def test_get_lattices(self):
sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5,
primitive_cell=True, scale=True,
attempt_supercell=False)
l1 = Lattice.from_lengths_and_angles([1, 2.1, 1.9], [90, 89, 91])
l2 = Lattice.from_lengths_and_angles([1.1, 2, 2], [89, 91, 90])
s1 = Structure(l1, [], [])
s2 = Structure(l2, [], [])
lattices = list(sm._get_lattices(s=s1, target_lattice=s2.lattice))
self.assertEqual(len(lattices), 16)
l3 = Lattice.from_lengths_and_angles([1.1, 2, 20], [89, 91, 90])
s3 = Structure(l3, [], [])
lattices = list(sm._get_lattices(s=s1, target_lattice=s3.lattice))
self.assertEqual(len(lattices), 0)
def from_string(header_str):
"""
Reads Header string and returns Header object if header was
generated by pymatgen.
Note: Checks to see if generated by pymatgen, if not it is impossible
to generate structure object so it is not possible to generate
header object and routine ends
Args:
header_str: pymatgen generated feff.inp header
Returns:
Structure object.
"""
lines = tuple(clean_lines(header_str.split("\n"), False))
comment1 = lines[0]
feffpmg = comment1.find("pymatgen")
if feffpmg:
comment2 = ' '.join(lines[1].split()[2:])
source = ' '.join(lines[2].split()[2:])
basis_vec = lines[6].split(":")[-1].split()
# a, b, c
a = float(basis_vec[0])
b = float(basis_vec[1])
c = float(basis_vec[2])
lengths = [a, b, c]
# alpha, beta, gamma
basis_ang = lines[7].split(":")[-1].split()
alpha = float(basis_ang[0])
beta = float(basis_ang[1])
gamma = float(basis_ang[2])
angles = [alpha, beta, gamma]
lattice = Lattice.from_lengths_and_angles(lengths, angles)
natoms = int(lines[8].split(":")[-1].split()[0])
atomic_symbols = []
for i in range(9, 9 + natoms):
atomic_symbols.append(lines[i].split()[2])
# read the atomic coordinates
coords = []
for i in range(natoms):
toks = lines[i + 9].split()
coords.append([float(s) for s in toks[3:]])
struct = Structure(lattice, atomic_symbols, coords, False,
False, False)
h = Header(struct, source, comment2)
return h
else:
return "Header not generated by pymatgen, cannot return header object"
def setUp(self):
self.cubic = Structure(
Lattice.from_lengths_and_angles(
[1.0, 1.0, 1.0], [90.0, 90.0, 90.0]),
["H"], [[0.0, 0.0, 0.0]], validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=False,
site_properties=None)
self.bcc = Structure(
Lattice.from_lengths_and_angles(
[1.0, 1.0, 1.0], [90.0, 90.0, 90.0]),
["H", "H"], [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False, site_properties=None)
self.fcc = Structure(
Lattice.from_lengths_and_angles(
[1.0, 1.0, 1.0], [90.0, 90.0, 90.0]),
["H", "H", "H", "H"], [[0.0, 0.0, 0.0], [0.0, 0.5, 0.5],
[0.5, 0.0, 0.5], [0.5, 0.5, 0.0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False, site_properties=None)
self.hcp = Structure(
Lattice.from_lengths_and_angles(
[1.0, 1.0, 1.633], [90.0, 90.0, 120.0]),
["H", "H"],
[[0.3333, 0.6667, 0.25], [0.6667, 0.3333, 0.75]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False, site_properties=None)
self.diamond = Structure(
Lattice.from_lengths_and_angles(
[1.0, 1.0, 1.0], [90.0, 90.0, 90.0]),
["H", "H", "H", "H", "H", "H", "H", "H"],
[[0.0, 0.0, 0.5], [0.75, 0.75, 0.75],
[0.0, 0.5, 0.0], [0.75, 0.25, 0.25],
[0.5, 0.0, 0.0], [0.25, 0.75, 0.25],
[0.5, 0.5, 0.5], [0.25, 0.25, 0.75]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False, site_properties=None)
def setUp(self):
self.silicon = Structure(
Lattice.from_lengths_and_angles(
[5.47, 5.47, 5.47],
[90.0, 90.0, 90.0]),
["Si", "Si", "Si", "Si", "Si", "Si", "Si", "Si"],
[[0.000000, 0.000000, 0.500000],
[0.750000, 0.750000, 0.750000],
[0.000000, 0.500000, 1.000000],
[0.750000, 0.250000, 0.250000],
[0.500000, 0.000000, 1.000000],
[0.250000, 0.750000, 0.250000],
[0.500000, 0.500000, 0.500000],
[0.250000, 0.250000, 0.750000]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False, site_properties=None)
self.diamond = Structure(
Lattice([[2.189, 0, 1.264], [0.73, 2.064, 1.264],
[0, 0, 2.528]]), ["C0+", "C0+"], [[2.554, 1.806, 4.423],
[0.365, 0.258, 0.632]],
validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
self.nacl = Structure(
Lattice([[3.485, 0, 2.012], [1.162, 3.286, 2.012],
[0, 0, 4.025]]), ["Na1+", "Cl1-"], [[0, 0, 0],
[2.324, 1.643, 4.025]],
validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
self.cscl = Structure(
Lattice([[4.209, 0, 0], [0, 4.209, 0], [0, 0, 4.209]]),
["Cl1-", "Cs1+"], [[2.105, 2.105, 2.105], [0, 0, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.square_pyramid = Structure(
Lattice([[100, 0, 0], [0, 100, 0], [0, 0, 100]]),
["C", "C", "C", "C", "C", "C"], [
[0, 0, 0], [1, 0, 0], [-1, 0, 0], [0, 1, 0], [0, -1, 0], \
