class pyxtal:
"""
Class for handling atomic crystals based on symmetry constraints.
Examples
--------
>>> from pyxtal import pyxtal
>>> struc = pyxtal()
>>> struc.from_random(3, 227, ['C'], [8])
>>> struc.get_site_labels()
{'C': ['8a']}
>>> struc
------Crystal from random------
Dimension: 3
Composition: C8
Group: Fd-3m (227)
cubic lattice: 4.3529 4.3529 4.3529 90.0000 90.0000 90.0000
Wyckoff sites:
C @ [0.1250 0.1250 0.1250], WP: 8a, Site symmetry: -4 3 m
The structure object can be easily manipulated via `apply_perturbtation`
or `subgroup` function
>>> struc2 = struc.subgroup(H=141, once=True)
>>> struc2
------Crystal from Wyckoff Split------
Dimension: 3
Composition: C8
Group: I41/amd (141)
tetragonal lattice: 3.3535 3.3535 4.6461 90.0000 90.0000 90.0000
Wyckoff sites:
C @ [0.0000 0.2500 0.3750], WP: 4b, Site symmetry: -4 m 2
Alternatively, one can also easily compute its XRD via the `pyxtal.XRD` class
>>> xrd = struc.get_XRD()
>>> xrd
2theta d_hkl hkl Intensity Multi
32.706 2.738 [ 1 1 1] 100.00 8
54.745 1.677 [ 2 2 0] 40.95 12
65.249 1.430 [ 3 1 1] 20.65 24
81.116 1.186 [ 4 0 0] 5.15 6
90.236 1.088 [ 3 3 1] 8.24 24
105.566 0.968 [ 4 2 2] 14.44 24
115.271 0.913 [ 5 1 1] 10.03 24
133.720 0.838 [ 4 4 0] 9.80 12
148.177 0.802 [ 5 3 1] 28.27 48
Finally, the structure can be saved to different formats
>>> struc.to_file('my.cif')
>>> struc.to_file('my_poscar', fmt='poscar')
or to Pymatgen/ASE structure object
>>> pmg_struc = struc.to_pymatgen()
>>> ase_struc = struc.to_ase()
"""
def __init__(self, molecular=False):
self.valid = False
self.molecular = molecular
self.diag = False
self.numIons = None
self.numMols = None
def __str__(self):
if self.valid:
s = "------Crystal from {:s}------".format(self.source)
s += "\nDimension: {}".format(self.dim)
s += "\nComposition: {}".format(self.formula)
if self.group.number in [7, 14, 15] and self.diag:
symbol = self.group.alias
else:
symbol = self.group.symbol
s += "\nGroup: {} ({})".format(symbol, self.group.number)
s += "\n{}".format(self.lattice)
s += "\nWyckoff sites:"
if self.molecular:
for wyc in self.mol_sites:
s += "\n\t{}".format(wyc)
else:
for wyc in self.atom_sites:
s += "\n\t{}".format(wyc)
else:
s = "\nStructure not available."
return s
def __repr__(self):
return str(self)
def get_dof(self):
"""
get the number of dof for the given structures:
"""
if self.molecular:
sites = self.mol_sites
else:
sites = self.atom_sites
dof = 0
for site in sites:
dof += site.dof
return self.lattice.dof + dof
def get_site_labels(self):
"""
quick function to get the site_labels as a dictionary
"""
if self.molecular:
sites = self.mol_sites
names = [site.molecule.name for site in sites]
else:
sites = self.atom_sites
names = [site.specie for site in sites]
dicts = {}
for name, site in zip(names, sites):
label = str(site.wp.multiplicity) + site.wp.letter
if name not in dicts.keys():
dicts[name] = [label]
else:
dicts[name].append(label)
return dicts
def from_random(
self,
dim=3,
group=None,
species=None,
numIons=None,
factor=1.1,
thickness=None,
area=None,
lattice=None,
sites=None,
conventional=True,
diag=False,
t_factor=1.0,
max_count=10,
force_pass=False,
):
if self.molecular:
prototype = "molecular"
else:
prototype = "atomic"
tm = Tol_matrix(prototype=prototype, factor=t_factor)
count = 0
quit = False
while True:
count += 1
if self.molecular:
if dim == 3:
struc = molecular_crystal(group,
species,
numIons,
factor,
lattice=lattice,
sites=sites,
conventional=conventional,
diag=diag,
tm=tm)
elif dim == 2:
struc = molecular_crystal_2D(group,
species,
numIons,
factor,
thickness=thickness,
sites=sites,
conventional=conventional,
tm=tm)
elif dim == 1:
struc = molecular_crystal_1D(group,
species,
numIons,
factor,
area=area,
sites=sites,
conventional=conventional,
tm=tm)
else:
if dim == 3:
struc = random_crystal(group, species, numIons, factor,
lattice, sites, conventional, tm)
elif dim == 2:
struc = random_crystal_2D(group, species, numIons, factor,
thickness, lattice, sites,
conventional, tm)
elif dim == 1:
struc = random_crystal_1D(group, species, numIons, factor,
area, lattice, sites,
conventional, tm)
else:
struc = random_cluster(group, species, numIons, factor,
lattice, sites, tm)
if force_pass:
quit = True
break
elif struc.valid:
quit = True
break
if count >= max_count:
raise RuntimeError(
"It takes long time to generate the structure, check inputs"
)
if quit:
self.valid = struc.valid
self.dim = dim
try:
self.lattice = struc.lattice
if self.molecular:
self.numMols = struc.numMols
self.molecules = struc.molecules
self.mol_sites = struc.mol_sites
self.diag = struc.diag
else:
self.numIons = struc.numIons
self.species = struc.species
self.atom_sites = struc.atom_sites
self.group = struc.group
self.PBC = struc.PBC
self.source = 'random'
self.factor = struc.factor
self.number = struc.number
self._get_formula()
except:
pass
