mirror of https://github.com/phonopy/phono3py.git
Fix issues #42 by improving the algorithm
This commit is contained in:
Atsushi Togo
parent
545af58938
commit
9a8d107c42
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@ -76,7 +76,9 @@ def direction_to_displacement(direction_dataset,
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lattice = supercell.cell.T
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new_dataset = {}
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new_dataset['natom'] = len(supercell)
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new_dataset['duplicates'] = duplicates
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if duplicates:
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new_dataset['duplicates'] = duplicates
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if cutoff_distance is not None:
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new_dataset['cutoff_distance'] = cutoff_distance
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@ -333,28 +335,73 @@ def _get_orbits(atom_index, cell, site_symmetry, symprec=1e-5):
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def _find_duplicates(direction_dataset):
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direction_sets = []
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id_offset = len(direction_dataset) + 1
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direction_sets = {}
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idx = len(direction_dataset) + 1
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pair_idx = {}
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# (List index of direction_sets + id_offset + 1) gives the displacement id.
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# This id is stamped in direction_to_displacement by the sequence of
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# the loops. Therefore the same system of the loops should be used here.
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for direction1 in direction_dataset:
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number1 = direction1['number']
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n1 = direction1['number']
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d1 = direction1['direction']
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for directions2 in direction1['second_atoms']:
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number2 = directions2['number']
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for d2 in directions2['directions']:
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direction_sets.append([number1, number2] + d1 + d2)
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n2 = directions2['number']
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if (n1, n2) not in direction_sets:
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direction_sets[(n1, n2)] = []
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pair_idx[(n1, n2)] = []
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for i, d2 in enumerate(directions2['directions']):
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direction_sets[(n1, n2)].append(d1 + d2)
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pair_idx[(n1, n2)].append(idx + i)
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idx += len(directions2['directions'])
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direction_sets = np.array(direction_sets)
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flip_sets = direction_sets[:, [1, 0, 5, 6, 7, 2, 3, 4]]
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_duplucates = []
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for i, dset in enumerate(direction_sets):
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eq_indices = np.where(np.abs(flip_sets - dset).sum(axis=1) == 0)[0]
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duplucates = []
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done = []
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for i, direction1 in enumerate(direction_dataset):
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n1 = direction1['number']
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for directions2 in direction1['second_atoms']:
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n2 = directions2['number']
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if (n2 > n1 and (n2, n1) not in done and
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(n2, n1) in direction_sets):
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done.append((n2, n1))
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duplucates += _compare(
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n1, n2,
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direction_sets[(n1, n2)], direction_sets[(n2, n1)],
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pair_idx[(n1, n2)], pair_idx[(n2, n1)])
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done = []
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for i, direction1 in enumerate(direction_dataset):
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n1 = direction1['number']
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for directions2 in direction1['second_atoms']:
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n2 = directions2['number']
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if n1 == n2 and n1 not in done:
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done.append(n1)
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duplucates += _compare_opposite(
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n1,
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direction_sets[(n1, n1)],
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pair_idx[(n1, n1)])
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return duplucates
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def _compare(n1, n2, dset1, dset2, pidx1, pidx2):
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flip_sets = np.array(dset2)[:, [3, 4, 5, 0, 1, 2]]
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duplucates = []
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for i, d1 in enumerate(dset1):
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eq_indices = np.where(np.abs(flip_sets - d1).sum(axis=1) == 0)[0]
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if len(eq_indices) > 0:
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_duplucates += [[i + id_offset, j] for j in eq_indices + id_offset]
