def test_xyz(self):
op=SymmOp([[1, -1, 0, 0], [0, -1, 0, 0],
[0, 0, -1, 0], [0, 0, 0, 1]])
s=op.as_xyz_string()
self.assertEqual(s, 'x-y, -y, -z')
self.assertEqual(op, SymmOp.from_xyz_string(s))
op2=SymmOp([[0, -1, 0, 0.5], [1, 0, 0, 0.5],
[0, 0, 1, 0.5 + 1e-7], [0, 0, 0, 1]])
s2=op2.as_xyz_string()
self.assertEqual(s2, '-y+1/2, x+1/2, z+1/2')
self.assertEqual(op2, SymmOp.from_xyz_string(s2))
op2=SymmOp([[3, -2, -1, 0.5], [-1, 0, 0, 12. / 13],
[0, 0, 1, 0.5 + 1e-7], [0, 0, 0, 1]])
s2=op2.as_xyz_string()
self.assertEqual(s2, '3x-2y-z+1/2, -x+12/13, z+1/2')
self.assertEqual(op2, SymmOp.from_xyz_string(s2))
op3=SymmOp.from_xyz_string('3x - 2y - z+1 /2 , -x+12/ 13, z+1/2')
self.assertEqual(op2, op3)
# Ensure strings can be read in any order
op4=SymmOp.from_xyz_string('1 /2 + 3X - 2y - z , 12/ 13-x, z+1/2')
op5=SymmOp.from_xyz_string('+1 /2 + 3x - 2y - z , 12/ 13-x, +1/2+z')
self.assertEqual(op4, op3)
self.assertEqual(op4, op5)
self.assertEqual(op3, op5)
self.assertRaises(ValueError, self.op.as_xyz_string)
o=SymmOp.from_xyz_string('0.5+x, 0.25+y, 0.75+z')
self.assertArrayAlmostEqual(o.translation_vector, [0.5, 0.25, 0.75])
o=SymmOp.from_xyz_string('x + 0.5, y + 0.25, z + 0.75')
self.assertArrayAlmostEqual(o.translation_vector, [0.5, 0.25, 0.75])
def test_xyz(self):
op = SymmOp([[1, -1, 0, 0], [0, -1, 0, 0], [0, 0, -1, 0], [0, 0, 0,
1]])
s = op.as_xyz_string()
self.assertEqual(s, 'x-y, -y, -z')
self.assertEqual(op, SymmOp.from_xyz_string(s))
op2 = SymmOp([[0, -1, 0, 0.5], [1, 0, 0, 0.5], [0, 0, 1, 0.5 + 1e-7],
[0, 0, 0, 1]])
s2 = op2.as_xyz_string()
self.assertEqual(s2, '-y+1/2, x+1/2, z+1/2')
self.assertEqual(op2, SymmOp.from_xyz_string(s2))
op2 = SymmOp([[3, -2, -1, 0.5], [-1, 0, 0, 12. / 13],
[0, 0, 1, 0.5 + 1e-7], [0, 0, 0, 1]])
s2 = op2.as_xyz_string()
self.assertEqual(s2, '3x-2y-z+1/2, -x+12/13, z+1/2')
self.assertEqual(op2, SymmOp.from_xyz_string(s2))
op3 = SymmOp.from_xyz_string('3x - 2y - z+1 /2 , -x+12/ 13, z+1/2')
self.assertEqual(op2, op3)
# Ensure strings can be read in any order
op4 = SymmOp.from_xyz_string('1 /2 + 3X - 2y - z , 12/ 13-x, z+1/2')
op5 = SymmOp.from_xyz_string('+1 /2 + 3x - 2y - z , 12/ 13-x, +1/2+z')
self.assertEqual(op4, op3)
self.assertEqual(op4, op5)
self.assertEqual(op3, op5)
self.assertRaises(ValueError, self.op.as_xyz_string)
o = SymmOp.from_xyz_string('0.5+x, 0.25+y, 0.75+z')
self.assertArrayAlmostEqual(o.translation_vector, [0.5, 0.25, 0.75])
o = SymmOp.from_xyz_string('x + 0.5, y + 0.25, z + 0.75')
self.assertArrayAlmostEqual(o.translation_vector, [0.5, 0.25, 0.75])
def get_wyckoffs(sg):
wyckoff_strings = eval(wyckoff_df["0"][sg])
wyckoffs = []
for x in wyckoff_strings:
wyckoffs.append([])
for y in x:
wyckoffs[-1].append(SymmOp.from_xyz_string(y))
return wyckoffs
def test_xyz(self):
op = SymmOp([[1, -1, 0, 0], [0, -1, 0, 0],
[0, 0, -1, 0], [0, 0, 0, 1]])
s = op.as_xyz_string()
self.assertEqual(s, 'x-y, -y, -z')
self.assertEqual(op, SymmOp.from_xyz_string(s))
op2 = SymmOp([[0, -1, 0, 0.5], [1, 0, 0, 0.5],
[0, 0, 1, 0.5+1e-7], [0, 0, 0, 1]])
s2 = op2.as_xyz_string()
self.assertEqual(s2, '-y+1/2, x+1/2, z+1/2')
self.assertEqual(op2, SymmOp.from_xyz_string(s2))
op2 = SymmOp([[3, -2, -1, 0.5], [-1, 0, 0, 12./13],
[0, 0, 1, 0.5+1e-7], [0, 0, 0, 1]])
s2 = op2.as_xyz_string()
self.assertEqual(s2, '3x-2y-z+1/2, -x+12/13, z+1/2')
self.assertEqual(op2, SymmOp.from_xyz_string(s2))
op3 = SymmOp.from_xyz_string('3x - 2y - z+1 /2 , -x+12/ 13, z+1/2')
self.assertEqual(op2, op3)
self.assertRaises(ValueError, self.op.as_xyz_string)
def get_wyckoff_generators(sg):
'''
Returns a list of Wyckoff generators for a given space group.