def from_seed(self, seed, molecule=None, relax_h=False):
"""
Load the seed structure from Pymatgen/ASE/POSCAR/CIFs
Internally they will be handled by Pymatgen
"""
from ase import Atoms
from pymatgen import Structure
if self.molecular:
from pyxtal.molecule import pyxtal_molecule
pmol = pyxtal_molecule(molecule).mol
struc = structure_from_ext(seed, pmol, relax_h=relax_h)
if struc.match():
self.mol_sites = [struc.make_mol_site()]
self.group = Group(struc.wyc.number)
self.lattice = struc.lattice
self.molecules = [
pyxtal_molecule(struc.molecule, symmetrize=False)
]
self.numMols = struc.numMols
self.diag = struc.diag
self.valid = True # Need to add a check function
else:
raise ValueError(
"Cannot extract the molecular crystal from cif")
else:
if isinstance(seed, dict):
self.from_dict()
elif isinstance(seed, Atoms): #ASE atoms
from pymatgen.io.ase import AseAtomsAdaptor
pmg_struc = AseAtomsAdaptor.get_structure(seed)
self._from_pymatgen(pmg_struc)
elif isinstance(seed, Structure): #Pymatgen
self._from_pymatgen(seed)
elif isinstance(seed, str):
pmg_struc = Structure.from_file(seed)
self._from_pymatgen(pmg_struc)
self.factor = 1.0
self.number = self.group.number
self.source = 'Seed'
self.dim = 3
self.PBC = [1, 1, 1]
self._get_formula()
def _from_pymatgen(self, structure):
"""
Load structure from Pymatgen
should not be used directly
"""
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer as sga
self.valid = True
try:
# needs to do it twice in order to get the conventional cell
s = sga(structure)
structure = s.get_refined_structure()
s = sga(structure)
sym_struc = s.get_symmetrized_structure()
number = s.get_space_group_number()
except:
print("Failed to load the Pymatgen structure")
self.valid = False
if self.valid:
d = sym_struc.composition.as_dict()
species = [key for key in d.keys()]
numIons = []
for ele in species:
numIons.append(int(d[ele]))
self.numIons = numIons
self.species = species
self.group = Group(number)
atom_sites = []
for i, site in enumerate(sym_struc.equivalent_sites):
pos = site[0].frac_coords
wp = Wyckoff_position.from_group_and_index(
number, sym_struc.wyckoff_symbols[i])
specie = site[0].specie.number
atom_sites.append(atom_site(wp, pos, specie))
self.atom_sites = atom_sites
matrix, ltype = sym_struc.lattice.matrix, self.group.lattice_type
self.lattice = Lattice.from_matrix(matrix, ltype=ltype)
def check_short_distances(self, r=0.7, exclude_H=True):
"""
A function to check short distance pairs
Mainly used for debug, powered by pymatgen
Args:
r: the given cutoff distances
exclude_H: whether or not exclude the H atoms
Returns:
list of pairs within the cutoff
"""
if self.dim > 0:
pairs = []
pmg_struc = self.to_pymatgen()
if exclude_H:
pmg_struc.remove_species('H')
res = pmg_struc.get_all_neighbors(r)
for i, neighs in enumerate(res):
for n in neighs:
pairs.append(
[pmg_struc.sites[i].specie, n.specie, n.nn_distance])
else:
raise NotImplementedError("Does not support cluster for now")
return pairs
def to_file(self, filename=None, fmt=None, permission='w', sym_num=None):
"""
Creates a file with the given filename and file type to store the structure.
By default, creates cif files for crystals and xyz files for clusters.
For other formats, Pymatgen is used
Args:
filename: the file path
fmt: the file type (`cif`, `xyz`, etc.)
permission: `w` or `a+`
Returns:
Nothing. Creates a file at the specified path
"""
if self.valid:
if fmt is None:
if self.dim == 0:
fmt = 'xyz'
else:
fmt = 'cif'
if fmt == "cif":
if self.dim == 3:
return write_cif(self,
filename,
"from_pyxtal",
permission,
sym_num=sym_num)
else:
pmg_struc = self.to_pymatgen()
if self.molecular:
pmg_struc.sort()
return pmg_struc.to(fmt=fmt, filename=filename)
else:
pmg_struc = self.to_pymatgen()
if self.molecular:
pmg_struc.sort()
return pmg_struc.to(fmt=fmt, filename=filename)
else:
raise RuntimeError(
"Cannot create file: structure did not generate")
def subgroup(self,
H=None,
eps=0.05,
idx=None,
once=False,
group_type='t',
max_index=4):
"""
generate a structure with lower symmetry
Args:
H: space group number (int)
eps: pertubation term (float)
idx: list
once: generate only one structure, otherwise output all
Returns:
a list of pyxtal structures with lower symmetries
"""
#randomly choose a subgroup from the available list
if group_type == 't':
dicts = self.group.get_max_t_subgroup() #['subgroup']
else:
dicts = self.group.get_max_k_subgroup() #['subgroup']
Hs = dicts['subgroup']
indices = dicts['index']
if idx is None:
idx = [i for i, id in enumerate(indices) if id <= max_index]
#idx = range(len(Hs))
else:
for id in idx:
if id >= len(Hs):
raise ValueError(
"The idx exceeds the number of possible splits")
if H is not None:
idx = [id for id in idx if Hs[id] == H]
if len(idx) == 0:
raise RuntimeError("No subgroup to perform the split")
if self.molecular:
struc_sites = self.mol_sites
