atat-mirror/glue/vasp/robustrelax_vasp

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2023-08-31 20:30:18 +02:00
#!/bin/bash
dohelp=0
cutoff="0"
cmdsuffix=""
volrelaxcommand="runstruct_vasp -w vaspvol.wrap"
relaxcommand="runstruct_vasp -w vasp.wrap"
chaincommand="runstruct_vasp -w vaspneb.wrap"
staticcommand="runstruct_vasp -w vaspstatic.wrap"
infdetcommand="runstruct_vasp -p -w vaspid.wrap"
doid=0
idopt="-d"
idf="0.5"
idja="0.0"
idjc="0.0"
doneb=0
doextract=0
nimage=6
dovib=0
makevaspfiles=0
contif=0
if [[ $1 == "" || $1 == "-h" ]]
then
cat - <<EOF
This command implements the "inflection-detection" method introduced in
A. van de Walle, Q. Hong, S. Kadkhodaei and R. Sun, "The free energy of mechanically unstable phases"
Nat. Com. 6, 7559 (2015) doi:10.1038/ncomms8559 .
and
A. van de Walle and S. Kadkhodaei and R. Sun and Q.-J. Hong, "Epicycle method for elasticity limit calculations",
Phys. Rev. B 95 144113 (2017) doi:10.1103/PhysRevB.95.144113 .
It calculates the energy of a structure that is potentially mechanically unstable.
In a nutshell: the method finds either a local minimum (for a mechanically stable phase)
or the inflection point on a path joining the unrelaxed and fully relaxed structures
(for a mechanically unstable phase).
Syntax: robustrelax_vasp [options] command_prefix
where options are
-id Inflection Detection method
-idop "options" Options passed to the infdet command.
-neb Use the Nudged Elastic Band method to find minimum energy path
Otherwise: simply interpolate linearly.
-ex Only extract data form VASP files. Do not run anything.
-c [real] Relaxation magnitude cutoff needed to activate robust relax algorithm (default: 0).
-ni [integer] Number of images in the minimum energy path (default: 6).
-rc [string] Command for full relaxation (Default: runstruct_vasp -w vasp.wrap).
-vc [string] Command for volume only relaxation (Default: runstruct_vasp -w vaspvol.wrap).
-cc [string] Command for chain (neb) calculations (Default: runstruct_vasp -w vaspneb.wrap).
-sc [string] Command for static runs (Default: runstruct_vasp -w vaspstatic.wrap).
-ic [string] Command for inflection-detection runs (-id option) (Default: runstruct_vasp -p -w vaspid.wrap).
-idf [real] Starting point fraction for inflection detection (default: 0.5)
-ja
-jc By how much to jitter atoms (-ja) and cell parameters (-jt) for the initial conditions
for inflection-detection method.
-vib Update vibrational data in svib_ht file from vol_0/svib_ht file.
-mk Make auxiliary vasp input files (vaspvol.wrap, vaspneb.wrap, vaspstatic.wrap, vaspf.wrap) from vasp.wrap.
Do not run anything.
-cln clean files for a full restart.
-cip continue (an prior run) if possible (only implemented for -id algorithm).
-d Use all defaults values.
-h Display more help.
command_prefix Prefix needed for vasp to run on a remote machine or in parallel (e.g. mpirun).
Note: the commands specified by -rc,-vc,-cc,-sc can be set to empty "" to skip the corresponding
calculation step (useful to restart an aborted run).
EOF
if [[ $1 == "" ]]
then
exit
fi
fi
while [[ $1 != "" ]]
do
if [[ $1 == "-d" ]]
then
echo -n
elif [[ $1 == "-h" ]]
then
dohelp=1
elif [[ $1 == "-mk" ]]
then
makevaspfiles=1
elif [[ $1 == "-cln" ]]
then
clnrestart=1
elif [[ $1 == "-vib" ]]
then
dovib=1
elif [[ $1 == "-cc" ]]
then
shift
chaincommand="$1";
elif [[ $1 == "-rc" ]]
then
shift
relaxcommand="$1";
elif [[ $1 == "-vc" ]]
then
shift
volrelaxcommand="$1";
elif [[ $1 == "-sc" ]]
then
shift
staticcommand="$1";
elif [[ $1 == "-ic" ]]
then
shift
infdetcommand="$1";
elif [[ $1 == "-cip" ]]
then
contif=1;
elif [[ $1 == "-c" ]]
then
shift
cutoff=$1
elif [[ $1 == "-ni" ]]
then
shift
nimage=$1
elif [[ $1 == "-id" ]]
then
doid=1
elif [[ $1 == "-idop" ]]
then
shift
idopt="$1"
elif [[ $1 == "-idf" ]]
then
shift
idf="$1"
elif [[ $1 == "-ja" ]]
then
shift
idja="$1"
elif [[ $1 == "-jc" ]]
then
shift
idjc="$1"
elif [[ $1 == "-neb" ]]
then
doneb=1
elif [[ $1 == "-ex" ]]
then
doextract=1
else
cmdsuffix="$*"
break
fi
shift
done
if [[ $dohelp == 1 ]]
then
cat - <<EOF
This command does the following:
1) Fully relax the structure (in str_hint.out or str.out) to create str_relax.out,
just like runstruct_vasp.
