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Added example files for Si_LAMMPS
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@ttadano
ttadano committed Oct 30, 2017
1 parent 2ec7f80 commit 9b9ba3b
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398 changes: 398 additions & 0 deletions example/Si_LAMMPS/run_all.sh
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#!/bin/bash

# Binaries

LAMMPS=${HOME}/src/lammps/src/lmp_serial
ALAMODE_ROOT=${HOME}/Work/alamode/

# Generate displacement patterns

cat << EOF > si_alm0.in
&general
PREFIX = si222
MODE = suggest
NAT = 64; NKD = 1
KD = Si
/
&interaction
NORDER = 2 # 1: harmonic, 2: cubic, ..
/
&cell
20.406 # factor in Bohr unit
1.0 0.0 0.0 # a1
0.0 1.0 0.0 # a2
0.0 0.0 1.0 # a3
/
&cutoff
Si-Si 7.4 7.4
/
&position
1 0.0000000000000000 0.0000000000000000 0.0000000000000000
1 0.0000000000000000 0.0000000000000000 0.5000000000000000
1 0.0000000000000000 0.2500000000000000 0.2500000000000000
1 0.0000000000000000 0.2500000000000000 0.7500000000000000
1 0.0000000000000000 0.5000000000000000 0.0000000000000000
1 0.0000000000000000 0.5000000000000000 0.5000000000000000
1 0.0000000000000000 0.7500000000000000 0.2500000000000000
1 0.0000000000000000 0.7500000000000000 0.7500000000000000
1 0.1250000000000000 0.1250000000000000 0.1250000000000000
1 0.1250000000000000 0.1250000000000000 0.6250000000000000
1 0.1250000000000000 0.3750000000000000 0.3750000000000000
1 0.1250000000000000 0.3750000000000000 0.8750000000000000
1 0.1250000000000000 0.6250000000000000 0.1250000000000000
1 0.1250000000000000 0.6250000000000000 0.6250000000000000
1 0.1250000000000000 0.8750000000000000 0.3750000000000000
1 0.1250000000000000 0.8750000000000000 0.8750000000000000
1 0.2500000000000000 0.0000000000000000 0.2500000000000000
1 0.2500000000000000 0.0000000000000000 0.7500000000000000
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1 0.2500000000000000 0.5000000000000000 0.7500000000000000
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1 0.2500000000000000 0.7500000000000000 0.5000000000000000
1 0.3750000000000000 0.1250000000000000 0.3750000000000000
1 0.3750000000000000 0.1250000000000000 0.8750000000000000
1 0.3750000000000000 0.3750000000000000 0.1250000000000000
1 0.3750000000000000 0.3750000000000000 0.6250000000000000
1 0.3750000000000000 0.6250000000000000 0.3750000000000000
1 0.3750000000000000 0.6250000000000000 0.8750000000000000
1 0.3750000000000000 0.8750000000000000 0.1250000000000000
1 0.3750000000000000 0.8750000000000000 0.6250000000000000
1 0.5000000000000000 0.0000000000000000 0.0000000000000000
1 0.5000000000000000 0.0000000000000000 0.5000000000000000
1 0.5000000000000000 0.2500000000000000 0.2500000000000000
1 0.5000000000000000 0.2500000000000000 0.7500000000000000
1 0.5000000000000000 0.5000000000000000 0.0000000000000000
1 0.5000000000000000 0.5000000000000000 0.5000000000000000
1 0.5000000000000000 0.7500000000000000 0.2500000000000000
1 0.5000000000000000 0.7500000000000000 0.7500000000000000
1 0.6250000000000000 0.1250000000000000 0.1250000000000000
1 0.6250000000000000 0.1250000000000000 0.6250000000000000
1 0.6250000000000000 0.3750000000000000 0.3750000000000000
1 0.6250000000000000 0.3750000000000000 0.8750000000000000
1 0.6250000000000000 0.6250000000000000 0.1250000000000000
1 0.6250000000000000 0.6250000000000000 0.6250000000000000
1 0.6250000000000000 0.8750000000000000 0.3750000000000000
1 0.6250000000000000 0.8750000000000000 0.8750000000000000
1 0.7500000000000000 0.0000000000000000 0.2500000000000000
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1 0.7500000000000000 0.5000000000000000 0.7500000000000000
1 0.7500000000000000 0.7500000000000000 0.0000000000000000
1 0.7500000000000000 0.7500000000000000 0.5000000000000000
1 0.8750000000000000 0.1250000000000000 0.3750000000000000
1 0.8750000000000000 0.1250000000000000 0.8750000000000000
1 0.8750000000000000 0.3750000000000000 0.1250000000000000
1 0.8750000000000000 0.3750000000000000 0.6250000000000000
1 0.8750000000000000 0.6250000000000000 0.3750000000000000
1 0.8750000000000000 0.6250000000000000 0.8750000000000000
1 0.8750000000000000 0.8750000000000000 0.1250000000000000
1 0.8750000000000000 0.8750000000000000 0.6250000000000000
/
EOF

