def read_compared_result_from_json(filename='structure compare.json'):
import json
import re
from method.atom import Atom
with open(filename, 'r+') as fp:
result_json = json.load(fp)
result = []
for element_json in result_json:
element_json = json.loads(element_json)
for key, value in element_json.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.loads(atom)
tmp.append(Atom(atom_json['pos'], type=atom_json['type'], num=atom_json['num']))
atom_list.append(tmp)
element_json[key] = atom_list
else:
atom_list = []
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
def remove_doped_atoms(structure, remove_dict):
temp = []
for atom in structure:
if atom.type in remove_dict.keys():
value = remove_dict[atom.type]
if value != '':
temp.append(Atom(atom.pos, value))
else:
temp.append(Atom(atom.pos, atom.type))
structure.clear()
structure.extend(temp)
return structure
def get_species(structure):
species = {}
i = 0
for atom in structure:
if species.get(atom.type):
species[atom.type].append(Atom(atom.pos, atom.type, num=i))
else:
species[atom.type] = [
Atom(atom.pos, atom.type, num=i),
]
i = i + 1
return species
def remove_doped_atoms(structure, remove_dict):
temp = []
for atom in structure:
if atom.type in remove_dict.keys():
value = remove_dict[atom.type]
if value != '':
temp.append(Atom(atom.pos, value))
else:
temp.append(Atom(atom.pos, atom.type))
new_structure = Structure(structure.cell, scale=structure.scale)
new_structure.extend(temp)
return new_structure
def symmetrically_inequivalent_sites(structure,
specie=None,
center=None,
tolerance=1e-3,
symprec=0.1):
from method import error
from method.atom import Atom
from method.utilities import are_periodic_images
from numpy import dot
from numpy.linalg import norm
if specie is None:
raise error.RuntimeError("specie is None!")
ops = get_symmetrical_operations(structure, symprec=symprec)
temp = structure.copy()
result = []
for i in range(len(temp)):
equivalent_sites = []
if temp[i].type != specie:
continue
else:
atom = Atom(temp[i].pos, type=temp[i].type, index=i)
equivalent_sites.append(atom)
for op in ops:
rotation = op[:3]
translation = op[3]
transform = dot(rotation, temp[i].pos) + translation
for j in range(i + 1, len(temp)):
if temp[j].type != specie:
continue
if are_periodic_images(transform,
temp[j].pos,
cell=structure.cell,
tolerance=tolerance):
atom = Atom(temp[j].pos, type=temp[j].type, index=j)
equivalent_sites.append(atom)
temp[j].type = 'Used'
result.append(equivalent_sites)
indices = []
for equivalent in result:
if center is None:
indices.append(equivalent[0].index)
else:
center = dot(temp.cell, center)
minimum = norm(equivalent[0].pos - center)
index = equivalent[0].index
for site in equivalent:
if norm(site.pos - center) < minimum:
minimum = norm(site.pos - center)
index = site.index
indices.append(index)
return indices
def build_shell(structure,
pure_substrate=False,
doped_atom=None,
remove_dict=None,
cluster_r=5,
shell_r=30):
"""
:param structure: Pylada.crystal.Structure
:param pure_substrate: Bool type
:param doped_atom: Pylada.crystal.Atom
:param remove_dict: dict
:param cluster_r: float
:param shell_r: float
:return:
"""
if pure_substrate is True:
pass
else:
if doped_atom is None:
species = structure_species(structure)
doped_name = species[0][0]
num = species[0][1]
if num != 1:
print(
'WARNING: The number of doped atom is not exclusive, please give doped atom name and position.\n'
)
for atom in structure:
if atom.type == doped_name:
doped_atom = Atom(atom.pos, atom.type)
break
if pure_substrate is False:
if remove_dict is None:
print(
'ERROR: remove_list can not be None when substrate includes doped atoms.\n'
)
exit(1)
structure = remove_doped_atoms(structure, remove_dict)
supercell = extend_structure(structure, shell_r)
shell = Structure(structure.cell, scale=structure.scale)
doped_center = doped_atom.pos
temp = []
for atom in supercell:
position = atom.pos
d = np.linalg.norm(position - doped_center)
if cluster_r < d <= shell_r:
temp.append(Atom(position - doped_center, atom.type))
shell.extend(temp)
return shell
def extend_structure(structure, shell_r, pure_substrate=True, remove_dict=None):
if pure_substrate is False:
if remove_dict is None:
print('ERROR: remove_list can not be None when substrate includes doped atoms.\n')
exit(1)
structure = remove_doped_atoms(structure, remove_dict)
cell = structure.cell.T
volume = structure.volume
hz = volume/np.linalg.norm(np.cross(cell[0], cell[1]))
hx = volume/np.linalg.norm(np.cross(cell[1], cell[2]))