2) If the relaxation cutoff (-c=...) no exceeded, stop. Typically, should be set to -c=0.05.
3) Relax the volume only of structure in str_sup.out or str.out. Results are in directory 00/
4) Do a neb (-neb) or infection detection (-id) calculation between the two structures obtained in step 1 and 3
or just a linear interpolation between them (if no -neb or -id). Results are in directories ??/
Note that you need VTST Tools from http://theory.cm.utexas.edu/vtsttools/ for the neb method
with variable cell shape.
5) Do static calculations in each directory ??/
6) Find the inflection point on the path optimized in step 4. If it does not exist, find the
minimum energy along that path.
7) Report the energy found in 6 in the file energy and the corresponding geometry in str_relax.out
Notes:
1) str_beg.out and str_end.out contain the extremities of the path.
If you want to restart from scratch, delete these files.
2) For high symmetry phases (e.g. bcc,fcc,hcp) you may need to break the symmetry of the phase for it to relax.
For that purpose, you can use, e.g.,
symbrklib W fcc bcc
or
cellcvrt -ja=0.01 -jc=0.01 < str.out > str_hint.out .
Sometimes a supercell is needed (a phonon analysis will tell you that - or symbrklib for bcc,fcc,hcp).
EOF
exit
fi
if [[ $makevaspfiles == 1 ]]
then
if [[ ! -e vasp.wrap ]]
then
echo Please provide a vasp.wrap file.
exit
fi
grep -v -i -e ISIF -e DOSTATIC vasp.wrap > vaspvol.wrap
echo ISIF = 7 >> vaspvol.wrap
grep -v -i -e ISMEAR -e SIGMA -e NSW -e IBRION -e ISIF -e DOSTATIC vasp.wrap > vaspstatic.wrap
cat - >> vaspstatic.wrap <<EOF
ISMEAR = -5
IBRION = -1
ISIF = 2
EOF
grep -v -i -e IBRION -e DOSTATIC vasp.wrap > vaspneb.wrap
echo IMAGES = $(( nimage -2 )) >> vaspneb.wrap
cat - >>vaspneb.wrap <<EOF
SPRING = -5
LCLIMB = .FALSE.
LNEBCELL = .TRUE.
IBRION = 3
POTIM = 0
EDIFFG = -5e-2
IOPT = 3
EOF
grep -v -i -e NSW -e IBRION -e ISIF -e DOSTATIC vasp.wrap > vaspf.wrap
cat - >> vaspf.wrap <<EOF
LREAL = AUTO
ICHARG = 1
ISTART = 2
IBRION = -1
ISIF = 2
EOF
grep -v -i -e NSW -e IBRION -e ISIF -e DOSTATIC -e KPPRA -e EDIFF -e EDIFFG vasp.wrap > vaspid.wrap
cat - >> vaspid.wrap <<EOF
IBRION = -1
ISIF = 2
ICHARG = 1
KPPRA = UPDIR
ISYM = 0
EDIFF = 1e-5
ISTART = 2
EOF
exit
fi
if [[ $clnrestart == 1 ]]
then
rm str_beg.out str_end.out
rm -r [0-9][0-9]
exit
fi
if [[ $contif == 1 ]]
then
if [[ -e OSZICAR && ! -e str_relax.out ]]
then
runstruct_vasp -ex
rm -f error
if [[ -e str_relax.out ]]
then
if [[ -e str_hint.out ]]
then
cp str_hint.out str_hint.out.org
fi
echo Re-relaxing pre-relaxed geometry...