[0, 0, 1]], validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.trigonal_bipyramid = Structure(
Lattice([[100, 0, 0], [0, 100, 0], [0, 0, 100]]),
["P", "Cl", "Cl", "Cl", "Cl", "Cl"], [
[0, 0, 0], [0, 0, 2.14], [0, 2.02, 0], [1.74937, -1.01, 0], \
[-1.74937, -1.01, 0], [0, 0, -2.14]], validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
def setUp(self):
self.single_bond = Structure(
Lattice.from_lengths_and_angles(
[10, 10, 10], [90, 90, 90]),
["H", "H", "H"], [[1, 0, 0], [0, 0, 0], [6, 0, 0]],
validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
self.linear = Structure(
Lattice.from_lengths_and_angles(
[10, 10, 10], [90, 90, 90]),
["H", "H", "H"], [[1, 0, 0], [0, 0, 0], [2, 0, 0]],
validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
self.bent45 = Structure(
Lattice.from_lengths_and_angles(
[10, 10, 10], [90, 90, 90]), ["H", "H", "H"],
[[0, 0, 0], [0.707, 0.707, 0], [0.707, 0, 0]],
validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
self.cubic = Structure(
Lattice.from_lengths_and_angles(
[1, 1, 1], [90, 90, 90]),
["H"], [[0, 0, 0]], validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=False,
site_properties=None)
self.bcc = Structure(
Lattice.from_lengths_and_angles(
[1, 1, 1], [90, 90, 90]),
["H", "H"], [[0, 0, 0], [0.5, 0.5, 0.5]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False, site_properties=None)
self.fcc = Structure(
Lattice.from_lengths_and_angles(
[1, 1, 1], [90, 90, 90]), ["H", "H", "H", "H"],
[[0, 0, 0], [0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False, site_properties=None)
self.hcp = Structure(
Lattice.from_lengths_and_angles(
[1, 1, 1.633], [90, 90, 120]), ["H", "H"],
[[0.3333, 0.6667, 0.25], [0.6667, 0.3333, 0.75]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False, site_properties=None)
self.diamond = Structure(
Lattice.from_lengths_and_angles(
[1, 1, 1], [90, 90, 90]), ["H", "H", "H", "H", "H", "H", "H", "H"],
[[0, 0, 0.5], [0.75, 0.75, 0.75], [0, 0.5, 0], [0.75, 0.25, 0.25],
[0.5, 0, 0], [0.25, 0.75, 0.25], [0.5, 0.5, 0.5],
[0.25, 0.25, 0.75]], validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False, site_properties=None)
self.trigonal_off_plane = Structure(
Lattice.from_lengths_and_angles(
[100, 100, 100], [90, 90, 90]),
["H", "H", "H", "H"],
[[0.50, 0.50, 0.50], [0.25, 0.75, 0.25], \
[0.25, 0.25, 0.75], [0.75, 0.25, 0.25]], \
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.regular_triangle = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), ["H", "H", "H", "H"],
[[15, 15.28867, 15.65], [14.5, 15, 15], [15.5, 15, 15], \
[15, 15.866, 15]], validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.trigonal_planar = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), ["H", "H", "H", "H"],
[[15, 15.28867, 15], [14.5, 15, 15], [15.5, 15, 15], \
[15, 15.866, 15]], validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.square_planar = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), ["H", "H", "H", "H", "H"],
[[15, 15, 15], [14.75, 14.75, 15], [14.75, 15.25, 15], \
[15.25, 14.75, 15], [15.25, 15.25, 15]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.square = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), ["H", "H", "H", "H", "H"],
[[15, 15, 15.707], [14.75, 14.75, 15], [14.75, 15.25, 15], \
[15.25, 14.75, 15], [15.25, 15.25, 15]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.T_shape = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), ["H", "H", "H", "H"],
[[15, 15, 15], [15, 15, 15.5], [15, 15.5, 15],
[15, 14.5, 15]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.square_pyramid = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), ["H", "H", "H", "H", "H", "H"],
[[15, 15, 15], [15, 15, 15.3535], [14.75, 14.75, 15],
[14.75, 15.25, 15], [15.25, 14.75, 15], [15.25, 15.25, 15]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.pentagonal_planar = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), ["Xe", "F", "F", "F", "F", "F"],
[[0, -1.6237, 0], [1.17969, 0, 0], [-1.17969, 0, 0], \
[1.90877, -2.24389, 0], [-1.90877, -2.24389, 0], [0, -3.6307, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.pentagonal_pyramid = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), ["Xe", "F", "F", "F", "F", "F", "F"],
[[0, -1.6237, 0], [0, -1.6237, 1.17969], [1.17969, 0, 0], \
[-1.17969, 0, 0], [1.90877, -2.24389, 0], \
[-1.90877, -2.24389, 0], [0, -3.6307, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.pentagonal_bipyramid = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]),
["Xe", "F", "F", "F", "F", "F", "F", "F"],
[[0, -1.6237, 0], [0, -1.6237, -1.17969], \
[0, -1.6237, 1.17969], [1.17969, 0, 0], \
