def test_impose_symmetry():
total_path = os.path.dirname(os.path.abspath(__file__))
os.chdir(total_path)
# initialize the dynamical matrix
dyn = CC.Phonons.Phonons("old_dyn", full_name=True)
# Print the symmetry group at high threshold
GROUP = spglib.get_spacegroup(dyn.structure.get_ase_atoms(), 0.05)
s_group_expected = spglib.get_spacegroup(dyn.structure.get_ase_atoms())
print ("Space group with high threshold:", s_group_expected)
print ("Space group with low threshold:", GROUP)
# Get the symmetries from the new spacegroup
symmetries = spglib.get_symmetry(dyn.structure.get_ase_atoms(), symprec = 0.05)
print("Number of symmetries: {}".format(len(symmetries["rotations"])))
# Transform the spglib symmetries into the CellConstructor data type
sym_mats = CC.symmetries.GetSymmetriesFromSPGLIB(symmetries, True)
# Force the symmetrization
dyn.structure.impose_symmetries(sym_mats)
# Check once again the symetry
s_group_after = spglib.get_spacegroup(dyn.structure.get_ase_atoms())
print ("New space group with high threshold:", s_group_after)
assert s_group_after == GROUP
def test_supercell_replica():
total_path = os.path.dirname(os.path.abspath(__file__))
os.chdir(total_path)
# Load the structure
struct = CC.Structure.Structure()
struct.read_scf("unit_cell_structure.scf")
# Generate a supercell
super_struct = struct.generate_supercell((2, 2, 1))
print("Space group before:")
print(spglib.get_spacegroup(super_struct.get_ase_atoms()), )
print(
len(spglib.get_symmetry(super_struct.get_ase_atoms())["translations"]))
# Get the symmetries in the supercell using spglib
spglib_syms = spglib.get_symmetry(super_struct.get_ase_atoms())
syms = CC.symmetries.GetSymmetriesFromSPGLIB(spglib_syms, False)
nsyms = len(syms)
# Generate a random distorted super structure
d_structure = super_struct.copy()
d_structure.coords += np.random.normal(scale=0.1,
size=np.shape(d_structure.coords))
# Get the new pool of structures
new_d_structures = []
for i in range(nsyms):
# Get irt
irt = CC.symmetries.GetIRT(super_struct, syms[i])
#print "Symmetry ", i
#print len(set(irt))
u_disp = d_structure.coords - super_struct.coords
new_u_disp = CC.symmetries.ApplySymmetryToVector(
syms[i], u_disp, super_struct.unit_cell, irt[:])
tmp = super_struct.copy()
tmp.coords += new_u_disp
tmp.save_scf("replica_%d.scf" % i)
new_d_structures.append(tmp)
# Average all the displacements to see if the symmetries are recovered correctly
new_structure = super_struct.copy()
new_structure.coords = np.sum([x.coords
for x in new_d_structures], axis=0) / nsyms
# Get again the symmetries
print("Symmetries after the sum:")
print(spglib.get_spacegroup(new_structure.get_ase_atoms()), )
print(
len(
spglib.get_symmetry(
new_structure.get_ase_atoms())["translations"]))
# Lets check if the structure is the same as before
# Should be 0 only if the symmeties are enaugh to have 0 force.
print("Difference from the first one:")
print(np.sqrt(np.sum((new_structure.coords - super_struct.coords)**2)))
def get_sym(cell, symprec=1e-5, print_atom=False, print_analysis=True):
'''Giving a cell, return symmetry analysis'''
# spglib only work with tuple
cell = tuple(cell)
#Space group info
spg_label, spg_number = spglib.get_spacegroup(cell, symprec).split(' ')
spg_number = spg_number.split("(")[1].split(")")[0]
Schoenflies_label = spglib.get_spacegroup(cell, symprec,
symbol_type=1).split(' ')[0]
sym = spglib.get_symmetry(cell, symprec)
rotations = sym['rotations']
translations = sym['translations']
equi_atoms = sym['equivalent_atoms']
is_std = is_prim = False
std_cell = spglib.refine_cell(cell, symprec)
prim_cell = spglib.find_primitive(cell, symprec)
if compare_cells(cell, std_cell): is_std = True
if compare_cells(cell, prim_cell): is_prim = True
atoms = utils.convert_atomtype(cell[2])
if print_analysis == True:
#Cell info
std_cell = spglib.refine_cell(cell, symprec)
prim_cell = spglib.find_primitive(cell, symprec)
#Print
misc.print_msg("Spacegroup number : %s" % (spg_number))
misc.print_msg("Short International symbol : %s" % (spg_label))
misc.print_msg("Schoenflies symbol : %s" %
(Schoenflies_label))
if print_atom == True:
misc.print_msg("Atoms list (No. - Sym - Symbol):")
for i, atom in enumerate(atoms):
misc.print_msg("%3d %3d %s" %
(i + 1, equi_atoms[i] + 1, atom))
misc.print_msg("Irreducible atoms:")
for i, index in enumerate(np.unique(equi_atoms)):
coord = cell[1][index]
misc.print_msg(
"%3d %3s %7f5 %7f5 %7f5" %
(i + 1, atoms[index], coord[0], coord[1], coord[2]))
misc.print_msg("Number of irreducible atoms : %d" %
(np.unique(equi_atoms).shape[0]))
misc.print_msg("Standard cell : %r" % (is_std))
misc.print_msg("Primitive cell : %r" % (is_prim))
else:
# Return an standard cell object with irreducible atoms
irred_idx = np.unique(equi_atoms)
lattice = cell[0]
irred_coord = cell[1][irred_idx, :]
irred_label = np.array(cell[2])[irred_idx]
irred_cell = (lattice, irred_coord, irred_label)