mv -f str_relax.out str_hint.out
fi
fi
if [[ -e str_end.out ]]
then
relaxcommand="";
echo Skipping relax step...
if [[ -e str_beg.out ]]
then
volrelaxcommand="";
echo Skipping volume relax step...
if [[ -e 01/cstr_relax.out ]]
then
infdetcommand="";
echo Skipping inflection detection step...
diff 01/cstr_relax.out str_relax.out > /dev/null
if [[ $? == 0 ]]
then
staticcommand="";
echo Skipping static run step...
fi
fi
fi
fi
fi
if [[ $dovib == 1 ]]
then
for subdir in vol_0 smsqs/vol_0
do
if [[ -e ${subdir}/svib_ht ]]
then
if [[ ! -e confmult.in ]]
then
echo using scaled ${subdir}/svib_ht
echo `cat ${subdir}/svib_ht` `cellcvrt -pn < str.out` `cellcvrt -pn < ${subdir}/str_relax.out` | awk '{print $1*$2/$3}' > svib_ht
else
echo using scaled ${subdir}/svib_ht and confmult.in
echo `cat ${subdir}/svib_ht` `cellcvrt -pn < str.out` `cellcvrt -pn < ${subdir}/str_relax.out` `cat confmult.in` | awk '{print $1*$2/$3+$2*log($4)}' > svib_ht
fi
exit
fi
done
echo No svib_ht file in `pwd`/vol_0 or `pwd`/smsqs/vol_0
exit
fi
if [[ $doextract == 0 ]]
then
if [[ $relaxcommand != "" ]]
then
echo $relaxcommand $cmdsuffix
$relaxcommand $cmdsuffix
fi
if [[ -e error ]]
then
echo Error during relaxation run.
exit 1
fi
relmag=`checkrelax -1`
# if [[ ! (( $relmag > $cutoff || -e str_sup.out )) ]]
if [[ ! (( $relmag > $cutoff )) ]]
then
if [[ $relaxcommand != "" ]]
then
mv energy energy_sup
echo `cat energy_sup` `cellcvrt -pn < str.out` `cellcvrt -pn < str_relax.out` | awk '{print $1*$2/$3}' > energy
fi
else
if [[ $relaxcommand != "" ]]
then
mv energy energy_end
if [[ ! -e str_end.out ]]
then
cp str_relax.out str_end.out
fi
fi
mkdir 00
if [[ $volrelaxcommand != "" ]]
then
if [[ -e str_sup.out ]]
then
cp str_sup.out 00/str.out
else
cp str.out 00/
fi
cd 00
echo "Now working in" `pwd`
echo $volrelaxcommand $cmdsuffix
$volrelaxcommand $cmdsuffix
if [[ -e error ]]
then
echo Error during static run in 00/
touch ../error
exit 1
fi
cd ..
fi
if [[ ! -e str_beg.out ]]
then
cp 00/str_relax.out str_beg.out
fi
if [[ $doid == 1 ]]
then
if [[ ! -e KPOINTS ]]
then
cp KPOINTS.static KPOINTS
fi
mkdir 01
if [[ -e 01/str_hint.in ]]
then
cp 01/str_hint.in 01/str.in
else
strpath -s1=str_beg.out -s2=str_end.out -f=${idf} | cellcvrt -ja=$idja -jc=$idjc > 01/str.in
fi
if [[ $infdetcommand != "" ]]
then
pushd 01 > /dev/null
echo "Now working in" `pwd`
if [[ -e str_hint.in ]]
then
cp str_hint.in str.in
fi
if [[ -e busy ]]
then
rm busy
fi
echo Running infdet $idopt
rm -f error stop busy
if [[ -e infdet.log ]]
then
for (( baknum=1 ; ; baknum++ ))
do
if [[ ! -e infdet.save${baknum} ]]
then
cp infdet.log infdet.save${baknum}
break;
fi
done
fi
( infdet $idopt > infdet.log ; if [[ $? == 1 ]] ; then touch error ; fi ; touch stop ) &
while [[ 1 ]]
do
while [[ ! -e busy && ! -e stop && ! -e error ]]
do
sleep 2
done
if [[ -e stop || -e error ]]
then
break
fi
echo vasp
rm stress.out force.out > /dev/null
$infdetcommand $cmdsuffix
cat stress.out force.out
rm busy
echo waiting
done
rm -f stop busy
