def get_orientations(self):
"""
Calculates the valid orientations for each Molecule and Wyckoff
position. Returns a list with 4 indices:
- index 1: the molecular prototype's index within self.molecules
- index 2: the Wyckoff position's 1st index (based on multiplicity)
- index 3: the WP's 2nd index (within the group of equal multiplicity)
- index 4: the index of the valid orientation for the molecule/WP pair
For example, self.valid_orientations[i][j][k] would be a list of valid
orientations for self.molecules[i], in the Wyckoff position
self.group.wyckoffs_organized[j][k]
"""
self.valid_orientations = []
for pyxtal_mol in self.molecules:
self.valid_orientations.append([])
wp_index = -1
for i, x in enumerate(self.group.wyckoffs_organized):
self.valid_orientations[-1].append([])
for j, wp in enumerate(x):
wp_index += 1
allowed = orientation_in_wyckoff_position(
pyxtal_mol.mol,
wp,
already_oriented=True,
allow_inversion=self.allow_inversion,
)
if allowed is not False:
self.valid_orientations[-1][-1].append(allowed)
else:
self.valid_orientations[-1][-1].append([])
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)