def _generate_orientation(self, pyxtal_mol, pt, oris, wp):
# Use a Wyckoff_site object for the current site
self.numattempts += 1
#ensure that the orientation is good
count = 0
while count < 100:
ori = random.choice(oris).copy()
ori.change_orientation(flip=True)
if self._check_ori_dist(ori):
#print("===good orientation", count, self._check_ori_dist(ori))
break
count += 1
#print(count, self.molecules[0].axes.T[0].dot(ori.r.as_matrix().T))
#print(ori.r.as_matrix())
ms0 = mol_site(pyxtal_mol, pt, ori, wp, self.lattice, self.diag)
# Check distances within the WP
if ms0.check_distances():
return ms0
else:
# Maximize the smallest distance for the general
# positions if needed
if len(pyxtal_mol.mol) > 1 and ori.degrees > 0:
# bisection method
def fun_dist(angle, ori, mo, pt):
ori0 = ori.copy()
ori.change_orientation(angle)
ms0 = mol_site(
mo,
pt,
ori,
wp,
self.lattice,
self.diag,
)
d = ms0.compute_distances()
return d
angle_lo = ori.angle
angle_hi = angle_lo + np.pi
fun_lo = fun_dist(angle_lo, ori, pyxtal_mol, pt)
fun_hi = fun_dist(angle_hi, ori, pyxtal_mol, pt)
fun = fun_hi
for it in range(self.ori_attempts):
self.numattempts += 1
if (fun > 0.8) & (ms0.check_distances()):
return ms0
angle = (angle_lo + angle_hi) / 2
fun = fun_dist(angle, ori, pyxtal_mol, pt)
#print('Bisection: ', it, fun)
if fun_lo > fun_hi:
angle_hi, fun_hi = angle, fun
else:
angle_lo, fun_lo = angle, fun
return None
def make_mol_site(self, ref=False):
if ref:
mol = self.ref_mol
ori = self.ori
else:
mol = self.molecule
ori = Orientation(np.eye(3))
mol = self.add_site_props(mol)
pmol = pyxtal_molecule(mol, symmetrize=False)
site = mol_site(pmol, self.position, ori, self.wyc, self.lattice, self.diag)
return site
def fun_dist(angle, ori, mo, pt):
ori0 = ori.copy()
ori.change_orientation(angle)
ms0 = mol_site(
mo,
pt,
ori,
wp,
self.lattice,
self.diag,
)
d = ms0.compute_distances()
return d
def make_mol_sites(self):
"""
generate the molecular wyckoff sites
"""
ori = Orientation(np.eye(3))
sites = []
for mol, pos, wp in zip(self.p_mols, self.positions, self.wps):
site = mol_site(mol, pos, ori, wp, self.lattice, self.diag)
#print(pos)
#print(self.lattice.matrix)
#print([a.value for a in site.molecule.mol.species])
#print(site.molecule.mol.cart_coords)
#print(site._get_coords_and_species(absolute=True)[0][:10])
sites.append(site)
return sites
def subgroup_by_splitter(self, splitter, eps=0.05):
"""
transform the crystal to subgroup symmetry from a splitter object
"""
lat1 = np.dot(splitter.R[:3, :3].T, self.lattice.matrix)
multiples = np.linalg.det(splitter.R[:3, :3])
new_struc = deepcopy(self)
new_struc.group = splitter.H
lattice = Lattice.from_matrix(lat1, ltype=new_struc.group.lattice_type)
lattice = lattice.mutate(degree=eps, frozen=True)
h = splitter.H.number
split_sites = []
if self.molecular:
# below only works when the cell does not change
for i, site in enumerate(self.mol_sites):
pos = site.position
mol = site.molecule
ori = site.orientation
coord0 = mol.mol.cart_coords.dot(ori.matrix.T)
wp1 = site.wp
ori.reset_matrix(np.eye(3))
for ops1, ops2 in zip(splitter.G2_orbits[i],
splitter.H_orbits[i]):
#reset molecule
coord1 = np.dot(coord0, ops1[0].affine_matrix[:3, :3].T)
_mol = mol.copy()