1st index: index of WP in sg (0 is the WP with largest multiplicity)
2nd index: a generator for the WP
'''
generators_strings = eval(wyckoff_generators_df["0"][sg])
generators = []
#Loop over Wyckoff positions
for wp in generators_strings:
generators.append([])
#Loop over points in WP
for op in wp:
generators[-1].append(SymmOp.from_xyz_string(op))
return generators
def test_xyz(self):
op = SymmOp([[1, -1, 0, 0], [0, -1, 0, 0], [0, 0, -1, 0], [0, 0, 0, 1]])
s = op.as_xyz_string()
self.assertEqual(s, "x-y, -y, -z")
self.assertEqual(op, SymmOp.from_xyz_string(s))
op2 = SymmOp(
[[0, -1, 0, 0.5], [1, 0, 0, 0.5], [0, 0, 1, 0.5 + 1e-7], [0, 0, 0, 1]]
)
s2 = op2.as_xyz_string()
self.assertEqual(s2, "-y+1/2, x+1/2, z+1/2")
self.assertEqual(op2, SymmOp.from_xyz_string(s2))
op2 = SymmOp(
[
[3, -2, -1, 0.5],
[-1, 0, 0, 12.0 / 13],
[0, 0, 1, 0.5 + 1e-7],
[0, 0, 0, 1],
]
)
s2 = op2.as_xyz_string()
self.assertEqual(s2, "3x-2y-z+1/2, -x+12/13, z+1/2")
self.assertEqual(op2, SymmOp.from_xyz_string(s2))
op3 = SymmOp.from_xyz_string("3x - 2y - z+1 /2 , -x+12/ 13, z+1/2")
self.assertEqual(op2, op3)
# Ensure strings can be read in any order
op4 = SymmOp.from_xyz_string("1 /2 + 3X - 2y - z , 12/ 13-x, z+1/2")
op5 = SymmOp.from_xyz_string("+1 /2 + 3x - 2y - z , 12/ 13-x, +1/2+z")
self.assertEqual(op4, op3)
self.assertEqual(op4, op5)
self.assertEqual(op3, op5)
# TODO: assertWarns not in Python 2.x unittest
# update PymatgenTest for unittest2?
# self.assertWarns(UserWarning, self.op.as_xyz_string)
o = SymmOp.from_xyz_string("0.5+x, 0.25+y, 0.75+z")
self.assertArrayAlmostEqual(o.translation_vector, [0.5, 0.25, 0.75])
o = SymmOp.from_xyz_string("x + 0.5, y + 0.25, z + 0.75")
self.assertArrayAlmostEqual(o.translation_vector, [0.5, 0.25, 0.75])
def get_symmetry(mol, already_oriented=False):
'''
Return a list of SymmOps for a molecule's point symmetry
already_oriented: whether or not the principle axes of mol are already reoriented
'''
pga = PointGroupAnalyzer(mol)
#Handle linear molecules
if '*' in pga.sch_symbol:
if already_oriented == False:
#Reorient the molecule
oriented_mol, P = reoriented_molecule(mol)
pga = PointGroupAnalyzer(oriented_mol)
pg = pga.get_pointgroup()
symm_m = []
for op in pg:
symm_m.append(op)
#Add 12-fold and reflections in place of ininitesimal rotation
for axis in [[1, 0, 0], [0, 1, 0], [0, 0, 1]]:
op = SymmOp.from_rotation_and_translation(aa2matrix(axis, pi / 6),
[0, 0, 0])
if pga.is_valid_op(op):
symm_m.append(op)
#Any molecule with infinitesimal symmetry is linear;
#Thus, it possess mirror symmetry for any axis perpendicular
#To the rotational axis. pymatgen does not add this symmetry
#for all linear molecules - for example, hydrogen
if axis == [1, 0, 0]:
symm_m.append(SymmOp.from_xyz_string('x,-y,z'))
symm_m.append(SymmOp.from_xyz_string('x,y,-z'))
elif axis == [0, 1, 0]:
symm_m.append(SymmOp.from_xyz_string('-x,y,z'))
symm_m.append(SymmOp.from_xyz_string('x,y,-z'))
elif axis == [0, 0, 1]:
symm_m.append(SymmOp.from_xyz_string('-x,y,z'))
symm_m.append(SymmOp.from_xyz_string('x,-y,z'))
#Generate a full list of SymmOps for the molecule's pointgroup
symm_m = generate_full_symmops(symm_m, 1e-3)
break
#Reorient the SymmOps into mol's original frame
if not already_oriented:
new = []
for op in symm_m:
new.append(P.inverse * op * P)
return new
elif already_oriented:
return symm_m
#Handle nonlinear molecules
else:
pg = pga.get_pointgroup()
symm_m = []
for op in pg:
symm_m.append(op)
return symm_m
def get_wyckoff_symmetry(sg):
'''
Returns a list of Wyckoff position site symmetry for a given space group.