return irred_cell, int(spg_number), spg_label, rotations, translations
def refine(ase_obj, accuracy=1E-03):
"""
Refine ASE structure using spglib
Args:
ase_obj: (object) ASE structure
accuracy: (float) spglib tolerance, normally within [1E-02, 1E-04]
Returns:
Refined ASE structure (object) *or* None
None *or* error (str)
"""
try:
symmetry = spglib.get_spacegroup(ase_obj, symprec=accuracy)
lattice, positions, numbers = spglib.refine_cell(ase_obj,
symprec=accuracy)
except:
return None, 'Error while structure refinement'
try:
spacegroup = int(symmetry.split()[1].replace("(", "").replace(")", ""))
except (ValueError, IndexError):
return None, 'Symmetry error (coinciding atoms?) in structure'
try:
return crystal(Atoms(numbers=numbers,
cell=lattice,
scaled_positions=positions,
pbc=True),
spacegroup=spacegroup,
primitive_cell=True,
onduplicates='replace'), None
except:
return None, 'Unrecognized sites or invalid site symmetry in structure'
def symmetrise(self, sbs=[], symprec=1e-2):
import spglib
if len(sbs) == 0:
sbs = range(self.nframes)
for i in sbs:
frame = self.frames[i]
frame.info['space_group'] = spglib.get_spacegroup(frame, symprec=symprec)
def main(fxyz, prefix, verbose, precision):
# read frames
if fxyz != 'none':
frames = read(fxyz, ':')
nframes = len(frames)
print("read xyz file:", fxyz, ", a total of", nframes, "frames")
standardized_frames = []
for frame in frames:
space_now = spglib.get_spacegroup(
frame,
symprec=precision) # spglib.get_symmetry(frame, symprec=1e-1))
print(space_now)
lattice, scaled_positions, numbers = spglib.standardize_cell(
frame, to_primitive=1, no_idealize=1, symprec=precision)
if verbose:
show_cell(lattice, scaled_positions, numbers)
# output
frtemp = atom(numbers=numbers,
cell=lattice,
scaled_positions=scaled_positions,
pbc=frame.get_pbc())
frtemp.info['space_group'] = space_now
standardized_frames.append(frtemp)
write(prefix + '-standardized.xyz', standardized_frames)
def get_primitive_cell(axis, atom_pos):
import spglib
import numpy as np
L = np.mat(axis)
pos = []
atom_type = []
atom_dic = {}
type_dic = {}
index = 0
for line in atom_pos:
pos.append(line[0:3])
if not line[4] in atom_dic.keys():
atom_dic[line[4]] = index
type_dic[index] = [line[3], line[4]]
index = index + 1
atom_type.append(atom_dic[line[4]])
D = np.mat(pos)
Cell = (L, D, atom_type)
prim_cell = spglib.find_primitive(Cell, symprec=2e-3)
equ_atoms = spglib.get_symmetry_dataset(prim_cell,
symprec=2e-3)['equivalent_atoms']
prim_axis = prim_cell[0].tolist()
prim_pos = prim_cell[1].tolist()
prim_type = prim_cell[2].tolist()
prim_atom_pos = []
for i in range(len(prim_pos)):
prim_atom_pos.append(prim_pos[i] + type_dic[prim_type[i]])
sym = spglib.get_spacegroup(Cell, symprec=2e-3).split('(')[1].split(')')[0]
[new_axis, new_pos, sym_typ] = axis_rotation(prim_axis, prim_atom_pos, sym)
return [new_axis, new_pos, sym_typ]
def get_lattice_type(self):
'''
Find the symmetry of the crystal using spglib symmetry finder.
Assign to sg_name i sg_nr members name of the space group and
its number extracted from the result. Based on the group number
identify also the lattice type (assigned to sg_type member) and
the Bravais lattice of the crystal (assigned to bravais member).
The returned value is the lattice type number.
The lattice type numbers are
(see also Crystal.ls, the numbering starts from 1):
Triclinic (1), Monoclinic (2), Orthorombic (3), Tetragonal (4)
Trigonal (5), Hexagonal (6), Cubic (7)
'''
# Table of lattice types and correcponding group numbers dividing
# the ranges. See get_lattice_type method for precise definition.
lattice_types = [[3, "Triclinic"], [16, "Monoclinic"],
[75, "Orthorombic"], [143, "Tetragonal"],
[168, "Trigonal"], [195, "Hexagonal"], [231, "Cubic"]]
sg = spg.get_spacegroup(self)
m = re.match('([A-Z].*\\b)\s*\(([0-9]*)\)', sg)
self.sg_name = m.group(1)
self.sg_nr = int(m.group(2))
for n, l in enumerate(lattice_types):
if self.sg_nr < l[0]:
lattice = l[1]
lattype = n + 1
break
self.sg_type = lattype
self.bravais = lattice
return lattype
def write_struct_boltztrap(structure, filename):
ao = io.read(structure)
spacegroup = spglib.get_spacegroup(ao, symprec=1e-5)
ao.info = {'spacegroup': spacegroup}
filename = str(filename + ".struct")
with open(filename, "w") as out:
out.write('HTE output' + '\n') # title
latt = ao.get_cell() / 0.5291772083
for i in range(3):
line = ''
for j in range(3):
line = line + "%12.5f" % latt[i][j]
out.write(line + '\n')
krot = get_kspace_operations(ao)
out.write(str(len(krot)) + '\n')
for iop in range(len(krot)):
for i in range(3):
for j in range(3):
out.write(str(krot[iop][i][j]) + ' ')
out.write('\n')
return
def get_interstitials(ats, ttol=0.5):
"""Function to return unique interstitial sites in the given structure.
Args:
Atoms(:ase:class:`Atoms`): atoms object.
ttol(float): tolerance on distance between interstitials to be considered unique.
Returns:
list of unique intestital sites (cartesian (x,y,z) as list) in the given structure.
