def run_method(self):
from method import structure_compare_donet
from method import read
from method.plot_crystal import plot_atoms
tolerance = float(self.tolerance.text())
percent = float(self.percent.text())
arrow_location, arrow = structure_compare_donet.exec(self.path.save_path,
self.host.text(), self.doped.text(), tolerance, percent)
self.figure.clear()
ax = self.figure.add_subplot(111, projection='3d')
structure = read.poscar(self.host.text())
draw_crystal_in_ax(ax, structure)
structure = read.poscar(self.doped.text())
plot_atoms(ax, structure)
ax.quiver(arrow_location[0], arrow_location[1], arrow_location[2], arrow[0], arrow[1], arrow[2])
self.canvas.draw()
def exec(inputPath, outputPath, types, subs, center, tolerance):
import platform
structure = read.poscar(inputPath, types=poscar_is_vasp5(inputPath))
doped_result, view_result = substitution(structure, types, subs, center, tolerance)
for doped_structure in doped_result:
output_name = os.path.join(outputPath, doped_structure.name)
if platform.system() == 'Windows':
output_name = output_name.replace('\\', '/')
poscar(doped_structure, file_name=output_name, vasp5=True)
return view_result
def readdoped(self):
from method import read
file_name, file_type = QFileDialog.getOpenFileName(None, 'Open', './', 'All Files (*)')
self.path.open_path = file_name
self.doped.setText(file_name)
self.figure.clear()
self.structure = read.poscar(self.path.open_path, types=poscar_is_vasp5(self.path.open_path))
ax = self.figure.add_subplot(111, projection='3d')
draw_crystal_in_ax(ax, self.structure)
self.canvas.draw()
def exec(inputPath, outputPath, insert, center, position, tolerance):
import platform
structure = read.poscar(inputPath, types=poscar_is_vasp5(inputPath))
doped_result, view_result = interstitial(structure, insert, position=position, center=center, tolerance=tolerance)
for doped_structure in doped_result:
output_name = os.path.join(outputPath, doped_structure.name)
if platform.system() == 'Windows':
output_name = output_name.replace('\\', '/')
poscar(doped_structure, file_name=output_name, vasp5=True)
poscar(view_result, file_name='inequivalent interstitial sites.vasp', vasp5=True)
return view_result
def time_stop(self):
from method import read
self.bar.setValue(100)
self.timer.stop()
self.status.setText('Finished.')
self.run_btn.setText('Run')
self.structure = read.poscar(self.write_path, types=poscar_is_vasp5(self.write_path))
self.figure.clear()
ax = self.figure.add_subplot(111, projection='3d')
draw_crystal_in_ax(ax, self.structure)
self.canvas.draw()
with open('interstitial log.txt', 'w') as file:
file.writelines('0%')
raise error.RuntimeError("Cannot find specie to substitute in structure!")
view_structure = structure.copy()
for specie in types:
indices = symmetrically_inequivalent_indices(structure, center=center, species=specie, symprec=tolerance)
for index in indices:
if subs is None:
doped_structure = structure.copy()
del doped_structure[index]
doped_structure.name = 'vacancy_of_{0}_in_site{1}'.format(specie, index+1)
result.append(doped_structure)
view_structure[index].type = 'Vac'
else:
for sub_specie in subs:
doped_structure = structure.copy()
doped_structure[index].type = sub_specie
doped_structure.name = 'substitution_{0}_in_site{1}'.format(sub_specie, index+1)
result.append(doped_structure)
view_structure[index].type = 'Sub'
return result, view_structure
if __name__ == "__main__":
from method.read import poscar
structure1 = poscar('R-3c.vasp')
# inequivalent = interstitial(structure1, 'O', center=[0.5, 0.5, 0.5])
test = substitution(structure1)
def read_poscar(raw):
from method import read
with open('POSCAR', 'w') as f:
f.write(raw)
structure = read.poscar('POSCAR', types=poscar_is_vasp5('POSCAR'))
return structure
for atom in value:
atom_json = json.loads(atom)