1st index: index of WP in sg (0 is the WP with largest multiplicity)
2nd index: a point within the WP
3rd index: a site symmetry SymmOp of the point
'''
symmetry_strings = eval(wyckoff_symmetry_df["0"][sg])
symmetry = []
#Loop over Wyckoff positions
for x in symmetry_strings:
symmetry.append([])
#Loop over points in WP
for y in x:
symmetry[-1].append([])
#Loop over
for z in y:
symmetry[-1][-1].append(SymmOp.from_xyz_string(z))
return symmetry
def test_inverse(self):
coord0 = [0.35, 0.1, 0.4]
coords = np.array([
[0.350, 0.100, 0.400],
[0.350, 0.100, 0.000],
[0.350, 0.100, 0.000],
[0.350, 0.000, 0.667],
[0.350, 0.000, 0.250],
[0.350, 0.350, 0.400],
[0.350, 0.350, 0.500],
[0.350, 0.350, 0.000],
[0.350, 0.350, 0.350],
[0.100, 0.100, 0.100],
[0.400, 0.400, 0.400],
[0.350, 0.000, 0.000],
[0.000, 0.100, 0.400],
[0.350, 0.000, 0.400],
])
xyzs = [
'x,y,z',
'x,y,0',
'y,x,0',
'x,0,2/3',
'0,x,1/4',
'x,x,z',
'x,-x,1/2',
'2x,x,0',
'-2x,-0.5x,-x+1/4',
'-2y,-0.5y,-y+1/4',
'-2z,-0.5z,-z+1/4',
'0,0,x',
'-y/2+1/2,-z,0',
'-z,-x/2+1/2,0',
]
for i, xyz in enumerate(xyzs):
op = SymmOp.from_xyz_string(xyz)
inv_op = get_inverse(op)
coord1 = op.operate(coord0)
coord2 = inv_op.operate(coord1)
self.assertTrue(np.allclose(coord2, coords[i], rtol=1e-2))
def test_xyz(self):
op = SymmOp([[1, -1, 0, 0], [0, -1, 0, 0],
[0, 0, -1, 0], [0, 0, 0, 1]])
s = op.as_xyz_string()
self.assertEqual(s, 'x-y, -y, -z')
self.assertEqual(op, SymmOp.from_xyz_string(s))
op2 = SymmOp([[0, -1, 0, 0.5], [1, 0, 0, 0.5],
[0, 0, 1, 0.5 + 1e-7], [0, 0, 0, 1]])
s2 = op2.as_xyz_string()
self.assertEqual(s2, '-y+1/2, x+1/2, z+1/2')
self.assertEqual(op2, SymmOp.from_xyz_string(s2))
op2 = SymmOp([[3, -2, -1, 0.5], [-1, 0, 0, 12. / 13],
[0, 0, 1, 0.5 + 1e-7], [0, 0, 0, 1]])
s2 = op2.as_xyz_string()
self.assertEqual(s2, '3x-2y-z+1/2, -x+12/13, z+1/2')
self.assertEqual(op2, SymmOp.from_xyz_string(s2))
op3 = SymmOp.from_xyz_string('3x - 2y - z+1 /2 , -x+12/ 13, z+1/2')
self.assertEqual(op2, op3)
# Ensure strings can be read in any order
op4 = SymmOp.from_xyz_string('1 /2 + 3X - 2y - z , 12/ 13-x, z+1/2')
op5 = SymmOp.from_xyz_string('+1 /2 + 3x - 2y - z , 12/ 13-x, +1/2+z')
self.assertEqual(op4, op3)
self.assertEqual(op4, op5)
self.assertEqual(op3, op5)
# TODO: assertWarns not in Python 2.x unittest
# update PymatgenTest for unittest2?
# self.assertWarns(UserWarning, self.op.as_xyz_string)
o = SymmOp.from_xyz_string('0.5+x, 0.25+y, 0.75+z')
self.assertArrayAlmostEqual(o.translation_vector, [0.5, 0.25, 0.75])
o = SymmOp.from_xyz_string('x + 0.5, y + 0.25, z + 0.75')
self.assertArrayAlmostEqual(o.translation_vector, [0.5, 0.25, 0.75])
def get_wyckoff_symmetry(sg, molecular=False):
'''
Returns a list of Wyckoff position site symmetry for a given space group.
1st index: index of WP in sg (0 is the WP with largest multiplicity)
2nd index: a point within the WP
3rd index: a site symmetry SymmOp of the point
molecular: whether or not to return the Euclidean point symmetry operations
If True, cuts off translational part of operation, and converts non-orthogonal
(3-fold and 6-fold rotation) operations to pure rotations
'''
P = SymmOp.from_rotation_and_translation(
[[1, -.5, 0], [0, sqrt(3) / 2, 0], [0, 0, 1]], [0, 0, 0])
symmetry_strings = eval(wyckoff_symmetry_df["0"][sg])
symmetry = []
convert = False
if molecular is True:
if sg >= 143 and sg <= 194:
convert = True
#Loop over Wyckoff positions
for x in symmetry_strings:
symmetry.append([])
#Loop over points in WP
for y in x:
symmetry[-1].append([])
#Loop over ops
for z in y:
op = SymmOp.from_xyz_string(z)
if convert is True:
#Convert non-orthogonal trigonal/hexagonal operations
op = P * op * P.inverse
if molecular is False:
symmetry[-1][-1].append(op)
elif molecular is True:
op = SymmOp.from_rotation_and_translation(
op.rotation_matrix, [0, 0, 0])
symmetry[-1][-1].append(op)
return symmetry
def get_wyckoffs(sg, organized=False):
'''
Returns a list of Wyckoff positions for a given space group.
1st index: index of WP in sg (0 is the WP with largest multiplicity)
2nd index: a SymmOp object in the WP
'''
wyckoff_strings = eval(wyckoff_df["0"][sg])
wyckoffs = []
for x in wyckoff_strings:
wyckoffs.append([])
for y in x:
wyckoffs[-1].append(SymmOp.from_xyz_string(y))
if organized:
wyckoffs_organized = [[]] #2D Array of WP's organized by multiplicity
old = len(wyckoffs[0])
for wp in wyckoffs:
mult = len(wp)
if mult != old:
wyckoffs_organized.append([])
old = mult
wyckoffs_organized[-1].append(wp)
return wyckoffs_organized
else:
return wyckoffs
from structure import *
from pymatgen.core.operations import SymmOp
print("---Site Symmetry for a point in a space group---")
sg = input("Space group Number (1-230): ")
point = input("Point (can have x,y,z variables): ")
gen_pos = get_wyckoff_positions(int(sg))[0][0]
point = SymmOp.from_xyz_string(point)
mylist = site_symm(point, gen_pos)
print("Found symmetry:")
for x in mylist:
print(x.as_xyz_string())
def get_symops(self, data):
"""
In order to generate symmetry equivalent positions, the symmetry
operations are parsed. If the symops are not present, the space
group symbol is parsed, and symops are generated.
