def from_1D_dicts(cls, dicts):
from pyxtal.molecule import pyxtal_molecule, Orientation
mol = pyxtal_molecule(mol=dicts['smile'] + '.smi')
rdkit_mol = mol.rdkit_mol(mol.smile)
conf = rdkit_mol.GetConformer(0)
#print("try")
#print(conf.GetPositions()[:3])
#print(dicts["rotor"])
if dicts['reflect']:
mol.set_torsion_angles(conf, dicts["rotor"], False)
# print(mol.set_torsion_angles(conf, dicts["rotor"], True))
# #import sys; sys.exit()
xyz = mol.set_torsion_angles(conf, dicts["rotor"], dicts['reflect'])
mol.reset_positions(xyz)
g = dicts["number"]
index = dicts["index"]
dim = dicts["dim"]
matrix = R.from_euler('zxy', dicts["orientation"],
degrees=True).as_matrix()
orientation = Orientation(matrix)
#if dicts['reflect']:
# print('load'); print(xyz[:3])
# print("aaaaaaaaaaaaaa"); print(xyz[:3].dot(orientation.matrix.T))
# print("matrix"); print(orientation.matrix)
wp = Wyckoff_position.from_group_and_index(g, index, dim)
diag = dicts["diag"]
lattice = Lattice.from_matrix(dicts["lattice"],
ltype=dicts["lattice_type"])
position = dicts[
"center"] #np.dot(dicts["center"], lattice.inv_matrix)
return cls(mol, position, orientation, wp, lattice, diag)
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 from_pymatgen(self, structure):
"""
Load the seed structure from Pymatgen/ASE/POSCAR/CIFs
"""
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer as sga
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
self.lattice = Lattice.from_matrix(sym_struc.lattice.matrix,
ltype=self.group.lattice_type)
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 _find_gen_wyckoff_in_subgroup(self, groups=None):
"""
Symmetry transformation
group -> subgroup
At the moment we only consider
for multiplicity 2: P-1, P21, P2, Pm and Pc
to add: for multiplicity 4: P21/c, P212121
Permutation is allowed
"""
from pyxtal.symmetry import Wyckoff_position
pos = self.position
wp0 = self.wp
pos0 = apply_ops(pos, wp0)
if len(wp0) == 2:
if self.diag: # P21/n -> Pn
#print("----------P21n----------")
wp1 = Wyckoff_position.from_group_and_index(7, 0)
wp1.diagonalize_symops()
axes = [[0, 1, 2], [2, 1, 0]]
for ax in axes:
pos1 = apply_ops(pos[ax], wp1)
diff = (pos1[:, ax] - pos0)[1]
diff -= np.floor(diff)
if len(diff[diff == 0]) >= 2:
#return wp1, ax, pos[ax] - 0.5*diff
return Wyckoff_position.from_group_and_index(
7, 0), ax, pos[ax] - 0.5 * diff
else:
if groups is None:
groups = [4, 3, 6, 7, 2]
if 15 < wp0.number < 71:
axes = [[0, 1, 2], [0, 2, 1], [1, 0, 2], [2, 1, 0]]
elif wp0.number < 15:
axes = [[0, 1, 2], [2, 1, 0]]
for group in groups:
wp1 = Wyckoff_position.from_group_and_index(group, 0)
for ax in axes:
pos1 = apply_ops(pos[ax], wp1)
diff = (pos1[:, ax] - pos0)[1]
diff -= np.floor(diff)
if len(diff[diff == 0]) >= 2:
return wp1, ax, pos[ax] - 0.5 * diff
def load_dict(cls, dicts):
"""
load the sites from a dictionary
"""
g = dicts["number"]
index = dicts["index"]
dim = dicts["dim"]
PBC = dicts["PBC"]
position = dicts["position"]
specie = dicts["specie"]
wp = Wyckoff_position.from_group_and_index(g, index, dim, PBC)
return cls(wp, position, specie)
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 load_dict(cls, dicts):
"""
load the sites from a dictionary
"""
from pyxtal.molecule import pyxtal_molecule, Orientation
g = dicts["number"]
index = dicts["index"]
dim = dicts["dim"]
mol = pyxtal_molecule.load_dict(dicts["molecule"])
position = dicts["position"]
orientation = Orientation.load_dict(dicts['orientation'])