[-1.17969, 0, 0], [1.90877, -2.24389, 0], \
[-1.90877, -2.24389, 0], [0, -3.6307, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.hexagonal_pyramid = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), \
["H", "Li", "C", "C", "C", "C", "C", "C"],
[[0, 0, 0], [0, 0, 1.675], [0.71, 1.2298, 0], \
[-0.71, 1.2298, 0], [0.71, -1.2298, 0], [-0.71, -1.2298, 0], \
[1.4199, 0, 0], [-1.4199, 0, 0]], \
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.hexagonal_bipyramid = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), \
["H", "Li", "Li", "C", "C", "C", "C", "C", "C"],
[[0, 0, 0], [0, 0, 1.675], [0, 0, -1.675], \
[0.71, 1.2298, 0], [-0.71, 1.2298, 0], \
[0.71, -1.2298, 0], [-0.71, -1.2298, 0], \
[1.4199, 0, 0], [-1.4199, 0, 0]], \
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.trigonal_pyramid = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), ["P", "Cl", "Cl", "Cl", "Cl"],
[[0, 0, 0], [0, 0, 2.14], [0, 2.02, 0],
[1.74937, -1.01, 0], [-1.74937, -1.01, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.trigonal_bipyramidal = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), ["P", "Cl", "Cl", "Cl", "Cl", "Cl"],
[[0, 0, 0], [0, 0, 2.14], [0, 2.02, 0],
[1.74937, -1.01, 0], [-1.74937, -1.01, 0], [0, 0, -2.14]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.cuboctahedron = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]),
["H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H"],
[[15, 15, 15], [15, 14.5, 14.5], [15, 14.5, 15.5],
[15, 15.5, 14.5], [15, 15.5, 15.5],
[14.5, 15, 14.5], [14.5, 15, 15.5], [15.5, 15, 14.5], [15.5, 15, 15.5],
[14.5, 14.5, 15], [14.5, 15.5, 15], [15.5, 14.5, 15], [15.5, 15.5, 15]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.see_saw = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]),
["H", "H", "H", "H", "H"],
[[15, 15, 15], [15, 15, 14], [15, 15, 16], [15, 14, 15], [14, 15, 15]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
def setUp(self):
self.linear = Structure(
Lattice.from_lengths_and_angles(
[10, 10, 10], [90, 90, 90]),
["H", "H", "H"], [[1, 0, 0], [0, 0, 0], [2, 0, 0]],
validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
self.bent45 = Structure(
Lattice.from_lengths_and_angles(
[10, 10, 10], [90, 90, 90]), ["H", "H", "H"],
[[0, 0, 0], [0.707, 0.707, 0], [0.707, 0, 0]],
validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
self.cubic = Structure(
Lattice.from_lengths_and_angles(
[1, 1, 1], [90, 90, 90]),
["H"], [[0, 0, 0]], validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=False,
site_properties=None)
self.bcc = Structure(
Lattice.from_lengths_and_angles(
[1, 1, 1], [90, 90, 90]),
["H", "H"], [[0, 0, 0], [0.5, 0.5, 0.5]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False, site_properties=None)
self.fcc = Structure(
Lattice.from_lengths_and_angles(
[1, 1, 1], [90, 90, 90]), ["H", "H", "H", "H"],
[[0, 0, 0], [0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False, site_properties=None)
self.hcp = Structure(
Lattice.from_lengths_and_angles(
[1, 1, 1.633], [90, 90, 120]), ["H", "H"],
[[0.3333, 0.6667, 0.25], [0.6667, 0.3333, 0.75]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False, site_properties=None)
self.diamond = Structure(
Lattice.from_lengths_and_angles(
[1, 1, 1], [90, 90, 90]), ["H", "H", "H", "H", "H", "H", "H", "H"],
[[0, 0, 0.5], [0.75, 0.75, 0.75], [0, 0.5, 0], [0.75, 0.25, 0.25],
[0.5, 0, 0], [0.25, 0.75, 0.25], [0.5, 0.5, 0.5],
[0.25, 0.25, 0.75]], validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False, site_properties=None)
self.regular_triangle = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), ["H", "H", "H", "H"],
[[15, 15.28867, 15.65], [14.5, 15, 15], [15.5, 15, 15], \
[15, 15.866, 15]], validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.square = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), ["H", "H", "H", "H", "H"],
[[15, 15, 15.707], [14.75, 14.75, 15], [14.75, 15.25, 15], \
[15.25, 14.75, 15], [15.25, 15.25, 15]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.square_pyramid = Structure(
Lattice.from_lengths_and_angles(
[30, 30, 30], [90, 90, 90]), ["H", "H", "H", "H", "H", "H"],
[[15, 15, 15], [15, 15, 15.3535], [14.75, 14.75, 15],
[14.75, 15.25, 15], [15.25, 14.75, 15], [15.25, 15.25, 15]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
def lat_in_to_sqs(atat_lattice_in, rename=True):
"""
Convert a string-like ATAT-style lattice.in to an abstract SQS.
Parameters
----------
atat_lattice_in : str
String-like of a lattice.in in the ATAT format.
rename : bool
If True, SQS format element names will be renamed, e.g. `a_B` -> `Xab`. Default is True.
Returns
-------
SQS
Abstract SQS.
