Embedded Files
All you need to get going is a vasp.in file with the RELAXED structure in it, as well as comp.config and fitfc.config files.
Typical usage:
autophonon > log.out
This will just show you progress and not actually launch any jobs automatically. To do that,
autophonon run > log.out
comp.config file:
# job identifier (careful, don't make it longer than 2 or 3 characters!)
FO
# nodes to use for relaxation
1
# number of cpus to use for relaxation
2
# walltime to use for relaxation
8
# nodes to use for static calculations
1
# number of cpus to use for static calculations
4
# walltime to use for static calculations
16
fitfc.config file:
# Format: value for er, then ns, then ms, then dr
5
3
0.04
0.1
autophonon script:
#!/bin/sh
function cleanhouse {
echo "Cleaning old files..."
foreachfile vasp.in rm OSZICAR OUTCAR *.q str_relax.out &> /dev/null
foreachfile -d 2 vasp.in rm OSZICAR OUTCAR *.q str_relax.out &> /dev/null
}
function jobsub {
jobname=$1
jobtype=$2
if [ $jobtype = "relax" ]; then
sed -e '/ISIF/d' INCAR > INCAR.new
echo "ISIF = 4" >> INCAR.new
mv INCAR.new INCAR
else
sed -e '/ISIF/d' INCAR > INCAR.new
echo "ISIF = 2" >> INCAR.new
mv INCAR.new INCAR
sed -e '/IBRION/d' INCAR > INCAR.new
echo "IBRION = -1" >> INCAR.new
mv INCAR.new INCAR
sed -e '/NSW/d' INCAR > INCAR.new
echo "NSW = 0" >> INCAR.new
mv INCAR.new INCAR
sed -e '/ISMEAR/d' INCAR > INCAR.new
echo "ISMEAR = -5" >> INCAR.new
mv INCAR.new INCAR
sed -e '/ALGO/d' INCAR > INCAR.new
echo "ALGO = FAST" >> INCAR.new
mv INCAR.new INCAR
fi
if [ $jobtype = "relax" -o $jobtype = "volstatic" ]; then
makeqfile $jobname $relaxnodes $relaxcpu $relaxtime
else makeqfile $jobname $staticnodes $staticcpu $statictime
fi
qsub $jobname.q
sleep 10
}
function statuscheck {
jobname=$1
jobtype=$2
user=`whoami`
if [ -e OSZICAR ]; then
tail -1 OSZICAR
else echo "No OSZICAR; this step has not made any progress"
fi
if [ "$runmode" = "run" ]; then
queuestatus=`qstat | grep $user | grep $jobname`
if [ "$queuestatus" ]; then
echo "Job $jobname is running"
echo $queuestatus
else echo "Job $jobname is not running"
jobsub $jobname $jobtype
fi
fi
}
function printenergy {
file=$1
grep TOTEN $1 | tail -1
}
function relax1check {
vol=$1
if [ -e OUTCAR.relax1 ]; then
echo "vol_$vol is done with the first relaxation!"
printenergy OUTCAR.relax1
elif [ -e OUTCAR ] && grep -q "required accuracy" OUTCAR && [ ! -e OUTCAR.relax1 ]; then
sleep 30
mv OUTCAR OUTCAR.relax1
mv OSZICAR OSZICAR.relax1
cp INCAR INCAR.relax1
cp CONTCAR POSCAR
elif [ ! -e OUTCAR.relax1 ]; then
echo "vol_$vol first relaxation in progress"
statuscheck "$id"v"$vol"r1 relax
fi
}
function relax2check {
vol=$1
if [ -e OUTCAR.relax2 ]; then
echo "vol_$vol is done with the second relaxation!"
printenergy OUTCAR.relax2
elif [ -e OUTCAR ] && [ -e OUTCAR.relax1 ] && grep -q "required accuracy" OUTCAR; then
sleep 30
mv OUTCAR OUTCAR.relax2
mv OSZICAR OSZICAR.relax2
cp INCAR INCAR.relax2
cp CONTCAR POSCAR
elif [ -e OUTCAR.relax1 ]; then
echo "vol_$vol second relaxation in progress"
statuscheck "$id"v"$vol"r2 relax
fi
}
function volstatic {
vol=$1
volindex=$2
if [ -e OUTCAR.static ]; then
echo "vol_$vol is done with its static calculation"
printenergy OUTCAR.static
let volindex=$volindex+1
if [ ! -e str_relax.out ]; then
extract_vasp
fi
elif [ -e OUTCAR ] && [ -e OUTCAR.relax2 ] && grep -q "aborting loop" OUTCAR; then
sleep 30
mv OUTCAR OUTCAR.static
mv OSZICAR OSZICAR.static
cp INCAR INCAR.static
elif [ -e OUTCAR.relax2 ]; then
echo "vol_$vol static calculation in progress"
statuscheck "$id"v"$vol"st volstatic
fi
return $[$volindex]
}
function staticcheck {
vol=$1
staticindex=0
staticdone=0
for file in $(ls); do
if [ -d $file ]; then
echo "Checking static calculation directory $file"
cd $file
if [ -e OUTCAR.static ]; then
echo "$file static calculation is done!"