"""
# s = deepcopy(structure)
# prim = primitive(s)
spg = spglib.get_spacegroup(ats, 0.1)
### Step 1: get unique sites in the primitive of the given structure
uniq_sites = get_unique_wyckoff(ats)
### Step 2: get all interstitial sites from Voronoi method
ints2 = get_all_interstitials(ats, uniq_sites)
### get interstital sites within primitive cell
ints_prim = get_ints_in_prim_cell(ats, ints2)
### Step 3: get unique interstitials after symmetry analysis
ints3 = get_unique_ints(ats, ints_prim, ttol=ttol)
return ints3
def mongo_atoms_doc(atoms):
"""Return a dictionary of an Atoms object."""
d = OrderedDict(atoms=[{
'symbol': atom.symbol,
'position': json.loads(encode(atom.position)),
'tag': atom.tag,
'index': atom.index,
'charge': atom.charge,
'momentum': json.loads(encode(atom.momentum)),
'magmom': atom.magmom
} for atom in atoms],
cell=atoms.cell,
pbc=atoms.pbc,
info=atoms.info,
constraints=[c.todict() for c in atoms.constraints])
# redundant information for search convenience.
d['natoms'] = len(atoms)
cell = atoms.get_cell()
if cell is not None and np.linalg.det(cell) > 0:
d['volume'] = atoms.get_volume()
d['mass'] = sum(atoms.get_masses())
syms = atoms.get_chemical_symbols()
d['chemical_symbols'] = list(set(syms))
d['symbol_counts'] = {sym: syms.count(sym) for sym in syms}
d['spacegroup'] = spglib.get_spacegroup(atoms)
d['hash'] = get_hash(atoms)
return json.loads(encode(d))
def _make_atoms_dict(atoms):
'''
Convert an ase.Atoms object into a dictionary for json storage.
Arg:
atoms ase.Atoms object
Returns:
atoms_dict A dictionary with various atoms information stored
'''
atoms_dict = OrderedDict(
atoms=[{
'symbol': atom.symbol,
'position': json.loads(encode(atom.position)),
'tag': atom.tag,
'index': atom.index,
'charge': atom.charge,
'momentum': json.loads(encode(atom.momentum)),
'magmom': atom.magmom
} for atom in atoms],
cell=atoms.cell,
pbc=atoms.pbc,
info=atoms.info,
constraints=[c.todict() for c in atoms.constraints])
# Redundant information for search convenience.
atoms_dict['natoms'] = len(atoms)
cell = atoms.get_cell()
atoms_dict['mass'] = sum(atoms.get_masses())
syms = atoms.get_chemical_symbols()
atoms_dict['chemical_symbols'] = list(set(syms))
atoms_dict['symbol_counts'] = {sym: syms.count(sym) for sym in syms}
atoms_dict['spacegroup'] = spglib.get_spacegroup(atoms)
if cell is not None and np.linalg.det(cell) > 0:
atoms_dict['volume'] = atoms.get_volume()
return json.loads(encode(atoms_dict))
def gulp_opt(stru):
gulp_inp = 'opt.gin'
tp_inp = 'tp_inp'
out = 'out'
cif_out = 'final.cif'
symprec = 0.01
ccell = standardize_cell((stru.cell, stru.get_scaled_positions(), stru.numbers), symprec=symprec)
if ccell:
symmetry = get_symmetry(ccell, symprec=symprec)
spacegroup = get_spacegroup(ccell, symprec=symprec)
else:
symmetry = get_symmetry((stru.cell, stru.get_scaled_positions(), stru.numbers), symprec=symprec)
spacegroup = get_spacegroup((stru.cell, stru.get_scaled_positions(), stru.numbers), symprec=symprec)
asymmetric_atoms = np.unique(symmetry.equivalent_atoms)
pass
def symmetry(self, symprec=1e-3):
""" Compute space group with spglib. """
from matador.utils.cell_utils import doc2spg
import spglib as spg
print('Refining symmetries...')
if self.mode == 'display':
print_warning('{}'.format('At symprec: ' + str(symprec)))
print_warning("{:^36}{:^16}{:^16}".format('text_id', 'new sg', 'old sg'))
for _, doc in enumerate(self.cursor):
try:
spg_cell = doc2spg(doc)
sg = spg.get_spacegroup(spg_cell, symprec=symprec).split(' ')[0]
if sg != doc['space_group']:
self.changed_count += 1
self.diff_cursor.append(doc)
if self.mode == 'display':
print_notify("{:^36}{:^16}{:^16}"
.format(doc['text_id'][0]+' '+doc['text_id'][1], sg, doc['space_group']))
doc['space_group'] = sg
else:
if self.mode == 'display':
print("{:^36}{:^16}{:^16}"
.format(doc['text_id'][0]+' '+doc['text_id'][1], sg, doc['space_group']))
except Exception:
self.failed_count += 1
if self.args.get('debug'):
print_exc()
print_failure('Failed for' + ' '.join(doc['text_id']))
def findsym(fname, prec=None, verbose=True):
'''
Reads cif file using ASE parser and extracts symmetry using spglib
over different levels of tolerence
'''
if prec:
assert (type(prec) == type(1e-10))
precs = [prec]
else:
t = [1, 2, 3, 5, 7]
precs = [1e-10, 1e-9, 1e-8, 1e-7, 1e-6] + [
i * j for i in [1e-5, 1e-4, 1e-3, 1e-2, 1e-1] for j in t
]
old = ''
if verbose: print('# Tolerance\tSpace group')
cell = ase.io.read(fname)
for prec in precs:
s = spglib.get_spacegroup(cell, symprec=prec)
if s != old:
if verbose: print(f'{prec}\t\t{s}')
old = s
sg, sgid = old.split(' (')
sgid = sgid.replace(')', '')
return sg, sgid
def get_spacegroup_and_kpath(structure, symprec=1.0e-9):
"""
:param: structure is an instance of crystal()
"""
lattice = structure.cell
positions = []
numbers = []
a = np.sqrt(structure.cell[0][0]**2 + structure.cell[0][1]**2 +
structure.cell[0][2]**2)
b = np.sqrt(structure.cell[1][0]**2 + structure.cell[1][1]**2 +
structure.cell[1][2]**2)
c = np.sqrt(structure.cell[2][0]**2 + structure.cell[2][1]**2 +
structure.cell[2][2]**2)
frac_coord = structure.get_fractional()
for i in range(len(frac_coord)):
positions.append(
[frac_coord[i][1], frac_coord[i][2],
frac_coord[i][3]]) # must be fractional coordinates
numbers.append(element[frac_coord[i][0]].number)
cell = (lattice, positions, numbers)
return [
spglib.get_spacegroup(cell, symprec=symprec),
seekpath.get_path(cell)
]
def mongo_atoms_doc(atoms):
"""Return a dictionary of an Atoms object."""
d = OrderedDict(atoms=[{'symbol': atom.symbol,
'position': json.loads(encode(atom.position)),
'tag': atom.tag,
'index': atom.index,
'charge': atom.charge,
'momentum': json.loads(encode(atom.momentum)),
'magmom': atom.magmom}
for atom in atoms],
cell=atoms.cell,
pbc=atoms.pbc,
info=atoms.info,
constraints=[c.todict() for c in atoms.constraints])
# redundant information for search convenience.
d['natoms'] = len(atoms)
cell = atoms.get_cell()
if cell is not None and np.linalg.det(cell) > 0:
d['volume'] = atoms.get_volume()
d['mass'] = sum(atoms.get_masses())
syms = atoms.get_chemical_symbols()
d['chemical_symbols'] = list(set(syms))
d['symbol_counts'] = {sym: syms.count(sym) for sym in syms}
d['spacegroup'] = spglib.get_spacegroup(atoms)
return json.loads(encode(d))
def get_lattice_type(cryst):
'''Find the symmetry of the crystal using spglib symmetry finder.