"""
# TODO: handle numeric species, e.g. 'g1'.
# Problems: parser has trouble with matching next line and we have to rename it so pymatgen
# doesn't think it's a charge.
# parse the data
parsed_data = _parse_atat_lattice(atat_lattice_in)
atat_coord_system = parsed_data[0]
atat_lattice = parsed_data[1]
atat_atoms = parsed_data[2]
# create the lattice
if len(atat_coord_system) == 3:
# we have a coordinate system matrix
coord_system = Lattice(list(atat_coord_system)).matrix
else:
# we have length and angles
coord_system = Lattice.from_lengths_and_angles(list(atat_coord_system[0]), list(atat_coord_system[1])).matrix
direct_lattice = Lattice(list(atat_lattice))
lattice = coord_system.dot(direct_lattice.matrix)
# create the list of atoms, converted to the right coordinate system
species_list = []
species_positions = []
subl_model = {} # format {'subl_name': 'atoms_found_in_subl, e.g. "aaabbbb"'}
for position, atoms in atat_atoms:
# atoms can be a list of atoms, e.g. for not abstract SQS
if len(atoms) > 1:
raise NotImplementedError('Cannot parse atom list {} because the sublattice is unclear.\nParsed data: {}'.format(atoms, atat_atoms))
atom = atoms[0]
if rename:
# change from `a_B` style to `Xab`
atom = atom.lower().split('_')
else:
raise NotImplementedError('Cannot rename because the atom name and sublattice name may be ambigous.')
# add the abstract atom to the sublattice model
subl = atom[0]
subl_atom = atom[1]
subl_model[subl] = subl_model.get(subl, set()).union({subl_atom})
# add the species and position to the lists
species_list.append('X'+subl+subl_atom)
species_positions.append(list(position))
# create the structure
sublattice_model = [[e for e in sorted(list(set(subl_model[s])))] for s in sorted(subl_model.keys())]
sublattice_names = [s for s in sorted(subl_model.keys())]
sqs = AbstractSQS(direct_lattice, species_list, species_positions, coords_are_cartesian=True,
sublattice_model=sublattice_model,
sublattice_names=sublattice_names)
sqs.modify_lattice(Lattice(lattice))
return sqs
#%%
import math
from pymatgen import Structure, Molecule, Lattice
import os
os.chdir(
'/home/jinho93/oxides/perobskite/lanthanum-aluminate/slab/gulp/nonstochio/La-vac/two'
)
m = Molecule.from_file('tail.xyz')
l = Lattice.from_lengths_and_angles([11.46615, 15.2882, 50], [90, 90, 90])
s = Structure(l, m.species, m.cart_coords, coords_are_cartesian=True)
s.make_supercell([[4, 0, 0], [0, 3, 0], [0, 0, 1]])
s.make_supercell([[1, 1, 0], [1, -1, 0], [0, 0, 1]])
s.sort()
# ll = Lattice.from_lengths_and_angles([s.lattice.a / 2, s.lattice.b / 2, s.lattice.c], s.lattice.angles)
ll = Lattice.from_lengths_and_angles(s.lattice.abc, s.lattice.angles)
s = Structure(ll, s.species, s.cart_coords, coords_are_cartesian=True)
indi = []
for i, site in enumerate(s.sites):
if site.x + site.y < ll.b / math.sqrt(2):
indi.append(i)
# s.remove_sites(indi)
# s = Structure(ll, s.species, s.cart_coords, coords_are_cartesian=True)
# s.to('POSCAR', 'POSCAR')
def _parse(self):
float_patt = re.compile(r"[+-]?\d+\.\d+[EFD]?[+-]?\d+") # -9.3892E+02
start_patt = re.compile(r"^\s*EEEEEEEEEE STARTING DATE \d+")
coord_patt = re.compile(r"^\s+(\d+)\s+(?P<aunit>[TF])\s+(?P<Z>\d+)\s+"
r"(?P<specie>\w+)\s+(?P<x>[+-]?\d+\.\d+E[+-]?\d+)"
r"\s+(?P<y>[+-]?\d+\.\d+E[+-]?\d+)\s+"
r"(?P<z>[+-]?\d+\.\d+E[+-]?\d+)")
coord_nanotube_patt = re.compile(r"^\s+(\d+)\s+(?P<aunit>[TF])\s+(?P<Z>\d+)\s+"
r"(?P<specie>\w+)\s+(?P<x>[+-]?\d+\.\d+E[+-]?\d+)"
r"\s+(?P<y>[+-]?\d+\.\d+E[+-]?\d+)\s+"
r"(?P<z>[+-]?\d+\.\d+E[+-]?\d+)\s+"
r"(?P<radius>\d+\.\d+)")
forces_patt = re.compile(r"^\s+(?P<iat>\d+)\s+(?P<Z>\d+)\s+"
r"(?P<x>[+-]?\d+\.\d+E[+-]?\d+)\s+"
r"(?P<y>[+-]?\d+\.\d+E[+-]?\d+)\s+"
r"(?P<z>[+-]?\d+\.\d+E[+-]?\d+)")
max_grad_patt = re.compile(r"^\sMAX GRADIENT\s+(?P<max_grad>\d+\.\d+)"
r"\s+THRESHOLD\s+(?P<max_grad_thr>\d+\.\d+)")
rms_grad_patt = re.compile(r"^\sRMS GRADIENT\s+(?P<rms_grad>\d+\.\d+)"
r"\s+THRESHOLD\s+(?P<rms_grad_thr>\d+\.\d+)")
max_displac_patt = re.compile(r"^\sMAX DISPLAC\.\s+(?P<max_displac>\d+\.\d+)"
r"\s+THRESHOLD\s+(?P<max_displac_thr>\d+\.\d+)")
rms_displac_patt = re.compile(r"^\sRMS DISPLAC\.\s+(?P<rms_displac>\d+\.\d+)"