hy = volume/np.linalg.norm(np.cross(cell[2], cell[0]))
if min(hx, hy, hz)/2 >= shell_r:
return structure
nz = int(np.ceil(shell_r/hz - 0.5))
nx = int(np.ceil(shell_r/hx - 0.5))
ny = int(np.ceil(shell_r/hy - 0.5))
temp = []
for i in range(-nx, nx+1):
for j in range(-ny, ny+1):
for k in range(-nz, nz+1):
for atom in structure:
position = atom.pos + i*cell[0] + j*cell[1] + k*cell[2]
temp.append(Atom(position, atom.type))
supercell = Structure(structure.cell, scale=structure.scale)
supercell.extend(temp)
return supercell
def insert(self, index, *args, **kwargs):
""" Insert atoms in given position """
from method.atom import Atom
if len(args) == 1 and len(kwargs) == 0 and isinstance(args[0], Atom):
atom = args[0]
else:
atom = Atom(*args, **kwargs)
self._atoms.insert(index, atom)
def extend(self, args):
""" Adds atoms to structure """
from collections import Sequence
from method.atom import Atom
from method import error
for arg in args:
if isinstance(arg, Atom):
self._atoms.append(arg)
elif isinstance(arg, Sequence):
self._atoms.append(Atom(*arg))
else:
raise error.TypeError("Cannot convert argument to Atom")
def supercell(structure, transform):
from method.structure import Structure
from method.atom import Atom
import numpy as np
from numpy import dot
epsilon = 1e-3
r = []
surface = []
for j in range(3):
minimum = 0
maximum = 0
for i in range(3):
if transform[i][j] <= 0:
minimum += transform[i][j]
else:
maximum += transform[i][j]
r.append([minimum, maximum])
result = Structure(dot(structure.cell, transform.T), scale=structure.scale)
inverse = np.linalg.inv(transform)
inv_cell = np.linalg.inv(structure.cell)
for i in range(len(structure)):
fractional = dot(inv_cell, structure[i].pos)
for a0 in range(r[0][0] - 1, r[0][1] + 1):
for a1 in range(r[1][0] - 1, r[1][1] + 1):
for a2 in range(r[2][0] - 1, r[2][1] + 1):
translation = np.array([a0, a1, a2])
temp = dot((translation + fractional), inverse)
if is_in_cell(temp, epsilon):
result.add_atom(dot(result.cell, temp),
structure[i].type)
elif is_in_surface(temp, epsilon):
surface.append(
Atom(dot(result.cell, temp),
structure[i].type,
flag=0))
surface = remove_reduplicate(surface, dot(structure.cell, transform.T),
epsilon)
result.extend(surface)
return result
def extend_structure(structure, shell_r=30):
cell = structure.cell.T
volume = structure.volume
hz = volume / np.linalg.norm(np.cross(cell[0], cell[1]))
hx = volume / np.linalg.norm(np.cross(cell[1], cell[2]))
hy = volume / np.linalg.norm(np.cross(cell[2], cell[0]))
if min(hx, hy, hz) >= shell_r:
return structure
nz = int(np.ceil(shell_r / hz - 0.5))
nx = int(np.ceil(shell_r / hx - 0.5))
ny = int(np.ceil(shell_r / hy - 0.5))
temp = []
for i in range(-nx, nx + 1):
for j in range(-ny, ny + 1):
for k in range(-nz, nz + 1):
for atom in structure:
position = atom.pos + i * cell[0] + j * cell[1] + k * cell[
2]
temp.append(Atom(position, atom.type))
supercell = Structure(structure.cell, scale=structure.scale)
supercell.extend(temp)
return supercell
def build_shell(structure,
center,
cluster_r,
shell_r,
pure_substrate=False,
remove_dict=None):
if pure_substrate is False:
if remove_dict is None:
print(
'ERROR: remove_list can not be None when substrate includes doped atoms.\n'
)
exit(1)
structure = remove_doped_atoms(structure, remove_dict)
supercell = extend_structure(structure, shell_r)
shell = Structure(structure.cell, scale=structure.scale)
temp = []
for atom in supercell:
position = atom.pos
d = np.linalg.norm(position - center)
if cluster_r < d <= shell_r:
temp.append(Atom(position - center, atom.type))
shell.extend(temp)
return shell
def append(self, *args, **kwargs):
from method.atom import Atom
if len(args) == 1 and len(kwargs) == 0 and isinstance(args[0], Atom):
self._atoms.append(args[0])
else:
self._atoms.append(Atom(*args, **kwargs))
result_json = json.load(fp)
result = []
for element in result_json:
element = json.loads(element)
for key, value in element.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.loads(atom)
tmp.append(
Atom(atom_json['pos'],
type=atom_json['type'],
num=atom_json['num']))
atom_list.append(tmp)
element[key] = atom_list
else:
atom_list = []
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[key] = atom_list
result.append(element)
print(result)
def build_cluster(structure,
cluster_r,
doped_atom_type=None,
center=None,
core_r=None,
tolerance=0.2):
from method.coordination_shells import coordination_shells
position = np.array([0.0, 0.0, 0.0])
species = structure_species(structure)
if doped_atom_type is None:
doped_atom_type = species[0][0]
