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import numpy as np
import periodictable
from copy import deepcopy, copy
from .latmatcher import LatMatch, SR
class PipelineLatMatch:
def __init__(self, Alat3D, Blat3D, Aatoms3D=None, Batoms3D=None, dim=10, sc_vec=None, optimize_angle=True,
optimize_strain=True, dz=4):
self.Alat3D = Alat3D
self.Blat3D = Blat3D
self.Alat = self.Alat3D[:2, :2][:2, :2]
self.Blat = self.Blat3D[:2, :2][:2, :2]
self.dz = dz
if sc_vec is not None:
self.sc_vec = sc_vec
# TODO: This should be computed
self.rez = None
else:
self.matcher4 = LatMatch(scdim=dim, reference=self.Alat, target=self.Blat,
optimize_angle=optimize_angle, optimize_strain=optimize_strain)
self.sc_vec = self.matcher4.supercell()
self.rez = self.matcher4.result
self.sc_vec3 = np.array([[self.sc_vec[0][0], self.sc_vec[0][1], 0],
[self.sc_vec[1][0], self.sc_vec[1][1], 0],
[0, 0, self.dz+self.Alat3D[2][2]+self.Blat3D[2][2]+0.001]])
self.Aatoms3D, self.Batoms3D = self.atom_shift(Aatoms3D, Batoms3D)
self.superA_xyz = []
self.superB_xyz = []
def atom_shift(self, Aatoms3D, Batoms3D):
shift_Aatoms3D = deepcopy(Aatoms3D)
shift_Batoms3D = deepcopy(Batoms3D)
za = []
for atom in Aatoms3D:
za.append(atom[1][-1])
zb = []
for atom in Batoms3D:
zb.append(atom[1][-1])
a_average = sum(za) / len(za)
b_average = sum(zb) / len(zb)
min_za=min(za) # min(za)+x=0
for i in range(len(za)):
za[i] = za[i] - min_za+0.001
min_zb = min(zb) # min(za)+x=0
for i in range(len(zb)):
zb[i] = zb[i] - min_zb
max_za = max(za)
for i in range(len(zb)):
zb[i] = zb[i] + max_za + self.dz+0.001
for i in range(len(shift_Aatoms3D)):
shift_Aatoms3D[i][1][-1] = za[i]
for i in range(len(shift_Batoms3D)):
shift_Batoms3D[i][1][-1] = zb[i]
self.Aatoms3D = shift_Aatoms3D
self.Batoms3D = shift_Batoms3D
return self.Aatoms3D, self.Batoms3D
def compute_super_atoms(self):
atoms = atoms_to_greed(self.Aatoms3D, lat_v=self.Alat3D, dim=(10, 10, 0)) # initial grid of atoms xyz
atoms_a = atom_change_basis2D(atoms, new_basis=self.Alat, old_basis=np.identity(2)) # grid of atoms in A basis
atoms_A = atom_change_basis2D(atoms_a, new_basis=self.sc_vec,
old_basis=self.Alat) # grid of atoms in super cell basis
superA = supar_atoms(atoms_A) # select the atoms from super cell
superA_xyz = atom_change_basis2D(superA, new_basis=np.identity(2),
old_basis=self.sc_vec) # move the atoms back to xyz basis
atoms = atoms_to_greed(self.Batoms3D, lat_v=self.Blat3D, dim=(10, 10, 0)) # initial grid of atoms
oBlat3D, atoms_b = rotate_guest(self.rez, self.Blat3D, atoms)
atoms_B = atom_change_basis2D(atoms_b, new_basis=self.sc_vec,
old_basis=np.identity(2)) # grid of atoms in super cell basis
superB = supar_atoms(atoms_B) # select the atoms from super cell
superB_xyz = atom_change_basis2D(superB, new_basis=np.identity(2),
old_basis=self.sc_vec) # move the atoms back to xyz basis
superA_xyz = uniq_list(superA_xyz)
superB_xyz = uniq_list(superB_xyz)
self.superA_xyz = superA_xyz
self.superB_xyz = superB_xyz
return self.superA_xyz, self.superB_xyz
def get_new_structure(self, inter_distance=[0,0,0]):
structure = {"atoms": [],
"lattice_vectors": self.sc_vec3,
"pbc": [True, True, False],
"positions": [],
"host_guest": [], }
superA_xyz, superB_xyz = self.compute_super_atoms()
atomic_numbers = []
positions = []
for element in superA_xyz:
structure["host_guest"].append("host")
symbol = element[0]
positions.append(element[1].tolist())
atomic_number = getattr(periodictable, symbol)
if atomic_number is not None:
atomic_numbers.append(atomic_number.number)
else:
print(f"Warning: Atomic number for element '{symbol}' not found.")
