Examples

ase_chgnet_Sr4Co4O12

Download

ase_chgnet_RS_Sr4Co4O12.tar.gz

cryspy.in

[basic]
algo = RS
calc_code = ASE
tot_struc = 10
nstage = 1
njob = 2
jobcmd = bash
jobfile = job_cryspy

[structure]
natot = 20
atype = Sr Co O
nat = 4  4  12
mindist_1 = 2.2  2.0  1.8
mindist_2 = 2.0  2.2  1.5
mindist_3 = 1.8  1.5  2.0

[ASE]
ase_python = chgnet_in.py

[option]

calc_in/

chgnet_in.py_1

from chgnet.model import StructOptimizer
from pymatgen.core import Structure


# ---------- input structure
# CrySPY outputs 'POSCAR' as an input file in work/xxxxxx directory
structure = Structure.from_file('POSCAR')

# ---------- relax
relaxer = StructOptimizer()
result = relaxer.relax(atoms=structure, fmax=0.01, steps=2000)

# ---------- opt. structure and energy
# [rule in ASE interface]
# output file for energy: 'log.tote' in eV/cell
#                         CrySPY reads the last line of 'log.tote'
# output file for structure: 'CONTCAR' in vasp format
# ------ energy
traj = result['trajectory']
e = traj.compute_energy()   # eV/cell
with open('log.tote', mode='w') as f:
    f.write(str(e))
# ------ struc
opt_struc = result["final_structure"]
opt_struc.to(fmt='poscar', filename='CONTCAR')

job_cryspy

#!/bin/sh

# ---------- ASE
python3 chgnet_in.py > out.log

# ---------- for error
if [ ! -f "log.tote" ]; then
    sed -i -e '3 s/^.*$/skip/' stat_job
    exit 1
fi

# ---------- CrySPY
sed -i -e '3 s/^.*$/done/' stat_job

ase_Cu8_RS

Download

ase_Cu8_RS.tar.gz

cryspy.in

[basic]
algo = RS
calc_code = ASE
tot_struc = 5
nstage = 1
njob = 2
jobcmd = zsh
jobfile = job_cryspy

[structure]
natot = 8
atype = Cu
nat = 8

[ASE]
ase_python = ase_in.py

[option]

calc_in/

ase_in.py_1

from ase.constraints import ExpCellFilter, StrainFilter
from ase.calculators.emt import EMT
from ase.calculators.lj import LennardJones
from ase.optimize.sciopt import SciPyFminCG
from ase.optimize import BFGS
from ase.spacegroup.symmetrize import FixSymmetry
import numpy as np
from ase.io import read, write

# ---------- input structure
# CrySPY outputs 'POSCAR' as an input file in work/xxxxxx directory
atoms = read('POSCAR', format='vasp')

# ---------- setting and run
atoms.calc = EMT()
atoms.set_constraint([FixSymmetry(atoms)])
atoms = ExpCellFilter(atoms, hydrostatic_strain=False)
opt = BFGS(atoms)
#opt=SciPyFminCG(atoms)
opt.run()

# ---------- opt. structure and energy
# [rule in ASE interface]
# output file for energy: 'log.tote' in eV/cell
#                         CrySPY reads the last line of 'log.tote'
# output file for structure: 'CONTCAR' in vasp format
e = atoms.atoms.get_total_energy()
with open('log.tote', mode='w') as f:
    f.write(str(e))

write('CONTCAR', atoms.atoms, format='vasp')

job_cryspy

#!/bin/sh

# ---------- ASE
python3 ase_in.py

# ---------- CrySPY
sed -i -e '3 s/^.*$/done/' stat_job

soiap_Si8_RS

Download

soiap_Si8_RS.tar.gz

cryspy.in

[basic]
algo = RS
calc_code = soiap
tot_struc = 5
nstage = 1
njob = 2
jobcmd = zsh
jobfile = job_cryspy

[structure]
natot = 8
atype = Si
nat = 8

[soiap]
soiap_infile = soiap.in
soiap_outfile = soiap.out
soiap_cif = initial.cif

