def set_point_vacancy(self, index):
n = len(self._symbols)
if index < 0 or index > n - 1:
sys.stderr.write("At least a pair of point and symbol or "
"a pair of point and number have to be set.\n")
else:
builder = CellBuilder(self._original_cell)
builder.pop(index)
self.set_cell(builder.get_cell())
def set_point_vacancy(self, index):
n = len(self._symbols)
if index < 0 or index > n - 1:
sys.stderr.write(
"At least a pair of point and symbol or "
"a pair of point and number have to be set.\n")
else:
builder = CellBuilder(self._original_cell)
builder.pop(index)
self.set_cell(builder.get_cell())
import numpy as np
import cogue
from cogue.crystal.builder import CellBuilder
import cogue.calculator.vasp as vasp
symbols = ['Si'] * 2 + ['O'] * 4
lattice = [[4.65, 0, 0],
[0, 4.75, 0],
[0, 0, 3.25]] # Orthorhombic
points=np.transpose([[0.0, 0.0, 0.0],
[0.5, 0.5, 0.5],
[0.3, 0.3, 0.0],
[0.7, 0.7, 0.0],
[0.2, 0.8, 0.5],
[0.8, 0.2, 0.5]])
cell = cogue.cell(lattice=lattice,
points=points,
symbols=symbols)
builder = CellBuilder(cell)
builder.push(point=[0.1, 0.1, 0.1],
symbol='Si')
builder.pop(4)
# To use get_cell restricts the cell to be an object of Cell but not CellBuilder
vasp.write_poscar(builder.get_cell())
import numpy as np
import cogue
from cogue.crystal.builder import CellBuilder
import cogue.calculator.vasp as vasp
symbols = ['Si'] * 2 + ['O'] * 4
lattice = [[4.65, 0, 0], [0, 4.75, 0], [0, 0, 3.25]] # Orthorhombic
points = np.transpose([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5], [0.3, 0.3, 0.0],
[0.7, 0.7, 0.0], [0.2, 0.8, 0.5], [0.8, 0.2, 0.5]])
cell = cogue.cell(lattice=lattice, points=points, symbols=symbols)
builder = CellBuilder(cell)
builder.push(point=[0.1, 0.1, 0.1], symbol='Si')
builder.pop(4)
# To use get_cell restricts the cell to be an object of Cell but not CellBuilder
vasp.write_poscar(builder.get_cell())
