def compare_wyckoffs(num1, num2, dim=3):
"""Given 2 groups, return whether the second point
group has equal or greater symmetry than the first group."""
from numpy import allclose
if num1 == "???":
print("Error: invalid value for num1 passed to compare_wyckoffs")
return
if num2 == "???":
return False
# Get general positions for both groups
if dim == 3:
from pyxtal.symmetry import get_wyckoffs
g1 = get_wyckoffs(num1)[0]
g2 = get_wyckoffs(num2)[0]
elif dim == 2:
from pyxtal.symmetry import get_layer
g1 = get_layer(num1)[0]
g2 = get_layer(num2)[0]
elif dim == 1:
from pyxtal.symmetry import get_rod
g1 = get_rod(num1)[0]
g2 = get_rod(num2)[0]
elif dim == 0:
from pyxtal.symmetry import get_point
g1 = get_point(num1)[0]
g2 = get_point(num2)[0]
# If group 2 has higher symmetry
if len(g2) > len(g1):
return True
# Compare point group operations
for i, op2 in enumerate(g2):
op1 = g1[i]
m1 = op1.rotation_matrix
m2 = op2.rotation_matrix
if not allclose(m1, m2):
return False
return True
def check_struct_group(crystal, group, dim=3, tol=1e-2):
# Supress pymatgen/numpy complex casting warnings
from pyxtal.crystal import random_crystal
from pyxtal.molecular_crystal import molecular_crystal
from copy import deepcopy
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore")
"""Given a pymatgen structure, group number, and dimension, return
whether or not the structure matches the group number."""
if isinstance(crystal, (random_crystal, molecular_crystal)):
lattice = crystal.struct.lattice.matrix
if dim != 0:
old_coords = deepcopy(crystal.struct.frac_coords)
old_species = deepcopy(crystal.struct.atomic_numbers)
elif dim == 0:
old_coords = deepcopy(crystal.cart_coords)
old_species = deepcopy(crystal.species)
else:
lattice = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
old_coords = np.array(crystal)
old_species = ["C"] * len(old_coords)
from pyxtal.symmetry import distance
from pyxtal.symmetry import filtered_coords
from copy import deepcopy
PBC = [1, 1, 1]
# Obtain the generators for the group
if dim == 3:
from pyxtal.symmetry import get_wyckoffs
generators = get_wyckoffs(group)[0]
elif dim == 2:
from pyxtal.symmetry import get_layer
generators = get_layer(group)[0]
PBC = [1, 1, 0]
elif dim == 1:
from pyxtal.symmetry import get_rod
generators = get_rod(group)[0]
PBC = [0, 0, 1]
elif dim == 0:
from pyxtal.symmetry import Group
generators = Group(group, dim=0)[0]
PBC = [0, 0, 0]
# TODO: Add check for lattice symmetry
# Apply SymmOps to generate new points
# old_coords = filtered_coords(struct.frac_coords,PBC=PBC)
new_coords = []
new_species = []
for i, point in enumerate(old_coords):
for j, op in enumerate(generators):
if j != 0:
new_coords.append(op.operate(point))
new_species.append(old_species[i])
# new_coords = filtered_coords(new_coords,PBC=PBC)
# Check that all points in new list are still in old
failed = False
i_list = list(range(len(new_coords)))
for i, point1 in enumerate(new_coords):
found = False
for j, point2 in enumerate(old_coords):
if new_species[i] == old_species[j]:
difference = filtered_coords(point2 - point1, PBC=PBC)
if distance(difference, lattice, PBC=PBC) <= tol:
found = True
break
if found is False:
failed = True
break
if failed is False:
return True
else:
return False
def test_molecular_1D():
global outstructs
global outstrings
print(
"=== Testing generation of molecular 1D crystals. This may take some time. ==="
)
from time import time
from spglib import get_symmetry_dataset
from pyxtal.symmetry import get_rod
from pyxtal.molecular_crystal import molecular_crystal_1D
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
slow = []
failed = []
print(" Rod group | Gen sg. (SPG) | Gen. sg (PMG) |Time Elapsed")
skip = [] # slow to generate
for num in range(1, 76):
if num not in skip:
multiplicity = len(
get_rod(num)[0]) # multiplicity of the general position
start = time()
rand_crystal = molecular_crystal_1D(num, ["H2O"], [multiplicity],
4.0)
end = time()
timespent = np.around((end - start), decimals=2)
t = str(timespent)
if len(t) == 3:
t += "0"
t += " s"
if timespent >= 1.0:
t += " ~"
if timespent >= 3.0:
t += "~"
if timespent >= 10.0:
t += "~"
if timespent >= 60.0:
t += "~"
slow.append(num)
if rand_crystal.valid:
try:
ans1 = get_symmetry_dataset(rand_crystal.spg_struct,
symprec=1e-1)
except:
ans1 = "???"
if ans1 is None or ans1 == "???":
ans1 = "???"
else:
ans1 = ans1["number"]
sga = SpacegroupAnalyzer(rand_crystal.struct)
try:
ans2 = sga.get_space_group_number()
except:
ans2 = "???"