r"\s+THRESHOLD\s+(?P<rms_displac_thr>\d+\.\d+)")
norm_grad_patt = re.compile(r"^\s+GRADIENT NORM\s+(?P<norm_grad>\d+\.\d+)"
r"\s+GRADIENT THRESHOLD\s+(?P<norm_grad_thr>\d+\.\d+)")
self.title = ""
self.system = ""
self.group = ""
self.slab = False
self.nanotube = False
self.volumes = list()
self.energies = list()
self.forces = list()
self.convergence_data = list()
self.geometry_converge = False
self.scf_converge = False
external_geometry = False
with open(self.filename, "r", encoding=self.encoding) as f:
# look for starting message
for line in f:
if start_patt.match(line):
self.title = f.readline().strip()
break
# ------------------------------------------------------------------
# first, read the initial geometry & identify the type of structure
# ------------------------------------------------------------------
for line in f:
if re.match(r"^\sGEOMETRY INPUT FROM EXTERNAL FILE", line):
external_geometry = True
line = f.readline()
if "SLAB" in line:
self.slab = True
if "NANOTUBE" in line:
self.nanotube = True
print("WARNING: Geometry from an external file.")
break
if re.match(r"^\sSLAB CALCULATION", line):
self.slab = True
system_patt = re.compile(r"^\sSYSTEM AND LATTICE")
group_patt = re.compile(r" PLANE GROUP N.")
break
if re.match(r"^\sCRYSTAL CALCULATION", line):
system_patt = re.compile(r"^\sCRYSTAL FAMILY")
group_patt = re.compile(r"^\sSPACE GROUP")
break
# look for initial geometry: GEOMETRY FOR WAVEFUNCTION
# read group and crystallographic system
# check if a SLAB or NANOTUBE is built by GEOMETRY EDITING
geom_for_wf = False
for line in f:
if not external_geometry and system_patt.search(line):
self.system = line.split(":")[1].strip()
if not external_geometry and group_patt.search(line):
self.group = line.split(":")[1].strip()
if " SLAB GENERATED " in line:
self.slab = True
# group and system no more relevant
self.group = ""
self.system = ""
if "CONSTRUCTION OF A NANOTUBE FROM A SLAB" in line:
self.nanotube = True
self.slab = False
# group and system no more relevant
self.group = ""
self.system = ""
if re.match(r"^\sGEOMETRY FOR WAVE FUNCTION", line):
geom_for_wf = True
break
if line == "":
# end of file, geometry for wavefunction not found
break
if not geom_for_wf:
# STOP case, add TESTGEOM to d12
raise ValueError("GEOMETRY FOR WAVEFUNCTION NOT FOUND.\n"
"Please, add TESTGEOM in the d12 input file.")
# read until calculation start
# read starting geometry and look for PRIMITIVE or CRYSTALLOGRAPHIC
read_geom = False
while "CRYSTAL - SCF - TYPE OF CALCULATION" not in line:
line = f.readline()
if line == "":
raise ValueError("End of file.")
# search PRIMITIVE CELL
if re.match(r"^\sPRIMITIVE CELL", line):
read_geom = True
geom_patt = re.compile(r"^\sPRIMITIVE CELL")
# search CRYSTALLOGRAPHIC CELL if exist
if re.match(r"^\sCRYSTALLOGRAPHIC CELL", line):
read_geom = True
geom_patt = re.compile(r"^\sCRYSTALLOGRAPHIC CELL")
if read_geom:
if not self.slab and not self.nanotube:
volume = float(line.split("=")[1].split()[0].strip(")"))
self.volumes.append(volume)
f.readline()
# lattice parameters
line = f.readline()
params = [float(val) for val in re.findall(r"\d+\.\d+", line)]
lattice = Lattice.from_lengths_and_angles(params[0:3], params[3:])
# step on for 4 lines
[f.readline() for _ in range(4)]
# read coordinates
species = list() # atom names
uniq = list() # True if atom belong to the asymmetric unit
radius = list() # distance from the axes of the nanotube
coords = list()
while line != "\n":
read = False
line = f.readline()
if self.nanotube and coord_nanotube_patt.match(line):
data = coord_nanotube_patt.match(line).groupdict()
read = True
elif coord_patt.match(line):
data = coord_patt.match(line).groupdict()
read = True
if read:
specie = data["specie"]
specie = specie if len(specie) == 1 else specie[0] + specie[1].lower()
species.append(specie)
coord = [float(data[k]) for k in "xyz"]
uniq.append(True if data["aunit"] == "T" else False)
if self.slab:
coord[2] /= lattice.c
elif self.nanotube:
coord[1] /= lattice.b
coord[2] /= lattice.c
radius.append(float(data["radius"]))
coords.append(coord)
self.structures = [Structure(lattice, species, coords,
site_properties={"aunit": uniq})]