${ALAMODE_ROOT}/alm/alm si_alm0.in > alm.log


# Generate structure files of LAMMPS
mkdir displace; cd displace/

python ${ALAMODE_ROOT}/tools/displace.py --LAMMPS ../Si222.lammps --prefix harm --mag 0.01 ../Si222_2.pattern_HARMONIC >> run.log
python ${ALAMODE_ROOT}/tools/displace.py --LAMMPS ../Si222.lammps --prefix cubic --mag 0.04 ../Si222_2.pattern_ANHARM3 >> run.log

cp ../Si.sw .
cp ../in.sw .

# Run LAMMPS
for ((i=1; i<=1; i++))
do
cp harm${i}.lammps tmp.lammps
$LAMMPS < in.sw >> run.log
mv COORD COORD.harm${i}
mv FORCE FORCE.harm${i}
done

for ((i=1; i<=20; i++))
do
suffix=`echo ${i} | awk '{printf("%02d", $1)}'`
cp cubic${suffix}.lammps tmp.lammps
$LAMMPS < in.sw >> run.log
mv COORD COORD.cubic${suffix}
mv FORCE FORCE.cubic${suffix}
done

# Collect data
python ${ALAMODE_ROOT}/tools/extract.py --LAMMPS ../Si222.lammps --get disp COORD.harm* > disp_harm.dat
python ${ALAMODE_ROOT}/tools/extract.py --LAMMPS ../Si222.lammps --get force FORCE.harm* > force_harm.dat
python ${ALAMODE_ROOT}/tools/extract.py --LAMMPS ../Si222.lammps --get disp COORD.cubic* > disp_cubic.dat
python ${ALAMODE_ROOT}/tools/extract.py --LAMMPS ../Si222.lammps --get force FORCE.cubic* > force_cubic.dat