wp = Wyckoff_position.from_group_and_index(g, index, dim)
diag = dicts["diag"]
lattice = Lattice.from_matrix(dicts["lattice"])
return cls(mol, position, orientation, wp, lattice, diag)
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
def _from_pymatgen(self, struc, tol=1e-3):
"""
Load structure from Pymatgen
should not be used directly
"""
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer as sga
from pyxtal.util import symmetrize
#import pymatgen.analysis.structure_matcher as sm
self.valid = True
try:
# needs to do it twice in order to get the conventional cell
pmg = symmetrize(struc, tol)
s = sga(pmg, symprec=tol)
sym_struc = s.get_symmetrized_structure()
number = s.get_space_group_number()
#print(sym_struc)
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, search=True))
self.atom_sites = atom_sites
matrix, ltype = sym_struc.lattice.matrix, self.group.lattice_type
self.lattice = Lattice.from_matrix(matrix, ltype=ltype)
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
def test_modules():
print("====== Testing functionality for pyXtal version 0.1dev ======")
global failed_package
failed_package = False # Record if errors occur at any level
reset()
print("Importing sys...")
try:
import sys
print("Success!")
except Exception as e:
fail(e)
sys.exit(0)
print("Importing numpy...")
try:
import numpy as np
print("Success!")
except Exception as e:
fail(e)
sys.exit(0)
I = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
print("Importing pymatgen...")
try:
import pymatgen
print("Success!")
except Exception as e:
fail(e)
sys.exit(0)
try:
from pymatgen.core.operations import SymmOp
except Exception as e:
fail(e)
sys.exit(0)
print("Importing pandas...")
try:
import pandas
print("Success!")
except Exception as e:
fail(e)
sys.exit(0)
print("Importing spglib...")
try:
import spglib
print("Success!")
except Exception as e:
fail(e)
sys.exit(0)
print("Importing openbabel...")
try:
import ase
print("Success!")
except:
print(
"Error: could not import openbabel. Try reinstalling the package.")
print("Importing pyxtal...")
try:
import pyxtal
print("Success!")
except Exception as e:
fail(e)
sys.exit(0)
print("=== Testing modules ===")
# =====database.element=====
print("pyxtal.database.element")
reset()
try:
import pyxtal.database.element
except Exception as e:
fail(e)
print(" class Element")
try:
from pyxtal.database.element import Element
except Exception as e:
fail(e)
if passed():
for i in range(1, 95):
if passed():
try:
ele = Element(i)
except:
fail("Could not access Element # " + str(i))
try:
y = ele.sf
y = ele.z
y = ele.short_name
y = ele.long_name
y = ele.valence
y = ele.valence_electrons
y = ele.covalent_radius
y = ele.vdw_radius
y = ele.get_all(0)
except:
fail("Could not access attribute for element # " + str(i))
try:
ele.all_z()
ele.all_short_names()
ele.all_long_names()
ele.all_valences()
ele.all_valence_electrons()
ele.all_covalent_radii()
ele.all_vdw_radii()
except:
fail("Could not access class methods")
check()
# =====database.hall=====
print("pyxtal.database.hall")
reset()
try:
import pyxtal.database.hall
except Exception as e:
fail(e)
print(" hall_from_hm")
try:
from pyxtal.database.hall import hall_from_hm
except Exception as e:
fail(e)
if passed():
for i in range(1, 230):
if passed():
try:
hall_from_hm(i)
except:
fail("Could not access hm # " + str(i))
check()
# =====database.collection=====
print("pyxtal.database.collection")
reset()
try:
import pyxtal.database.collection
except Exception as e:
fail(e)
print(" Collection")
try:
from pyxtal.database.collection import Collection
except Exception as e:
fail(e)
if passed():
for i in range(1, 230):
if passed():
try:
molecule_collection = Collection("molecules")
except:
fail("Could not access hm # " + str(i))
check()
# =====operations=====
print("pyxtal.operations")
reset()
try:
import pyxtal.operations
except Exception as e:
fail(e)
print(" random_vector")
try:
from pyxtal.operations import random_vector
except Exception as e:
fail(e)
if passed():
try:
for i in range(10):
random_vector()
except Exception as e:
fail(e)
check()
print(" angle")
try:
from pyxtal.operations import angle
except Exception as e:
fail(e)
if passed():
try:
for i in range(10):
v1 = random_vector()
v2 = random_vector()
angle(v1, v2)
except Exception as e:
fail(e)
check()
print(" random_shear_matrix")
try:
from pyxtal.operations import random_shear_matrix
except Exception as e:
fail(e)
if passed():
try:
for i in range(10):
random_shear_matrix()
except Exception as e:
fail(e)
check()
print(" is_orthogonal")
try:
from pyxtal.operations import is_orthogonal
except Exception as e:
fail(e)
if passed():
try:
a = is_orthogonal([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
b = is_orthogonal([[0, 0, 1], [1, 0, 0], [1, 0, 0]])
if a is True and b is False:
pass
else:
fail()
except Exception as e:
fail(e)
check()
print(" aa2matrix")
try:
from pyxtal.operations import aa2matrix
except Exception as e:
fail(e)
if passed():
try:
for i in range(10):
aa2matrix(1, 1, random=True)
except Exception as e:
fail(e)
check()
print(" matrix2aa")
try:
from pyxtal.operations import matrix2aa
except Exception as e:
fail(e)
if passed():
try:
for i in range(10):
m = aa2matrix(1, 1, random=True)
aa = matrix2aa(m)
except Exception as e:
fail(e)
check()
print(" rotate_vector")
try:
from pyxtal.operations import rotate_vector
except Exception as e:
fail(e)
if passed():
try:
for i in range(10):
v1 = random_vector()
v2 = random_vector()
rotate_vector(v1, v2)
except Exception as e:
fail(e)
check()
print(" are_equal")
try:
from pyxtal.operations import are_equal
except Exception as e:
fail(e)
if passed():
try:
op1 = SymmOp.from_xyz_string("x,y,z")
op2 = SymmOp.from_xyz_string("x,y,z+1")
a = are_equal(op1, op2, PBC=[0, 0, 1])
b = are_equal(op1, op2, PBC=[1, 0, 0])
if a is True and b is False:
pass
else:
fail()
except Exception as e:
fail(e)
check()
print(" class OperationAnalyzer")
try:
from pyxtal.operations import OperationAnalyzer
except Exception as e:
fail(e)
if passed():
try:
for i in range(10):
m = aa2matrix(1, 1, random=True)
t = random_vector()
op1 = SymmOp.from_rotation_and_translation(m, t)
OperationAnalyzer(op1)
except Exception as e:
fail(e)
check()
print(" class Orientation")
try:
from pyxtal.operations import Orientation
except Exception as e:
fail(e)
if passed():
try:
for i in range(10):
v1 = random_vector()
c1 = random_vector()
o = Orientation.from_constraint(v1, c1)
except Exception as e:
fail(e)
check()
# =====symmetry=====
print("pyxtal.symmetry")
reset()
try:
import pyxtal.symmetry
except Exception as e:
fail(e)
print(" get_wyckoffs (may take a moment)")
try:
from pyxtal.symmetry import get_wyckoffs
except Exception as e:
fail(e)
if passed():
try:
for i in [1, 2, 229, 230]:
get_wyckoffs(i)
get_wyckoffs(i, organized=True)
except:
fail(" Could not access Wyckoff positions for space group # " +
str(i))
check()
