#!/bin/tcsh -f
 
#
# Check command line arguments ...
#
if ( $# != 3 ) then
echo " "
echo "Usage   : NAMDjob <number of cores> <filename of namd script> <log filename>"
echo " "
exit
endif
 
#
# ... presence of script
#
if (! -es $2 ) then
echo "Missing file ($2) containing NAMD script ? Abort."
exit
endif
 
#
# ... write access
#
touch .test_$$
if (! -e .test_$$ ) then
echo "No write access in current directory ? Abort."
exit
endif
/bin/rm -rf .test_$$
 
#
# ... number of cores
#
if ( $1 != 4 && $1 != 8 && $1 != 12 && $1 != 16 && $1 != 20 && $1 != 24 && $1 != 28 && $1 != 32 ) then
echo "Number of cores requested ($1) must be a multiple of four."
exit 
endif
 
 
#
# If NAMD_THINGS is not defined, set it. Add ++local
# if we run on a single node
#
if ( ! $?NAMD_THINGS ) then
        if ( $1 == 4 ) then
        set NAMD_THINGS = '++local'
        else
        set NAMD_THINGS = ' '
        endif
else
        if ( $1 == 4 ) then
        set NAMD_THINGS = $NAMD_THINGS' ++local'
        endif
endif
 
 
#
# Now, prepare the slurm script. The initial fuss is about preparing the
# nodelist file. Take a good look at the sed line (don't you love unix ?-)
# The reason for the sed line is to prepare a nodelist file containing the IP
# addresses of both interfaces for each node.
# 
# The 'if' clause is for the unlikely event where the hosts appear up, but
# they do not respond to ssh.
#
# The env variable $NAMD_THINGS is for passing additional arguments to NAMD
#
cat > ./.NAMD_$$.slurm << EOF
#!/bin/tcsh -f
 
echo group main > ./.nodelist_$$
srun hostname -i | sort - | awk '{print "host " \$1}' >> ./.nodelist_$$
sed -i -s '3~2s/host 10\.0\.0/host 10\.0\.1/g' ./.nodelist_$$
 
if ( \`wc -l < ./.nodelist_$$\` != ($1 + 1) ) then
echo "Something went seriously wrong. Get help."
echo "No job will be submitted."
exit
endif
 
/usr/local/namd/charmrun ++nodelist .nodelist_$$ /usr/local/namd/namd2 +p$1 $NAMD_THINGS +giga $2
 
exit
EOF
 
 
#
# Submit it
#
sbatch -o $3 -n$1 .NAMD_$$.slurm
 
exit

#!/bin/tcsh -f
 
#
# Check command line arguments ...
#
if ( $# < 1 || $# > 2 ) then
echo " "
echo "Usage   : plotnamd <log filename> [lines to skip]"
echo " "
exit
endif
 
#
# ... presence of log
#
if (! -es $1 ) then
echo "Missing log file ? Abort."
exit
endif
 
if ( $# == 1 ) then
set skip = "+0"
else
set skip = "+$2"
endif
 
echo "TS vs. TOTAL"
grep -i '^ENERGY:' LOG | tail --lines=$skip | tee /tmp/$$ | awk '{print $2 " " $12}' | plot
 
echo "TS vs. TEMP"
awk '{print $2 " " $13}' /tmp/$$ | plot
 
echo "TS vs. PRESSURE"
awk '{print $2 " " $17}' /tmp/$$ | plot
 
echo "TS vs. ELECT"
awk '{print $2 " " $7}' /tmp/$$ | plot
 
echo "TS vs. VDW"
awk '{print $2 " " $8}' /tmp/$$ | plot
 
echo "TS vs. KINETIC"
awk '{print $2 " " $11}' /tmp/$$ | plot
 
echo "TS vs. BOND"
awk '{print $2 " " $3}' /tmp/$$ | plot
 
echo "TS vs. ANGLE"
awk '{print $2 " " $4}' /tmp/$$ | plot
 
echo "TS vs. DIHED"
awk '{print $2 " " $5}' /tmp/$$ | plot
 
echo "TS vs. IMPRP"
awk '{print $2 " " $6}' /tmp/$$ | plot
 
 
/bin/rm -rf /tmp/$$
 
exit