def _(sym, model, full_group): # pylint: disable=missing-docstring
sym_group = sr.SymmetryGroup(
symmetries=[sym],
full_group=full_group
or False # catches 'None', does nothing for 'True' or 'False'
)
return _symmetrize(sym_group, model, full_group)
def _(sym, model, full_group):
sym_group = sr.SymmetryGroup(
symmetries=[sym],
full_group=full_group
or False, # catches 'None', does nothing for 'True' or 'False'
)
return _symmetrize(sym_group, model, full_group)
def test_auto_repr(sample):
"""
Test that the symmetry group created with the automatic representation matrix
is the matches a reference.
"""
pos_In = (0, 0, 0) # pylint: disable=invalid-name
pos_As = (0.25, 0.25, 0.25) # pylint: disable=invalid-name
orbitals = []
for spin in (sr.SPIN_UP, sr.SPIN_DOWN):
orbitals.extend([
sr.Orbital(position=pos_In, function_string=fct, spin=spin)
for fct in sr.WANNIER_ORBITALS['s'] + sr.WANNIER_ORBITALS['p']
])
orbitals.extend([
sr.Orbital(position=pos_As, function_string=fct, spin=spin)
for fct in sr.WANNIER_ORBITALS['p']
])
symops, symops_cart = mg.loadfn(sample('InAs_symops.json'))
symmetry_group = sr.SymmetryGroup(symmetries=[
sr.SymmetryOperation.from_orbitals(
orbitals=orbitals,
real_space_operator=sr.RealSpaceOperator.from_pymatgen(
sym_reduced),
rotation_matrix_cartesian=sym_cart.rotation_matrix,
numeric=True)
for sym_reduced, sym_cart in zip(symops, symops_cart)
],
full_group=True)
reference = sr.io.load(sample('symmetries_InAs.hdf5'))
assert symmetry_group.full_group == reference.full_group
for sym1, sym2 in zip(symmetry_group.symmetries, reference.symmetries):
assert_allclose(sym1.real_space_operator.rotation_matrix,
sym2.real_space_operator.rotation_matrix,
atol=1e-12)
assert_allclose(sym1.real_space_operator.translation_vector,
sym2.real_space_operator.translation_vector,
atol=1e-12)
assert sym1.repr.has_cc == sym2.repr.has_cc
assert_allclose(sym1.repr.matrix, sym2.repr.matrix, atol=1e-12)
)
# get real-space representations
analyzer = mg.symmetry.analyzer.SpacegroupAnalyzer(structure)
symops = analyzer.get_symmetry_operations(cartesian=False)
symops_cart = analyzer.get_symmetry_operations(cartesian=True)
rots = [x.rotation_matrix for x in symops]
taus = [x.translation_vector for x in symops]
# get corresponding represesentations in the Hamiltonian basis
reps = []
for n, (rot, tau) in enumerate(zip(rots, taus)):
C = symops_cart[n].rotation_matrix
tauc = symops_cart[n].translation_vector
prep = C
spinrep = spin_reps(C)
R = np.kron(spinrep, la.block_diag(1.0, prep, prep))
reps.append(R)
# set up the space group symmetries
symmetries = [
sr.SymmetryOperation(
# r-space and k-space matrices are related by transposing and inverting
rotation_matrix=rot,
repr_matrix=repr_mat,
repr_has_cc=False,
) for rot, repr_mat in zip(rots, reps)
]
point_group = sr.SymmetryGroup(symmetries=symmetries, full_group=True)
sr.io.save([time_reversal, point_group], "results/symmetries.hdf5")
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import tempfile
import pytest
import numpy as np
import symmetry_representation as sr
SYM_OP = sr.SymmetryOperation(rotation_matrix=np.array([[1, 2, 3], [4, 5j,
9]]),
repr_matrix=np.array([[0, 1], [3, 5]]),
repr_has_cc=True)
REPR_MATRIX = sr.Representation(matrix=np.array([[1j, 0], [-2j, 3j]]))
SYM_GROUP = sr.SymmetryGroup(symmetries=[SYM_OP, SYM_OP], full_group=True)
@pytest.mark.parametrize('data', [
SYM_OP, [SYM_OP], REPR_MATRIX, [REPR_MATRIX],
[SYM_OP, [SYM_OP], REPR_MATRIX], SYM_GROUP,
[SYM_GROUP, SYM_OP, REPR_MATRIX]
])
def test_save_load(data):
with tempfile.NamedTemporaryFile() as f:
print(data)
sr.io.save(data, f.name)
result = sr.io.load(f.name)
np.testing.assert_equal(result, data)
for fct in sr.WANNIER_ORBITALS['s'] + sr.WANNIER_ORBITALS['p']:
for spin in (sr.SPIN_UP, sr.SPIN_DOWN):
orbitals.append(
sr.Orbital(position=POS_In, function_string=fct, spin=spin))
for fct in sr.WANNIER_ORBITALS['p']:
for spin in (sr.SPIN_UP, sr.SPIN_DOWN):
orbitals.append(
sr.Orbital(position=POS_Sb, function_string=fct, spin=spin))
structure = mg.Structure(lattice=[[0., 3.239, 3.239], [3.239, 0., 3.239],
[3.239, 3.239, 0.]],
species=['In', 'Sb'],
coords=np.array([[0, 0, 0], [0.25, 0.25, 0.25]]))
analyzer = mg.symmetry.analyzer.SpacegroupAnalyzer(structure)
symops = analyzer.get_symmetry_operations(cartesian=False)
symops_cart = analyzer.get_symmetry_operations(cartesian=True)
symmetry_group = sr.SymmetryGroup(symmetries=[
sr.SymmetryOperation.from_orbitals(
orbitals=orbitals,
real_space_operator=sr.RealSpaceOperator.from_pymatgen(sym_reduced),
rotation_matrix_cartesian=sym_cart.rotation_matrix,
numeric=True) for sym_reduced, sym_cart in zip(symops, symops_cart)
],
full_group=True)
time_reversal = sr.get_time_reversal(orbitals=orbitals, numeric=True)
sr.io.save([time_reversal, symmetry_group], 'inputs/symmetries.hdf5')