else:
struc_sites = self.atom_sites
sites = [
str(site.wp.multiplicity) + site.wp.letter for site in struc_sites
]
valid_splitters = []
bad_splitters = []
for id in idx:
splitter = wyckoff_split(G=self.group.number,
wp1=sites,
idx=id,
group_type=group_type)
if splitter.valid_split:
valid_splitters.append(splitter)
else:
bad_splitters.append(splitter)
if len(valid_splitters) == 0:
# do one more step
new_strucs = []
for splitter in bad_splitters:
trail_struc = self.subgroup_by_splitter(splitter)
new_strucs.append(
trail_struc.subgroup(once=True, group_type=group_type))
return new_strucs
else:
if once:
return self.subgroup_by_splitter(choice(valid_splitters),
eps=eps)
else:
new_strucs = []
for splitter in valid_splitters:
new_strucs.append(
self.subgroup_by_splitter(splitter, eps=eps))
return new_strucs
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 apply_perturbation(self, d_lat=0.05, d_coor=0.05, d_rot=1):
"""
perturb the structure without breaking the symmetry
Args:
d_coor: magnitude of perturbation on atomic coordinates (in A)
d_lat: magnitude of perturbation on lattice (in percentage)
"""
self.lattice = self.lattice.mutate(degree=d_lat)
if self.molecular:
for i, site in enumerate(self.mol_sites):
site.perturbate(lattice=self.lattice.matrix,
trans=d_coor,
rot=d_rot)
else:
for i, site in enumerate(self.atom_sites):
site.perturbate(lattice=self.lattice.matrix, magnitude=d_coor)
self.source = 'Perturbation'
def copy(self):
"""
simply copy the structure
"""
return deepcopy(self)
def _get_coords_and_species(self, absolute=False, unitcell=True):
"""
extract the coordinates and species information
Args:
abosulte: if True, return the cartesian coords otherwise fractional
Returns:
total_coords (N*3 numpy array) and the list of species
"""
species = []
total_coords = None
if self.molecular:
for site in self.mol_sites:
coords, site_species = site.get_coords_and_species(
absolute, unitcell=unitcell)
species.extend(site_species)
if total_coords is None:
total_coords = coords
else:
total_coords = np.append(total_coords, coords, axis=0)
else:
for site in self.atom_sites:
species.extend([site.specie] * site.multiplicity)
if total_coords is None:
total_coords = site.coords
else:
total_coords = np.append(total_coords, site.coords, axis=0)
if absolute:
total_coords = total_coords.dot(self.lattice.matrix)
return total_coords, species
def _get_formula(self):
"""
A quick function to get the formula.
"""
formula = ""
if self.molecular:
numspecies = self.numMols
species = [str(mol) for mol in self.molecules]
else:
numspecies = self.numIons
species = self.species
for i, s in zip(numspecies, species):
formula += "{:s}{:d}".format(s, int(i))
self.formula = formula
def to_ase(self, resort=True):
"""
export to ase Atoms object.
"""
from ase import Atoms
if self.valid:
if self.dim > 0:
lattice = self.lattice.copy()
if self.molecular:
coords, species = self._get_coords_and_species(True)
latt, coords = lattice.add_vacuum(coords,
frac=False,
PBC=self.PBC)
atoms = Atoms(species,
positions=coords,
cell=latt,
pbc=self.PBC)
if resort:
permutation = np.argsort(atoms.numbers)
atoms = atoms[permutation]
return atoms
else:
coords, species = self._get_coords_and_species()
latt, coords = lattice.add_vacuum(coords, PBC=self.PBC)
return Atoms(species,
scaled_positions=coords,
cell=latt,
pbc=self.PBC)
else:
coords, species = self._get_coords_and_species(True)
return Atoms(species, positions=coords)
else:
raise RuntimeError("No valid structure can be converted to ase.")
def to_pymatgen(self):
"""
export to Pymatgen structure object.
"""
from pymatgen.core.structure import Structure, Molecule
if self.valid:
if self.dim > 0:
lattice = self.lattice.copy()
coords, species = self._get_coords_and_species()
# Add space above and below a 2D or 1D crystals
latt, coords = lattice.add_vacuum(coords, PBC=self.PBC)
return Structure(latt, species, coords)
else:
# Clusters are handled as large molecules
coords, species = self._get_coords_and_species(True)
return Molecule(species, coords)
else:
raise RuntimeError(
"No valid structure can be converted to pymatgen.")
def get_XRD(self, **kwargs):
"""
compute the PXRD object.
** kwargs include
- wavelength (1.54184)
- thetas [0, 180]
- preferred_orientation: False
- march_parameter: None
"""
return XRD(self.to_ase(), **kwargs)
def show(self, **kwargs):
"""
display the crystal structure
"""
if self.molecular:
from pyxtal.viz import display_molecular
return display_molecular(self, **kwargs)
else:
from pyxtal.viz import display_atomic
return display_atomic(self, **kwargs)
def optimize_lattice(self):
"""
optimize the lattice if the cell has a bad inclination angles
"""
if self.molecular:
for i in range(5):
lattice, trans, opt = self.lattice.optimize()
if opt:
for site in self.mol_sites:
pos_abs = np.dot(site.position, self.lattice.matrix)