Derive name of the space group and its number extracted from the result.
Based on the group number identify also the lattice type and the Bravais
lattice of the crystal. The lattice type numbers are
(the numbering starts from 1):
Triclinic (1), Monoclinic (2), Orthorombic (3),
Tetragonal (4), Trigonal (5), Hexagonal (6), Cubic (7)
:param cryst: ASE Atoms object
:returns: tuple (lattice type number (1-7), lattice name, space group
name, space group number)
'''
# Table of lattice types and correcponding group numbers dividing
# the ranges. See get_lattice_type method for precise definition.
lattice_types = [[3, "Triclinic"], [16, "Monoclinic"], [75, "Orthorombic"],
[143, "Tetragonal"], [168, "Trigonal"],
[195, "Hexagonal"], [231, "Cubic"]]
sg = spg.get_spacegroup(cryst)
m = re.match(r'([A-Z].*\b)\s*\(([0-9]*)\)', sg)
sg_name = m.group(1)
sg_nr = int(m.group(2))
for n, l in enumerate(lattice_types):
if sg_nr < l[0]:
bravais = l[1]
lattype = n + 1
break
return lattype, bravais, sg_name, sg_nr
def test_spglib_symmetries(self):
self.assertTrue(__SPGLIB__)
self.assertTrue(__ASE__)
if __SPGLIB__ and __ASE__:
spacegroup = spglib.get_spacegroup(self.struct_ice.get_ase_atoms())
self.assertEqual(spacegroup, "Cmc2_1 (36)")
def space_group_analyse(lattice, pos):
numbers = [1, 2]
cell = (lattice, pos, numbers)
sp = spglib.get_spacegroup(cell, symprec=1e-5)
symm = spglib.get_symmetry(cell, symprec=1e-5)
#print(spglib.niggli_reduce(lattice, eps=1e-5))
#mesh = [8, 8, 8]
#mapping, grid = spglib.get_ir_reciprocal_mesh(mesh, cell, is_shift=[0, 0, 0])
## All k-points and mapping to ir-grid points
#for i, (ir_gp_id, gp) in enumerate(zip(mapping, grid)):
# print("%3d ->%3d %s" % (i, ir_gp_id, gp.astype(float) / mesh))
#
## Irreducible k-points
#print("Number of ir-kpoints: %d" % len(np.unique(mapping)))
#print(grid[np.unique(mapping)] / np.array(mesh, dtype=float))
#
##
## With shift
##
#mapping, grid = spglib.get_ir_reciprocal_mesh(mesh, cell, is_shift=[1, 1, 1])
#
## All k-points and mapping to ir-grid points
#for i, (ir_gp_id, gp) in enumerate(zip(mapping, grid)):
# print("%3d ->%3d %s" % (i, ir_gp_id, (gp + [0.5, 0.5, 0.5]) / mesh))
#
## Irreducible k-points
#print("Number of ir-kpoints: %d" % len(np.unique(mapping)))
#print((grid[np.unique(mapping)] + [0.5, 0.5, 0.5]) / mesh)
return sp, symm
def get_spacegroup(structure):
"""
returns the spacegorup of a given AiiDA structure
"""
import spglib
s_ase = structure.get_ase()
spacegroup = spglib.get_spacegroup(s_ase, symprec=1e-5)
return spacegroup
def test_check_fc_symmetry():
total_path = os.path.dirname(os.path.abspath(__file__))
os.chdir(total_path)
"""
This script check the symmetries of a dynamical matrix.
In the end the symmetry is constrained.
