CrySPY Utility

See Installation/CrySPY utility to download. Some (but not all) examples can also be downloaded from this document site.

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

# ---------- 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

Scripts

extract_struc.py

2023 April 16 update

Script to extract structures from init_struc_data.pkl or opt_struc_data.pkl. This script can print stucture information and output cif files.

One can specify structure ID(s) using -i option. Top k structures (the k most stable structures) can be extracted using -t option. -a option is for outputting all the structures. (note that many cif files will be output.) Symmetrized cif files can be generated with -s option. When outputting a symmetrized CIF file, you can also specify a tolerance with --tolerance. Structure information is printed with -p. If you use -p option, cif files are not output. You can also read a gzipped file (e.g., opt_struc_data.pkl.gz).

Update History

2024 April 16: –tolerance option, gzip
2023 July 21: –print option

Usage

python3 extract_struc.py -h

or if you put the script in your PATH, you can omit python3

extract_struc.py -h

usage: extract_struc.py [-h] [-p] [-a] [-i [INDEX ...]] [-t TOP] [-r] [-s] [--tolerance TOLERANCE] infile

positional arguments:
  infile                input file

options:
  -h, --help            show this help message and exit
  -p, --print           just print, e.g., extract_struc.py opt_struc_data.pkl -i 7 10 12 -ps
  -a, --all_id          all structures, e.g., extract_struc.py opt_struc_data.pkl -as
  -i [INDEX ...], --index [INDEX ...]
                        structure ID, e.g., extract_struc.py opt_struc_data.pkl -i 7 10 12 -s
  -t TOP, --top TOP     top k structures, e.g. (k = 3), extract_struc.py opt_struc_data.pkl -t 3 -s
  -r, --rank            add rank in file names, e.g., extract_struc.py opt_struc_data.pkl -t 3 -rs
  -s, --symmetrized     symmetrized structure, e.g., extract_struc.py opt_struc_data.pkl -i 7 10 12 -s
  --tolerance TOLERANCE
                        tolerance for symmetrization (default 0.01), e.g., extract_struc.py opt_struc_data.pkl -i 0 1 -s --tolerance 0.01

Examples

Print

The -p option can be used in combination with any option except for -s option.

extract_struc.py -p opt_struc_data.pkl -i 0 1

ID 0
Full Formula (Na8 Cl8)
Reduced Formula: NaCl
abc   :   6.823618   6.823618   7.566454
angles:  90.000000  90.000000  96.650518
pbc   :       True       True       True
Sites (16)
  #  SP           a         b         c
---  ----  --------  --------  --------
  0  Na    0         0         1
  1  Na    0         0         0.5
  2  Na    0.704707  0.295293  0.75
  3  Na    0.295293  0.704707  0.25
  4  Na    0.5       0         1
  5  Na    0.5       0         0.5
  6  Na    0         0.5       0.5
  7  Na    0         0.5       0
  8  Cl    0.5       0.5       0
  9  Cl    0.5       0.5       0.5
 10  Cl    0.484753  0.515247  0.75
 11  Cl    0.515247  0.484753  0.25
 12  Cl    0.828247  0.171753  0.851096
 13  Cl    0.171753  0.828247  0.351096
 14  Cl    0.828247  0.171753  0.648904
 15  Cl    0.171753  0.828247  0.148904

ID 1
Full Formula (Na8 Cl8)
Reduced Formula: NaCl
abc   :   8.145021   8.145021   4.324235
angles:  90.000000  90.000000 120.000000
pbc   :       True       True       True
Sites (16)
  #  SP            a          b         c
---  ----  ---------  ---------  --------
  0  Na     0.666667   0.333333  0.736206
  1  Na     0.666667   0.333333  0.263794
  2  Na     0.913147   0.086853  0.5
  3  Na     0.913147   0.826295  0.5
  4  Na     0.173705   0.086853  0.5
  5  Na     0.77711    0.22289   0
  6  Na     0.77711    0.55422   0
  7  Na     0.44578    0.22289   0
  8  Cl     0.027675   0.423376  0.5
  9  Cl    -0.423376  -0.395701  0.5
 10  Cl     0.395701  -0.027675  0.5
 11  Cl    -0.423376  -0.027675  0.5
 12  Cl     0.395701   0.423376  0.5
 13  Cl     0.027675  -0.395701  0.5
 14  Cl     0.333333   0.666667  0.5
 15  Cl     0          0         0

Structure ID

extract_struc.py opt_struc_data.pkl -i 7 10 12

7.cif, 10.cif, and 12.cif are output.

For symmetrized cif,

extract_struc.py opt_struc_data.pkl -i 7 10 12 -s

2024 April 16
With the tolerance parameter (default 0.01)

extract_struc.py opt_struc_data.pkl -i 7 10 12 -s --tolerance 0.01

Top k structures

Info

rslt_data.pkl is required in the same directory as the input.