read_geom = False
# ------------------------------------------------------------------
# from that point, SCF, or structure optimization start !
# continue up to the end of file
# ------------------------------------------------------------------
n_geom = 0
cvg_data = dict()
while line != "":
line = f.readline()
if " TOTAL ENERGY" in line:
self.energies.append(float(float_patt.findall(line)[0]))
self.scf_converge = True
if "CARTESIAN FORCES IN HARTREE/BOHR" in line:
# WARNING: Forces are not printed at each geom step
line = f.readline()
forces = list()
for _ in range(self.initial_structure.num_sites):
data = forces_patt.match(f.readline()).groupdict()
forces.append([float(data[c]) for c in "xyz"])
self.forces.append(np.array(forces))
if max_grad_patt.match(line):
cvg_data.update(max_grad_patt.match(line).groupdict())
if rms_grad_patt.match(line):
cvg_data.update(rms_grad_patt.match(line).groupdict())
if max_displac_patt.match(line):
cvg_data.update(max_displac_patt.match(line).groupdict())
if rms_displac_patt.match(line):
cvg_data.update(rms_displac_patt.match(line).groupdict())
if norm_grad_patt.match(line):
cvg_data.update(norm_grad_patt.match(line).groupdict())
if line == "":
# end of file ?
break
if "COORDINATE AND CELL OPTIMIZATION" in line:
cvg_data = {k: float(v) for k, v in cvg_data.items()}
# end of optimization cycle
self.convergence_data.append(cvg_data)
n_geom += 1
cvg_data = dict()
if "FINAL OPTIMIZED GEOMETRY" in line:
self.geometry_converge = True
n_geom += 1
# search structure data
if geom_patt.match(line):
# PRIMITVE or CRYSTALLOGRAPHIC depending on what is present
read_geom = True
if read_geom:
if not self.slab and not self.nanotube:
volume = float(line.split("=")[1].split()[0].strip(")"))
self.volumes.append(volume)
f.readline()
# lattice parameters
line = f.readline()
params = [float(val) for val in re.findall(r"\d+\.\d+", line)]
lattice = Lattice.from_lengths_and_angles(params[0:3], params[3:])
# step on for 4 lines
[f.readline() for _ in range(4)]
# read coordinates
species = list() # atom names
uniq = list() # True if atom belong to the asymmetric unit
radius = list() # distance from the axes of the nanotube
coords = list()
while line != "\n":
read = False
line = f.readline()
if self.nanotube and coord_nanotube_patt.match(line):
data = coord_nanotube_patt.match(line).groupdict()
read = True
elif coord_patt.match(line):
data = coord_patt.match(line).groupdict()
read = True
if read:
specie = data["specie"]
specie = specie if len(specie) == 1 else specie[0] + specie[1].lower()
species.append(specie)
coord = [float(data[k]) for k in "xyz"]
uniq.append(True if data["aunit"] == "T" else False)
if self.slab:
coord[2] /= lattice.c
elif self.nanotube:
coord[1] /= lattice.b
coord[2] /= lattice.c
radius.append(float(data["radius"]))
coords.append(coord)
self.structures.append(Structure(lattice, species, coords,
site_properties={"aunit": uniq}))
read_geom = False
def _parse(self):
float_patt = re.compile(r"[+-]?\d+\.\d+[EFD]?[+-]?\d+") # -9.3892E+02
start_patt = re.compile(r"^\s*EEEEEEEEEE STARTING DATE \d+")
coord_patt = re.compile(
r"^\s+(\d+)\s+(?P<aunit>[TF])\s+(?P<Z>\d+)\s+"
r"(?P<specie>\w+)\s+(?P<x>[+-]?\d+\.\d+E[+-]?\d+)"
r"\s+(?P<y>[+-]?\d+\.\d+E[+-]?\d+)\s+"
r"(?P<z>[+-]?\d+\.\d+E[+-]?\d+)")
coord_nanotube_patt = re.compile(
r"^\s+(\d+)\s+(?P<aunit>[TF])\s+(?P<Z>\d+)\s+"
r"(?P<specie>\w+)\s+(?P<x>[+-]?\d+\.\d+E[+-]?\d+)"
r"\s+(?P<y>[+-]?\d+\.\d+E[+-]?\d+)\s+"
r"(?P<z>[+-]?\d+\.\d+E[+-]?\d+)\s+"
r"(?P<radius>\d+\.\d+)")
forces_patt = re.compile(r"^\s+(?P<iat>\d+)\s+(?P<Z>\d+)\s+"
r"(?P<x>[+-]?\d+\.\d+E[+-]?\d+)\s+"
r"(?P<y>[+-]?\d+\.\d+E[+-]?\d+)\s+"
r"(?P<z>[+-]?\d+\.\d+E[+-]?\d+)")
max_grad_patt = re.compile(
r"^\sMAX GRADIENT\s+(?P<max_grad>\d+\.\d+)"
r"\s+THRESHOLD\s+(?P<max_grad_thr>\d+\.\d+)")
rms_grad_patt = re.compile(
r"^\sRMS GRADIENT\s+(?P<rms_grad>\d+\.\d+)"
r"\s+THRESHOLD\s+(?P<rms_grad_thr>\d+\.\d+)")
max_displac_patt = re.compile(
r"^\sMAX DISPLAC\.\s+(?P<max_displac>\d+\.\d+)"
r"\s+THRESHOLD\s+(?P<max_displac_thr>\d+\.\d+)")
rms_displac_patt = re.compile(
r"^\sRMS DISPLAC\.\s+(?P<rms_displac>\d+\.\d+)"
r"\s+THRESHOLD\s+(?P<rms_displac_thr>\d+\.\d+)")
norm_grad_patt = re.compile(
r"^\s+GRADIENT NORM\s+(?P<norm_grad>\d+\.\d+)"
r"\s+GRADIENT THRESHOLD\s+(?P<norm_grad_thr>\d+\.\d+)")
self.title = ""
self.system = ""
self.group = ""
self.slab = False
self.nanotube = False
self.volumes = list()
self.energies = list()
self.forces = list()
self.convergence_data = list()
self.geometry_converge = False
self.scf_converge = False
external_geometry = False
with open(self.filename, "r", encoding=self.encoding) as f:
# look for starting message
for line in f:
if start_patt.match(line):
self.title = f.readline().strip()
break
# ------------------------------------------------------------------
# first, read the initial geometry & identify the type of structure
# ------------------------------------------------------------------
for line in f:
if re.match(r"^\sGEOMETRY INPUT FROM EXTERNAL FILE", line):
external_geometry = True
line = f.readline()
if "SLAB" in line:
self.slab = True
if "NANOTUBE" in line:
self.nanotube = True
print("WARNING: Geometry from an external file.")