atomic_numbers.append(None) # Or handle this case as you see fit
for element in superB_xyz:
structure["host_guest"].append("guest")
symbol = element[0]
pos=element[1].tolist()+inter_distance
positions.append(element[1].tolist())
atomic_number = getattr(periodictable, symbol)
if atomic_number is not None:
atomic_numbers.append(atomic_number.number)
else:
print(f"Warning: Atomic number for element '{symbol}' not found.")
atomic_numbers.append(None) # Or handle this case as you see fit
structure["atoms"] = atomic_numbers
structure["positions"] = positions
return structure
def is_element_in_list(element, lst):
for item in lst:
if item[0] == element[0] and np.allclose(item[1], element[1]):
return True
return False
def uniq_list(super_brut):
uniq = []
for c in super_brut:
if is_element_in_list(c, uniq) is False:
uniq.append(c)
return uniq
def atoms_to_greed(atoms, lat_v, dim):
"""
Construct a greed of atoms knowing the atoms lattice vectors and dim
:param atoms:
:param lat_v:
:param dim:
:return:
"""
atom_list = deepcopy(atoms)
# translation lat_v-x
new_atoms = []
for i in range(1, dim[0] + 1):
for atom in atom_list:
new_atom = deepcopy(atom)
new_atom[1][0] += i * lat_v[0][0]
new_atom[1][1] += i * lat_v[1][0]
new_atom[1][2] += i * lat_v[2][0]
new_atoms.append(new_atom)
new_atom = deepcopy(atom)
new_atom[1][0] -= i * lat_v[0][0]
new_atom[1][1] -= i * lat_v[1][0]
new_atom[1][2] -= i * lat_v[2][0]
new_atoms.append(new_atom)
atom_list.extend(new_atoms)
# translation lat_v-y
for i in range(1, dim[1] + 1):
for atom in atom_list:
new_atom = deepcopy(atom)
new_atom[1][0] += i * lat_v[0][1]
new_atom[1][1] += i * lat_v[1][1]
new_atom[1][2] += i * lat_v[2][1]
new_atoms.append(new_atom)
new_atom = deepcopy(atom)
new_atom[1][0] -= i * lat_v[0][1]
new_atom[1][1] -= i * lat_v[1][1]
new_atom[1][2] -= i * lat_v[2][1]
new_atoms.append(new_atom)
atom_list.extend(new_atoms)
# translation lat_v-z
for i in range(1, dim[2] + 1):
for atom in atom_list:
new_atom = deepcopy(atom)
new_atom[1][0] += i * lat_v[0][2]
new_atom[1][1] += i * lat_v[1][2]
new_atom[1][2] += i * lat_v[2][2]
new_atoms.append(new_atom)
new_atom = deepcopy(atom)
new_atom[1][0] -= i * lat_v[0][2]
new_atom[1][1] -= i * lat_v[1][2]
new_atom[1][2] -= i * lat_v[2][2]
new_atoms.append(new_atom)
atom_list.extend(new_atoms)
return atom_list
# atoms in new basis:
def atom_change_basis2D(atoms, new_basis, old_basis=np.identity(2)):
new_basis = [[new_basis[0][0], new_basis[0][1]],
[new_basis[1][0], new_basis[1][1]]]
old_basis = [[old_basis[0][0], old_basis[0][1]],
[old_basis[1][0], old_basis[1][1]]]
atom_list = deepcopy(atoms)
change_base = np.linalg.inv(new_basis) @ old_basis
new_atoms = []
for atom in atom_list:
new_atom = deepcopy(atom)
nd = (change_base @ (np.array(new_atom[1][:2]).T)).T
new_atom[1][0] = nd[0]
new_atom[1][1] = nd[1]
new_atoms.append(new_atom)
atom_list = deepcopy(new_atoms)
return atom_list
def supar_atoms(atoms, eps=0.01):
atom_list = deepcopy(atoms)
# change_base=np.linalg.inv(new_basis)
new_atoms = []
for atom in atom_list:
if ((atom[1][0] >= -eps) and (atom[1][0] < 1)) and ((atom[1][1] >= -eps) and (atom[1][1] < 1)):
new_atoms.append(atom)
atom_list = deepcopy(new_atoms)
return atom_list
def rotate_guest(rez, Blat3D, atoms):
Batoms3D = [a[1] for a in atoms]
s1, s2, theta = rez
Tr = np.eye(3)
Tr[:2, :2] = SR(s1, s2, theta)
oBlat3D = copy(Blat3D)
oBlat3D = (Tr @ (oBlat3D.T)).T
rs = [Tr @ r for r in Batoms3D]
new_atoms = [[atoms[i][0], rs[i]] for i in range(len(atoms))]
return oBlat3D, new_atoms
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