pos_frac = pos_abs.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
_, 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 save(self, filename=None):
# """
# Save the structure
# Args:
# filename: the file to save txt information
# """
# dict0 = self.save_dict(db_filename)
# with open(filename, "w") as fp:
# json.dump(dict0, fp)
#
# print("save the GP model to", filename, "and database to", db_filename)
#
# def load(self, filename=None):
# """
# load the structure
# Args:
# filename: the file to save txt information
# """
# #print(filename)
# with open(filename, "r") as fp:
# dict0 = json.load(fp)
# self.load_from_dict(dict0, N_max=N_max, device=device)
# self.fit(opt=opt)
# print("load the GP model from ", filename)
#
def save_dict(self):
"""
save the model as a dictionary
"""
sites = []
if self.molecular:
for site in self.mol_sites:
sites.append(site.save_dict())
else:
for site in self.atom_sites:
sites.append(site.save_dict())
dict0 = {
"lattice": self.lattice.matrix,
"sites": sites,
"group": self.group.number,
"molecular": self.molecular,
"numIons": self.numIons,
"numMols": self.numMols,
"factor": self.factor,
"PBC": self.PBC,
"formula": self.formula,
"source": self.source,
"dim": self.dim,
"valid": self.valid,
}
return dict0
def load_dict(self, dict0):
"""
load the structure from a dictionary
"""
self.group = Group(dict0["group"])
self.lattice = Lattice.from_matrix(dict0["lattice"],
ltype=self.group.lattice_type)
self.molecular = dict0["molecular"]
self.number = self.group.number
self.factor = dict0["factor"]
self.source = dict0["source"]
self.dim = dict0["dim"]
self.PBC = dict0["PBC"]
self.numIons = dict0["numIons"]
self.numMols = dict0["numMols"]
self.valid = dict0["valid"]
self.formula = dict0["formula"]
sites = []
if dict0["molecular"]:
for site in dict0["sites"]:
sites.append(mol_site.load_dict(site))
self.mol_sites = sites
else:
for site in dict0["sites"]:
sites.append(atom_site.load_dict(site))
self.atom_sites = sites
class pyxtal:
"""
Class for handling atomic crystals based on symmetry constraints
Examples
--------
To create a new structure instance
>>> from pyxtal import pyxtal
>>> struc = pyxtal()
one can either use pyxtal to generate a random symmetric structure
>>> struc.from_random(3, 227, ['C'], [8])
or load a structure from a file or ASE atoms or Pymatgen structure object
>>> struc.from_seed('diamond.cif') # as a string
>>> struc.from_seed(diamond_ase) # as a ase atoms object
>>> struc.from_seed(diamond_pymatgen) # as a pymatgen structure object
as long as the struc is created, you can check their symmetry as follows
>>> struc.get_site_labels()
{'C': ['8a']}
>>> struc
------Crystal from random------
Dimension: 3
Composition: C8
Group: Fd-3m (227)
cubic lattice: 4.3529 4.3529 4.3529 90.0000 90.0000 90.0000
Wyckoff sites:
C @ [0.1250 0.1250 0.1250], WP: 8a, Site symmetry: -4 3 m
The structure object can be easily manipulated via `apply_perturbtation`
or `subgroup` function
>>> struc2 = struc.subgroup_once(H=141)
>>> struc2
------Crystal from Wyckoff Split------
Dimension: 3
Composition: C8
Group: I41/amd (141)
tetragonal lattice: 3.3535 3.3535 4.6461 90.0000 90.0000 90.0000
Wyckoff sites:
C @ [0.0000 0.2500 0.3750], WP: 4b, Site symmetry: -4 m 2
Alternatively, one can also easily compute its XRD via the `pyxtal.XRD` class
>>> xrd = struc.get_XRD()
>>> xrd
2theta d_hkl hkl Intensity Multi
32.706 2.738 [ 1 1 1] 100.00 8
54.745 1.677 [ 2 2 0] 40.95 12
65.249 1.430 [ 3 1 1] 20.65 24
81.116 1.186 [ 4 0 0] 5.15 6
90.236 1.088 [ 3 3 1] 8.24 24
105.566 0.968 [ 4 2 2] 14.44 24
115.271 0.913 [ 5 1 1] 10.03 24
133.720 0.838 [ 4 4 0] 9.80 12
148.177 0.802 [ 5 3 1] 28.27 48
Finally, the structure can be saved to different formats
>>> struc.to_file('my.cif')
>>> struc.to_file('my_poscar', fmt='poscar')
or to Pymatgen/ASE structure object
>>> pmg_struc = struc.to_pymatgen()
>>> ase_struc = struc.to_ase()
"""
def __init__(self, molecular=False):
self.valid = False
self.molecular = molecular
self.diag = False
self.numIons = None
self.numMols = None
self.source = None
self.formula = None
self.species = None
self.group = None
self.lattice = None
self.dim = 3
self.factor = 1.0
self.PBC = [1,1,1]
if molecular:
self.molecules = []
self.mol_sites = []
else:
self.atom_sites = []
def __str__(self):
if self.valid:
s = "\n------Crystal from {:s}------".format(self.source)
s += "\nDimension: {}".format(self.dim)
s += "\nComposition: {}".format(self.formula)
if self.group.number in [7, 14, 15] and self.diag:
symbol = self.group.alias
else:
symbol = self.group.symbol
s += "\nGroup: {} ({})".format(symbol, self.group.number)
s += "\n{}".format(self.lattice)
s += "\nWyckoff sites:"
if self.molecular:
for wyc in self.mol_sites:
s += "\n\t{}".format(wyc)
else:
for wyc in self.atom_sites:
s += "\n\t{}".format(wyc)
else:
s = "\nStructure not available."