[option]

calc_in/

soiap.in_1

crystal initial.cif ! CIF file for the initial structure
symmetry 1 ! 0: not symmetrize displacements of the atoms or 1: symmetrize

md_mode_cell 3 ! cell-relaxation method
               ! 0: FIRE, 2: quenched MD, or 3: RFC5
number_max_relax_cell 1000 ! max. number of the cell relaxation
number_max_relax 1 ! max. number of the atom relaxation
max_displacement 0.1 ! max. displacement of atoms in Bohr

external_stress_v 0.0 0.0 0.0 ! external pressure in GPa

th_force 5d-5 ! convergence threshold for the force in Hartree a.u.
th_stress 5d-7 ! convergence threshold for the stress in Hartree a.u.

force_field 1 ! force field
              ! 1: Stillinger-Weber for Si, 2: Tsuneyuki potential for SiO2,
              ! 3: ZRL for Si-O-N-H, 4: ADP for Nd-Fe-B, 5: Jmatgen, or
              ! 6: Lennard-Jones

job_cryspy

#!/bin/sh

# ---------- soiap
EXEPATH=/path/to/soiap
$EXEPATH/soiap soiap.in > soiap.out 2>&1

# ---------- CrySPY
sed -i -e '3 s/^.*$/done/' stat_job

soiap_Si8_RS_mindist

Info

For mindist, see also Features > Restriction on interatomic distances.

Download

soiap_Si8_RS_mindist.tar.gz

cryspy.in

[basic]
algo = RS
calc_code = soiap
tot_struc = 5
nstage = 1
njob = 2
jobcmd = zsh
jobfile = job_cryspy

[structure]
natot = 8
atype = Si
nat = 8
mindist_1 = 2.0

[soiap]
soiap_infile = soiap.in
soiap_outfile = soiap.out
soiap_cif = initial.cif

[option]

calc_in/

soiap.in_1

crystal initial.cif ! CIF file for the initial structure
symmetry 1 ! 0: not symmetrize displacements of the atoms or 1: symmetrize

md_mode_cell 3 ! cell-relaxation method
               ! 0: FIRE, 2: quenched MD, or 3: RFC5
number_max_relax_cell 1000 ! max. number of the cell relaxation
number_max_relax 1 ! max. number of the atom relaxation
max_displacement 0.1 ! max. displacement of atoms in Bohr

external_stress_v 0.0 0.0 0.0 ! external pressure in GPa

th_force 5d-5 ! convergence threshold for the force in Hartree a.u.
th_stress 5d-7 ! convergence threshold for the stress in Hartree a.u.

force_field 1 ! force field
              ! 1: Stillinger-Weber for Si, 2: Tsuneyuki potential for SiO2,
              ! 3: ZRL for Si-O-N-H, 4: ADP for Nd-Fe-B, 5: Jmatgen, or
              ! 6: Lennard-Jones

job_cryspy

#!/bin/sh

# ---------- soiap
EXEPATH=/path/to/soiap
$EXEPATH/soiap soiap.in > soiap.out 2>&1

# ---------- CrySPY
sed -i -e '3 s/^.*$/done/' stat_job

vasp_Na8Cl8_RS

Download

vasp_Na8Cl8_RS.tar.gz

cryspy.in

[basic]
algo = RS
calc_code = VASP
tot_struc = 5
nstage = 2
njob = 2
jobcmd = qsub
jobfile = job_cryspy

[structure]
natot = 16
atype = Na Cl
nat = 8 8
mindist_1 = 2.5 1.5
mindist_2 = 1.5 2.5

[VASP]
kppvol = 40 80

[option]

calc_in/

INCAR_1

SYSTEM = NaCl
!!!LREAL = Auto
Algo = Fast
NSW = 40

LWAVE = .FALSE.
!LCHARG = .FALSE.

ISPIN =  1

ISMEAR = 0
SIGMA = 0.1

IBRION = 2
ISIF = 2

EDIFF = 1e-5
EDIFFG = -0.01

INCAR_2

SYSTEM = NaCl
!!LREAL = Auto
Algo = Fast
NSW = 200

ENCUT = 341

!!LWAVE = .FALSE.
!!LCHARG = .FALSE.