cd ../

# Extract harmonic force constants
cat << EOF > si_alm1.in
&general
PREFIX = si222_harm
MODE = fitting
NAT = 64; NKD = 1
KD = Si
/
&fitting
NDATA = 1
DFILE = displace/disp_harm.dat
FFILE = displace/force_harm.dat
/
&interaction
NORDER = 1 # 1: harmonic, 2: cubic, ..
/
&cell
20.406 # factor in Bohr unit
1.0 0.0 0.0 # a1
0.0 1.0 0.0 # a2
0.0 0.0 1.0 # a3
/
&cutoff
Si-Si 7.4 7.4
/
&position
1 0.0000000000000000 0.0000000000000000 0.0000000000000000
1 0.0000000000000000 0.0000000000000000 0.5000000000000000
1 0.0000000000000000 0.2500000000000000 0.2500000000000000
1 0.0000000000000000 0.2500000000000000 0.7500000000000000
1 0.0000000000000000 0.5000000000000000 0.0000000000000000
1 0.0000000000000000 0.5000000000000000 0.5000000000000000
1 0.0000000000000000 0.7500000000000000 0.2500000000000000
1 0.0000000000000000 0.7500000000000000 0.7500000000000000
1 0.1250000000000000 0.1250000000000000 0.1250000000000000
1 0.1250000000000000 0.1250000000000000 0.6250000000000000
1 0.1250000000000000 0.3750000000000000 0.3750000000000000
1 0.1250000000000000 0.3750000000000000 0.8750000000000000
1 0.1250000000000000 0.6250000000000000 0.1250000000000000
1 0.1250000000000000 0.6250000000000000 0.6250000000000000
1 0.1250000000000000 0.8750000000000000 0.3750000000000000
1 0.1250000000000000 0.8750000000000000 0.8750000000000000
1 0.2500000000000000 0.0000000000000000 0.2500000000000000
1 0.2500000000000000 0.0000000000000000 0.7500000000000000
1 0.2500000000000000 0.2500000000000000 0.0000000000000000
1 0.2500000000000000 0.2500000000000000 0.5000000000000000
1 0.2500000000000000 0.5000000000000000 0.2500000000000000
1 0.2500000000000000 0.5000000000000000 0.7500000000000000
1 0.2500000000000000 0.7500000000000000 0.0000000000000000
1 0.2500000000000000 0.7500000000000000 0.5000000000000000
1 0.3750000000000000 0.1250000000000000 0.3750000000000000
1 0.3750000000000000 0.1250000000000000 0.8750000000000000
1 0.3750000000000000 0.3750000000000000 0.1250000000000000
1 0.3750000000000000 0.3750000000000000 0.6250000000000000
1 0.3750000000000000 0.6250000000000000 0.3750000000000000
1 0.3750000000000000 0.6250000000000000 0.8750000000000000
1 0.3750000000000000 0.8750000000000000 0.1250000000000000
1 0.3750000000000000 0.8750000000000000 0.6250000000000000
1 0.5000000000000000 0.0000000000000000 0.0000000000000000
1 0.5000000000000000 0.0000000000000000 0.5000000000000000
1 0.5000000000000000 0.2500000000000000 0.2500000000000000
1 0.5000000000000000 0.2500000000000000 0.7500000000000000
1 0.5000000000000000 0.5000000000000000 0.0000000000000000
1 0.5000000000000000 0.5000000000000000 0.5000000000000000
1 0.5000000000000000 0.7500000000000000 0.2500000000000000
1 0.5000000000000000 0.7500000000000000 0.7500000000000000
1 0.6250000000000000 0.1250000000000000 0.1250000000000000
1 0.6250000000000000 0.1250000000000000 0.6250000000000000
1 0.6250000000000000 0.3750000000000000 0.3750000000000000
1 0.6250000000000000 0.3750000000000000 0.8750000000000000
1 0.6250000000000000 0.6250000000000000 0.1250000000000000
1 0.6250000000000000 0.6250000000000000 0.6250000000000000
1 0.6250000000000000 0.8750000000000000 0.3750000000000000
1 0.6250000000000000 0.8750000000000000 0.8750000000000000
1 0.7500000000000000 0.0000000000000000 0.2500000000000000
1 0.7500000000000000 0.0000000000000000 0.7500000000000000
1 0.7500000000000000 0.2500000000000000 0.0000000000000000
1 0.7500000000000000 0.2500000000000000 0.5000000000000000
1 0.7500000000000000 0.5000000000000000 0.2500000000000000
1 0.7500000000000000 0.5000000000000000 0.7500000000000000
1 0.7500000000000000 0.7500000000000000 0.0000000000000000
1 0.7500000000000000 0.7500000000000000 0.5000000000000000
1 0.8750000000000000 0.1250000000000000 0.3750000000000000
1 0.8750000000000000 0.1250000000000000 0.8750000000000000
1 0.8750000000000000 0.3750000000000000 0.1250000000000000
1 0.8750000000000000 0.3750000000000000 0.6250000000000000
1 0.8750000000000000 0.6250000000000000 0.3750000000000000
1 0.8750000000000000 0.6250000000000000 0.8750000000000000
1 0.8750000000000000 0.8750000000000000 0.1250000000000000
1 0.8750000000000000 0.8750000000000000 0.6250000000000000
/
EOF
${ALAMODE_ROOT}/alm/alm si_alm1.in >> alm.log