"""
symops = []
for symmetry_label in ["_symmetry_equiv_pos_as_xyz",
"_symmetry_equiv_pos_as_xyz_",
"_space_group_symop_operation_xyz",
"_space_group_symop_operation_xyz_"]:
if data.data.get(symmetry_label):
xyz = data.data.get(symmetry_label)
if isinstance(xyz, six.string_types):
warnings.warn("A 1-line symmetry op P1 CIF is detected!")
xyz = [xyz]
try:
symops = [SymmOp.from_xyz_string(s)
for s in xyz]
break
except ValueError:
continue
if not symops:
# Try to parse symbol
for symmetry_label in ["_symmetry_space_group_name_H-M",
"_symmetry_space_group_name_H_M",
"_symmetry_space_group_name_H-M_",
"_symmetry_space_group_name_H_M_",
"_space_group_name_Hall",
"_space_group_name_Hall_",
"_space_group_name_H-M_alt",
"_space_group_name_H-M_alt_",
"_symmetry_space_group_name_hall",
"_symmetry_space_group_name_hall_",
"_symmetry_space_group_name_h-m",
"_symmetry_space_group_name_h-m_"]:
sg = data.data.get(symmetry_label)
if sg:
sg = sub_spgrp(sg)
try:
spg = space_groups.get(sg)
if spg:
symops = SpaceGroup(spg).symmetry_ops
warnings.warn(
"No _symmetry_equiv_pos_as_xyz type key found. "
"Spacegroup from %s used." % symmetry_label)
break
except ValueError:
# Ignore any errors
pass
try:
for d in _get_cod_data():
if sg == re.sub("\s+", "",
d["hermann_mauguin"]) :
xyz = d["symops"]
symops = [SymmOp.from_xyz_string(s)
for s in xyz]
warnings.warn(
"No _symmetry_equiv_pos_as_xyz type key found. "
"Spacegroup from %s used." % symmetry_label)
break
except Exception as ex:
continue
if symops:
break
if not symops:
# Try to parse International number
for symmetry_label in ["_space_group_IT_number",
"_space_group_IT_number_",
"_symmetry_Int_Tables_number",
"_symmetry_Int_Tables_number_"]:
if data.data.get(symmetry_label):
try:
i = int(str2float(data.data.get(symmetry_label)))
symops = SpaceGroup.from_int_number(i).symmetry_ops
break
except ValueError:
continue
if not symops:
warnings.warn("No _symmetry_equiv_pos_as_xyz type key found. "
"Defaulting to P1.")
symops = [SymmOp.from_xyz_string(s) for s in ['x', 'y', 'z']]
return symops
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 _get_structure(self, data, primitive):
"""
Generate structure from part of the cif.
"""
lengths = [
str2float(data["_cell_length_" + i]) for i in ["a", "b", "c"]
]
angles = [
str2float(data["_cell_angle_" + i])
for i in ["alpha", "beta", "gamma"]
]
lattice = Lattice.from_lengths_and_angles(lengths, angles)
try:
sympos = data["_symmetry_equiv_pos_as_xyz"]
except KeyError:
try:
sympos = data["_symmetry_equiv_pos_as_xyz_"]
except KeyError:
warnings.warn("No _symmetry_equiv_pos_as_xyz type key found. "
"Defaulting to P1.")
sympos = ['x, y, z']
self.symmetry_operations = [SymmOp.from_xyz_string(s) for s in sympos]
def parse_symbol(sym):
# capitalization conventions are not strictly followed, eg Cu will be CU
m = re.search("([A-Za-z]*)", sym)
if m:
return m.group(1)[:2].capitalize()
return ""
try:
oxi_states = {
data["_atom_type_symbol"][i]:
str2float(data["_atom_type_oxidation_number"][i])
for i in range(len(data["_atom_type_symbol"]))
}
except (ValueError, KeyError):
oxi_states = None
coord_to_species = OrderedDict()
for i in range(len(data["_atom_site_label"])):
symbol = parse_symbol(data["_atom_site_label"][i])
# make sure symbol was properly parsed from _atom_site_label
# otherwise get it from _atom_site_type_symbol
try:
Element(symbol)
except KeyError:
symbol = parse_symbol(data["_atom_site_type_symbol"][i])
if oxi_states is not None:
# sometimes the site doesn't have the type_symbol.
# we then hope the type_symbol can be parsed from the label
if "_atom_site_type_symbol" in data.data.keys():
k = data["_atom_site_type_symbol"][i]
else:
k = symbol
el = Specie(symbol, oxi_states[k])
else:
el = Element(symbol)
x = str2float(data["_atom_site_fract_x"][i])
y = str2float(data["_atom_site_fract_y"][i])
z = str2float(data["_atom_site_fract_z"][i])
try:
occu = str2float(data["_atom_site_occupancy"][i])
except (KeyError, ValueError):
occu = 1
if occu > 0:
coord = (x, y, z)
if coord not in coord_to_species:
coord_to_species[coord] = {el: occu}
else:
coord_to_species[coord][el] = occu
allspecies = []
allcoords = []
for coord, species in coord_to_species.items():
coords = self._unique_coords(coord)
allcoords.extend(coords)
allspecies.extend(len(coords) * [species])
#rescale occupancies if necessary
for species in allspecies:
totaloccu = sum(species.values())
if 1 < totaloccu <= self._occupancy_tolerance:
for key, value in six.iteritems(species):
species[key] = value / totaloccu
struct = Structure(lattice, allspecies, allcoords)
if primitive:
struct = struct.get_primitive_structure().get_reduced_structure()
return struct.get_sorted_structure()
def get_symops(self, data):
"""
In order to generate symmetry equivalent positions, the symmetry
operations are parsed. If the symops are not present, the space
group symbol is parsed, and symops are generated.