return s
def __repr__(self):
return str(self)
def get_dof(self):
"""
get the number of dof for the given structures:
"""
if self.molecular:
sites = self.mol_sites
else:
sites = self.atom_sites
dof = 0
for site in sites:
dof += site.dof
return self.lattice.dof + dof
def get_site_labels(self):
"""
quick function to get the site_labels as a dictionary
"""
if self.molecular:
sites = self.mol_sites
names = [site.molecule.name for site in sites]
else:
sites = self.atom_sites
names = [site.specie for site in sites]
dicts = {}
for name, site in zip(names, sites):
label = str(site.wp.multiplicity) + site.wp.letter
if name not in dicts.keys():
dicts[name] = [label]
else:
dicts[name].append(label)
return dicts
def from_random(
self,
dim = 3,
group=None,
species=None,
numIons=None,
factor=1.1,
thickness = None,
area = None,
lattice=None,
sites = None,
conventional = True,
diag = False,
t_factor = 1.0,
max_count = 10,
force_pass = False,
):
if self.molecular:
prototype = "molecular"
else:
prototype = "atomic"
tm = Tol_matrix(prototype=prototype, factor=t_factor)
count = 0
quit = False
while True:
count += 1
if self.molecular:
if dim == 3:
struc = molecular_crystal(group, species, numIons, factor,
lattice=lattice, sites=sites, conventional=conventional, diag=diag, tm=tm)
elif dim == 2:
struc = molecular_crystal_2D(group, species, numIons, factor,
thickness=thickness, sites=sites, conventional=conventional, tm=tm)
elif dim == 1:
struc = molecular_crystal_1D(group, species, numIons, factor,
area=area, sites=sites, conventional=conventional, tm=tm)
else:
if dim == 3:
struc = random_crystal(group, species, numIons, factor,
lattice, sites, conventional, tm)
elif dim == 2:
struc = random_crystal_2D(group, species, numIons, factor,
thickness, lattice, sites, conventional, tm)
elif dim == 1:
struc = random_crystal_1D(group, species, numIons, factor,
area, lattice, sites, conventional, tm)
else:
struc = random_cluster(group, species, numIons, factor,
lattice, sites, tm)
if force_pass:
quit = True
break
elif struc.valid:
quit = True
break
if count >= max_count:
raise RuntimeError("It takes long time to generate the structure, check inputs")
if quit:
self.valid = struc.valid
self.dim = dim
try:
self.lattice = struc.lattice
if self.molecular:
self.numMols = struc.numMols
self.molecules = struc.molecules
self.mol_sites = struc.mol_sites
self.diag = struc.diag
else:
self.numIons = struc.numIons
self.species = struc.species
self.atom_sites = struc.atom_sites
self.group = struc.group
self.PBC = struc.PBC
self.source = 'random'
self.factor = struc.factor
self._get_formula()
except:
pass
def from_seed(self, seed, molecule=None, tol=1e-4, a_tol=5.0, relax_h=False, backend='pymatgen'):
"""
Load the seed structure from Pymatgen/ASE/POSCAR/CIFs
Internally they will be handled by Pymatgen
"""
if self.molecular:
pmol = pyxtal_molecule(molecule).mol
struc = structure_from_ext(seed, pmol, relax_h=relax_h)
if struc.match():
self.mol_sites = [struc.make_mol_site()]
self.group = Group(struc.wyc.number)
self.lattice = struc.lattice
self.molecules = [pyxtal_molecule(struc.molecule, symmetrize=False)]
self.numMols = struc.numMols
self.diag = struc.diag
self.valid = True # Need to add a check function
else:
raise ValueError("Cannot extract the molecular crystal from cif")
else:
if isinstance(seed, dict):
self.from_dict()
elif isinstance(seed, Atoms): #ASE atoms
from pymatgen.io.ase import AseAtomsAdaptor
pmg_struc = AseAtomsAdaptor.get_structure(seed)
self._from_pymatgen(pmg_struc, tol, a_tol)
elif isinstance(seed, Structure): #Pymatgen
self._from_pymatgen(seed, tol)
elif isinstance(seed, str):
if backend=='pymatgen':
pmg_struc = Structure.from_file(seed)
self._from_pymatgen(pmg_struc, tol, a_tol)
else:
self.lattice, self.atom_sites = read_cif(seed)
self.group = Group(self.atom_sites[0].wp.number)
self.diag = self.atom_sites[0].diag
self.valid = True
self.factor = 1.0
self.source = 'Seed'
self.dim = 3
self.PBC = [1, 1, 1]
self._get_formula()
def _from_pymatgen(self, struc, tol=1e-3, a_tol=5.0):
"""
Load structure from Pymatgen
should not be used directly
"""
from pyxtal.util import get_symmetrized_pmg
#import pymatgen.analysis.structure_matcher as sm
self.valid = True
try:
sym_struc, number = get_symmetrized_pmg(struc, tol, a_tol)
#print(sym_struc)
#import sys; sys.exit()
except TypeError:
print("Failed to load the Pymatgen structure")
# print(struc)
# self.valid = False
if self.valid:
d = sym_struc.composition.as_dict()
species = [key for key in d.keys()]
numIons = []
for ele in species:
numIons.append(int(d[ele]))
self.numIons = numIons
self.species = species
self.group = Group(number)
matrix, ltype = sym_struc.lattice.matrix, self.group.lattice_type
self.lattice = Lattice.from_matrix(matrix, ltype=ltype)
atom_sites = []
for i, site in enumerate(sym_struc.equivalent_sites):
pos = site[0].frac_coords
wp = Wyckoff_position.from_group_and_index(number, sym_struc.wyckoff_symbols[i])
specie = site[0].specie.number
pos1 = search_matched_position(self.group, wp, pos)
if pos1 is not None:
atom_sites.append(atom_site(wp, pos1, specie))
else:
break
if len(atom_sites) != len(sym_struc.equivalent_sites):
raise RuntimeError("Cannot extract the right mapping from spglib")
else:
self.atom_sites = atom_sites
#import pymatgen.analysis.structure_matcher as sm
#self.dim = 3
#self.PBC = [1, 1, 1]
#pmg1 = self.to_pymatgen()
#if not sm.StructureMatcher().fit(struc, pmg1):
# raise RuntimeError("The structure is inconsistent after conversion")
def check_short_distances(self, r=0.7, exclude_H = True):
"""
A function to check short distance pairs
Mainly used for debug, powered by pymatgen
Args:
r: the given cutoff distances
exclude_H: whether or not exclude the H atoms
Returns:
list of pairs within the cutoff
"""
if self.dim > 0:
pairs = []
pmg_struc = self.to_pymatgen()
if exclude_H:
pmg_struc.remove_species('H')
res = pmg_struc.get_all_neighbors(r)
for i, neighs in enumerate(res):
for n in neighs:
pairs.append([pmg_struc.sites[i].specie, n.specie, n.nn_distance])
else:
raise NotImplementedError("Does not support cluster for now")
return pairs
def check_short_distances_by_dict(self, dicts):
"""
A function to check short distance pairs
Mainly used for debug, powered by pymatgen
Args:
dicts: e.g., {"H-H": 1.0, "O-O": 2.0}
Returns:
N_pairs: number of atomic pairs within the cutoff
"""
if self.dim > 0:
N_pairs = 0
r_cut = max([dicts[key] for key in dicts.keys()])
pmg_struc = self.to_pymatgen()
res = pmg_struc.get_all_neighbors(r_cut)
for i, neighs in enumerate(res):
ele1 = pmg_struc.sites[i].specie.value
for n in neighs:
ele2 = n.specie.value
key1 = ele1 + '-' + ele2
key2 = ele2 + '-' + ele1
if key1 in dicts.keys() and n.nn_distance < dicts[key1]:
N_pairs += 1
elif key1 != key2 and key2 in dicts.keys() and n.nn_distance < dicts[key2]:
N_pairs += 1
else:
raise NotImplementedError("Does not support cluster for now")
return N_pairs
def to_file(self, filename=None, fmt=None, permission='w', sym_num=None):
"""
Creates a file with the given filename and file type to store the structure.