print(" get_wyckoff_symmetry (may take a moment)")
try:
from pyxtal.symmetry import get_wyckoff_symmetry
except Exception as e:
fail(e)
if passed():
try:
for i in [1, 2, 229, 230]:
get_wyckoff_symmetry(i)
get_wyckoff_symmetry(i, molecular=True)
except:
fail("Could not access Wyckoff symmetry for space group # " +
str(i))
check()
print(" get_wyckoffs_generators (may take a moment)")
try:
from pyxtal.symmetry import get_wyckoff_generators
except Exception as e:
fail(e)
if passed():
try:
for i in [1, 2, 229, 230]:
get_wyckoff_generators(i)
except:
fail("Could not access Wyckoff generators for space group # " +
str(i))
check()
print(" letter_from_index")
try:
from pyxtal.symmetry import letter_from_index
except Exception as e:
fail(e)
if passed():
try:
if letter_from_index(0, get_wyckoffs(47)) == "A":
pass
else:
fail()
except Exception as e:
fail(e)
check()
print(" index_from_letter")
try:
from pyxtal.symmetry import index_from_letter
except Exception as e:
fail(e)
if passed():
try:
if index_from_letter("A", get_wyckoffs(47)) == 0:
pass
else:
fail()
except Exception as e:
fail(e)
check()
print(" jk_from_i")
try:
from pyxtal.symmetry import jk_from_i
except Exception as e:
fail(e)
if passed():
try:
w = get_wyckoffs(2, organized=True)
j, k = jk_from_i(1, w)
if j == 1 and k == 0:
pass
else:
print(j, k)
fail()
except Exception as e:
fail(e)
check()
print(" i_from_jk")
try:
from pyxtal.symmetry import i_from_jk
except Exception as e:
fail(e)
if passed():
try:
w = get_wyckoffs(2, organized=True)
j, k = jk_from_i(1, w)
i = i_from_jk(j, k, w)
if i == 1:
pass
else:
print(j, k)
fail()
except Exception as e:
fail(e)
check()
print(" ss_string_from_ops")
try:
from pyxtal.symmetry import ss_string_from_ops
except Exception as e:
fail(e)
if passed():
try:
strings = ["1", "4 . .", "2 3 ."]
for i, sg in enumerate([1, 75, 195]):
ops = get_wyckoffs(sg)[0]
ss_string_from_ops(ops, sg, dim=3)
except Exception as e:
fail(e)
check()
print(" Wyckoff_position")
try:
from pyxtal.symmetry import Wyckoff_position
except Exception as e:
fail(e)
if passed():
try:
wp = Wyckoff_position.from_group_and_index(20, 1)
except Exception as e:
fail(e)
check()
print(" Group")
try:
from pyxtal.symmetry import Group
except Exception as e:
fail(e)
if passed():
try:
g3 = Group(230)
g2 = Group(80, dim=2)
g1 = Group(75, dim=1)
except Exception as e:
fail(e)
check()
# =====crystal=====
print("pyxtal.crystal")
reset()
try:
import pyxtal.crystal
except Exception as e:
fail(e)
print(" random_crystal")
try:
from pyxtal.crystal import random_crystal
except Exception as e:
fail(e)
if passed():
try:
c = random_crystal(1, ["H"], [1], 10.0)
if c.valid is True:
pass
else:
fail()
except Exception as e:
fail(e)
check()
print(" random_crystal_2D")
try:
from pyxtal.crystal import random_crystal_2D
except Exception as e:
fail(e)
if passed():
try:
c = random_crystal_2D(1, ["H"], [1], 10.0)
if c.valid is True:
pass
else:
fail()
except Exception as e:
fail(e)
check()
# =====molecule=====
print("pyxtal.molecule")
reset()
try:
import pyxtal.molecule
except Exception as e:
fail(e)
check()
print(" Collections")
try:
from pyxtal.molecule import mol_from_collection
except Exception as e:
fail(e)
if passed():
try:
h2o = mol_from_collection("H2O")
ch4 = mol_from_collection("CH4")
except Exception as e:
fail(e)
print(" get_inertia_tensor")
try:
from pyxtal.molecule import get_inertia_tensor
except Exception as e:
fail(e)
if passed():
try:
get_inertia_tensor(h2o)
