def from_seed(self,
seed,
molecule=None,
tol=1e-4,
relax_h=False,
backend='pymatgen'):
"""
Load the seed structure from Pymatgen/ASE/POSCAR/CIFs
Internally they will be handled by Pymatgen
"""
from ase import Atoms
from pymatgen import Structure
if self.molecular:
from pyxtal.molecule import pyxtal_molecule
pmol = pyxtal_molecule(molecule).mol
struc = structure_from_ext(seed, pmol, relax_h=relax_h)
if struc.match():
self.mol_sites = [struc.make_mol_site()]
self.group = Group(struc.wyc.number)
self.lattice = struc.lattice
self.molecules = [
pyxtal_molecule(struc.molecule, symmetrize=False)
]
self.numMols = struc.numMols
self.diag = struc.diag
self.valid = True # Need to add a check function
else:
raise ValueError(
"Cannot extract the molecular crystal from cif")
else:
if isinstance(seed, dict):
self.from_dict()
elif isinstance(seed, Atoms): #ASE atoms
from pymatgen.io.ase import AseAtomsAdaptor
pmg_struc = AseAtomsAdaptor.get_structure(seed)
self._from_pymatgen(pmg_struc, tol)
elif isinstance(seed, Structure): #Pymatgen
self._from_pymatgen(seed, tol)
elif isinstance(seed, str):
if backend == 'pymatgen':
pmg_struc = Structure.from_file(seed)
self._from_pymatgen(pmg_struc, tol)
else:
self.lattice, self.atom_sites = read_cif(seed)
self.group = Group(self.atom_sites[0].wp.number)
self.diag = self.atom_sites[0].diag
self.valid = True
self.factor = 1.0
self.source = 'Seed'
self.dim = 3
self.PBC = [1, 1, 1]
self._get_formula()
def from_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 make_mol_site(self, ref=False):
if ref:
mol = self.ref_mol
ori = self.ori
else:
mol = self.molecule
ori = Orientation(np.eye(3))
mol = self.add_site_props(mol)
pmol = pyxtal_molecule(mol, symmetrize=False)
site = mol_site(pmol, self.position, ori, self.wyc, self.lattice, self.diag)
return site
def __init__(self, struc, ref_mols, 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_mols: a list of reference molecule (xyz file or Pyxtal molecule)
tol: scale factor for covalent bond distance
relax_h: whether or not relax the position for hydrogen atoms in structure
"""
for ref_mol in ref_mols:
if isinstance(ref_mol, str):
ref_mol = pyxtal_molecule(ref_mol)
elif isinstance(ref_mol, pyxtal_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.ref_mols = ref_mols
self.tol = tol
self.diag = False
self.relax_h = relax_h
sym_struc, number = get_symmetrized_pmg(pmg_struc)
group = Group(number)
self.group = group
self.wyc = group[0]
self.perm = [0,1,2]
molecules = search_molecules_in_crystal(sym_struc, self.tol)
if self.relax_h: molecules = self.addh(molecules)
self.pmg_struc = sym_struc
self.lattice = Lattice.from_matrix(sym_struc.lattice.matrix, ltype=group.lattice_type)
self.resort(molecules)
self.numMols = [len(self.wyc)]
def init_common(
self,
molecules,
numMols,
volume_factor,
select_high,
allow_inversion,
orientations,
group,
lattice,
tm,
sites,
):
# init functionality which is shared by 3D, 2D, and 1D crystals
self.valid = False
self.numattempts = 0 # number of attempts to generate the crystal.
if type(group) == Group:
self.group = group
"""A pyxtal.symmetry.Group object storing information about the space/layer
/Rod/point group, and its Wyckoff positions."""
else:
self.group = Group(group, dim=self.dim)
self.number = self.group.number
"""
The international group number of the crystal:
1-230 for 3D space groups
1-80 for 2D layer groups
1-75 for 1D Rod groups
1-32 for crystallographic point groups
None otherwise
"""
self.Msgs()
self.factor = volume_factor # volume factor for the unit cell.
numMols = np.array(numMols) # must convert it to np.array
self.numMols0 = numMols # in the PRIMITIVE cell
self.numMols = self.numMols0 * cellsize(
self.group) # in the CONVENTIONAL cell
# boolean numbers
self.allow_inversion = allow_inversion
self.select_high = select_high
# Set the tolerance matrix
# The Tol_matrix object for checking inter-atomic distances within the structure.
if type(tm) == Tol_matrix:
self.tol_matrix = tm
else:
try:
self.tol_matrix = Tol_matrix(prototype=tm)
# TODO remove bare except
except:
msg = "Error: tm must either be a Tol_matrix object +\n"
msg += "or a prototype string for initializing one."