ISPIN =  1

ISMEAR = 0
SIGMA = 0.1

IBRION = 2
ISIF = 3

EDIFF = 1e-5
EDIFFG = -0.01

job_cryspy

#!/bin/sh
#$ -cwd
#$ -V -S /bin/bash
####$ -V -S /bin/zsh
#$ -N Na8Cl8_CrySPY_ID
#$ -pe smp 20
####$ -q ibis1.q
####$ -q ibis2.q
####$ -q ibis3.q
####$ -q ibis4.q

# ---------- vasp
VASPROOT=/usr/local/vasp/vasp.6.4.2/bin
mpirun -np $NSLOTS $VASPROOT/vasp_std

# ---------- CrySPY
sed -i -e '3 s/^.*$/done/' stat_job

vasp_Sr4O4_RS_pv_term

Download

vasp_Sr4O4_RS_pv_term.tar.gz

cryspy.in

[basic]
algo = RS
calc_code = VASP
tot_struc = 10
nstage = 2
njob = 4
jobcmd = qsub
jobfile = job_cryspy

[structure]
natot = 8
atype = Sr O
nat = 4 4

[VASP]
kppvol = 40 80

[option]

calc_in/

INCAR_1

SYSTEM = SrO
Algo = Fast
NSW = 60

LWAVE = .FALSE.
!LCHARG = .FALSE.

ISPIN =  1

ISMEAR = 0
SIGMA = 0.1

IBRION = 2
ISIF = 2

EDIFF = 1e-5
EDIFFG = -0.01

PSTRESS = 400

INCAR_2

SYSTEM = NaCl
LREAL = Auto
Algo = Fast
NSW = 200

ENCUT = 520

!!LWAVE = .FALSE.
!!LCHARG = .FALSE.


ISPIN =  1

ISMEAR = 0
SIGMA = 0.1

IBRION = 2
ISIF = 3

EDIFF = 1e-5
EDIFFG = -0.01

PSTRESS = 400

job_cryspy

#!/bin/sh
#$ -cwd
#$ -V -S /bin/bash
####$ -V -S /bin/zsh
#$ -N SrO_CrySPY_ID
#$ -pe smp 20
####$ -q ibis1.q
####$ -q ibis2.q
####$ -q ibis3.q
####$ -q ibis4.q

# ---------- vasp
VASPROOT=/usr/local/vasp/vasp.6.4.2/bin
mpirun -np $NSLOTS $VASPROOT/vasp_std

# ---------- CrySPY
sed -i -e '3 s/^.*$/done/' stat_job

qe_Si8_RS

Download

qe_Si8_RS.tar.gz

cryspy.in

[basic]
algo = RS
calc_code = QE
tot_struc = 5
nstage = 2
njob = 2
jobcmd = qsub
jobfile = job_cryspy

[structure]
natot = 8
atype = Si
nat = 8

[QE]
qe_infile = pwscf.in
qe_outfile = pwscf.out
kppvol =  40  80

[option]

calc_in/

pwscf.in_1

 &control
    title = 'Si8'
    calculation = 'relax'
    nstep = 100
    restart_mode = 'from_scratch',
    pseudo_dir = '/usr/local/pslibrary.1.0.0/pbe/PSEUDOPOTENTIALS/'
    outdir='./out.d/'
 /

 &system
    ibrav = 0
    nat = 8
    ntyp = 1
    ecutwfc = 44.0
    occupations = 'smearing'
    degauss = 0.01
 /

 &electrons
 /

 &ions
 /

 &cell
 /

ATOMIC_SPECIES
  Si  28.086  Si.pbe-n-kjpaw_psl.1.0.0.UPF

pwscf.in_2

 &control
    title = 'Si8'
    calculation = 'vc-relax'
    nstep = 200
    restart_mode = 'from_scratch',
    pseudo_dir = '/usr/local/pslibrary.1.0.0/pbe/PSEUDOPOTENTIALS/'
    outdir='./out.d/'
 /

 &system
    ibrav = 0
    nat = 8
    ntyp = 1
    ecutwfc = 44.0
    occupations = 'smearing'
    degauss = 0.01
 /