"""
RyToCm = 109691.40235
# Read the dynamical matrix
PH = CC.Phonons.Phonons("hydrogen_dyn", nqirr=1)
print("Loaded hydrogen_dyn1")
print("Symmetry group:",
spglib.get_spacegroup(PH.structure.get_ase_atoms(), 0.01))
# Get info about the symmetries of the structure
symmetries = spglib.get_symmetry(PH.structure.get_ase_atoms(), 0.01)
print("Number of symmetries:", len(symmetries["rotations"]))
# Convert the spglib symmetries into the cellconstructor format
sym_mats = CC.symmetries.GetSymmetriesFromSPGLIB(symmetries)
# Impose the symmetries on the structure
PH.structure.fix_coords_in_unit_cell()
PH.structure.impose_symmetries(sym_mats)
# get a random matrix
nat = PH.structure.N_atoms
#PH.dynmats[0][:,:] = np.random.uniform(size = (3 * nat, 3*nat))
#PH.dynmats[0] += PH.dynmats[0].T
# Get frequencies of the original matrix
w, pols = PH.DyagDinQ(0)
PH_new = PH.Copy()
# Force the symmetrization
#PH_new.SymmetrizeSupercell((1,1,1))
qe_sym = CC.symmetries.QE_Symmetry(PH.structure)
#qe_sym.SetupQPoint(verbose = True)
qe_sym.SetupFromSPGLIB()
#qe_sym.SymmetrizeDynQ(PH_new.dynmats[0], np.array([0,0,0]))
qe_sym.ApplySymmetriesToV2(PH_new.dynmats[0])
CC.symmetries.CustomASR(PH_new.dynmats[0])
new_w, new_pols = PH_new.DyagDinQ(0)
# Symmetrize using the quantum espresso
PH.Symmetrize()
w_qe, p_qe = PH.DyagDinQ(0)
print("Old Matrix | Python Symmetries | QE Symmetries | ")
print("\n".join([
"%12.2f\t%12.2f\t%12.2f cm-1" %
(w[k] * RyToCm, new_w[k] * RyToCm, w_qe[k] * RyToCm)
for k in range(0, len(w))
]))
def get_sym(cell, symprec=1e-5, print_atom=False, export_operator=False):
#Space group info
intl_label, number = spglib.get_spacegroup(cell, symprec).split(' ')
number = number.split("(")[1].split(")")[0]
Schoenflies_label = spglib.get_spacegroup(cell, symprec,
symbol_type=1).split(' ')[0]
sym = spglib.get_symmetry(cell, symprec)
rotations = sym['rotations']
translations = sym['translations']
equi_atoms = sym['equivalent_atoms']
is_std = is_prim = False
std_cell = spglib.refine_cell(cell, symprec)
prim_cell = spglib.find_primitive(cell, symprec)
if compare_cells(cell, std_cell): is_std = True
if compare_cells(cell, prim_cell): is_prim = True
atoms = utils.convert_atomtype(cell[2])
if export_operator == False:
#Cell info
std_cell = spglib.refine_cell(cell, symprec)
prim_cell = spglib.find_primitive(cell, symprec)
#Print
misc.print_msg("Spacegroup number : %s" % (number))
misc.print_msg("Short International symbol : %s" % (intl_label))
misc.print_msg("Schoenflies symbol : %s" %
(Schoenflies_label))
if print_atom == True:
misc.print_msg("Atoms list (No. - Sym - Symbol):")
for i, atom in enumerate(atoms):
misc.print_msg("%3d %3d %s" %
(i + 1, equi_atoms[i] + 1, atom))
misc.print_msg("Irreducible atoms:")
for i, index in enumerate(np.unique(equi_atoms)):
misc.print_msg("%3d %3s %7f5 %7f5 %7f5" %
(i + 1, atoms[index], cell[1][index][0],
cell[1][index][1], cell[1][index][2]))
misc.print_msg("Number of irreducible atoms : %d" %
(np.unique(equi_atoms).shape[0]))
misc.print_msg("Standard cell : %r" % (is_std))
misc.print_msg("Primitive cell : %r" % (is_prim))
return is_std, is_prim
else:
return (number, intl_label), equi_atoms, rotations, translations
def spacegroup(self, symprec=1e-3):
"""Get spacegroup of the atoms object."""
import spglib
sg = spglib.get_spacegroup(
(self.lattice_mat, self.frac_coords, self.atomic_numbers),
symprec=symprec,
)
return sg
def get_spacegroup(self, tilde_obj):
try:
symmetry = spg.get_spacegroup(tilde_obj['structures'][-1], symprec=self.accuracy, angle_tolerance=self.angle_tolerance)
except Exception as ex:
self.error = 'Symmetry finder error: %s' % ex
else:
symmetry = symmetry.split()
self.i = symmetry[0]
try: self.n = int( symmetry[1].replace("(", "").replace(")", "") )
except (ValueError, IndexError): self.n = 0
if self.n == 0:
self.error = 'Symmetry finder error (probably, coinciding atoms)'
def spginfo(self):
cell = (self.a, self.frac, self.charges)
print("[get_spacegroup]")
print(" Spacegroup of cell is %s" % spg.get_spacegroup(cell))
print("[get_symmetry]")
print(" Symmetry operations of unitcell are")
symmetry = spg.get_symmetry(cell)
show_symmetry(symmetry)
print("[get_pointgroup]")
print(" Pointgroup of cell is %s" %
spg.get_pointgroup(symmetry['rotations'])[0])
dataset = spg.get_symmetry_dataset(cell)
print("[get_symmetry_dataset] ['international']")
print(" Spacegroup of cell is %s (%d)" %
(dataset['international'], dataset['number']))
print("[get_symmetry_dataset] ['pointgroup']")
print(" Pointgroup of cell is %s" % (dataset['pointgroup']))
print("[get_symmetry_dataset] ['hall']")
print(" Hall symbol of cell is %s (%d)." %
(dataset['hall'], dataset['hall_number']))
print("[get_symmetry_dataset] ['wyckoffs']")
alphabet = "abcdefghijklmnopqrstuvwxyz"
print(" Wyckoff letters of cell are ", dataset['wyckoffs'])
print("[get_symmetry_dataset] ['equivalent_atoms']")
print(" Mapping to equivalent atoms of cell ")
for i, x in enumerate(dataset['equivalent_atoms']):
print(" %d -> %d" % (i + 1, x + 1))
print("[get_symmetry_dataset] ['rotations'], ['translations']")
print(" Symmetry operations of unitcell are:")
for i, (rot, trans) in enumerate(
zip(dataset['rotations'], dataset['translations'])):
print(" --------------- %4d ---------------" % (i + 1))
print(" rotation:")
for x in rot:
print(" [%2d %2d %2d]" % (x[0], x[1], x[2]))
print(" translation:")
print(" (%8.5f %8.5f %8.5f)" % (trans[0], trans[1], trans[2]))
reduced_lattice = spg.niggli_reduce(self.a)
print("[niggli_reduce]")
print(" Original lattice")
show_lattice(self.a)
print(" Reduced lattice")
show_lattice(reduced_lattice)
mapping, grid = spg.get_ir_reciprocal_mesh([11, 11, 11],
cell,
is_shift=[0, 0, 0])
num_ir_kpt = len(numpy.unique(mapping))
print("[get_ir_reciprocal_mesh]")
print(" Number of irreducible k-points of primitive")
print(" 11x11x11 Monkhorst-Pack mesh is %d " % num_ir_kpt)
return self
def get_spacegroup(self,
symprec: float = 1e-5,
angle_tolerance: float = -1,
symbol_type: int = 0) -> Union[str, None]:
"""Return International space group short symbol and number or Schoenflies symbol
:params symprec: distance tolerance in Cartesian coordinates to find crystal symmetry. Default: 1e-5
:params angle_tolerance: tolerance of angle between basis vectors in degrees to be tolerated in the symmetry finding. Default: -1
:params symbol_type: 0 - International, 1 - Schoenflies
"""
import spglib
return spglib.get_spacegroup(self.spgcell, symprec, angle_tolerance,
symbol_type)
def identify_spacegroup(spg_cell, max_iterations=200, minimum_distance=.9):
"""This function aims to identify the best spacegroup
based on allowing some amount of deviation. Accepts a spglib
compatible cell tuple as the argument."""