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if dset[0] == dset[1] and (dset[2:5] + dset[5:8] == 0).all():
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_duplucates.append([i + id_offset, 0])
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duplucates += [[pidx2[j], pidx1[i]] for j in eq_indices]
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return [[i, j] for (i, j) in _duplucates if i > j]
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return [[i, j] for (i, j) in duplucates if i > j]
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def _compare_opposite(n1, dset1, pidx1):
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flip_sets = np.array(dset1)[:, [3, 4, 5, 0, 1, 2]]
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duplucates = []
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for i, d1 in enumerate(dset1):
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eq_indices = np.where(np.abs(flip_sets + d1).sum(axis=1) == 0)[0]
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if len(eq_indices) > 0:
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duplucates += [[pidx1[j], 0] for j in eq_indices]
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return [[i, j] for (i, j) in duplucates if i > j]
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@ -1,200 +1,32 @@
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lattice:
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- [ 9.8130133395493626, 0.0000000000000000, 0.0000000000000000 ] # a
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- [ 0.0000000000000000, 12.9607729652407464, 0.0000000000000000 ] # b
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- [ 0.0000000000000000, 0.0000000000000000, 9.9776294309342557 ] # c
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- [ 3.2918783299999999, 0.0000000000000000, 0.0000000000000000 ] # a
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- [ 0.0000000000000000, 6.4164678799999999, 0.0000000000000000 ] # b
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- [ 0.0000000000000000, 0.0000000000000000, 4.9969270100000003 ] # c
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points:
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- symbol: N # 1 -> 1
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coordinates: [ 0.0010190549685383, 0.2500000000000000, 0.1952475607335603 ]
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- symbol: N # 2 -> 2
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coordinates: [ 0.3333333333333333, 0.2500000000000000, 0.1952475607335603 ]
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- symbol: N # 3 -> 3
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coordinates: [ 0.6666666666666666, 0.2500000000000000, 0.1952475607335603 ]
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- symbol: N # 4 -> 4
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coordinates: [ 0.0000000000000000, 0.7500000000000000, 0.1952475607335603 ]
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- symbol: N # 5 -> 5
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coordinates: [ 0.3333333333333333, 0.7500000000000000, 0.1952475607335603 ]
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- symbol: N # 6 -> 6
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coordinates: [ 0.6666666666666666, 0.7500000000000000, 0.1952475607335603 ]
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- symbol: N # 7 -> 7
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coordinates: [ 0.0000000000000000, 0.2500000000000000, 0.6952475607335603 ]
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- symbol: N # 8 -> 8
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coordinates: [ 0.3333333333333333, 0.2500000000000000, 0.6952475607335603 ]
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- symbol: N # 9 -> 9
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coordinates: [ 0.6666666666666666, 0.2500000000000000, 0.6952475607335603 ]
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- symbol: N # 10 -> 10
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coordinates: [ 0.0000000000000000, 0.7500000000000000, 0.6952475607335603 ]
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- symbol: N # 11 -> 11
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coordinates: [ 0.3333333333333333, 0.7500000000000000, 0.6952475607335603 ]
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- symbol: N # 12 -> 12
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coordinates: [ 0.6666666666666666, 0.7500000000000000, 0.6952475607335603 ]
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- symbol: O # 13 -> 25
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coordinates: [ 0.0000000000000000, 0.3318936741729317, 0.2635067655175194 ]
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- symbol: O # 14 -> 26
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coordinates: [ 0.3333333333333333, 0.3318936741729317, 0.2635067655175194 ]
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- symbol: O # 15 -> 27
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coordinates: [ 0.6666666666666666, 0.3318936741729317, 0.2635067655175194 ]
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- symbol: O # 16 -> 28
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coordinates: [ 0.0000000000000000, 0.8318936741729317, 0.2635067655175194 ]
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- symbol: O # 17 -> 29
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coordinates: [ 0.3333333333333333, 0.8318936741729317, 0.2635067655175194 ]
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- symbol: O # 18 -> 30
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coordinates: [ 0.6666666666666666, 0.8318936741729317, 0.2635067655175194 ]
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- symbol: O # 19 -> 31
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coordinates: [ 0.0000000000000000, 0.3318936741729317, 0.7635067655175194 ]
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- symbol: O # 20 -> 32
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coordinates: [ 0.3333333333333333, 0.3318936741729317, 0.7635067655175194 ]
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- symbol: O # 21 -> 33
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coordinates: [ 0.6666666666666666, 0.3318936741729317, 0.7635067655175194 ]