# Extract cubic force constants
cat << EOF > si_alm2.in
&general
PREFIX = si222_cubic
MODE = fitting
NAT = 64; NKD = 1
KD = Si
/
&fitting
NDATA = 20
DFILE = displace/disp_cubic.dat
FFILE = displace/force_cubic.dat
FC2XML = si222_harm.xml
/
&interaction
NORDER = 2 # 1: harmonic, 2: cubic, ..
/
&cell
20.406 # factor in Bohr unit
1.0 0.0 0.0 # a1
0.0 1.0 0.0 # a2
0.0 0.0 1.0 # a3
/
&cutoff
Si-Si 7.4 7.4
/
&position
1 0.0000000000000000 0.0000000000000000 0.0000000000000000
1 0.0000000000000000 0.0000000000000000 0.5000000000000000
1 0.0000000000000000 0.2500000000000000 0.2500000000000000
1 0.0000000000000000 0.2500000000000000 0.7500000000000000
1 0.0000000000000000 0.5000000000000000 0.0000000000000000
1 0.0000000000000000 0.5000000000000000 0.5000000000000000
1 0.0000000000000000 0.7500000000000000 0.2500000000000000
1 0.0000000000000000 0.7500000000000000 0.7500000000000000
1 0.1250000000000000 0.1250000000000000 0.1250000000000000
1 0.1250000000000000 0.1250000000000000 0.6250000000000000
1 0.1250000000000000 0.3750000000000000 0.3750000000000000
1 0.1250000000000000 0.3750000000000000 0.8750000000000000
1 0.1250000000000000 0.6250000000000000 0.1250000000000000
1 0.1250000000000000 0.6250000000000000 0.6250000000000000
1 0.1250000000000000 0.8750000000000000 0.3750000000000000
1 0.1250000000000000 0.8750000000000000 0.8750000000000000
1 0.2500000000000000 0.0000000000000000 0.2500000000000000
1 0.2500000000000000 0.0000000000000000 0.7500000000000000
1 0.2500000000000000 0.2500000000000000 0.0000000000000000
1 0.2500000000000000 0.2500000000000000 0.5000000000000000
1 0.2500000000000000 0.5000000000000000 0.2500000000000000
1 0.2500000000000000 0.5000000000000000 0.7500000000000000
1 0.2500000000000000 0.7500000000000000 0.0000000000000000
1 0.2500000000000000 0.7500000000000000 0.5000000000000000
1 0.3750000000000000 0.1250000000000000 0.3750000000000000
1 0.3750000000000000 0.1250000000000000 0.8750000000000000
1 0.3750000000000000 0.3750000000000000 0.1250000000000000
1 0.3750000000000000 0.3750000000000000 0.6250000000000000
1 0.3750000000000000 0.6250000000000000 0.3750000000000000
1 0.3750000000000000 0.6250000000000000 0.8750000000000000
1 0.3750000000000000 0.8750000000000000 0.1250000000000000
1 0.3750000000000000 0.8750000000000000 0.6250000000000000
1 0.5000000000000000 0.0000000000000000 0.0000000000000000
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1 0.5000000000000000 0.2500000000000000 0.7500000000000000
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1 0.5000000000000000 0.7500000000000000 0.2500000000000000
1 0.5000000000000000 0.7500000000000000 0.7500000000000000
1 0.6250000000000000 0.1250000000000000 0.1250000000000000
1 0.6250000000000000 0.1250000000000000 0.6250000000000000
1 0.6250000000000000 0.3750000000000000 0.3750000000000000
1 0.6250000000000000 0.3750000000000000 0.8750000000000000
1 0.6250000000000000 0.6250000000000000 0.1250000000000000
1 0.6250000000000000 0.6250000000000000 0.6250000000000000
1 0.6250000000000000 0.8750000000000000 0.3750000000000000
1 0.6250000000000000 0.8750000000000000 0.8750000000000000
1 0.7500000000000000 0.0000000000000000 0.2500000000000000
1 0.7500000000000000 0.0000000000000000 0.7500000000000000
1 0.7500000000000000 0.2500000000000000 0.0000000000000000
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1 0.7500000000000000 0.5000000000000000 0.7500000000000000
1 0.7500000000000000 0.7500000000000000 0.0000000000000000
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1 0.8750000000000000 0.1250000000000000 0.3750000000000000
1 0.8750000000000000 0.1250000000000000 0.8750000000000000
1 0.8750000000000000 0.3750000000000000 0.1250000000000000
1 0.8750000000000000 0.3750000000000000 0.6250000000000000
1 0.8750000000000000 0.6250000000000000 0.3750000000000000
1 0.8750000000000000 0.6250000000000000 0.8750000000000000
1 0.8750000000000000 0.8750000000000000 0.1250000000000000
1 0.8750000000000000 0.8750000000000000 0.6250000000000000
/
EOF
${ALAMODE_ROOT}/alm/alm si_alm2.in >> alm.log

# Phonon dispersion
cat << EOF > phband.in
&general
PREFIX = si222
MODE = phonons
FCSXML =si222_harm.xml
NKD = 1; KD = Si
MASS = 28.0855
/
&cell
10.203
0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0
/
&kpoint
1 # KPMODE = 1: line mode
G 0.0 0.0 0.0 X 0.5 0.5 0.0 51
X 0.5 0.5 1.0 G 0.0 0.0 0.0 51
G 0.0 0.0 0.0 L 0.5 0.5 0.5 51
/
EOF

mpirun -np 1 ${ALAMODE_ROOT}/anphon/anphon phband.in > phband.log

# Thermal conductivity
cat << EOF > RTA.in
&general
PREFIX = si222_10
MODE = RTA
FCSXML = si222_cubic.xml
NKD = 1; KD = Si
MASS = 28.0855
/
&cell
10.203
0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0
/
&kpoint2
2
10 10 10
/
EOF

mpirun -np 4 ${ALAMODE_ROOT}/anphon/anphon RTA.in > RTA.log

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