# Note that while precision to spglib is in cartesian distance,
# input positions are fractional coordinates
prec = 5 * minimum_distance
precs = []
grps = []
grp = 'None'
highest_symmetry_group = 'None'
max_group = 0
# Try a range of precisions and record the determined spacegroups
counter = 0
while grp is None or grp.split()[-1] not in ['(1)', '(2)']:
counter += 1
if counter > max_iterations:
break
grp = spglib.get_spacegroup(spg_cell, symprec=prec)
grps.append(grp)
precs.append(prec)
prec /= 2
if grp is not None:
group_num = int(grp.split()[-1].replace('(', '').replace(')', ''))
if group_num > max_group:
max_group = group_num
highest_symmetry_group = grp
if all(g is None for g in grps):
raise ValueError("No symmetry groups found!")
# One measure of best group is the highest symmetry group
highest_symmetry_group_prec = precs[::-1][grps[::-1].index(
highest_symmetry_group)]
# An alternative measure is the most commonly occurring group
counts = Counter(grps)
if None in counts:
del counts[None]
most_common_group = counts.most_common(1)[0][0]
most_common_group_prec = precs[::-1][grps[::-1].index(most_common_group)]
return {
'common': (most_common_group, most_common_group_prec),
'highest': (highest_symmetry_group, highest_symmetry_group_prec),
'histogram': counts
}
def writeCIF(cell, prec, basename):
# Find spacegroup name and number
sg = spglib.get_spacegroup(cell, symprec=prec)
sg, sgid = sg.split(' (')
sgid = sgid.replace(')', '')
# Find detailed info about the refined cell
lattice, scaled_positions, numbers = spglib.refine_cell(cell, prec)
if len(numbers) != len(cell):
# create new cell
ncell = (lattice, scaled_positions, numbers)
else:
ncell = copy.deepcopy(cell)
sym = spglib.get_symmetry(ncell, prec)
uniques = np.unique(sym['equivalent_atoms'])
a, b, c, alpha, beta, gamma = cellParameters(lattice)
f = open((basename + '_' + sgid + '.cif').replace('/', '|'), 'w')
f.write(f'# Symmetrized structure with precision = {prec}\n')
f.write(f'data_{basename}{sg}\n'.replace(' ', '_'))
f.write('_cell_length_a %.7g\n' % a)
f.write('_cell_length_b %.7g\n' % b)
f.write('_cell_length_c %.7g\n' % c)
f.write('_cell_angle_alpha %.7g\n' % alpha)
f.write('_cell_angle_beta %.7g\n' % beta)
f.write('_cell_angle_gamma %.7g\n' % gamma)
f.write("_symmetry_space_group_name_H-M '" + sg + "'\n")
f.write('_symmetry_Int_Tables_number ' + str(sgid) + '\n')
# Write out atomic positions
f.write('''
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_occupancy
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
''')
for pos, at in zip(scaled_positions[uniques], numbers[uniques]):
sym = element_symbols[at]
f.write('%s %s 1.0 %.7f %.7f %.7f\n' %
(sym, sym, pos[0], pos[1], pos[2]))
f.close()
def writeCIF (cell, prec, basename):
# Find spacegroup name and number
sg = spglib.get_spacegroup(cell, symprec=prec)
sg, sgid = sg.split(" (")
sgid = sgid.replace(")", "")
# Find detailed info about the refined cell
lattice, scaled_positions, numbers = spglib.refine_cell (cell, prec)
if len(numbers)!=len(cell):
#create new cell
ncell = (lattice, scaled_positions, numbers)
else:
ncell = copy.deepcopy(cell)
sym = spglib.get_symmetry(ncell, prec)
uniques = np.unique(sym['equivalent_atoms'])
a, b, c, alpha, beta, gamma = cellParameters (lattice)
f = open((basename + "_" + sgid + ".cif").replace("/","|"), "w")
f.write ("# Symmetrized structure with precision = %g\n" % prec)
f.write (("data_" + basename + sg + "\n").replace(" ", "_"))
f.write ("_cell_length_a %.7g\n" % a)
f.write ("_cell_length_b %.7g\n" % b)
f.write ("_cell_length_c %.7g\n" % c)
f.write ("_cell_angle_alpha %.7g\n" % alpha)
f.write ("_cell_angle_beta %.7g\n" % beta)
f.write ("_cell_angle_gamma %.7g\n" % gamma)
f.write ("_symmetry_space_group_name_H-M '" + sg + "'\n")
f.write ("_symmetry_Int_Tables_number " + str(sgid) + "\n")
# Write out atomic positions
f.write ("""
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_occupancy
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
""")
for pos, at in zip(scaled_positions[uniques], numbers[uniques]):
sym = element_symbols[at]
f.write ("%s %s 1.0 %.7f %.7f %.7f\n" % (sym, sym, pos[0], pos[1], pos[2]))
f.close()
def writeCIF(cell, prec, basename):
# Find spacegroup name and number
sg = spglib.get_spacegroup(cell, symprec=prec)
sg, sgid = sg.split(' (')
sgid = sgid.replace(')', '')
# Find detailed info about the refined cell
lattice, scaled_positions, numbers = spglib.refine_cell(cell, prec)
if len(numbers) != len(cell):
# create new cell
ncell = (lattice, scaled_positions, numbers)
else:
ncell = copy.deepcopy(cell)
sym = spglib.get_symmetry(ncell, prec)
uniques = np.unique(sym['equivalent_atoms'])
a, b, c, alpha, beta, gamma = cellParameters(lattice)
f = open((basename + '_' + sgid + '.cif').replace('/', '|'), 'w')
f.write(f'# Symmetrized structure with precision = {prec}\n')
f.write(f'data_{basename}{sg}\n'.replace(' ', '_'))
f.write('_cell_length_a %.7g\n' % a)
f.write('_cell_length_b %.7g\n' % b)
f.write('_cell_length_c %.7g\n' % c)
f.write('_cell_angle_alpha %.7g\n' % alpha)