By default, creates cif files for crystals and xyz files for clusters.
For other formats, Pymatgen is used
Args:
filename: the file path
fmt: the file type (`cif`, `xyz`, etc.)
permission: `w` or `a+`
Returns:
Nothing. Creates a file at the specified path
"""
if self.valid:
if fmt is None:
if self.dim == 0:
fmt = 'xyz'
else:
fmt = 'cif'
if fmt == "cif":
if self.dim == 3:
return write_cif(self, filename, "from_pyxtal", permission, sym_num=sym_num)
else:
pmg_struc = self.to_pymatgen()
if self.molecular:
pmg_struc.sort()
return pmg_struc.to(fmt=fmt, filename=filename)
else:
pmg_struc = self.to_pymatgen()
if self.molecular:
pmg_struc.sort()
return pmg_struc.to(fmt=fmt, filename=filename)
else:
raise RuntimeError("Cannot create file: structure did not generate")
def supergroup(self, G=None, group_type='t', d_tol=1.0):
"""
generate a structure with lower symmetry
Args:
G: super space group number (list of integers)
group_type: `t`, `k` or `t+k`
d_tol: maximum tolerance
Returns:
a list of pyxtal structures with minimum super group symmetries
"""
from pyxtal.supergroup import supergroup
my_super = supergroup(self, G=G, group_type=group_type)
solutions = my_super.search_supergroup(d_tol=d_tol)
return my_super.make_supergroup(solutions)
def subgroup(self, permutations=None, H=None, eps=0.05, idx=None, group_type='t', max_cell=4):
"""
generate a structure with lower symmetry
Args:
permutations: e.g., {"Si": "C"}
H: space group number (int)
eps: pertubation term (float)
idx: list
group_type: `t`, `k` or `t+k`
max_cell: maximum cell reconstruction (float)
Returns:
a list of pyxtal structures with lower symmetries
"""
#randomly choose a subgroup from the available list
idx, sites, t_types, k_types = self._get_subgroup_ids(H, group_type, idx, max_cell)
valid_splitters = []
bad_splitters = []
for id in idx:
gtype = (t_types+k_types)[id]
if gtype == 'k':
id -= len(t_types)
splitter = wyckoff_split(G=self.group.number, wp1=sites, idx=id, group_type=gtype)
if not splitter.error:
if permutations is None:
if splitter.valid_split:
special = False
if self.molecular:
for i in range(len(self.mol_sites)):
for ops in splitter.H_orbits[i]:
if len(ops) < len(splitter.H[0]):
special = True
break
if not special:
valid_splitters.append(splitter)
else:
bad_splitters.append(splitter)
else:
bad_splitters.append(splitter)
else:
# apply permuation
if len(splitter.H_orbits) == 1:
if len(splitter.H_orbits[0]) > 1:
valid_splitters.append(splitter)
else:
bad_splitters.append(splitter)
else:
valid_splitters.append(splitter)
if len(valid_splitters) == 0:
#print("try do one more step")
new_strucs = []
for splitter in bad_splitters:
trail_struc = self._subgroup_by_splitter(splitter, eps=eps)
new_strucs.extend(trail_struc.subgroup(permutations, group_type=group_type))
return new_strucs
else:
#print(len(valid_splitters), "valid_splitters are present")
new_strucs = []
for splitter in valid_splitters:
if permutations is None:
new_struc = self._subgroup_by_splitter(splitter, eps=eps)
else:
new_struc = self._apply_substitution(splitter, permutations)
new_strucs.append(new_struc)
return new_strucs
def subgroup_once(self, eps=0.1, H=None, permutations=None, group_type='t', max_cell=4, mut_lat=True):
"""
generate a structure with lower symmetry (for atomic crystals only)
Args:
permutations: e.g., {"Si": "C"}
H: space group number (int)
idx: list
group_type: `t` or `k`
max_cell: maximum cell reconstruction (float)
Returns:
a list of pyxtal structures with lower symmetries
"""
idx, sites, t_types, k_types = self._get_subgroup_ids(H, group_type, None, max_cell)
# Try 100 times to see if a valid split can be found
count = 0
while count < 100:
id = choice(idx)
gtype = (t_types+k_types)[id]
if gtype == 'k':
id -= len(t_types)
#print(self.group.number, sites, id, gtype)
splitter = wyckoff_split(G=self.group.number, wp1=sites, idx=id, group_type=gtype)
if not splitter.error:
if permutations is not None:
if len(splitter.H_orbits) == 1:
if len(splitter.H_orbits[0]) > 1:
return self._apply_substitution(splitter, permutations)
else:
#print("try to find the next subgroup")
trail_struc = self._subgroup_by_splitter(splitter, eps=eps, mut_lat=mut_lat)
multiple = sum(trail_struc.numIons)/sum(self.numIons)
max_cell = max([1, max_cell/multiple])
ans = trail_struc.subgroup_once(eps, H, permutations, group_type, max_cell)
if ans.group.number > 1:
return ans
else:
return self._apply_substitution(splitter, permutations)
else:
if splitter.valid_split:
special = False
if self.molecular:
for i in range(len(self.mol_sites)):
for ops in splitter.H_orbits[i]:
if len(ops) < len(splitter.H[0]):
special = True
break
if not special:
return self._subgroup_by_splitter(splitter, eps=eps, mut_lat=mut_lat)
else:
#print("try to find the next subgroup")