break
if re.match(r"^\sSLAB CALCULATION", line):
self.slab = True
system_patt = re.compile(r"^\sSYSTEM AND LATTICE")
group_patt = re.compile(r" PLANE GROUP N.")
break
if re.match(r"^\sCRYSTAL CALCULATION", line):
system_patt = re.compile(r"^\sCRYSTAL FAMILY")
group_patt = re.compile(r"^\sSPACE GROUP")
break
# look for initial geometry: GEOMETRY FOR WAVEFUNCTION
# read group and crystallographic system
# check if a SLAB or NANOTUBE is built by GEOMETRY EDITING
geom_for_wf = False
for line in f:
if not external_geometry and system_patt.search(line):
self.system = line.split(":")[1].strip()
if not external_geometry and group_patt.search(line):
self.group = line.split(":")[1].strip()
if " SLAB GENERATED " in line:
self.slab = True
# group and system no more relevant
self.group = ""
self.system = ""
if "CONSTRUCTION OF A NANOTUBE FROM A SLAB" in line:
self.nanotube = True
self.slab = False
# group and system no more relevant
self.group = ""
self.system = ""
if re.match(r"^\sGEOMETRY FOR WAVE FUNCTION", line):
geom_for_wf = True
break
if line == "":
# end of file, geometry for wavefunction not found
break
if not geom_for_wf:
# STOP case, add TESTGEOM to d12
raise ValueError("GEOMETRY FOR WAVEFUNCTION NOT FOUND.\n"
"Please, add TESTGEOM in the d12 input file.")
# read until calculation start
# read starting geometry and look for PRIMITIVE or CRYSTALLOGRAPHIC
read_geom = False
while "CRYSTAL - SCF - TYPE OF CALCULATION" not in line:
line = f.readline()
if line == "":
raise ValueError("End of file.")
# search PRIMITIVE CELL
if re.match(r"^\sPRIMITIVE CELL", line):
read_geom = True
geom_patt = re.compile(r"^\sPRIMITIVE CELL")
# search CRYSTALLOGRAPHIC CELL if exist
if re.match(r"^\sCRYSTALLOGRAPHIC CELL", line):
read_geom = True
geom_patt = re.compile(r"^\sCRYSTALLOGRAPHIC CELL")
if read_geom:
if not self.slab and not self.nanotube:
volume = float(
line.split("=")[1].split()[0].strip(")"))
self.volumes.append(volume)
f.readline()
# lattice parameters
line = f.readline()
params = [
float(val) for val in re.findall(r"\d+\.\d+", line)
]
lattice = Lattice.from_lengths_and_angles(
params[0:3], params[3:])
# step on for 4 lines
[f.readline() for _ in range(4)]
# read coordinates
species = list() # atom names
uniq = list() # True if atom belong to the asymmetric unit
radius = list() # distance from the axes of the nanotube
coords = list()
while line != "\n":
read = False
line = f.readline()
if self.nanotube and coord_nanotube_patt.match(line):
data = coord_nanotube_patt.match(line).groupdict()
read = True
elif coord_patt.match(line):
data = coord_patt.match(line).groupdict()
read = True
if read:
specie = data["specie"]
specie = specie if len(
specie
) == 1 else specie[0] + specie[1].lower()
species.append(specie)
coord = [float(data[k]) for k in "xyz"]
uniq.append(True if data["aunit"] ==
"T" else False)
if self.slab:
coord[2] /= lattice.c
elif self.nanotube:
coord[1] /= lattice.b
coord[2] /= lattice.c
radius.append(float(data["radius"]))
coords.append(coord)
self.structures = [
Structure(lattice,
species,
coords,
site_properties={"aunit": uniq})
]