let staticdone=$staticdone+1
printenergy OUTCAR.static
if [ ! -e str_relax.out ]; then
extract_vasp
fi
elif [ -e OUTCAR ] && grep -q "aborting loop" OUTCAR; then
sleep 30
mv OUTCAR OUTCAR.static
mv OSZICAR OSZICAR.static
cp INCAR INCAR.static
elif [ -e ../OUTCAR.relax2 ]; then
echo "$file static calculation in progress"
statuscheck "$id"v"$vol"s"$staticindex" static
cd ..
fi
let staticindex=$staticindex+1
fi
done
return $[$staticindex-$staticdone]
}
# get necessary variables
runmode=$1
erval=`sed -n '2p' fitfc.config`
nsval=`sed -n '3p' fitfc.config`
msval=`sed -n '4p' fitfc.config`
drval=`sed -n '5p' fitfc.config`
id=`sed -n '2p' comp.config`
relaxnodes=`sed -n '4p' comp.config`
relaxcpu=`sed -n '6p' comp.config`
relaxtime=`sed -n '8p' comp.config`
staticnodes=`sed -n '10p' comp.config`
staticcpu=`sed -n '12p' comp.config`
statictime=`sed -n '14p' comp.config`
# set up str.out and str_relax.out files
function str_out {
rm str.out
sed -e '/./{H;$!d;}' -e 'x;/POSCAR/!d;' vasp.in | sed 's/^[ \t]*//' > tmp
sed -n '5,7p' tmp > str.out
latparam=`sed -n '4p' tmp | sed 's/^[ \t]*//'`
cat >> str.out << EOF
$latparam 0 0
0 $latparam 0
0 0 $latparam
EOF
sed '1,8d' tmp >> str.out
rm tmp
cp str.out str_relax.out
}
# set up vasp.wrap file
function vasp_wrap {
sed '/POSCAR/,$d' vasp.in > vasp.wrap
}
# get list of the volume folders ATAT creates
function getvollist {
i=1
for file in $(ls); do
if echo $file | grep vol_; then
vollist[i]=`echo $file`
fi
done
echo $vollist
}
# Function to generate a queue file for encina
# $1: name of .q file; $2: ncpus; $3: walltime
function makeqfile {
if [ `hostname` == "encina" ]; then
cat > $1.q << EOF
#PBS -l ncpus=$3
#PBS -l walltime=$4:00:00
cd $`echo PBS_O_WORKDIR`
echo Running on host \`hostname\`
echo Time is \`date\`
echo Directory is \`pwd\`
echo ""
mpirun -np $3 /usr/local/bin/vasp
EOF
elif [ `hostname` == "master.cl.northwestern.edu" ]; then
cat > $1.q << EOF
#PBS -l nodes=$2:ppn=$3
#PBS -l walltime=$4:00:00
# This job's working directory
# echo Working directory is $`echo PBS_O_WORKDIR`
cd $`echo PBS_O_WORKDIR`
echo ""
echo Running on host \`hostname\`
echo Time is \`date\`
echo Directory is \`pwd\`
echo This jobs runs on the following processors:
echo \`cat $`echo PBS_NODEFILE`\`
# Define number of processors
NPROCS=\`wc -l < $`echo PBS_NODEFILE`\`
echo This job has allocated $`echo NPROCS` nodes
echo ""
echo ==========================================================================
echo ""
mpirun -machinefile $`echo PBS_NODEFILE` -np $`echo NPROCS` /usr/local/bin/vasp
EOF
fi
}
# if runmode is "run", submit jobs; otherwise, just print status
function getnewcalcs {
fitfc -er=$erval -ns=$nsval -ms=$msval -dr=$drval
sleep 10
foreachfile str.out str2ezvasp
foreachfile -d 2 str.out str2ezvasp
foreachfile vasp.in ezvasp -n vasp.in
foreachfile -d 2 vasp.in ezvasp -n vasp.in
}
# main body of script
cleanhouse
str_out
vasp_wrap
getnewcalcs
vollist=`getvollist`
while [ 1 ]; do
sleep 15
voldone=0
staticremaining=0
for i in $vollist; do
echo "Checking $i..."
cd $i
relax1check $i
relax2check $i
volstatic $i $voldone
voldone=$?
dirs_here=`ls -l | egrep '^d'`
# prepare static calculations if all volumes are done and they do not already exist
if [ "$voldone" == "$nsval" ] && [ ! "$dirs_here" ]; then
cd ..
getnewcalcs
fi
staticcheck $i
let staticremaining=$staticremaining+$?
cd ..
done
if [ "$voldone" == "$nsval" ] && [ "$staticremaining" == "0" ] && ls vol_0 | grep p+; then
echo "Phonon calculation complete!"
break
fi
echo "$voldone of $nsval volume calculations complete"
echo "$staticremaining static calculations remaining"
echo "*****************************************"
done
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