trail_struc = self._subgroup_by_splitter(splitter, eps=eps, mut_lat=mut_lat)
multiple = sum(trail_struc.numIons)/sum(self.numIons)
max_cell = max([1, max_cell/multiple])
ans = trail_struc.subgroup_once(eps, H, None, group_type, max_cell)
if ans.group.number > 1:
return ans
count += 1
raise RuntimeError("Cannot find the splitter")
def _apply_substitution(self, splitter, permutations):
"""
dummy function to apply the substitution
"""
try:
new_struc = self._subgroup_by_splitter(splitter)
except:
print(self)
print(splitter)
print(len(splitter.H_orbits), len(splitter.G2_orbits), len(self.atom_sites))
self._subgroup_by_splitter(splitter)
site_ids = []
for site_id, site in enumerate(new_struc.atom_sites):
if site.specie in permutations.keys():
site_ids.append(site_id)
if len(site_ids) > 1:
N = choice(range(1, len(site_ids)))
else:
N = 1
sub_ids = sample(site_ids, N)
for sub_id in sub_ids:
key = new_struc.atom_sites[sub_id].specie
new_struc.atom_sites[sub_id].specie = permutations[key]
new_struc._get_formula()
return new_struc
def _get_subgroup_ids(self, H, group_type, idx, max_cell):
"""
generate the subgroup dictionary
"""
t_types = []
k_types = []
if group_type == 't':
dicts = self.group.get_max_t_subgroup()#['subgroup']
t_types = ['t']*len(dicts['subgroup'])
elif group_type == 'k':
dicts = self.group.get_max_k_subgroup()#['subgroup']
k_types = ['k']*len(dicts['subgroup'])
else:
dicts = self.group.get_max_t_subgroup()#['subgroup']
dict2 = self.group.get_max_k_subgroup()#['subgroup']
t_types = ['t']*len(dicts['subgroup'])
k_types = ['k']*len(dict2['subgroup'])
for key in dicts.keys():
dicts[key].extend(dict2[key])
Hs = dicts['subgroup']
trans = dicts['transformation']
if idx is None:
idx = []
if not self.molecular:
for i, tran in enumerate(trans):
if np.linalg.det(tran[:3,:3])<=max_cell:
idx.append(i)
else:
# for molecular crystals, assume the cell does not change
for i, tran in enumerate(trans):
good = True
# QZ: This loop needs a generalization!
if abs(np.linalg.det(tran[:3,:3])-1)>1e-3:
good = False
elif self.group.number in [7, 14, 15] and self.diag and Hs[i]==4:
good = False
elif self.group.number in [31] and Hs[i]==7:
good = False
if good:
idx.append(i)
else:
for id in idx:
if id >= len(Hs):
raise ValueError("The idx exceeds the number of possible splits")
if H is not None:
idx = [id for id in idx if Hs[id] == H]
if len(idx) == 0:
raise RuntimeError("Cannot find the splitter")
if self.molecular:
struc_sites = self.mol_sites
else:
struc_sites = self.atom_sites
sites = [str(site.wp.multiplicity)+site.wp.letter for site in struc_sites]
return idx, sites, t_types, k_types
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 apply_perturbation(self, d_lat=0.05, d_coor=0.05, d_rot=1):
"""
perturb the structure without breaking the symmetry
Args:
d_coor: magnitude of perturbation on atomic coordinates (in A)
d_lat: magnitude of perturbation on lattice (in percentage)
"""
self.lattice = self.lattice.mutate(degree=d_lat)
if self.molecular:
for site in self.mol_sites:
site.perturbate(lattice=self.lattice.matrix, trans=d_coor, rot=d_rot)
else:
for site in self.atom_sites:
site.perturbate(lattice=self.lattice.matrix, magnitude=d_coor)
self.source = 'Perturbation'
def copy(self):
"""
simply copy the structure
"""
return deepcopy(self)
def _get_coords_and_species(self, absolute=False, unitcell=True):
"""
extract the coordinates and species information
Args:
abosulte: if True, return the cartesian coords otherwise fractional
Returns:
total_coords (N*3 numpy array) and the list of species
"""
species = []
total_coords = None
if self.molecular:
for site in self.mol_sites:
coords, site_species = site.get_coords_and_species(absolute, unitcell=unitcell)
species.extend(site_species)
if total_coords is None:
total_coords = coords
else:
total_coords = np.append(total_coords, coords, axis=0)
else:
for site in self.atom_sites:
species.extend([site.specie]*site.multiplicity)
if total_coords is None:
total_coords = site.coords
else:
total_coords = np.append(total_coords, site.coords, axis=0)
if absolute:
total_coords = total_coords.dot(self.lattice.matrix)
return total_coords, species
def _get_formula(self):
"""
A quick function to get the formula.
"""
formula = ""
if self.molecular:
numspecies = self.numMols
species = [str(mol) for mol in self.molecules]
else:
specie_list = []
for site in self.atom_sites:
specie_list.extend([site.specie]*site.wp.multiplicity)
species = list(set(specie_list))
numIons = np.zeros(len(species), dtype=int)
for i, sp in enumerate(species):
numIons[i] = specie_list.count(sp)
self.numIons = numIons
self.species = species
numspecies = self.numIons
for i, s in zip(numspecies, species):
formula += "{:s}{:d}".format(s, int(i))
self.formula = formula
def to_ase(self, resort=True):
"""
export to ase Atoms object.