read_geom = False
# ------------------------------------------------------------------
# from that point, SCF, or structure optimization start !
# continue up to the end of file
# ------------------------------------------------------------------
n_geom = 0
cvg_data = dict()
while line != "":
line = f.readline()
if " TOTAL ENERGY" in line:
self.energies.append(float(float_patt.findall(line)[0]))
self.scf_converge = True
if "CARTESIAN FORCES IN HARTREE/BOHR" in line:
# WARNING: Forces are not printed at each geom step
line = f.readline()
forces = list()
for _ in range(self.initial_structure.num_sites):
data = forces_patt.match(f.readline()).groupdict()
forces.append([float(data[c]) for c in "xyz"])
self.forces.append(np.array(forces))
if max_grad_patt.match(line):
cvg_data.update(max_grad_patt.match(line).groupdict())
if rms_grad_patt.match(line):
cvg_data.update(rms_grad_patt.match(line).groupdict())
if max_displac_patt.match(line):
cvg_data.update(max_displac_patt.match(line).groupdict())
if rms_displac_patt.match(line):
cvg_data.update(rms_displac_patt.match(line).groupdict())
if norm_grad_patt.match(line):
cvg_data.update(norm_grad_patt.match(line).groupdict())
if line == "":
# end of file ?
break
if "COORDINATE AND CELL OPTIMIZATION" in line:
cvg_data = {k: float(v) for k, v in cvg_data.items()}
# end of optimization cycle
self.convergence_data.append(cvg_data)
n_geom += 1
cvg_data = dict()
if "FINAL OPTIMIZED GEOMETRY" in line:
self.geometry_converge = True
n_geom += 1
# search structure data
if geom_patt.match(line):
# PRIMITVE or CRYSTALLOGRAPHIC depending on what is present
read_geom = True
if read_geom:
if not self.slab and not self.nanotube:
volume = float(
line.split("=")[1].split()[0].strip(")"))
self.volumes.append(volume)
f.readline()
# lattice parameters
line = f.readline()
params = [
float(val) for val in re.findall(r"\d+\.\d+", line)
]
lattice = Lattice.from_lengths_and_angles(
params[0:3], params[3:])
# step on for 4 lines
[f.readline() for _ in range(4)]
# read coordinates
species = list() # atom names
uniq = list() # True if atom belong to the asymmetric unit
radius = list() # distance from the axes of the nanotube
coords = list()
while line != "\n":
read = False
line = f.readline()
if self.nanotube and coord_nanotube_patt.match(line):
data = coord_nanotube_patt.match(line).groupdict()
read = True
elif coord_patt.match(line):
data = coord_patt.match(line).groupdict()
read = True
if read:
specie = data["specie"]
specie = specie if len(
specie
) == 1 else specie[0] + specie[1].lower()
species.append(specie)
coord = [float(data[k]) for k in "xyz"]
uniq.append(True if data["aunit"] ==
"T" else False)
if self.slab:
coord[2] /= lattice.c
elif self.nanotube:
coord[1] /= lattice.b
coord[2] /= lattice.c
radius.append(float(data["radius"]))
coords.append(coord)
self.structures.append(
Structure(lattice,
species,
coords,
site_properties={"aunit": uniq}))
read_geom = False
def build_gb(self,
vacuum=0.0,
add_if_dist=0.0,
to_primitive=True,
delete_layer="0b0t0b0t",
tol=0.25):
"""
Build the GB based on the given crystal, uc of grain A and B, if_model,
vacuum thickness, distance between two grains and tolerance factor.
Args:
vacuum (float), Angstrom: Vacuum thickness for GB.
Default to 0.0
add_if_dist (float), Angstrom: Add extra distance at the interface
between two grains.
Default to 0.0
to_primitive (bool): Whether to get primitive structure of GB.
Default to true.
delete_layer (str): Delete interface layers on both sides of each grain.
8 characters in total. The first 4 characters is for grain A and
the other 4 is for grain B. "b" means bottom layer and "t" means
top layer. Integer represents the number of layers to be deleted.
Default to "0b0t0b0t", which means no deletion of layers. The
direction of top and bottom layers is based on gb_direction.
tol (float), Angstrom: Tolerance factor to determine whether two
atoms are at the same plane.
Default to 0.25
Returns:
GB structure (Grain)
"""
ind = self.gb_direction
delete_layer = delete_layer.lower()
delete = re.findall('(\d+)(\w)', delete_layer)
if len(delete) != 4:
raise ValueError(
"'%s' is not supported. Please make sure the format "
"is 0b0t0b0t.")
for i, v in enumerate(delete):
for j in range(int(v[0])):
if i <= 1:
self.grain_a.delete_bt_layer(v[1], tol, ind)
else:
self.grain_b.delete_bt_layer(v[1], tol, ind)
abc_a = list(self.grain_a.lattice.abc)
abc_b, angles = self.grain_b.lattice.lengths_and_angles
if ind == 1:
l = (abc_a[ind] + add_if_dist) * sin(radians(angles[2]))
else:
l = abc_a[ind] + add_if_dist
abc_a[ind] += abc_b[ind] + 2 * add_if_dist + vacuum
new_lat = Lattice.from_lengths_and_angles(abc_a, angles)
a_fcoords = new_lat.get_fractional_coords(self.grain_a.cart_coords)
grain_a = Grain(new_lat, self.grain_a.species, a_fcoords)
l_vector = [0, 0]
l_vector.insert(ind, l)
b_fcoords = new_lat.get_fractional_coords(self.grain_b.cart_coords +
l_vector)
grain_b = Grain(new_lat, self.grain_b.species, b_fcoords)
gb = Grain.from_sites(grain_a[:] + grain_b[:])
gb = gb.get_sorted_structure()
if to_primitive:
gb = gb.get_primitive_structure()
return gb
