def subgroup_by_splitter(self, splitter, eps=0.05):
lat1 = np.dot(splitter.R[:3, :3].T, self.lattice.matrix)
multiples = np.linalg.det(splitter.R[:3, :3])
split_sites = []
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,
group=splitter.H.number,
permutation=False)
split_sites.append(atom_site(wp, pos0, site.specie))
new_struc = deepcopy(self)
new_struc.group = splitter.H
lattice = Lattice.from_matrix(lat1, ltype=new_struc.group.lattice_type)
new_struc.lattice = lattice.mutate(degree=0.01, frozen=True)
new_struc.atom_sites = split_sites
new_struc.numIons = [
int(multiples * numIon) for numIon in self.numIons
]
new_struc.source = 'Wyckoff Split'
return new_struc
def optimize_lattice(self):
"""
optimize the lattice if the cell has a bad inclination angles
"""
for i in range(5):
lattice, trans, opt = self.lattice.optimize()
if opt:
for site in self.mol_sites:
pos_absolute = np.dot(site.position, self.lattice.matrix)
pos_frac = pos_absolute.dot(lattice.inv_matrix)
site.position = pos_frac - np.floor(pos_frac)
site.lattice = lattice
# for P21/c, Pc, C2/c, check if opt the inclination angle
if self.group.number in [7, 14, 15]:
for j, op in enumerate(site.wp.ops):
vec = op.translation_vector.dot(trans)
vec -= np.floor(vec)
op1 = op.from_rotation_and_translation(
op.rotation_matrix, vec)
site.wp.ops[j] = op1
#to do needs to update diag if necessary
_, perm = Wyckoff_position.from_symops(site.wp.ops,
self.group.number)
if not isinstance(perm, list):
self.diag = True
else:
self.diag = False
self.lattice = lattice
else:
break
def test_P21n(self):
strs = [
"x, y, z",
"-x, -y, -z",
"-x+1/2, y+1/2, -z+1/2",
"x+1/2, -y+1/2, z+1/2",
]
wyc, perm = Wyckoff_position.from_symops(strs)
self.assertTrue(wyc.number == 14)
def optimize_lattice(self, iterations=3):
"""
optimize the lattice if the cell has a bad inclination angles
"""
#if self.molecular:
count = 0
for i in range(iterations):
lattice, trans, opt = self.lattice.optimize()
#print(self.lattice, "->", lattice)
if opt:
if self.molecular:
sites = self.mol_sites
else:
sites = self.atom_sites
for j, site in enumerate(sites):
count += 1
pos_abs = np.dot(site.position, self.lattice.matrix)
pos_frac = pos_abs.dot(lattice.inv_matrix)
pos_frac -= np.floor(pos_frac)
if self.molecular:
site.lattice = lattice
# for P21/c, Pc, C2/c, check if opt the inclination angle
ops = site.wp.ops.copy()
diag = False
if self.group.number in [7, 14, 15]:
for k, op in enumerate(ops):
vec = op.translation_vector.dot(trans)
#print(vec)
vec -= np.floor(vec)
op1 = op.from_rotation_and_translation(
op.rotation_matrix, vec)
ops[k] = op1
wp, perm = Wyckoff_position.from_symops(
ops, self.group.number)
if not isinstance(perm, list):
diag = True
else:
diag = False
pos_frac = pos_frac[perm]
sites[j] = atom_site(wp, pos_frac, site.specie, diag)
#print(sites[j].wp)
#site.update()
self.lattice = lattice
self.diag = diag
else:
break
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 __init__(self, struc, ref_mol=None, tol=0.2, relax_h=False):
"""
extract the mol_site information from the give cif file
and reference molecule
Args:
struc: cif/poscar file or a Pymatgen Structure object
ref_mol: xyz file or a reference Pymatgen molecule object
tol: scale factor for covalent bond distance
relax_h: whether or not relax the position for hydrogen atoms in structure
"""
if isinstance(ref_mol, str):
ref_mol = Molecule.from_file(ref_mol)
elif isinstance(ref_mol, Molecule):
ref_mol = ref_mol
else:
print(type(ref_mol))
raise NameError("reference molecule cannot be defined")
if isinstance(struc, str):
pmg_struc = Structure.from_file(struc)
elif isinstance(struc, Structure):
pmg_struc = struc
else:
print(type(struc))
raise NameError("input structure cannot be intepretted")
self.props = ref_mol.site_properties
self.ref_mol = ref_mol.get_centered_molecule()
self.tol = tol
self.diag = False
self.relax_h = relax_h
sga = SpacegroupAnalyzer(pmg_struc)
ops = sga.get_space_group_operations()
self.wyc, perm = Wyckoff_position.from_symops(
ops, sga.get_space_group_number())
if self.wyc is not None:
self.group = Group(self.wyc.number)
if isinstance(perm, list):
if perm != [0, 1, 2]:
lattice = Lattice.from_matrix(pmg_struc.lattice.matrix,
self.group.lattice_type)
latt = lattice.swap_axis(ids=perm,
random=False).get_matrix()
coor = pmg_struc.frac_coords[:, perm]
pmg_struc = Structure(latt, pmg_struc.atomic_numbers, coor)
else:
self.diag = True
self.perm = perm
coords, numbers = search_molecule_in_crystal(pmg_struc, self.tol)
#coords -= np.mean(coords, axis=0)
if self.relax_h:
self.molecule = self.addh(Molecule(numbers, coords))
else:
self.molecule = Molecule(numbers, coords)
self.pmg_struc = pmg_struc
self.lattice = Lattice.from_matrix(pmg_struc.lattice.matrix,
self.group.lattice_type)
else:
raise ValueError(
"Cannot find the space group matching the symmetry operation")
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
def test_Pmn21(self):
strs = ["x, y, z", "-x+1/2, -y, z+1/2", "-x, y, z", "x+1/2, -y, z+1/2"]
wyc, perm = Wyckoff_position.from_symops(strs)
self.assertTrue(wyc.number == 31)
def test_P21(self):
strs = ["x, y, z", "-x, y+1/2, -z"]
wyc, perm = Wyckoff_position.from_symops(strs)
self.assertTrue(wyc.number == 4)