f.write('_cell_angle_beta %.7g\n' % beta)
f.write('_cell_angle_gamma %.7g\n' % gamma)
f.write("_symmetry_space_group_name_H-M '" + sg + "'\n")
f.write('_symmetry_Int_Tables_number ' + str(sgid) + '\n')
# Write out atomic positions
f.write('''
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_occupancy
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
''')
for pos, at in zip(scaled_positions[uniques], numbers[uniques]):
sym = element_symbols[at]
f.write('%s %s 1.0 %.7f %.7f %.7f\n' % (sym, sym, pos[0], pos[1], pos[2]))
f.close()
def get_spacegroup(self, tilde_obj):
try:
symmetry = spg.get_spacegroup(tilde_obj['structures'][-1],
symprec=self.accuracy,
angle_tolerance=self.angle_tolerance)
except Exception as ex:
self.error = 'Symmetry finder error: %s' % ex
else:
symmetry = symmetry.split()
self.i = symmetry[0]
try:
self.n = int(symmetry[1].replace("(", "").replace(")", ""))
except (ValueError, IndexError):
self.n = 0
if self.n == 0:
self.error = 'Symmetry finder error (probably, coinciding atoms)'
def _findsym(self,inPOSCAR,cell):
if cell is None: cell=self.__cell_vasp(inPOSCAR=inPOSCAR)
# cell1=tuple( [cell.lattice,cell.positions,cell.numbers] )
# print (cell)
print('')
print('\n ----------INFORMATION ABOUT THE UNIT CELL----------- \n')
print('')
print ('Primitive vectors : \n',cell[0],'\n Atomic positions: \n',cell[1],'\n Atom type indices: \n',cell[2])
symmetries = spglib.get_symmetry( cell )
# print ("symmetriesreturned by spglib : ",symmetries)
symmetries = [ SymmetryOperation(rot,symmetries['translations'][i],cell[0],ind=i+1,spinor=self.spinor)
for i,rot in enumerate(symmetries['rotations']) ]
nsym=len(symmetries)
s=spglib.get_spacegroup(cell).split(" ")
return symmetries,s[0],int(s[1].strip("()")) ,cell[0]
def get_lattice_type(cryst):
'''Find the symmetry of the crystal using spglib symmetry finder.
Derive name of the space group and its number extracted from the result.
Based on the group number identify also the lattice type and the Bravais
lattice of the crystal. The lattice type numbers are
(the numbering starts from 1):
Triclinic (1), Monoclinic (2), Orthorombic (3),
Tetragonal (4), Trigonal (5), Hexagonal (6), Cubic (7)
:param cryst: ASE Atoms object
:returns: tuple (lattice type number (1-7), lattice name, space group
name, space group number)
'''
# Table of lattice types and correcponding group numbers dividing
# the ranges. See get_lattice_type method for precise definition.
lattice_types = [
[3, "Triclinic"],
[16, "Monoclinic"],
[75, "Orthorombic"],
[143, "Tetragonal"],
[168, "Trigonal"],
[195, "Hexagonal"],
[231, "Cubic"]
]
sg = spg.get_spacegroup(cryst)
m = re.match(r'([A-Z].*\b)\s*\(([0-9]*)\)', sg)
sg_name = m.group(1)
sg_nr = int(m.group(2))
for n, l in enumerate(lattice_types):
if sg_nr < l[0]:
bravais = l[1]
lattype = n+1
break
return lattype, bravais, sg_name, sg_nr
def get_lattice_type(self):
'''
Find the symmetry of the crystal using spglib symmetry finder.
Assign to sg_name i sg_nr members name of the space group and
its number extracted from the result. Based on the group number
identify also the lattice type (assigned to sg_type member) and
the Bravais lattice of the crystal (assigned to bravais member).
The returned value is the lattice type number.
The lattice type numbers are
(see also Crystal.ls, the numbering starts from 1):
Triclinic (1), Monoclinic (2), Orthorombic (3), Tetragonal (4)
Trigonal (5), Hexagonal (6), Cubic (7)
'''
# Table of lattice types and correcponding group numbers dividing
# the ranges. See get_lattice_type method for precise definition.
lattice_types=[
[3, "Triclinic"],
[16, "Monoclinic"],
[75, "Orthorombic"],
[143, "Tetragonal"],
[168, "Trigonal"],
[195, "Hexagonal"],
[231, "Cubic"]
]
sg=spg.get_spacegroup(self)
m=re.match('([A-Z].*\\b)\s*\(([0-9]*)\)',sg)
self.sg_name=m.group(1)
self.sg_nr=int(m.group(2))
for n,l in enumerate(lattice_types) :
if self.sg_nr < l[0] :
lattice=l[1]
lattype=n+1
break
self.sg_type=lattype
self.bravais=lattice
return lattype
c = 3.52
MgB2 = Atoms( symbols=['Mg']+['B']*2,
cell=[ ( a, 0, 0 ),
( -a/2, a/2*np.sqrt(3), 0 ),
( 0, 0, c ) ],
scaled_positions=[ ( 0, 0, 0 ),
( 1.0/3, 2.0/3, 0.5 ),
( 2.0/3, 1.0/3, 0.5 ) ],
pbc=True )
# For VASP case
# import vasp
# bulk = vasp.read_vasp(sys.argv[1])
print "[get_spacegroup]"
print " Spacegroup of Silicon is ", spglib.get_spacegroup(silicon)
print
print "[get_spacegroup]"
print " Spacegroup of Rutile is ", spglib.get_spacegroup(rutile)
print
print "[get_spacegroup]"
print " Spacegroup of MgB2 is ", spglib.get_spacegroup(MgB2)
print
print "[get_symmetry]"
print " Symmetry operations of Rutile unitcell are:"
print
symmetry = spglib.get_symmetry( rutile )
show_symmetry(symmetry)
print
print "[get_pointgroup]"
def write_cell_params(fh, a, p):
'''
Write the specification of the cell using a traditional A,B,C,
alpha, beta, gamma scheme. The symmetry and parameters are determined
from the atoms (a) object. The atoms object is translated into a
primitive unit cell but *not* converted. This is just an internal procedure.