print('\nTry to use *{0}* atoms as doped atoms\n'.format(
doped_atom_type))
if center is None:
num = 0
for atom in structure:
if atom.type == doped_atom_type:
position += atom.pos
num += 1
center = position / num
if cluster_r > min(distance_of_center_and_surface(center,
structure.cell.T)):
print(
'\nERROR: the cluster is out range of the CONTCAR supercell structure. '
'Please use a bigger supercell or a smaller cluster_r parameter\n')
exit(1)
cluster = Structure(structure.cell, scale=structure.scale)
if core_r is None:
print(
'\nTry to use the nearest neighbor of doped atoms to build core structure.\n'
)
nearest_neighbors = []
for atom in structure:
if atom.type == doped_atom_type:
neighbors = coordination_shells(structure,
nshells=5,
center=atom.pos,
tolerance=tolerance)
nearest_neighbors.append(atom)
atom.pseudo = 0
for item in neighbors[0]:
atom = item[0]
nearest_neighbors.append(atom)
atom.pseudo = 0
atom = neighbors[0][0][0]
nearest_name = atom.type
print('\nSet *{0}* atoms as nearest neighbor.\n'.format(
nearest_name))
flag = 0
for i in range(1, 5):
temp = []
if flag != 0:
break
for item in neighbors[i]:
atom = item[0]
if nearest_name == atom.type:
if not hasattr(atom, 'pseudo'):
temp.append(atom)
atom.pseudo = 0
else:
flag = 1
nearest_neighbors.extend(temp)
# nearest neighbor might be outside of CONTCAR
with open('core structure.txt', 'w+') as fp:
for atom in nearest_neighbors:
fp.writelines(atom.type + ' ' + str(atom.pos) + '\n')
for atom in structure:
position = atom.pos
d = np.linalg.norm(center - position)
if d <= cluster_r:
if hasattr(atom, 'pseudo'):
cluster.append(Atom(atom.pos - center, atom.type,
pseudo=0))
else:
cluster.append(
Atom(atom.pos - center, atom.type, pseudo=-1))
else:
for atom in structure:
d = np.linalg.norm(center - atom.pos)
if d <= core_r:
cluster.append(Atom(atom.pos - center, atom.type, pseudo=0))
elif d <= cluster_r:
cluster.append(Atom(atom.pos - center, atom.type, pseudo=-1))
return cluster, center
def build_cluster(structure,
doped_atom=None,
cluster_r=5,
core_r=None,
tolerance=0.2):
from coordination_shells import coordination_shells
"""
:param structure: Pylada.crystal.Structure
:param doped_atom: Pylada.crystal.Atom
:param cluster_r: float
:param core_r: float
:return: cluster, Pylada.crystal.Structure
"""
if doped_atom is None:
species = structure_species(structure)
doped_name = species[0][0]
num = species[0][1]
if num != 1:
print(
'WARNING: The number of doped atom is not exclusive, please give doped atom name and position.\n'
)
for atom in structure:
if atom.type == doped_name:
doped_atom = Atom(atom.pos, atom.type)
break
cluster = Structure(structure.cell, scale=structure.scale)
doped_center = doped_atom.pos
if core_r is not None:
for atom in structure:
position = atom.pos
d = np.linalg.norm(doped_center - position)
if d <= core_r:
cluster.append(
Atom(atom.pos - doped_center, atom.type, pseudo=0))
elif d <= cluster_r:
cluster.append(
Atom(atom.pos - doped_center, atom.type, pseudo=-1))
else:
# try to find the nearest neighbors of doped atom
neighbors = coordination_shells(structure,
nshells=4,
center=doped_center,
tolerance=tolerance)
nearest_neighbors = []
flag = 0
for item in neighbors[0]:
atom = item[0]
nearest_neighbors.append(atom)
atom.pseudo = 0
if len(sorted({a.type for a in nearest_neighbors})) > 1:
print(
'WARNING: The species of nearest neighbor atoms are more than one.\n'
)
atom = neighbors[0][0][0]
nearest_name = atom.type
for i in range(1, 4):
if flag != 0:
break
temp = [item[0] for item in neighbors[i]]
if len(sorted({a.type for a in temp})) > 1:
print('WARNING: The species of next nearest neighbor atoms:\n')
print(sorted({a.type for a in temp}))
print(
'\nwhich means the tolerance parameter might be too big to distinguish different shell of '
'neighbors\n')
# when this situation happened, we discard this shell.
break
for item in neighbors[i]:
atom = item[0]
if nearest_name == atom.type:
nearest_neighbors.append(atom)
atom.pseudo = 0
else:
flag = 1
for atom in structure:
position = atom.pos
d = np.linalg.norm(doped_center - position)
if d <= cluster_r:
if hasattr(atom, 'pseudo'):
cluster.append(
Atom(atom.pos - doped_center, atom.type, pseudo=0))
elif atom.type == doped_atom.type and d < 0.01:
cluster.append(
Atom(atom.pos - doped_center, atom.type, pseudo=0))
else:
cluster.append(
Atom(atom.pos - doped_center, atom.type, pseudo=-1))
return cluster
def build_mosaic_structure(cluster, shell):
for atom in shell:
cluster.append(Atom(atom.pos, atom.type, pseudo=-1))
return cluster