"""
symops = []
for symmetry_label in [
"_symmetry_equiv_pos_as_xyz", "_symmetry_equiv_pos_as_xyz_",
"_space_group_symop_operation_xyz",
"_space_group_symop_operation_xyz_"
]:
if data.data.get(symmetry_label):
xyz = data.data.get(symmetry_label)
if isinstance(xyz, six.string_types):
warnings.warn("A 1-line symmetry op P1 CIF is detected!")
xyz = [xyz]
try:
symops = [SymmOp.from_xyz_string(s) for s in xyz]
break
except ValueError:
continue
if not symops:
# Try to parse symbol
for symmetry_label in [
"_symmetry_space_group_name_H-M",
"_symmetry_space_group_name_H_M",
"_symmetry_space_group_name_H-M_",
"_symmetry_space_group_name_H_M_",
"_space_group_name_Hall", "_space_group_name_Hall_",
"_space_group_name_H-M_alt", "_space_group_name_H-M_alt_",
"_symmetry_space_group_name_hall",
"_symmetry_space_group_name_hall_",
"_symmetry_space_group_name_h-m",
"_symmetry_space_group_name_h-m_"
]:
sg = data.data.get(symmetry_label)
if sg:
sg = sub_spgrp(sg)
try:
spg = space_groups.get(sg)
if spg:
symops = SpaceGroup(spg).symmetry_ops
warnings.warn(
"No _symmetry_equiv_pos_as_xyz type key found. "
"Spacegroup from %s used." % symmetry_label)
break
except ValueError:
# Ignore any errors
pass
try:
for d in _get_cod_data():
if sg == re.sub(r"\s+", "", d["hermann_mauguin"]):
xyz = d["symops"]
symops = [
SymmOp.from_xyz_string(s) for s in xyz
]
warnings.warn(
"No _symmetry_equiv_pos_as_xyz type key found. "
"Spacegroup from %s used." %
symmetry_label)
break
except Exception as ex:
continue
if symops:
break
if not symops:
# Try to parse International number
for symmetry_label in [
"_space_group_IT_number", "_space_group_IT_number_",
"_symmetry_Int_Tables_number",
"_symmetry_Int_Tables_number_"
]:
if data.data.get(symmetry_label):
try:
i = int(str2float(data.data.get(symmetry_label)))
symops = SpaceGroup.from_int_number(i).symmetry_ops
break
except ValueError:
continue
if not symops:
warnings.warn("No _symmetry_equiv_pos_as_xyz type key found. "
"Defaulting to P1.")
symops = [SymmOp.from_xyz_string(s) for s in ['x', 'y', 'z']]
return symops
def __init__(self, int_symbol):
"""
Initializes a Space Group from its full or abbreviated international
symbol. Only standard settings are supported.
Args:
int_symbol (str): Full International (e.g., "P2/m2/m2/m") or
Hermann-Mauguin Symbol ("Pmmm") or abbreviated symbol. The
notation is a LaTeX-like string, with screw axes being
represented by an underscore. For example, "P6_3/mmc". Note
that for rhomohedral cells, the hexagonal setting can be
accessed by adding a "H", e.g., "R-3mH".
"""
gen_matrices = get_symm_data("generator_matrices")
# POINT_GROUP_ENC = SYMM_DATA["point_group_encoding"]
sgencoding = get_symm_data("space_group_encoding")
abbrev_sg_mapping = get_symm_data("abbreviated_spacegroup_symbols")
translations = {k: Fraction(v) for k, v in get_symm_data(
"translations").items()}
full_sg_mapping = {
v["full_symbol"]: k
for k, v in get_symm_data("space_group_encoding").items()}
int_symbol = re.sub(" ", "", int_symbol)
if int_symbol in abbrev_sg_mapping:
int_symbol = abbrev_sg_mapping[int_symbol]
elif int_symbol in full_sg_mapping:
int_symbol = full_sg_mapping[int_symbol]
for spg in SpaceGroup.SYMM_OPS:
if re.sub(" ", "", spg["hermann_mauguin"]) == int_symbol or re.sub(":", "", re.sub(" ", "", spg["universal_h_m"])) == int_symbol:
ops = [SymmOp.from_xyz_string(s) for s in spg["symops"]]
self.symbol = re.sub(":", "",
re.sub(" ", "", spg["universal_h_m"]))
if int_symbol in sgencoding:
self.full_symbol = sgencoding[int_symbol]["full_symbol"]
self.point_group = sgencoding[int_symbol]["point_group"]
else:
self.full_symbol = re.sub(" ", "",
spg["universal_h_m"])
self.point_group = spg["schoenflies"]
self.int_number = spg["number"]
self.order = len(ops)
self._symmetry_ops = ops
break
else:
if int_symbol not in sgencoding:
raise ValueError("Bad international symbol %s" % int_symbol)
data = sgencoding[int_symbol]
self.symbol = int_symbol
# TODO: Support different origin choices.
enc = list(data["enc"])
inversion = int(enc.pop(0))
ngen = int(enc.pop(0))
symm_ops = [np.eye(4)]
if inversion:
symm_ops.append(np.array(
[[-1, 0, 0, 0], [0, -1, 0, 0], [0, 0, -1, 0],
[0, 0, 0, 1]]))
for i in range(ngen):
m = np.eye(4)
m[:3, :3] = gen_matrices[enc.pop(0)]
m[0, 3] = translations[enc.pop(0)]
m[1, 3] = translations[enc.pop(0)]
m[2, 3] = translations[enc.pop(0)]
symm_ops.append(m)
self.generators = symm_ops
self.full_symbol = data["full_symbol"]
self.int_number = data["int_number"]
self.order = data["order"]
self._symmetry_ops = None
def __init__(self, int_symbol):
"""
Initializes a Space Group from its full or abbreviated international
symbol. Only standard settings are supported.
