def _get_smat_cell(cell, options):
s_mat = np.array([int(x) for x in options.s_mat.split()])
s_mat = _get_matrix(s_mat)
if s_mat is False:
sys.stderr.write("Supercell matrix is not correctly set.\n")
return False
else:
if options.is_verbose:
print "Transform cell using supercell matrix:"
print s_mat
return get_supercell(cell, s_mat)
def _get_smat_cell(cell, options):
s_mat = np.array([int(x) for x in options.s_mat.split()])
s_mat = _get_matrix(s_mat)
if s_mat is False:
sys.stderr.write("Supercell matrix is not correctly set.\n")
return False
else:
if options.is_verbose:
print "Transform cell using supercell matrix:"
print s_mat
return get_supercell(cell, s_mat)
def transform_cell(cell, options, is_shift=True):
if options.shift and is_shift:
set_shift(cell, options)
if options.t_mat:
cell = _get_tmat_cell(cell, options)
if options.is_r2h:
if options.is_verbose:
print "Transform cell by transformation matrix of rhombohedral to hexagonal:"
print np.array(r2h)
cell = get_supercell(cell, r2h)
if options.s_mat:
cell = _get_smat_cell(cell, options)
return cell
def transform_cell(cell, options, is_shift=True):
if options.shift and is_shift:
set_shift(cell, options)
if options.t_mat:
cell = _get_tmat_cell(cell, options)
if options.is_r2h:
if options.is_verbose:
print "Transform cell by transformation matrix of rhombohedral to hexagonal:"
print np.array(r2h)
cell = get_supercell(cell, r2h)
if options.s_mat:
cell = _get_smat_cell(cell, options)
return cell
import numpy as np
import cogue
import cogue.calculator.vasp as vasp
from cogue.crystal.point_defect import PointDefect
from cogue.crystal.supercell import get_supercell
symbols = ['Cu'] * 4
lattice = [[3.61, 0, 0],
[0, 3.61, 0],
[0, 0, 3.61]] # Orthorhombic
points=np.transpose([[0.0, 0.0, 0.0],
[0.0, 0.5, 0.5],
[0.5, 0.0, 0.5],
[0.5, 0.5, 0.0]])
cell = cogue.cell(lattice=lattice,
points=points,
symbols=symbols)
supercell = get_supercell(cell, np.diag([2, 2, 2]))
vacancy_cell = PointDefect(supercell)
vacancy_cell.set_point_vacancy(3)
# To use get_cell restricts the cell to be an object of Cell but not CellBuilder
vasp.write_poscar(vacancy_cell)