 &electrons
 /

 &ions
 /

 &cell
 /

ATOMIC_SPECIES
  Si  28.086  Si.pbe-n-kjpaw_psl.1.0.0.UPF

job_cryspy

#!/bin/sh
#$ -cwd
#$ -V -S /bin/bash
####$ -V -S /bin/zsh
#$ -N Si8_CrySPY_ID
#$ -pe smp 20
####$ -q ibis1.q
####$ -q ibis2.q

mpirun -np $NSLOTS /path/to/pw.x < pwscf.in > pwscf.out


if [ -e "CRASH" ]; then
    sed -i -e '3 s/^.*$/skip/' stat_job
    exit 1
fi

sed -i -e '3 s/^.*$/done/' stat_job

qe_benzene_2_RS_mol

Download

qe_benzene_2_RS_mol.tar.gz

cryspy.in

[basic]
algo = RS
calc_code = QE
tot_struc = 6
nstage = 2
njob = 2
jobcmd = qsub
jobfile = job_cryspy

[structure]
struc_mode = mol
natot = 24
atype = H C
nat = 12 12
mol_file = benzene
nmol = 2

[QE]
qe_infile = pwscf.in
qe_outfile = pwscf.out
kppvol = 40  60

[option]

calc_in/

pwscf.in_1

 &control
    title = '2 benzene'
    calculation = 'relax'
    nstep = 30
    restart_mode = 'from_scratch',
    pseudo_dir = '/usr/local/pslibrary.1.0.0/pbe/PSEUDOPOTENTIALS/'
    outdir='./outdir/'
 /

 &system
    ibrav = 0
    nat = 24
    ntyp = 2
    ecutwfc = 35.00
    ecutrho = 300.00
    occupations = 'smearing'
    degauss = 0.01
 /

 &electrons
 /

 &ions
 /

 &cell
 /

ATOMIC_SPECIES
   H  1.008  H.pbe-kjpaw_psl.1.0.0.UPF
   C  12.01  C.pbe-n-kjpaw_psl.1.0.0.UPF

pwscf.in_2

 &control
    title = '2 benzene'
    calculation = 'vc-relax'
    nstep = 200
    restart_mode = 'from_scratch',
    pseudo_dir = '/usr/local/pslibrary.1.0.0/pbe/PSEUDOPOTENTIALS/'
    outdir='./outdir/'
 /

 &system
    ibrav = 0
    nat = 24
    ntyp = 2
    ecutwfc = 46.00
    ecutrho = 326.00
    occupations = 'smearing'
    degauss = 0.01
 /

 &electrons
 /

 &ions
 /

 &cell
 /

ATOMIC_SPECIES
   H  1.008  H.pbe-kjpaw_psl.1.0.0.UPF
   C  12.01  C.pbe-n-kjpaw_psl.1.0.0.UPF

job_cryspy

#!/bin/sh
#$ -cwd
#$ -V -S /bin/bash
####$ -V -S /bin/zsh
#$ -N bz_CrySPY_ID
#$ -pe smp 20

# ---------- qe run
mpirun -np $NSLOTS /path/to/pw.x  < pwscf.in > pwscf.out

# ---------- qe if crash
if [ -e "CRASH" ]; then
    sed -i -e '3 s/^.*$/skip/' stat_job
    exit 1
fi

# ---------- cryspy
sed -i -e '3 s/^.*$/done/' stat_job

qe_Sr4O4_RS_pv_term

Download

qe_Sr4O4_RS_pv_term.tar.gz

cryspy.in

[basic]
algo = RS
calc_code = QE
tot_struc = 10
nstage = 2
njob = 4
jobcmd = qsub
jobfile = job_cryspy

[structure]
natot = 8
atype = Sr O
nat = 4 4

[QE]
qe_infile = pwscf.in
qe_outfile = pwscf.out
kppvol =  40  80
pv_term = True

[option]

calc_in/

pwscf.in_1

 &control
    title = 'SrO'
    calculation = 'relax'
    nstep = 100
    restart_mode = 'from_scratch',
    pseudo_dir = '/usr/local/gbrv/all_pbe_UPF_v1.5/'
    outdir='./out.d/'
 /

 &system
    ibrav = 0
    nat = 8
    ntyp = 2
    ecutwfc = 40
    ecutrho = 200
    occupations = 'smearing'
    degauss = 0.01
 /

 &electrons
 /

 &ions
 /

 &cell
    press = 400
 /

ATOMIC_SPECIES
  Sr  -1.0  sr_pbe_v1.uspp.F.UPF
   O  -1.0  o_pbe_v1.2.uspp.F.UPF

pwscf.in_2

 &control
    title = 'SrO'
    calculation = 'vc-relax'
    nstep = 200
    restart_mode = 'from_scratch',
    pseudo_dir = '/usr/local/gbrv/all_pbe_UPF_v1.5/'
    outdir='./out.d/'
 /