Args:
int_symbol (str): Full International (e.g., "P2/m2/m2/m") or
Hermann-Mauguin Symbol ("Pmmm") or abbreviated symbol. The
notation is a LaTeX-like string, with screw axes being
represented by an underscore. For example, "P6_3/mmc".
Alternative settings can be access by adding a ":identifier".
For example, the hexagonal setting for rhombohedral cells can be
accessed by adding a ":H", e.g., "R-3m:H". To find out all
possible settings for a spacegroup, use the get_settings
classmethod. Alternative origin choices can be indicated by a
translation vector, e.g., 'Fm-3m(a-1/4,b-1/4,c-1/4)'.
"""
int_symbol = re.sub(r" ", "", int_symbol)
if int_symbol in SpaceGroup.abbrev_sg_mapping:
int_symbol = SpaceGroup.abbrev_sg_mapping[int_symbol]
elif int_symbol in SpaceGroup.full_sg_mapping:
int_symbol = SpaceGroup.full_sg_mapping[int_symbol]
for spg in SpaceGroup.SYMM_OPS:
if int_symbol in [spg["hermann_mauguin"], spg["universal_h_m"]]:
ops = [SymmOp.from_xyz_string(s) for s in spg["symops"]]
self.symbol = re.sub(r":", "",
re.sub(r" ", "", spg["universal_h_m"]))
if int_symbol in SpaceGroup.sgencoding:
self.full_symbol = SpaceGroup.sgencoding[int_symbol]["full_symbol"]
self.point_group = SpaceGroup.sgencoding[int_symbol]["point_group"]
else:
self.full_symbol = re.sub(r" ", "",
spg["universal_h_m"])
self.point_group = spg["schoenflies"]
self.int_number = spg["number"]
self.order = len(ops)
self._symmetry_ops = ops
break
else:
if int_symbol not in SpaceGroup.sgencoding:
raise ValueError("Bad international symbol %s" % int_symbol)
data = SpaceGroup.sgencoding[int_symbol]
self.symbol = int_symbol
# TODO: Support different origin choices.
enc = list(data["enc"])
inversion = int(enc.pop(0))
ngen = int(enc.pop(0))
symm_ops = [np.eye(4)]
if inversion:
symm_ops.append(np.array(
[[-1, 0, 0, 0], [0, -1, 0, 0], [0, 0, -1, 0],
[0, 0, 0, 1]]))
for i in range(ngen):
m = np.eye(4)
m[:3, :3] = SpaceGroup.gen_matrices[enc.pop(0)]
m[0, 3] = SpaceGroup.translations[enc.pop(0)]
m[1, 3] = SpaceGroup.translations[enc.pop(0)]
m[2, 3] = SpaceGroup.translations[enc.pop(0)]
symm_ops.append(m)
self.generators = symm_ops
self.full_symbol = data["full_symbol"]
self.int_number = data["int_number"]
self.order = data["order"]
self._symmetry_ops = None
from pymatgen import Structure
from pymatgen import symmetry
from pymatgen.ext.matproj import MPRester
from pymatgen.io.cif import CifWriter
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.core.operations import SymmOp
from IPython.display import Image
with MPRester("izD7mJmnjhUOKyWGtZ") as m:
# Structure for material id
structure = m.get_structure_by_material_id("mp-27869")
w = CifWriter(structure)
w.write_file('mp-27869.cif')
sGP = SpacegroupAnalyzer(structure)
print("2ème élément de symétrie (Ci:0 0 0):")
Op1 = SymmOp.from_xyz_string("-x, -y, -z")
print("Effet sur P1 #2:")
Eff1 = Op1.operate((0, 0, 1 / 2))
print(Eff1)
display(Image(filename='sym1.jpg'))
print("4ème élément de symétrie (3-bar axis:y,-x+y,-z):")
Op2 = SymmOp.from_xyz_string("y,-x+y,-z")
print("Effet sur BaO1 #4:")
Eff2 = Op2.operate((0, 0, 0.24))
print(Eff2)
display(Image(filename='sym2.jpg'))
print("5ème élément de symétrie (3-bar axis:-x+y,-x,z):")
Op3 = SymmOp.from_xyz_string("-x+y,-x,z")
print("Effet sur BaO6 #5:")
Eff3 = Op3.operate((0.67, 0.33, 0.57))
print(Eff3)
def get_symops(self, data):
"""
In order to generate symmetry equivalent positions, the symmetry
operations are parsed. If the symops are not present, the space
group symbol is parsed, and symops are generated.
