def loop(self):
if not os.path.exists(f'conf{self.n}'):
os.mkdir(f'conf{self.n}')
shutil.copy('INCAR', f'conf{self.n}')
shutil.copy('KPOINTS', f'conf{self.n}')
shutil.copy('POTCAR', f'conf{self.n}')
self.s.to('POSCAR', f'conf{self.n}/POSCAR')
self.move()
if self.n > 0:
shutil.copy2(f'conf{self.n - 1}/CHGCAR', f'conf{self.n}')
shutil.copy2(f'conf{self.n - 1}/WAVECAR', f'conf{self.n}')
pathlib.Path(f'conf{self.n}/wait').touch()
else:
self.s = Structure.from_file(f'conf{self.n}/POSCAR')
self.move()
os.chdir(f'conf{self.n}')
self.calculate()
os.chdir('..')
from pymatgen.io.vasp.outputs import Structure
import os
os.chdir('/home/jinho93/new/oxides/perobskite/lanthanum-aluminate/bulk/hse/polaron')
s = Structure.from_file('POSCAR')
s.translate_sites(range(len(s.sites)), [0.5, 0.5, 0], frac_coords=True)
s.to('POSCAR', 'POSCAR')
from pymatgen.io.vasp.outputs import Structure, Element
import os
import numpy as np
def aver(arr:np.ndarray):
return arr.sum() / len(arr)
if __name__ == '__main__':
os.chdir('/home/jinho93/oxides/cluster/zno/vasp/3.slab/2.80')
os.chdir('/home/jinho93/oxides/cluster/zno/vasp/3.slab/1.zn_vac/3.LDIPOL_from_ini')
os.chdir('/home/jinho93/oxides/cluster/zno/cp2k/3.slab/2.wann')
os.chdir('/home/jinho93/oxides/cluster/zno/vasp/4.supc/1.fix/two')
s = Structure.from_file('CONTCAR')
z_coords = []
p = []
for i in s.sites:
if i.specie == Element.Zn:
if len(s.get_neighbors(i, 2.5)) is 4:
z = [_[0].z for _ in s.get_neighbors(i, 2.5)]
z_coords.append(i.z)
p.append(i.z - sum(z) / 4)
arr = np.array([z_coords, p]).transpose()
arr = arr[arr[:, 0].argsort()]
n = 2
for i in range(len(arr) // n):
print(arr[n*i][0], aver(arr[n * i: n * (i + 1), 1]))
def __init__(self):
self.s = Structure.from_file('POSCAR')
self.n = 0
self.output = []
self.displacement = -0.1
from pymatgen.io.vasp.outputs import Element, Structure
import os
import numpy as np
os.chdir('/home/ksrc5/FTJ/bfo')
s = Structure.from_file('r3c_gaf_relaxed.vasp')
output2 = np.zeros(3)
for i in s.sites:
if i.specie == Element.Fe or i.specie == Element.Bi:
output = np.zeros(3)
n = 0
for j in s.get_neighbors(i, 2.7):
output += j[0].coords
n += 1
output2 += (output / n - i.coords)
print(output2)