_mol.reset_positions(coord1)
pos0 = apply_ops(pos, ops1)[0]
pos0 -= np.floor(pos0)
pos0 += eps * (np.random.sample(3) - 0.5)
wp, _ = Wyckoff_position.from_symops(ops2,
h,
permutation=False)
split_sites.append(mol_site(_mol, pos0, ori, wp, lattice))
new_struc.mol_sites = split_sites
new_struc.numMols = [
int(multiples * numMol) for numMol in self.numMols
]
else:
for i, site in enumerate(self.atom_sites):
pos = site.position
for ops1, ops2 in zip(splitter.G2_orbits[i],
splitter.H_orbits[i]):
pos0 = apply_ops(pos, ops1)[0]
pos0 -= np.floor(pos0)
pos0 += eps * (np.random.sample(3) - 0.5)
wp, _ = Wyckoff_position.from_symops(ops2,
h,
permutation=False)
split_sites.append(atom_site(wp, pos0, site.specie))
new_struc.atom_sites = split_sites
new_struc.numIons = [
int(multiples * numIon) for numIon in self.numIons
]
new_struc.lattice = lattice
new_struc.source = 'Wyckoff Split'
return new_struc
def _subgroup_by_splitter(self, splitter, eps=0.05, mut_lat=True):
"""
transform the crystal to subgroup symmetry from a splitter object
Args:
splitter: wyckoff splitter object
eps (float): maximum atomic displacement in Angstrom
mut_lat (bool): whether or not mutate the lattice
"""
lat1 = np.dot(splitter.R[:3,:3].T, self.lattice.matrix)
multiples = np.linalg.det(splitter.R[:3,:3])
new_struc = self.copy()
new_struc.group = splitter.H
lattice = Lattice.from_matrix(lat1, ltype=new_struc.group.lattice_type)
if mut_lat:
lattice=lattice.mutate(degree=eps, frozen=True)
h = splitter.H.number
split_sites = []
if self.molecular:
# below only works when the cell does not change
for i, site in enumerate(self.mol_sites):
pos = site.position
mol = site.molecule
ori = site.orientation
coord0 = mol.mol.cart_coords.dot(ori.matrix.T)
coord0 = np.dot(coord0, splitter.R[:3,:3])
wp1 = site.wp
ori.reset_matrix(np.eye(3))
id = 0
for ops1, ops2 in zip(splitter.G2_orbits[i], splitter.H_orbits[i]):
#reset molecule
rot = wp1.generators_m[id].affine_matrix[:3,:3].T
coord1 = np.dot(coord0, rot)
_mol = mol.copy()
_mol.reset_positions(coord1)
pos0 = apply_ops(pos, ops1)[0]
pos0 -= np.floor(pos0)
dis = (np.random.sample(3) - 0.5).dot(self.lattice.matrix)
dis /= np.linalg.norm(dis)
pos0 += eps*dis*(np.random.random()-0.5)
wp, _ = Wyckoff_position.from_symops(ops2, h, permutation=False)
if h in [7, 14] and self.group.number == 31:
diag = True
else:
diag = self.diag
split_sites.append(mol_site(_mol, pos0, ori, wp, lattice, diag))
id += wp.multiplicity
new_struc.mol_sites = split_sites
new_struc.numMols = [int(multiples*numMol) for numMol in self.numMols]
else:
for i, site in enumerate(self.atom_sites):
pos = site.position
for ops1, ops2 in zip(splitter.G2_orbits[i], splitter.H_orbits[i]):
pos0 = apply_ops(pos, ops1)[0]
pos0 -= np.floor(pos0)
dis = (np.random.sample(3) - 0.5).dot(self.lattice.matrix)
dis /= np.linalg.norm(dis)
pos0 += np.dot(eps*dis*(np.random.random()-0.5), self.lattice.inv_matrix)
wp, _ = Wyckoff_position.from_symops(ops2, h, permutation=False)
split_sites.append(atom_site(wp, pos0, site.specie))
new_struc.atom_sites = split_sites
new_struc.numIons = [int(multiples*numIon) for numIon in self.numIons]
new_struc.lattice = lattice
new_struc.source = 'subgroup'
return new_struc