"""
symops = []
for symmetry_label in ["_symmetry_equiv_pos_as_xyz",
"_symmetry_equiv_pos_as_xyz_",
"_space_group_symop_operation_xyz",
"_space_group_symop_operation_xyz_"]:
if data.data.get(symmetry_label):
try:
symops = [SymmOp.from_xyz_string(s)
for s in data.data.get(symmetry_label)]
break
except ValueError:
continue
if not symops:
# Try to parse symbol
for symmetry_label in ["_symmetry_space_group_name_H-M",
"_symmetry_space_group_name_H_M",
"_symmetry_space_group_name_H-M_",
"_symmetry_space_group_name_H_M_",
"_space_group_name_Hall",
"_space_group_name_Hall_",
"_space_group_name_H-M_alt",
"_space_group_name_H-M_alt_",
"_symmetry_space_group_name_hall",
"_symmetry_space_group_name_hall_",
"_symmetry_space_group_name_h-m",
"_symmetry_space_group_name_h-m_"]:
if data.data.get(symmetry_label):
try:
spg = space_groups.get(sub_spgrp(
data.data.get(symmetry_label)))
if spg:
symops = SpaceGroup(spg).symmetry_ops
break
except ValueError:
continue
if not symops:
# Try to parse International number
for symmetry_label in ["_space_group_IT_number",
"_space_group_IT_number_",
"_symmetry_Int_Tables_number",
"_symmetry_Int_Tables_number_"]:
if data.data.get(symmetry_label):
try:
i = int(str2float(data.data.get(symmetry_label)))
symops = SpaceGroup.from_int_number(i).symmetry_ops
break
except ValueError:
continue
if not symops:
warnings.warn("No _symmetry_equiv_pos_as_xyz type key found. "
"Defaulting to P1.")
symops = [SymmOp.from_xyz_string(s) for s in ['x', 'y', 'z']]
return symops
def get_symops(self, data):
"""
In order to generate symmetry equivalent positions, the symmetry
operations are parsed. If the symops are not present, the space
group symbol is parsed, and symops are generated.
"""
symops = []
for symmetry_label in [
"_symmetry_equiv_pos_as_xyz", "_symmetry_equiv_pos_as_xyz_",
"_space_group_symop_operation_xyz",
"_space_group_symop_operation_xyz_"
]:
if data.data.get(symmetry_label):
try:
symops = [
SymmOp.from_xyz_string(s)
for s in data.data.get(symmetry_label)
]
break
except ValueError:
continue
if not symops:
# Try to parse symbol
for symmetry_label in [
"_symmetry_space_group_name_H-M",
"_symmetry_space_group_name_H_M",
"_symmetry_space_group_name_H-M_",
"_symmetry_space_group_name_H_M_",
"_space_group_name_Hall", "_space_group_name_Hall_",
"_space_group_name_H-M_alt", "_space_group_name_H-M_alt_",
"_symmetry_space_group_name_hall",
"_symmetry_space_group_name_hall_",
"_symmetry_space_group_name_h-m",
"_symmetry_space_group_name_h-m_"
]:
if data.data.get(symmetry_label):
try:
spg = space_groups.get(
sub_spgrp(data.data.get(symmetry_label)))
if spg:
symops = SpaceGroup(spg).symmetry_ops
break
except ValueError:
continue
if not symops:
# Try to parse International number
for symmetry_label in [
"_space_group_IT_number", "_space_group_IT_number_",
"_symmetry_Int_Tables_number",
"_symmetry_Int_Tables_number_"
]:
if data.data.get(symmetry_label):
try:
symops = SpaceGroup.from_int_number(
str2float(
data.data.get(symmetry_label))).symmetry_ops
break
except ValueError:
continue
if not symops:
warnings.warn("No _symmetry_equiv_pos_as_xyz type key found. "
"Defaulting to P1.")
symops = [SymmOp.from_xyz_string(s) for s in ['x', 'y', 'z']]
return symops
def get_symmop(data):
symops = []
for symmetry_label in [
"_symmetry_equiv_pos_as_xyz", "_symmetry_equiv_pos_as_xyz_",
"_space_group_symop_operation_xyz",
"_space_group_symop_operation_xyz_"
]:
if data.get(symmetry_label):
xyz = data.get(symmetry_label)
if isinstance(xyz, str):
msg = "A 1-line symmetry op P1 CIF is detected!"
warnings.warn(msg)
xyz = [xyz]
try:
symops = [SymmOp.from_xyz_string(s) for s in xyz]
break
except ValueError:
continue
if not symops:
# Try to parse symbol
for symmetry_label in [
"_symmetry_space_group_name_H-M",
"_symmetry_space_group_name_H_M",
"_symmetry_space_group_name_H-M_",
"_symmetry_space_group_name_H_M_", "_space_group_name_Hall",
"_space_group_name_Hall_", "_space_group_name_H-M_alt",
"_space_group_name_H-M_alt_",
"_symmetry_space_group_name_hall",
"_symmetry_space_group_name_hall_",
"_symmetry_space_group_name_h-m",
"_symmetry_space_group_name_h-m_"
]:
sg = data.get(symmetry_label)
if sg:
sg = sub_spgrp(sg)
try:
spg = space_groups.get(sg)
if spg:
symops = SpaceGroup(spg).symmetry_ops
msg = "No _symmetry_equiv_pos_as_xyz type key found. " \
"Spacegroup from %s used." % symmetry_label
warnings.warn(msg)
break
except ValueError:
# Ignore any errors
pass
try:
for d in _get_cod_data():
if sg == re.sub(r"\s+", "", d["hermann_mauguin"]):
xyz = d["symops"]
symops = [SymmOp.from_xyz_string(s) for s in xyz]
msg = "No _symmetry_equiv_pos_as_xyz type key found. " \
"Spacegroup from %s used." % symmetry_label
warnings.warn(msg)
break
except Exception:
continue
if symops:
break
if not symops:
# Try to parse International number
for symmetry_label in [
"_space_group_IT_number", "_space_group_IT_number_",
"_symmetry_Int_Tables_number", "_symmetry_Int_Tables_number_"
]:
if data.get(symmetry_label):
try:
i = int(braket2float(data.get(symmetry_label)))
symops = SpaceGroup.from_int_number(i).symmetry_ops
break
except ValueError:
continue
if not symops:
msg = "No _symmetry_equiv_pos_as_xyz type key found. " \
"Defaulting to P1."
warnings.warn(msg)
symops = [SymmOp.from_xyz_string(s) for s in ['x', 'y', 'z']]
return symops
def __init__(self, int_symbol):
"""
Initializes a Space Group from its full or abbreviated international
symbol. Only standard settings are supported.