printx(msg, priority=1)
return
self.molecules = [] # A pyxtal_molecule objects,
for mol in molecules:
self.molecules.append(pyxtal_molecule(mol, self.tol_matrix))
self.sites = {}
for i, mol in enumerate(self.molecules):
if sites is not None and sites[i] is not None:
self.check_consistency(sites[i], self.numMols[i])
self.sites[i] = sites[i]
else:
self.sites[i] = None
# if seeds, directly parse the structure from cif
# At the moment, we only support one specie
if self.seed is not None:
seed = structure_from_ext(self.seed,
self.molecules[0].mol,
relax_h=self.relax_h)
if seed.match():
self.mol_sites = [seed.make_mol_site()]
self.group = Group(seed.wyc.number)
self.lattice = seed.lattice
self.molecules = [pyxtal_molecule(seed.molecule)]
self.diag = seed.diag
self.valid = True # Need to add a check function
else:
raise ValueError("Cannot extract the structure from cif")
# The valid orientations for each molecule and Wyckoff position.
# May be copied when generating a new molecular_crystal to save a
# small amount of time
if orientations is None:
self.get_orientations()
else:
self.valid_orientations = orientations
if self.seed is None:
if lattice is not None:
# Use the provided lattice
self.lattice = lattice
self.volume = lattice.volume
# Make sure the custom lattice PBC axes are correct.
if lattice.PBC != self.PBC:
self.lattice.PBC = self.PBC
printx("\n Warning: converting custom lattice PBC to " +
str(self.PBC))
else:
# Determine the unique axis
if self.dim == 2:
if self.number in range(3, 8):
unique_axis = "c"
else:
unique_axis = "a"
elif self.dim == 1:
if self.number in range(3, 8):
unique_axis = "a"
else:
unique_axis = "c"
else:
unique_axis = "c"
# Generate a Lattice instance
self.volume = self.estimate_volume()
# The Lattice object used to generate lattice matrices
if self.dim == 3 or self.dim == 0:
self.lattice = Lattice(
self.group.lattice_type,
self.volume,
PBC=self.PBC,
unique_axis=unique_axis,
)
elif self.dim == 2:
self.lattice = Lattice(
self.group.lattice_type,
self.volume,
PBC=self.PBC,
unique_axis=unique_axis,
thickness=self.thickness,
)
elif self.dim == 1:
self.lattice = Lattice(
self.group.lattice_type,
self.volume,
PBC=self.PBC,
unique_axis=unique_axis,
area=self.area,
)
self.generate_crystal()
def init_common(
self,
molecules,
numMols,
volume_factor,
select_high,
allow_inversion,
orientations,
group,
lattice,
sites,
conventional,
tm,
):
# init functionality which is shared by 3D, 2D, and 1D crystals
self.valid = False
self.numattempts = 0 # number of attempts to generate the crystal.
if type(group) == Group:
self.group = group
else:
self.group = Group(group, dim=self.dim)
self.number = self.group.number
"""
The international group number of the crystal:
1-230 for 3D space groups
1-80 for 2D layer groups
1-75 for 1D Rod groups
1-32 for crystallographic point groups
None otherwise
"""
self.factor = volume_factor # volume factor for the unit cell.
numMols = np.array(numMols) # must convert it to np.array
if not conventional:
mul = cellsize(self.group)
else:
mul = 1
self.numMols = numMols * mul
# boolean numbers
self.allow_inversion = allow_inversion
self.select_high = select_high
# Set the tolerance matrix
# The Tol_matrix object for checking inter-atomic distances within the structure.
if type(tm) == Tol_matrix:
self.tol_matrix = tm
else:
try:
self.tol_matrix = Tol_matrix(prototype=tm)
# TODO remove bare except
except:
msg = "Error: tm must either be a Tol_matrix object +\n"
msg += "or a prototype string for initializing one."