If you wish to work with primitive unit cells in ASE, you need to make
a conversion yourself. The cell params are in angstrom.
Input
-----
fh file handle of the opened pw.in file
a atoms object
p parameters dictionary
Output
------
Primitive cell tuple of arrays: (lattice, atoms, atomic numbers)
'''
assert(p['use_symmetry'])
# Get a spacegroup name and number for the a
sg,sgn=spglib.get_spacegroup(a).split()
# Extract the number
sgn=int(sgn[1:-1])
# Extract the lattice type
ltyp=sg[0]
# Find a primitive unit cell for the system
# puc is a tuple of (lattice, atoms, atomic numbers)
puc=spglib.find_primitive(a)
cell=puc[0]
apos=puc[1]
anum=puc[2]
icell=a.get_cell()
A=norm(icell[0])
B=norm(icell[1])
C=norm(icell[2])
# Select appropriate ibrav
if sgn >= 195 :
# Cubic lattice
if ltyp=='P':
p['ibrav']=1 # Primitive
qepc=array([[1,0,0],[0,1,0],[0,0,1]])
elif ltyp=='F':
p['ibrav']=2 # FCC
qepc=array([[-1,0,1],[0,1,1],[-1,1,0]])/2.0
elif ltyp=='I':
p['ibrav']=3 # BCC
qepc=array([[1,1,1],[-1,1,1],[-1,-1,1]])/2.0
else :
print 'Impossible lattice symmetry! Contact the author!'
raise NotImplementedError
#a=sqrt(2)*norm(cell[0])
qepc=A*qepc
fh.write(' A = %f,\n' % (A,))
elif sgn >= 143 :
# Hexagonal and trigonal
if ltyp=='P' :
p['ibrav']=4 # Primitive
qepc=array([[1,0,0],[-1/2,sqrt(3)/2,0],[0,0,C/A]])
elif ltyp=='R' :
p['ibrav']=5 # Trigonal rhombohedral
raise NotImplementedError
else :
print 'Impossible lattice symmetry! Contact the author!'
raise NotImplementedError
qepc=A*qepc
fh.write(' A = %f,\n' % (A,))
fh.write(' C = %f,\n' % (C,))
elif sgn >= 75 :
raise NotImplementedError
elif sgn ==1 :
# P1 symmetry - no special primitive cell signal to the caller
p['ibrav']=0
return None
else :
raise NotImplementedError
cp=Atoms(cell=puc[0], scaled_positions=puc[1], numbers=puc[2], pbc=True)
qepc=Atoms(cell=qepc,
positions=cp.get_positions(),
numbers=cp.get_atomic_numbers(), pbc=True)
return qepc.get_cell(), qepc.get_scaled_positions(), qepc.get_atomic_numbers()
def get_spacegroup(self, symprec=1e-5):
return spg.get_spacegroup(cell=self.spglib_cell, symprec=symprec)
spec.append(a[0])
print("Input data:")
print("Cell:")
i=0
for v in b:
print("a%d= % 9.7f % 9.7f % 9.7f" % (i,v[0],v[1],v[2]))
i+=1
print(spec)
print('Atomic positions:')
print(dp)
structure=[b,dp,spec]
res=seekpath.getpaths.get_path(structure, with_time_reversal=True, recipe='hpkot', threshold=1e-07, symprec=1e-05, angle_tolerance=-1.0)
print("Output data:")
print("Space group: %s" %spl.get_spacegroup(cell=(b,dp,spec), symprec=1e-5))
print('Primitive lattice:')
for v in res['primitive_lattice']:
print("a1= % 9.7f % 9.7f % 9.7f" % (v[0],v[1],v[2]))
print('Atomic positions:')
for i in range(len(res['primitive_positions'])):
print("%2d %s" % (res['primitive_types'][i], "".join(" % 12.9f" % val for val in res['primitive_positions'][i])))
print('Crystallographic lattice:')
for v in res['conv_lattice']:
print("a1= % 9.7f % 9.7f % 9.7f" % (v[0],v[1],v[2]))
print('Points:')
for pt in res['point_coords'].items():
print(pt)
print('PATH:')
print (res['path'])
[(0, 0, 0),
(1.0/3, 2.0/3, 0.5),
(2.0/3, 1.0/3, 0.5)],
[12, 5, 5])
a = [3., 0., 0.]
b = [-3.66666667, 3.68178701, 0.]
c = [-0.66666667, -1.3429469, 1.32364995]
niggli_lattice = np.array([a, b, c])
# For VASP case
# import vasp
# bulk = vasp.read_vasp(sys.argv[1])
print("[get_spacegroup]")
print(" Spacegroup of Silicon is %s." % spglib.get_spacegroup(silicon))
print('')
print("[get_spacegroup]")
print(" Spacegroup of Silicon (ASE Atoms-like format) is %s." %
spglib.get_spacegroup(silicon_ase))
print('')
print("[get_spacegroup]")
print(" Spacegroup of Rutile is %s." % spglib.get_spacegroup(rutile))
print('')
print("[get_spacegroup]")
print(" Spacegroup of MgB2 is %s." % spglib.get_spacegroup(MgB2))
print('')
print("[get_symmetry]")
print(" Symmetry operations of Rutile unitcell are:")
print('')
symmetry = spglib.get_symmetry(rutile)
print(f'Usage: {prog} file.cif')
sys.exit(1)
try:
cell = ase.io.read(sys.argv[1])
except Exception as e:
print('Could not read CIF structure from file: ' + sys.argv[1])
print('Error message is: ' + str(e))
sys.exit(1)
if sys.argv[1][-4:] == '.cif':
basename = sys.argv[1][:-4]
else:
basename = sys.argv[1]
t = [1, 2, 3, 5, 7]
precs = [1e-10, 1e-9, 1e-8, 1e-7, 1e-6] + [i * j for i in [1e-5, 1e-4, 1e-3, 1e-2, 1e-1] for j in t]
old = ''
print('# Tolerance\tSpace group')
for prec in precs:
s = spglib.get_spacegroup(cell, symprec=prec)
if s != old:
print(f'{prec}\t\t{s}')
writeCIF(cell, prec, basename)
old = s
sys.exit(0)