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- symbol: O # 22 -> 34
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coordinates: [ 0.0000000000000000, 0.8318936741729317, 0.7635067655175194 ]
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- symbol: O # 23 -> 35
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coordinates: [ 0.3333333333333333, 0.8318936741729317, 0.7635067655175194 ]
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- symbol: O # 24 -> 36
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coordinates: [ 0.6666666666666666, 0.8318936741729317, 0.7635067655175194 ]
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- symbol: O # 25 -> 37
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coordinates: [ 0.0000000000000000, 0.1681063258270684, 0.2635067655175194 ]
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- symbol: O # 26 -> 38
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coordinates: [ 0.3333333333333333, 0.1681063258270684, 0.2635067655175194 ]
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- symbol: O # 27 -> 39
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coordinates: [ 0.6666666666666666, 0.1681063258270684, 0.2635067655175194 ]
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- symbol: O # 28 -> 40
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coordinates: [ 0.0000000000000000, 0.6681063258270684, 0.2635067655175194 ]
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- symbol: O # 29 -> 41
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coordinates: [ 0.3333333333333333, 0.6681063258270684, 0.2635067655175194 ]
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- symbol: O # 30 -> 42
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coordinates: [ 0.6666666666666666, 0.6681063258270684, 0.2635067655175194 ]
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- symbol: O # 31 -> 43
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coordinates: [ 0.0000000000000000, 0.1681063258270684, 0.7635067655175194 ]
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- symbol: O # 32 -> 44
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coordinates: [ 0.3333333333333333, 0.1681063258270684, 0.7635067655175194 ]
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- symbol: O # 33 -> 45
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coordinates: [ 0.6666666666666666, 0.1681063258270684, 0.7635067655175194 ]
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- symbol: O # 34 -> 46
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coordinates: [ 0.0000000000000000, 0.6681063258270684, 0.7635067655175194 ]
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- symbol: O # 35 -> 47
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coordinates: [ 0.3333333333333333, 0.6681063258270684, 0.7635067655175194 ]
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- symbol: O # 36 -> 48
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coordinates: [ 0.6666666666666666, 0.6681063258270684, 0.7635067655175194 ]
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- symbol: Ag # 37 -> 73
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coordinates: [ 0.0000000000000000, 0.2500000000000000, 0.4777389082314037 ]
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- symbol: Ag # 38 -> 74
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coordinates: [ 0.3333333333333333, 0.2500000000000000, 0.4777389082314037 ]
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- symbol: Ag # 39 -> 75
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coordinates: [ 0.6666666666666666, 0.2500000000000000, 0.4777389082314037 ]
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- symbol: Ag # 40 -> 76
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coordinates: [ 0.0000000000000000, 0.7500000000000000, 0.4777389082314037 ]
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- symbol: Ag # 41 -> 77
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coordinates: [ 0.3333333333333333, 0.7500000000000000, 0.4777389082314037 ]
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- symbol: Ag # 42 -> 78
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coordinates: [ 0.6666666666666666, 0.7500000000000000, 0.4777389082314037 ]
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- symbol: Ag # 43 -> 79
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coordinates: [ 0.0000000000000000, 0.2500000000000000, 0.9777389082314037 ]
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- symbol: Ag # 44 -> 80
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coordinates: [ 0.3333333333333333, 0.2500000000000000, 0.9777389082314037 ]
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- symbol: Ag # 45 -> 81
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coordinates: [ 0.6666666666666666, 0.2500000000000000, 0.9777389082314037 ]
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- symbol: Ag # 46 -> 82
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coordinates: [ 0.0000000000000000, 0.7500000000000000, 0.9777389082314037 ]
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- symbol: Ag # 47 -> 83
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coordinates: [ 0.3333333333333333, 0.7500000000000000, 0.9777389082314037 ]
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- symbol: Ag # 48 -> 84
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coordinates: [ 0.6666666666666666, 0.7500000000000000, 0.9777389082314037 ]
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- symbol: N # 49 -> 13
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coordinates: [ 0.1666666666666667, 0.0000000000000000, 0.4452475607335603 ]
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- symbol: N # 50 -> 14
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coordinates: [ 0.5000000000000000, 0.0000000000000000, 0.4452475607335603 ]
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- symbol: N # 51 -> 15
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coordinates: [ 0.8333333333333334, 0.0000000000000000, 0.4452475607335603 ]
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- symbol: N # 52 -> 16
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coordinates: [ 0.1666666666666667, 0.5000000000000000, 0.4452475607335603 ]
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- symbol: N # 53 -> 17
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coordinates: [ 0.5000000000000000, 0.5000000000000000, 0.4452475607335603 ]