printx(msg, priority=1)
return
self.molecules = [] # A pyxtal_molecule objects,
for mol in molecules:
self.molecules.append(pyxtal_molecule(mol, self.tol_matrix))
self.sites = {}
for i, mol in enumerate(self.molecules):
if sites is not None and sites[i] is not None:
self.check_consistency(sites[i], self.numMols[i])
self.sites[i] = sites[i]
else:
self.sites[i] = None
# The valid orientations for each molecule and Wyckoff position.
# May be copied when generating a new molecular_crystal to save a
# small amount of time
if orientations is None:
self.get_orientations()
else:
self.valid_orientations = orientations
if lattice is not None:
# Use the provided lattice
self.lattice = lattice
self.volume = lattice.volume
# Make sure the custom lattice PBC axes are correct.
if lattice.PBC != self.PBC:
self.lattice.PBC = self.PBC
printx("\n Warning: converting custom lattice PBC to " + str(self.PBC))
else:
# Determine the unique axis
if self.dim == 2:
if self.number in range(3, 8):
unique_axis = "c"
else:
unique_axis = "a"
elif self.dim == 1:
if self.number in range(3, 8):
unique_axis = "a"
else:
unique_axis = "c"
else:
unique_axis = "c"
# Generate a Lattice instance
self.volume = self.estimate_volume()
# The Lattice object used to generate lattice matrices
if self.dim == 3 or self.dim == 0:
self.lattice = Lattice(
self.group.lattice_type,
self.volume,
PBC=self.PBC,
unique_axis=unique_axis,
)
elif self.dim == 2:
self.lattice = Lattice(
self.group.lattice_type,
self.volume,
PBC=self.PBC,
unique_axis=unique_axis,
thickness=self.thickness,
)
elif self.dim == 1:
self.lattice = Lattice(
self.group.lattice_type,
self.volume,
PBC=self.PBC,
unique_axis=unique_axis,
area=self.area,
)
self.generate_crystal()
def test_modules():
fprint("====== Testing functionality for pyXtal version 0.1dev ======")
global failed_package
failed_package = False # Record if errors occur at any level
reset()
fprint("Importing sys...")
try:
import sys
fprint("Success!")
except Exception as e:
fail(e)
sys.exit(0)
fprint("Importing numpy...")
try:
import numpy as np
fprint("Success!")
except Exception as e:
fail(e)
sys.exit(0)
fprint("Importing pymatgen...")
try:
import pymatgen
fprint("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)
fprint("Importing pandas...")
try:
import pandas
fprint("Success!")
except Exception as e:
fail(e)
sys.exit(0)
fprint("Importing spglib...")
try:
import spglib
fprint("Success!")
except Exception as e:
fail(e)
sys.exit(0)
fprint("Importing ase...")
try:
import ase
fprint("Success!")
except:
fprint("Error: could not import openbabel. Try reinstalling the package.")
fprint("=== Testing modules ===")
# =====database.element=====
fprint("pyxtal.database.element")
reset()
try:
import pyxtal.database.element
except Exception as e:
fail(e)
fprint(" 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=====
fprint("pyxtal.database.hall")
reset()
try:
import pyxtal.database.hall
except Exception as e:
fail(e)
fprint(" 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=====
fprint("pyxtal.database.collection")
reset()
try:
import pyxtal.database.collection
except Exception as e:
fail(e)
fprint(" 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=====
fprint("pyxtal.operations")
reset()
try:
import pyxtal.operations
except Exception as e:
fail(e)
from pyxtal.lattice import random_shear_matrix, random_vector
fprint(" 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()
fprint(" 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()
fprint(" 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()
fprint(" 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()
fprint(" class OperationAnalyzer")
try:
from pyxtal.operations import OperationAnalyzer
except Exception as e:
fail(e)
if passed():
try:
m = np.eye(3)
t = random_vector()
op1 = SymmOp.from_rotation_and_translation(m, t)
OperationAnalyzer(op1)
except Exception as e:
fail(e)
check()
fprint(" class Orientation")
try:
from pyxtal.molecule 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=====
fprint("pyxtal.symmetry")
reset()
try:
import pyxtal.symmetry
except Exception as e:
fail(e)
fprint(" 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()
fprint(" 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()
fprint(" 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()
fprint(" 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()
fprint(" 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()
fprint(" 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:
fprint(j, k)
fail()
except Exception as e:
fail(e)
check()
fprint(" 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:
fprint(j, k)
fail()
except Exception as e:
fail(e)
check()
fprint(" 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()
fprint(" 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()
fprint(" 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()
# =====molecule=====
fprint("pyxtal.molecule")
reset()
try:
from pyxtal.molecule import pyxtal_molecule
except Exception as e:
fail(e)
if passed():
try:
h2o = pyxtal_molecule("H2O").mol
ch4 = pyxtal_molecule("CH4").mol
except Exception as e:
fail(e)
check()
fprint(" 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()
fprint(" 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()
end(condition=2)