if ans2 is None:
ans2 = "???"
check = True
# output cif files for incorrect space groups
if check is True:
if check_struct_group(rand_crystal, num, dim=1):
pass
else:
t += " xxxxx"
outstructs.append(rand_crystal.struct)
outstrings.append(
str("1D_Molecular_" + str(num) + ".vasp"))
print("\t" + str(num) + "\t|\t" + str(ans1) + "\t|\t" +
str(ans2) + "\t|\t" + t)
else:
print("~~~~ Error: Could not generate layer group " +
str(num) + " after " + t)
failed.append(num)
if slow != []:
print(
"~~~~ The following layer groups took more than 60 seconds to generate:"
)
for i in slow:
print(" " + str(i))
if failed != []:
print("~~~~ The following layer groups failed to generate:")
for i in failed:
print(" " + str(i))
def check_struct_group(struct, group, dim=3, tol=1e-2):
"""Given a pymatgen structure, group number, and dimension, return
whether or not the structure matches the group number."""
from pyxtal.symmetry import distance
from pyxtal.symmetry import filtered_coords
from copy import deepcopy
lattice = struct.lattice.matrix
PBC = [1,1,1]
#Obtain the generators for the group
if dim == 3:
from pyxtal.symmetry import get_wyckoffs
generators = get_wyckoffs(group)[0]
elif dim == 2:
from pyxtal.symmetry import get_layer
generators = get_layer(group)[0]
PBC = [1,1,0]
elif dim == 1:
from pyxtal.symmetry import get_rod
generators = get_rod(group)[0]
PBC = [0,0,1]
elif dim == 0:
from pyxtal.symmetry import get_point
generators = get_point(group)[0]
PBC = [0,0,0]
#TODO: Add check for lattice symmetry
#Apply SymmOps to generate new points
#old_coords = filtered_coords(struct.frac_coords,PBC=PBC)
old_coords = deepcopy(struct.frac_coords)
if dim == 0:
old_coords = old_coords - 0.5
old_species = deepcopy(struct.atomic_numbers)
new_coords = []
new_species = []
for i, point in enumerate(old_coords):
for j, op in enumerate(generators):
if j != 0:
new_coords.append(op.operate(point))
new_species.append(old_species[i])
#new_coords = filtered_coords(new_coords,PBC=PBC)
#Check that all points in new list are still in old
failed = False
i_list = list(range(len(new_coords)))
for i, point1 in enumerate(new_coords):
found = False
for j, point2 in enumerate(old_coords):
if new_species[i] == old_species[j]:
difference = filtered_coords(point2 - point1, PBC=PBC)
if distance(difference, lattice, PBC=PBC) <= tol:
found = True
break
if found is False:
failed = True
break
if failed is False:
return True
else:
return False
def test_atomic_1D():
global outstructs
global outstrings
fprint("=== Testing generation of atomic 1D crystals. This may take some time. ===")
slow = []
failed = []
fprint(" Rod group | Gen sg. (SPG) | Gen. sg (PMG) |Time Elapsed")
skip = [] # slow to generate
for num in range(1, 76):
if num not in skip:
multiplicity = len(get_rod(num)[0]) # multiplicity of the general position
start = time()
rand_crystal = pyxtal()
rand_crystal.from_random(1, num, ["H"], [multiplicity], 4.0)
end = time()
timespent = np.around((end - start), decimals=2)
t = str(timespent)
if len(t) == 3:
t += "0"
t += " s"
if timespent >= 1.0:
t += " ~"
if timespent >= 3.0:
t += "~"
if timespent >= 10.0:
t += "~"
if timespent >= 60.0:
t += "~"
slow.append(num)
if rand_crystal.valid:
try:
ans1 = get_symmetry_dataset(rand_crystal.to_ase(), symprec=1e-1)
except:
ans1 = "???"
if ans1 is None or ans1 == "???":
ans1 = "???"
else:
ans1 = ans1["number"]
sga = SpacegroupAnalyzer(rand_crystal.to_pymatgen())
try:
ans2 = sga.get_space_group_number()
except:
ans2 = "???"
if ans2 is None:
ans2 = "???"
check = True
# output cif files for incorrect space groups
if check is True:
if check_struct_group(rand_crystal, num, dim=1):
pass
else:
t += " xxxxx"
outstructs.append(rand_crystal.to_pymatgen)
outstrings.append(str("1D_Atomic_" + str(num) + ".vasp"))
fprint("\t{}\t|\t{}\t|\t{}\t|\t{}".format(num, ans1, ans2, t))
else:
fprint(
"~~~~ Error: Could not generate layer group {} after {}".format(
num, t
)
)
failed.append(num)
if slow != []:
fprint("~~~~ The following layer groups took more than 60 seconds to generate:")
for i in slow:
fprint(" " + str(i))
if failed != []:
fprint("~~~~ The following layer groups failed to generate:")
for i in failed:
fprint(" " + str(i))