 &system
    ibrav = 0
    nat = 8
    ntyp = 2
    ecutwfc = 40
    ecutrho = 200
    occupations = 'smearing'
    degauss = 0.01
 /

 &electrons
 /

 &ions
 /

 &cell
    press = 400
 /

ATOMIC_SPECIES
  Sr  -1.0  sr_pbe_v1.uspp.F.UPF
   O  -1.0  o_pbe_v1.2.uspp.F.UPF

job_cryspy

#!/bin/sh
#$ -cwd
#$ -V -S /bin/bash
####$ -V -S /bin/zsh
#$ -N SrO_CrySPY_ID
#$ -pe smp 20
####$ -q ibis1.q
####$ -q ibis2.q

# ---------- qe run
mpirun -np $NSLOTS /path/to/pw.x  < pwscf.in > pwscf.out

# ---------- qe if crash
if [ -e "CRASH" ]; then
    sed -i -e '3 s/^.*$/skip/' stat_job
    exit 1
fi

# ---------- cryspy
sed -i -e '3 s/^.*$/done/' stat_job

qe_Si16_LAQA

Download

qe_Si16_LAQA.tar.gz

cryspy.in

[basic]
algo = LAQA
calc_code = QE
tot_struc = 50
nstage = 1
njob = 10
jobcmd = qsub
jobfile = job_cryspy

[structure]
natot = 16
atype = Si
nat = 16
mindist_1 = 1.5

[QE]
qe_infile = pwscf.in
qe_outfile = pwscf.out
kppvol =  80

[LAQA]
nselect_laqa = 4

[option]

calc_in/

pwscf.in_1

&control
    calculation = 'vc-relax'
    pseudo_dir = '/usr/local/gbrv/all_pbe_UPF_v1.5/'
    outdir='./outdir/'
    nstep = 10
/

&system
    ibrav = 0
    nat = 16
    ntyp = 1
    ecutwfc = 40
    ecutrho = 200
    occupations = 'smearing'
    degauss = 0.01
/

&electrons
/

&ions
/

&cell
/

ATOMIC_SPECIES
  Si -1.0 si_pbe_v1.uspp.F.UPF

job_cryspy

#!/bin/sh
#$ -cwd
#$ -V -S /bin/bash
####$ -V -S /bin/zsh
#$ -N Si_CrySPY_ID
#$ -pe smp 20
####$ -q ibis1.q
####$ -q ibis2.q

# ---------- qe run
mpirun -np $NSLOTS /path/to/pw.x  < pwscf.in > pwscf.out

# ---------- qe if crash
if [ -e "CRASH" ]; then
    sed -i -e '3 s/^.*$/skip/' stat_job
    exit 1
fi

# ---------- cryspy
sed -i -e '3 s/^.*$/done/' stat_job

Examples

Table of contents

Subsections of Examples

ase_chgnet_Sr4Co4O12

Download

cryspy.in

calc_in/

chgnet_in.py_1

job_cryspy

ase_Cu8_RS

Download

cryspy.in

calc_in/

ase_in.py_1

job_cryspy

soiap_Si8_RS

Download

cryspy.in

calc_in/

soiap.in_1

job_cryspy

soiap_Si8_RS_mindist

Download

cryspy.in

calc_in/

soiap.in_1

job_cryspy

vasp_Na8Cl8_RS

Download

cryspy.in

calc_in/

INCAR_1

INCAR_2

job_cryspy

vasp_Sr4O4_RS_pv_term

Download

cryspy.in

calc_in/

INCAR_1

INCAR_2

job_cryspy

qe_Si8_RS

Download

cryspy.in

calc_in/

pwscf.in_1

pwscf.in_2

job_cryspy

qe_benzene_2_RS_mol

Download

cryspy.in

calc_in/

pwscf.in_1

pwscf.in_2

job_cryspy

qe_Sr4O4_RS_pv_term

Download

cryspy.in

calc_in/

pwscf.in_1

pwscf.in_2

job_cryspy

qe_Si16_LAQA

Download

cryspy.in

calc_in/

pwscf.in_1

job_cryspy