get_inertia_tensor(ch4)
except Exception as e:
fail(e)
check()
print(" get_moment_of_inertia")
try:
from pyxtal.molecule import get_moment_of_inertia
except Exception as e:
fail(e)
if passed():
try:
v = random_vector()
get_moment_of_inertia(h2o, v)
get_moment_of_inertia(ch4, v)
except Exception as e:
fail(e)
check()
print(" reoriented_molecule")
try:
from pyxtal.molecule import reoriented_molecule
except Exception as e:
fail(e)
if passed():
try:
reoriented_molecule(h2o)
reoriented_molecule(ch4)
except Exception as e:
fail(e)
check()
print(" orientation_in_wyckoff_position")
try:
from pyxtal.molecule import orientation_in_wyckoff_position
except Exception as e:
fail(e)
if passed():
try:
w = get_wyckoffs(20)
ws = get_wyckoff_symmetry(20, molecular=True)
wp = Wyckoff_position.from_group_and_index(20, 1)
orientation_in_wyckoff_position(h2o, wp)
orientation_in_wyckoff_position(ch4, wp)
except Exception as e:
fail(e)
check()
# =====molecular_crystal=====
print("pyxtal.molecular_crystal")
reset()
try:
import pyxtal.crystal
except Exception as e:
fail(e)
print(" molecular_crystal")
try:
from pyxtal.molecular_crystal import molecular_crystal
except Exception as e:
fail(e)
if passed():
try:
c = molecular_crystal(1, ["H2O"], [1], 10.0)
if c.valid is True:
pass
else:
fail()
except Exception as e:
fail(e)
check()
print(" molecular_crystal_2D")
try:
from pyxtal.molecular_crystal import molecular_crystal_2D
except Exception as e:
fail(e)
if passed():
try:
c = molecular_crystal_2D(1, ["H2O"], [1], 10.0)
if c.valid is True:
pass
else:
fail()
except Exception as e:
fail(e)
check()
end(condition=2)
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
# import gemmi as gm
# import spglib
from pyxtal.symmetry import Group
from pyxtal.symmetry import Wyckoff_position as wp
#################
#####################################################
#####################################################
# Testing pyxtal.symmetry Module:
g = Group(19)
sym_Ops = g.Wyckoff_positions[0]
sym_Ops2 = wp.from_group_and_index(19, 0)
# temp_dat=str(sym_Ops2)
# temp_dat_split=temp_dat.split()[14:]
# symm_Ops_lst=[]
# for i in temp_dat_split:
# i.replace('x','X')
# x=re.sub('x','X',i)
# x=re.sub('y','Y',x)
# x=re.sub('z','Z',x)
# symm_Ops_lst.append(x)
# # print(symm_Ops_lst)
# index=0
# lenList=len(symm_Ops_lst)
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)
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.core.operations import SymmOp
from pyxtal import pyxtal
from pyxtal.lattice import Lattice
from pyxtal.symmetry import Group, Wyckoff_position, get_wyckoffs
from pyxtal.wyckoff_site import WP_merge
from pyxtal.XRD import Similarity
from pyxtal.operations import get_inverse
cif_path = resource_filename("pyxtal", "database/cifs/")
l0 = Lattice.from_matrix([[4.08, 0, 0], [0, 9.13, 0], [0, 0, 5.50]])
l1 = Lattice.from_matrix([[4.08, 0, 0], [0, 9.13, 0], [0, 0, 5.50]])
l2 = Lattice.from_para(4.08, 9.13, 5.50, 90, 90, 90)
l3 = Lattice.from_para(4.08, 7.13, 5.50, 90, 38, 90, ltype="monoclinic")
wp1 = Wyckoff_position.from_group_and_index(36, 0)
wp2 = Wyckoff_position.from_group_and_index(36, "4a")
class TestGroup(unittest.TestCase):
def test_list_wyckoff_combinations(self):
g = Group(64)
a1, _ = g.list_wyckoff_combinations([4, 2])
self.assertTrue(a1 is None)
a2, _ = g.list_wyckoff_combinations([4, 8], quick=False)
self.assertTrue(len(a2) == 8)
class TestOptLat(unittest.TestCase):
def test_atomic(self):
c1 = pyxtal()