S /bin/bash
#PBS -j oe
#PBS -m ae
#PBS -M ngirmang.1@osu.edu
#PBS -A __projectid__
#PBS -q standard_lw


PBSBASE=glyions1o
#source $HOME/.bashrc

#This outputs the name of the root node
#to the directory where you submitted this PBS job
echo $HOSTNAME > $PBS_O_WORKDIR/hostname.txt
cat $PBS_NODEFILE | uniq > $PBS_O_WORKDIR/nodesfile.txt


cd "$PBS_O_WORKDIR"


aprun -n 5632 ./lsp-10-3d $PBSBASE.lsp >$PBS_O_WORKDIR/$PBSBASE.o.txt

@@ -0,0 +1,25 @@
#PBS -l walltime=48:0:00
#PBS -l select=128:ncpus=44:mpiprocs=44
#PBS -N glyions1o
#PBS -S /bin/bash
#PBS -j oe
#PBS -m ae
#PBS -M ngirmang.1@osu.edu
#PBS -A __projectid__
#PBS -q standard_lw


PBSBASE=glyions1o
#source $HOME/.bashrc

#This outputs the name of the root node
#to the directory where you submitted this PBS job
echo $HOSTNAME > $PBS_O_WORKDIR/hostname.txt
cat $PBS_NODEFILE | uniq > $PBS_O_WORKDIR/nodesfile.txt


cd "$PBS_O_WORKDIR"


aprun -n 5632 ./lsp-10-3d $PBSBASE.lsp >$PBS_O_WORKDIR/$PBSBASE.o.txt

@@ -0,0 +1,25 @@
#PBS -l walltime=1:0:00
#PBS -l select=128:ncpus=44:mpiprocs=44
#PBS -N glyions1o
#PBS -S /bin/bash
#PBS -j oe
#PBS -m ae
#PBS -M ngirmang.1@osu.edu
#PBS -A __projectid__
#PBS -q debug


PBSBASE=glyions1o
#source $HOME/.bashrc

#This outputs the name of the root node
#to the directory where you submitted this PBS job
echo $HOSTNAME > $PBS_O_WORKDIR/hostname.txt
cat $PBS_NODEFILE | uniq > $PBS_O_WORKDIR/nodesfile.txt


cd "$PBS_O_WORKDIR"


aprun -n 5632 ./lsp-10-3d $PBSBASE.lsp >$PBS_O_WORKDIR/$PBSBASE.o.txt

@@ -0,0 +1,25 @@
#PBS -l walltime=24:0:00
#PBS -l select=128:ncpus=44:mpiprocs=44
#PBS -N glyions1o
#PBS -S /bin/bash
#PBS -j oe
#PBS -m ae
#PBS -M ngirmang.1@osu.edu
#PBS -A __projectid__
#PBS -q standard_sm


PBSBASE=glyions1o
#source $HOME/.bashrc

#This outputs the name of the root node
#to the directory where you submitted this PBS job
echo $HOSTNAME > $PBS_O_WORKDIR/hostname.txt
cat $PBS_NODEFILE | uniq > $PBS_O_WORKDIR/nodesfile.txt


cd "$PBS_O_WORKDIR"


aprun -n 5632 ./lsp-10-3d $PBSBASE.lsp >$PBS_O_WORKDIR/$PBSBASE.o.txt

@@ -0,0 +1,2 @@
#!/usr/bin/env bash
while true; do ./$1 && echo sleeping... && sleep 60; done
@@ -0,0 +1,32 @@
#!/usr/bin/env bash
CONDAFILE=${CONDAFILE:-"$HOME/conda"}
[ -e "$CONDAFILE" ] && source $CONDAFILE
WAITDELAY=${WAITDELAY:-1}
DIR=${1:-"."}
if [ ! -n "$OUTDIR" ]; then
OUTDIR=${2:-"movne-laser"}
fi
mkdir -p "$OUTDIR"
INTENSITY=${INTENSITY:-"5.000000e+17"}
LIMS=${LIMS:-"(1e+19, 1e+23)"}
HIGHLIGHT=${HIGHLIGHT:-"1.832437e+21"}
QUANTITY=${QUANTITY:-"RhoN17"}
NPROCS=${NPROCS:-1}
source ~/.bashrc

for i in $(ls "$DIR" | grep 'sclr[0-9]\+\.p4' | sort -V); do
n=$(echo ${i#sclr*} | sed 's/\.p4.*$//')
I=$(printf '%05d' "$n" )
[ -e "$OUTDIR"/$I.png ] && [ ! -n "$DONTSKIP" ] && echo skipping...$i && continue;
while [ $(pgrep -f 'python[23]* *.*sclrq.py' | wc -l ) -ge $NPROCS ]; do sleep $WAITDELAY; done;
sleep 0.25;
echo $i...
sclrq.py -D "$DIR" $n "$OUTDIR"/$I.png --intensity="$INTENSITY" $EXTRA_MOVNE_ARGS \
-l --lims="$LIMS" --highlight="$HIGHLIGHT" --laser -Q "$QUANTITY" &
done
while [ $(pgrep -f 'python[23]* *.*sclrq.py' | wc -l ) -gt 0 ]; do
echo waiting...
sleep 5; done;
OUTMOV=${OUTMOV:-"glyions1o-ne-laser.mp4"}
ffmpeg -pattern_type glob -i "$OUTDIR/*.png" -c:v libx264 -pix_fmt yuv420p -y $OUTMOV
[ -e $OUTMOV ] && rcp $OUTMOV $PBS_O_WORKDIR

Large diffs are not rendered by default.

@@ -434,6 +434,11 @@ def genregions(**kw):
{data}
end
'''

plainconst_tmpl = '''type 1
coefficients {data} end
'''

tempdefaults = sd(
lspdefaults,
thermal_energy = (1.0, 1.0, 1.0),
@@ -497,8 +502,16 @@ def process_temp(iq):
def gendens(**kw):
getkw = mk_getkw(kw, densdefaults);
speciesl = getkw('speciesl');
outputfmt = "n_{}";
if test(kw,'target_density'):
Q = kw['target_density'];
fracs = getkw('fracs');
if test(kw, 'target_density_plainconst'):
ret = {
outputfmt.format(species) : plainconst_tmpl.format(data=Q*f)
for species,f in zip(speciesl,fracs) };
kw.update(ret);
return kw;
if type(Q) == tuple:
#the reason for tuple and not a general iterable
#is when we pass a single scale, for example, which
@@ -519,6 +532,7 @@ def gendens(**kw):
outputfmt.format(species) : densitypairs_tmpl.format(data = iQ)
for species,iQ in zip(speciesl,Q) };
kw.update(ret)
return kw;
else:
kw['dens_dat'] = getkw('dens_dat');
kw['dens_imul'] = getkw('dens_imul');
@@ -536,9 +550,8 @@ def copy_kw(l):
type = kw['dens_type'][i],
imul = kw['dens_imul'][i],
dmul = kw['fracs'][i]);
pass;
return kw;

return kw;
pass;
outletdefaults = sd(
lspdefaults,
lasertfunc=1,