Let us suppose

./data/pkl_data/opt_struc_data.pkl
./data/pkl_data/rslt_data.pkl

and cryspy_rslt_energy_asc file is as follows:

    Spg_num     Spg_sym  Spg_num_opt Spg_sym_opt    E_eV_atom  Magmom      Opt
9       110      I4_1cd          110      I4_1cd -1284.708037     NaN  not_yet
16        4        P2_1            4        P2_1 -1284.693651     NaN     done
97       92    P4_12_12           91      P4_122 -1284.692494     NaN     done
8        57        Pbcm           57        Pbcm -1284.668504     NaN     done
81       19  P2_12_12_1           19  P2_12_12_1 -1284.635684     NaN     done
...

Top k(=3) structures can be extracted with:

extract_struc.py ./data/pkl_data/opt_struc_data.pkl -t 3

In this example, rlst_data.pkl must be in ./data/pkl_data/. 9.cif, 16.cif, and 97.cif are output.

The rank can be included in cif file names with -r option:

extract_struc.py ./data/pkl_data/opt_struc_data.pkl -t 3 -r

1_9.cif, 2_16.cif, and 3_97.cif are output.

For symmetrized cif:

extract_struc.py ./data/pkl_data/opt_struc_data.pkl -t 3 -rs

All the structures

You should make a directory.

mkdir init_cifs
cd init_cifs
extract_struc.py /path/to/opt_struc_data.pkl -a

For symmetrized cif,

extract_struc.py /path/to/init_struc_data.pkl -as

Gzipped files

2024 April 16
Gzipped files (end with .gz) can be read:

extract_struc.py opt_struc_data.pkl.gz -i 0 1 -s

pos2pkl.py

2023 July 23 update

Script to convert structre data into init_struc_data.pkl. The default input format is init_POSCARS. Single structure data such as POSCAR and cif files can be optionally converted. Output is init_struc_data.pkl. Structure data can be added to an already existing init_struc_data.pkl. The structure ID is not taken into account and is newly assigned. If the number of atoms is different, an error is generated.

init_struc_data.pkl can be loaded at the start of the simulation in CrySPY.

You can remove and sort species with -f option. Note that without this option, pymatgen will sort the species in electronegativity order!

Usage

usage: pos2pkl.py [-h] [-s [SINGLE ...]] [-f [FILTER ...]] [-p] [infile ...]

positional arguments:
  infile                input file: init_POSCARS

options:
  -h, --help            show this help message and exit
  -s [SINGLE ...], --single [SINGLE ...]
                        input file: single structure file (POSCAR, cif)
  -f [FILTER ...], --filter [FILTER ...]
                        filter (sort): remove species and sort
  -p, --permit_diff_comp
                        flag for permitting different composition

Examples

init_POSCARS –> init_struc_data.pkl

It can be used to convert init_POSCARS generated by CrySPY to init_struc_data.pkl in another machine such as a supercomputer. Multiple input files can be converted.

python3 pos2pkl.py init_POSCARS

If you put the pos2pkl.py in your PATH, you can omit python3.

pos2pkl.py init_POSCARS

Composition: Na8 Cl8

Converted. The number of structures: 4
Save init_struc_data.pkl

Multiple inputs:

python3 pos2pkl.py init_POSCARS init_POSCARS2 init_POSCARS3

Composition: Na8 Cl8

Converted. The number of structures: 12
Save init_struc_data.pkl

If init_struc_data.pkl already exists in the current directory and you want to append to it:

python3 pos2pkl.py init_POSCARS

init_struc_data.pkl already exists.
Append to init_struc_data.pkl? [y/n]: y

Load init_struc_data
Composition: Na8 Cl8
The number of structures: 12

Converted. The number of structures: 16
Save init_struc_data.pkl

POSCAR or cif –> init_struc_data.pkl

Single structure data such as POSCAR and cif files can also be converted. -s/--single option is required.

python3 pos2pkl.py -s POSCAR test.cif

Composition: Na8 Cl8

Converted. The number of structures: 2
Save init_struc_data.pkl

init_POSCARS, POSCAR –> init_struc_data.pkl

python3 pos2pkl.py init_POSCARS -s POSCAR

Composition: Na8 Cl8

Converted. The number of structures: 5
Save init_struc_data.pkl

Warning

The following is wrong. The init_POSCARS is also treated as a single structure.

python3 pos2pkl.py -s POSCAR init_POSCARS

Filter (remove and sort)

Here we consider a cif file with the composition of Sr8 Co8 O20 X4, including 4 dummy atoms (X4). -f/--filter option can be used to remove and sort species. Specify the same as atype in cryspy.in.

python3 pos2pkl.py -s Sr8Co8O20X4.cif -f Sr Co O

Removed species: {'X0+'}
Composition: Sr8 Co8 O20

Converted. The number of structures: 1
Save init_struc_data.pkl

With extract_struc.py you can see how it was registered in init_struc_data.pkl.

python3 extract_struc.py init_struc_data.pkl -pa

ID 0
Full Formula (Sr8 Co8 O20)
Reduced Formula: Sr2Co2O5
...