atom_list.append(Atom(atom_json['pos'], type=atom_json['type'], num=atom_json['num']))
element_json[key] = atom_list
result.append(element_json)
return result
if __name__ == "__main__":
doped_crystal = '2Tisc960.vasp'
substrate = 'hostsc960.vasp'
unit_cell_file = 'primitive.vasp'
doped_element = 'Ti'
already_compared_structure = True
doped_structure = poscar(doped_crystal)
substrate_structure = poscar(substrate)
primitive = poscar(unit_cell_file)
original = []
if already_compared_structure:
doped_atoms = read_compared_result_from_json()
for element in doped_atoms:
if element['type'] == doped_element:
for pairs in element['sub']:
for atom in pairs:
if atom.type == doped_element:
original.append(atom)
else:
doped_atoms = compare_structure(substrate_structure, doped_structure, tolerance=1.0, compare_type='M')
for element in doped_atoms:
from method.read import poscar
from method.compare_structure import compare_structure
from copy import deepcopy
import json
import re
if __name__ == "__main__":
doped_crystal = '2Tisc960.vasp'
substrate = 'hostsc960.vasp'
doped_structure = poscar(doped_crystal)
substrate_structure = poscar(substrate)
doped_atoms = compare_structure(substrate_structure, doped_structure, tolerance=1.0, compare_type='Q')
doped_atoms_json = []
for element in doped_atoms:
element_json = deepcopy(element)
for key, value in element.__dict__.items():
if re.match('type', key):
continue
elif re.match('su', key) or re.match('un', key):
atom_list = []
for pair in value:
tmp = []
for atom in pair:
atom_json = json.dumps({'type': atom.type, 'num': atom.num, 'pos': atom.pos.tolist()})
tmp.append(atom_json)
atom_list.append(tmp)
element_json.__dict__[key] = atom_list
else:
atom_list = []
for atom in value:
def exec(outputPath, host_path, doped_path, tolerance, percent):
host = read.poscar(host_path, types=poscar_is_vasp5(host_path))
doped = read.poscar(doped_path, types=poscar_is_vasp5(doped_path))
arrow_location, arrow, tmp_result = structure_compare(
outputPath, host, doped, tolerance, percent)
return arrow_location, arrow
species = []
nb_atoms = [int(u) for u in line]
poscar.readline()
for n in nb_atoms:
flag = 0
for i in range(n):
line = poscar.readline().split()
if flag is 0:
species.append(line[3])
flag = 1
poscar.close()
return species
def exec(outputPath, host_path, doped_path, tolerance, percent):
host = read.poscar(host_path, types=poscar_is_vasp5(host_path))
doped = read.poscar(doped_path, types=poscar_is_vasp5(doped_path))
arrow_location, arrow, tmp_result = structure_compare(
outputPath, host, doped, tolerance, percent)
return arrow_location, arrow
if __name__ == "__main__":
host_path = 'host'
doped_path = 'defect'
host = read.poscar(host_path, types=poscar_is_vasp5(host_path))
doped = read.poscar(doped_path, types=poscar_is_vasp5(doped_path))
save_path = ''
result = structure_compare(save_path, host, doped)
print(result)
sum2 = special.erfc(eta * coeff3) / coeff3
sum2[np.isinf(sum2)] = -2 * eta / np.sqrt(np.pi)
result = np.sum(sum1) + np.sum(sum2)
if np.imag(result) > 1e-10:
print(
'\nERROR: the potential {0} is not a real, unknown problem, please check the code!\n'
.format(result))
exit(1)
return np.real(result)
if __name__ == "__main__":
tic = time.time()
file_name = 'YPO4primitive.vasp'
charge = {'Y': 3, 'O': -2, 'P': 5}
structure = poscar(file_name)
atom_list = [[], []]
multipler = (120, 120, 120)
eta = 1 * 2 * np.pi
for atom in structure:
atom_list[0].append(atom.pos)
atom_list[1].append(atom.type)
for atom in structure:
vectors = atom.pos - np.array(atom_list[0])
potential = 0.0
for i in range(len(vectors)):
potential += charge[atom_list[1][i]] * madelung_potential_new(
structure.cell.T, vectors[i], extend=multipler, eta=eta)
print(atom, potential)
toc = time.time()
print('Time:{0}'.format(toc - tic))