if [[ -e error ]]
then
echo Error during inflection detection run in 01/
touch ../error
exit 1
fi
if [[ ! -e cstr_relax.out ]]
then
cp str_current.out cstr_relax.out
fi
popd
fi
if [[ $staticcommand != "" ]]
then
pushd 01
cp cstr_relax.out str.out
echo "$staticcommand $cmdsuffix"
$staticcommand $cmdsuffix
popd
fi
if [[ -e error ]]
then
echo Error during static run in 01/
exit 1
fi
echo `cat 01/energy` `cellcvrt -pn < str.out` `cellcvrt -pn < 01/str_relax.out` | awk '{print $1*$2/$3}' > energy
( echo `cellcvrt -pn < str.out` `cellcvrt -pn < 01/str_relax.out` ; cat 01/dos.out )| awk 'BEGIN {getline; sc=$1/$2; getline; print $1*sc,$2,$3} {print $1*sc;}' > dos.out
cp 01/cstr_relax.out str_relax.out
exit 0
elif [[ $doneb == 1 ]]
then
strpath -s1=str_beg.out -s2=str_end.out -ni=$nimage
if [[ $chaincommand != "" ]]
then
lastdir=`ls -d -1 ?? | sort -n | tail -n -1`
cp ${lastdir}/str.out ${lastdir}/str_relax.out
echo "$chaincommand -nr"
foreachfile str.out "$chaincommand -nr"
for file in POTCAR KPOINTS INCAR vasp.in
do
rm ??/${file}
done
echo $chaincommand "$cmdsuffix"
$chaincommand "$cmdsuffix"
foreachfile str.out "$chaincommand -ex"
foreachfile str_relax.out cp str_relax.out str_hint.out
foreachfile str_relax.out cp OSZICAR OSZICAR.neb
cp OUTCAR OUTCAR.neb \; gzip OUTCAR.neb
if [[ $staticcommand != "" ]]
then
echo "$staticcommand $cmdsuffix"
foreachfile str_relax.out "$staticcommand $cmdsuffix"
fi
fi
else
strpath -s1=str_beg.out -s2=str_end.out -ni=$nimage
if [[ $volrelaxcommand != "" ]]
then
echo "$volrelaxcommand $cmdsuffix"
foreachfile str.out "$volrelaxcommand $cmdsuffix"
fi
if [[ $staticcommand != "" ]]
then
echo "$staticcommand $cmdsuffix"
foreachfile str_relax.out "$staticcommand $cmdsuffix"
fi
fi
fi
fi
if [[ $doextract == 1 || (( $relmag > $cutoff || -e str_sup.out )) ]]
then
if [[ ! -e 00 ]]
then
runstruct_vasp -ex
cp energy energy_end
echo `cat energy_end` `cellcvrt -pn < str.out` `cellcvrt -pn < str_relax.out` | awk '{print $1*$2/$3}' > energy
else
if [[ ! -e energy_end ]]
then
cp energy energy_end
fi
lastenergy=`ls -d -1 ?? | sort -n | tail -n -1`
#echo $lastenergy
if [[ ! -e ${lastenergy}/energy ]]
then
cp energy_end ${lastenergy}/energy
fi
((curnimage=lastenergy+0))
#echo $curnimage
cat `ls -1 ??/energy | sort -n` > epath.out
# cat epath.out | strpath -ci > energy
echo `cat epath.out | strpath -ci` `cellcvrt -pn < str.out` `cellcvrt -pn < str_beg.out` | awk '{print $1*$2/$3}' > energy
iploc=$(cat epath.out | strpath -cil | awk '{print $1*('$curnimage')}')
#echo $iploc
dirb=$(echo $iploc | awk '{n=int($1); printf("%02i",n)}')
#echo $dirb
if [[ $iploc == $curnimage ]]
then
#echo cp only
cp ${dirb}/str_relax.out .
else
dire=$(echo $iploc | awk '{n=int($1)+1; printf("%02i",n)}')
#echo $dire
frac=$(echo $iploc | awk '{print $1-int($1);}')
#echo $frac
strpath -f=${frac} -s1=${dirb}/str_relax.out -s2=${dire}/str_relax.out > str_relax.out
echo strpath -f=${frac} -s1=${dirb}/str_relax.out -s2=${dire}/str_relax.out
fi
fi
fi