Args:
int_symbol (str): Full International (e.g., "P2/m2/m2/m") or
Hermann-Mauguin Symbol ("Pmmm") or abbreviated symbol. The
notation is a LaTeX-like string, with screw axes being
represented by an underscore. For example, "P6_3/mmc".
Alternative settings can be access by adding a ":identifier".
For example, the hexagonal setting for rhombohedral cells can be
accessed by adding a ":H", e.g., "R-3m:H". To find out all
possible settings for a spacegroup, use the get_settings
classmethod. Alternative origin choices can be indicated by a
translation vector, e.g., 'Fm-3m(a-1/4,b-1/4,c-1/4)'.
"""
int_symbol = re.sub(r" ", "", int_symbol)
if int_symbol in SpaceGroup.abbrev_sg_mapping:
int_symbol = SpaceGroup.abbrev_sg_mapping[int_symbol]
elif int_symbol in SpaceGroup.full_sg_mapping:
int_symbol = SpaceGroup.full_sg_mapping[int_symbol]
for spg in SpaceGroup.SYMM_OPS:
if int_symbol in [spg["hermann_mauguin"], spg["universal_h_m"]]:
ops = [SymmOp.from_xyz_string(s) for s in spg["symops"]]
self.symbol = re.sub(r":", "",
re.sub(r" ", "", spg["universal_h_m"]))
if int_symbol in SpaceGroup.sgencoding:
self.full_symbol = SpaceGroup.sgencoding[int_symbol][
"full_symbol"]
self.point_group = SpaceGroup.sgencoding[int_symbol][
"point_group"]
else:
self.full_symbol = re.sub(r" ", "", spg["universal_h_m"])
self.point_group = spg["schoenflies"]
self.int_number = spg["number"]
self.order = len(ops)
self._symmetry_ops = ops
break
else:
if int_symbol not in SpaceGroup.sgencoding:
raise ValueError("Bad international symbol %s" % int_symbol)
data = SpaceGroup.sgencoding[int_symbol]
self.symbol = int_symbol
# TODO: Support different origin choices.
enc = list(data["enc"])
inversion = int(enc.pop(0))
ngen = int(enc.pop(0))
symm_ops = [np.eye(4)]
if inversion:
symm_ops.append(
np.array([[-1, 0, 0, 0], [0, -1, 0, 0], [0, 0, -1, 0],
[0, 0, 0, 1]]))
for i in range(ngen):
m = np.eye(4)
m[:3, :3] = SpaceGroup.gen_matrices[enc.pop(0)]
m[0, 3] = SpaceGroup.translations[enc.pop(0)]
m[1, 3] = SpaceGroup.translations[enc.pop(0)]
m[2, 3] = SpaceGroup.translations[enc.pop(0)]
symm_ops.append(m)
self.generators = symm_ops
self.full_symbol = data["full_symbol"]
self.point_group = data["point_group"]
self.int_number = data["int_number"]
self.order = data["order"]
self._symmetry_ops = None
def _get_structure(self, data, primitive):
"""
Generate structure from part of the cif.
"""
lengths = [str2float(data["_cell_length_" + i])
for i in ["a", "b", "c"]]
angles = [str2float(data["_cell_angle_" + i])
for i in ["alpha", "beta", "gamma"]]
lattice = Lattice.from_lengths_and_angles(lengths, angles)
try:
sympos = data["_symmetry_equiv_pos_as_xyz"]
except KeyError:
try:
sympos = data["_symmetry_equiv_pos_as_xyz_"]
except KeyError:
warnings.warn("No _symmetry_equiv_pos_as_xyz type key found. "
"Defaulting to P1.")
sympos = ['x, y, z']
self.symmetry_operations = [SymmOp.from_xyz_string(s) for s in sympos]
def parse_symbol(sym):
m = re.search("([A-Z][a-z]*)", sym)
if m:
return m.group(1)
return ""
try:
oxi_states = {
data["_atom_type_symbol"][i]:
str2float(data["_atom_type_oxidation_number"][i])
for i in range(len(data["_atom_type_symbol"]))}
except (ValueError, KeyError):
oxi_states = None
coord_to_species = OrderedDict()
for i in range(len(data["_atom_site_type_symbol"])):
symbol = parse_symbol(data["_atom_site_type_symbol"][i])
if oxi_states is not None:
el = Specie(symbol,
oxi_states[data["_atom_site_type_symbol"][i]])
else:
el = Element(symbol)
x = str2float(data["_atom_site_fract_x"][i])
y = str2float(data["_atom_site_fract_y"][i])
z = str2float(data["_atom_site_fract_z"][i])
try:
occu = str2float(data["_atom_site_occupancy"][i])
except (KeyError, ValueError):
occu = 1
if occu > 0:
coord = (x, y, z)
if coord not in coord_to_species:
coord_to_species[coord] = {el: occu}
else:
coord_to_species[coord][el] = occu
allspecies = []
allcoords = []
for coord, species in coord_to_species.items():
coords = self._unique_coords(coord)
allcoords.extend(coords)
allspecies.extend(len(coords) * [species])
#rescale occupancies if necessary
for species in allspecies:
totaloccu = sum(species.values())
if 1 < totaloccu <= self._occupancy_tolerance:
for key, value in six.iteritems(species):
species[key] = value / totaloccu
struct = Structure(lattice, allspecies, allcoords)
if primitive:
struct = struct.get_primitive_structure().get_reduced_structure()
return struct.get_sorted_structure()