-f option can allow you to sort.

python3 pos2pkl.py -s Sr8Co8O20X4.cif -f O Co

Removed species: {'Sr', 'X0+'}
Composition: O20 Co8

Converted. The number of structures: 1
Save init_struc_data.pkl

kpt_check.py

kpt_check.py can check a k-point mesh with a given kppvol. This script supports POSCAR, CONTCAR, and init_struc_data.pkl. pymatgen library is required.

After generating initial structures, you can try to see how much the value of kppvol should be.

Usage

python3 kpt_check.py -h

or if you put the script in your PATH, you can omit python3

kpt_check.py -h

usage: kpt_check.py [-h] [-w] [-n NSTRUC] infile kppvol

positional arguments:
  infile                input file: POSCAR, CONTCAR, or init_struc_data.pkl
  kppvol                kppvol

options:
  -h, --help            show this help message and exit
  -w, --write           write KPOINTS
  -n NSTRUC, --nstruc NSTRUC
                        number of structure to check

Example

POSCAR with a given kppvol

kpt_check.py POSCAR 100

a = 10.689217
b = 10.689217
c = 10.730846
    Lattice vector
10.689217 0.000000 0.000000
0.000000 10.689217 0.000000
0.000000 0.000000 10.730846

kppvol:  100
k-points:  [2, 2, 2]

Write KPOINTS file

You can generate a KPOINTS file using -w option.

kpt_check.py -w POSCAR 100

$ cat KPOINTS
pymatgen 4.7.6+ generated KPOINTS with grid density = 607 / atom
0
Monkhorst
2 2 2

Check k-point meshes for init_struc_data.pkl

In checking k-point meshes for init_struc_data.pkl, first five structures are automatically checked in the default setting. You can change the number of structures using -n option.

kpt_check.py -n 3 init_struc_data.pkl 100

# ---------- 0th structure
a = 8.0343076893
b = 8.03430768936
c = 9.1723323373
    Lattice vector
8.034308 0.000000 0.000000
-4.017154 6.957915 0.000000
0.000000 0.000000 9.172332

kppvol:  100
k-points:  [3, 3, 3]


# ---------- 1th structure
a = 9.8451944096
b = 9.84519440959
c = 6.8764313585
    Lattice vector
9.845194 0.000000 0.000000
-4.922597 8.526188 0.000000
0.000000 0.000000 6.876431

kppvol:  100
k-points:  [3, 3, 4]


# ---------- 2th structure
a = 7.5760383679
b = 7.57603836797
c = 6.6507478296
    Lattice vector
7.576038 0.000000 0.000000
-3.788019 6.561042 0.000000
0.000000 0.000000 6.650748

kppvol:  100
k-points:  [4, 4, 4]

repeat_cryspy

You may find it tedious to run cryspy over and over again. This auto script could help you. This runs cryspy once every 5 minutes.

#!/bin/bash

set -e

while :
do
    cryspy -n
    LOG_LASTLINE=`tail -n 1 log_cryspy`
    if  [ "$LOG_LASTLINE" = "Done all structures!" ]
    then
        exit 0
    # ---------- for EA
    elif [ "${LOG_LASTLINE:0:17}" = "Reached maxgen_ea" ]
    then
        exit 0
    elif [ "$LOG_LASTLINE" = "EA is ready" ]
    then
        cryspy -n    # EA
        LOG_LASTLINE=`tail -n 1 log_cryspy`
        if [ "${LOG_LASTLINE:0:17}" = "Reached maxgen_ea" ]
        then
            exit 0
        fi
        cryspy -n    # submit jobs
    # ---------- for BO
    elif [ "${LOG_LASTLINE:0:21}" = "Reached max_select_bo" ]
    then
        exit 0
    elif [ "$LOG_LASTLINE" = "BO is ready" ]
    then
        cryspy -n    # selection
        LOG_LASTLINE=`tail -n 1 log_cryspy`
        if [ "${LOG_LASTLINE:0:21}" = "Reached max_select_bo" ]
        then
            exit 0
        fi
        cryspy -n    # submit jobs
    # ---------- for LAQA
    elif [ "$LOG_LASTLINE" = "LAQA is ready" ]
    then
        cryspy -n    # selection
        cryspy -n    # submit jobs
    fi
    sleep 5m
done

CrySPY Utility

Table of contents

Subsections of CrySPY Utility

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

Scripts

Table of contents

Subsections of Scripts

extract_struc.py

Update History

Usage

Examples

Print

Structure ID