"""
if self.valid:
if self.dim > 0:
lattice = self.lattice.copy()
if self.molecular:
coords, species = self._get_coords_and_species(True)
latt, coords = lattice.add_vacuum(coords, frac=False, PBC=self.PBC)
atoms = Atoms(species, positions=coords, cell=latt, pbc=self.PBC)
else:
coords, species = self._get_coords_and_species()
latt, coords = lattice.add_vacuum(coords, PBC=self.PBC)
atoms = Atoms(species, scaled_positions=coords, cell=latt, pbc=self.PBC)
if resort:
permutation = np.argsort(atoms.numbers)
atoms = atoms[permutation]
return atoms
else:
coords, species = self._get_coords_and_species(True)
return Atoms(species, positions=coords)
else:
raise RuntimeError("No valid structure can be converted to ase.")
def to_pymatgen(self, resort=True):
"""
export to Pymatgen structure object.
"""
if self.valid:
if self.dim > 0:
lattice = self.lattice.copy()
coords, species = self._get_coords_and_species()
if resort:
permutation = sorted(range(len(species)),key=species.__getitem__)
#permutation = np.argsort(species)
species = [species[id] for id in permutation]
coords = coords[permutation]
# Add space above and below a 2D or 1D crystals
latt, coords = lattice.add_vacuum(coords, PBC=self.PBC)
return Structure(latt, species, coords)
else:
# Clusters are handled as large molecules
coords, species = self._get_coords_and_species(True)
return Molecule(species, coords)
else:
raise RuntimeError("No valid structure can be converted to pymatgen.")
def get_XRD(self, **kwargs):
"""
compute the PXRD object.
** kwargs include
- wavelength (1.54184)
- thetas [0, 180]
- preferred_orientation: False
- march_parameter: None
"""
return XRD(self.to_ase(), **kwargs)
def show(self, **kwargs):
"""
display the crystal structure
"""
if self.molecular:
return display_molecular(self, **kwargs)
else:
return display_atomic(self, **kwargs)
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 save(self, filename=None):
# """
# Save the structure
# Args:
# filename: the file to save txt information
# """
# dict0 = self.save_dict(db_filename)
# with open(filename, "w") as fp:
# json.dump(dict0, fp)
#
# print("save the GP model to", filename, "and database to", db_filename)
#
# def load(self, filename=None):
# """
# load the structure
# Args:
# filename: the file to save txt information
# """
# #print(filename)
# with open(filename, "r") as fp:
# dict0 = json.load(fp)
# self.load_from_dict(dict0, N_max=N_max, device=device)
# self.fit(opt=opt)
# print("load the GP model from ", filename)
#
def save_dict(self):
"""
save the model as a dictionary
"""
sites = []
if self.molecular:
for site in self.mol_sites:
sites.append(site.save_dict())
else:
for site in self.atom_sites:
sites.append(site.save_dict())
dict0 = {"lattice": self.lattice.matrix,
"sites": sites,
"group": self.group.number,
"molecular": self.molecular,
"numIons": self.numIons,
"numMols": self.numMols,
"factor": self.factor,
"PBC": self.PBC,
"formula": self.formula,
"source": self.source,
"dim": self.dim,
"valid": self.valid,
}
return dict0
def load_dict(self, dict0):
"""
load the structure from a dictionary
"""
self.group = Group(dict0["group"])
self.lattice = Lattice.from_matrix(dict0["lattice"], ltype=self.group.lattice_type)
self.molecular = dict0["molecular"]
self.factor = dict0["factor"]
self.source = dict0["source"]
self.dim = dict0["dim"]
self.PBC = dict0["PBC"]
self.numIons = dict0["numIons"]
self.numMols = dict0["numMols"]
self.valid = dict0["valid"]
self.formula = dict0["formula"]
sites = []
if dict0["molecular"]:
for site in dict0["sites"]:
sites.append(mol_site.load_dict(site))
self.mol_sites = sites
else:
for site in dict0["sites"]:
sites.append(atom_site.load_dict(site))
self.atom_sites = sites
def get_alternatives(self, include_self=True):
"""
get alternative structure representations
Args:
include_self (bool): return the original structure
Return:
list of structures
"""
if include_self:
new_strucs = [self]
else:
new_strucs = []
# the list of wyckoff indices in the original structure
# e.g. [0, 2, 2, 4] -> [a, c, c, e]
# ids = [len(self.group)-1-site.wp.index for site in self.atom_sites]
wyc_sets = self.group.get_alternatives()
No = len(wyc_sets['No.'])
if No > 1:
# skip the first setting since it is identity
for no in range(1,No):
new_struc, ids = self._get_alternative(wyc_sets, no)
new_strucs.append(new_struc)
return new_strucs
def _get_alternative(self, wyc_set, index):
"""
get alternative structure representations
Args:
tran: affine matrix
index: the list of transformed wps
Returns:
a new pyxtal structure after transformation
"""
new_struc = self.copy()
# xyz_string like 'x+1/4,y+1/4,z+1/4'
xyz_string = wyc_set['Coset Representative'][index]
op = get_inverse(SymmOp.from_xyz_string(xyz_string))
#op = SymmOp.from_xyz_string(xyz_string)
ids = []
for i, site in enumerate(new_struc.atom_sites):
id = len(self.group) - site.wp.index - 1
letter = wyc_set['Transformed WP'][index].split()[id]
ids.append(letters.index(letter))
wp = Wyckoff_position.from_group_and_index(self.group.number, letter)
pos = op.operate(site.position)
pos1 = search_matched_position(self.group, wp, pos)
if pos1 is not None:
new_struc.atom_sites[i] = atom_site(wp, pos1, site.specie)
else:
print(pos)
print(wp)
raise RuntimeError("Cannot find the right pos")
# switch lattice
R = op.affine_matrix[:3,:3] #rotation
matrix = np.dot(R, self.lattice.matrix)
new_struc.lattice = Lattice.from_matrix(matrix, ltype=self.group.lattice_type)
new_struc.source = "Alt. Wyckoff Set: " + xyz_string
return new_struc, ids