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- symbol: N # 54 -> 18
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coordinates: [ 0.8333333333333334, 0.5000000000000000, 0.4452475607335603 ]
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- symbol: N # 55 -> 19
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coordinates: [ 0.1666666666666667, 0.0000000000000000, 0.9452475607335603 ]
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- symbol: N # 56 -> 20
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coordinates: [ 0.5000000000000000, 0.0000000000000000, 0.9452475607335603 ]
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- symbol: N # 57 -> 21
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coordinates: [ 0.8333333333333334, 0.0000000000000000, 0.9452475607335603 ]
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- symbol: N # 58 -> 22
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coordinates: [ 0.1666666666666667, 0.5000000000000000, 0.9452475607335603 ]
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- symbol: N # 59 -> 23
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coordinates: [ 0.5000000000000000, 0.5000000000000000, 0.9452475607335603 ]
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- symbol: N # 60 -> 24
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coordinates: [ 0.8333333333333334, 0.5000000000000000, 0.9452475607335603 ]
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- symbol: O # 61 -> 49
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coordinates: [ 0.1666666666666667, 0.0818936741729317, 0.0135067655175194 ]
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- symbol: O # 62 -> 50
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coordinates: [ 0.5000000000000000, 0.0818936741729317, 0.0135067655175194 ]
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- symbol: O # 63 -> 51
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coordinates: [ 0.8333333333333334, 0.0818936741729317, 0.0135067655175194 ]
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- symbol: O # 64 -> 52
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coordinates: [ 0.1666666666666667, 0.5818936741729317, 0.0135067655175194 ]
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- symbol: O # 65 -> 53
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coordinates: [ 0.5000000000000000, 0.5818936741729317, 0.0135067655175194 ]
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- symbol: O # 66 -> 54
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coordinates: [ 0.8333333333333334, 0.5818936741729317, 0.0135067655175194 ]
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- symbol: O # 67 -> 55
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coordinates: [ 0.1666666666666667, 0.0818936741729317, 0.5135067655175194 ]
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- symbol: O # 68 -> 56
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coordinates: [ 0.5000000000000000, 0.0818936741729317, 0.5135067655175194 ]
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- symbol: O # 69 -> 57
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coordinates: [ 0.8333333333333334, 0.0818936741729317, 0.5135067655175194 ]
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- symbol: O # 70 -> 58
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coordinates: [ 0.1666666666666667, 0.5818936741729317, 0.5135067655175194 ]
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- symbol: O # 71 -> 59
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coordinates: [ 0.5000000000000000, 0.5818936741729317, 0.5135067655175194 ]
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- symbol: O # 72 -> 60
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coordinates: [ 0.8333333333333334, 0.5818936741729317, 0.5135067655175194 ]
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- symbol: O # 73 -> 61
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coordinates: [ 0.1666666666666667, 0.4181063258270684, 0.0135067655175194 ]
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- symbol: O # 74 -> 62
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coordinates: [ 0.5000000000000000, 0.4181063258270684, 0.0135067655175194 ]
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- symbol: O # 75 -> 63
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coordinates: [ 0.8333333333333334, 0.4181063258270684, 0.0135067655175194 ]
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- symbol: O # 76 -> 64
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coordinates: [ 0.1666666666666667, 0.9181063258270683, 0.0135067655175194 ]
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- symbol: O # 77 -> 65
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||||
coordinates: [ 0.5000000000000000, 0.9181063258270683, 0.0135067655175194 ]
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||||
- symbol: O # 78 -> 66
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coordinates: [ 0.8333333333333334, 0.9181063258270683, 0.0135067655175194 ]
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- symbol: O # 79 -> 67
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coordinates: [ 0.1666666666666667, 0.4181063258270684, 0.5135067655175194 ]
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- symbol: O # 80 -> 68
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||||
coordinates: [ 0.5000000000000000, 0.4181063258270684, 0.5135067655175194 ]
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||||
- symbol: O # 81 -> 69
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||||
coordinates: [ 0.8333333333333334, 0.4181063258270684, 0.5135067655175194 ]
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||||
- symbol: O # 82 -> 70
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||||
coordinates: [ 0.1666666666666667, 0.9181063258270683, 0.5135067655175194 ]
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- symbol: O # 83 -> 71
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coordinates: [ 0.5000000000000000, 0.9181063258270683, 0.5135067655175194 ]
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||||
- symbol: O # 84 -> 72
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coordinates: [ 0.8333333333333334, 0.9181063258270683, 0.5135067655175194 ]
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||||
- symbol: Ag # 85 -> 85
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||||
coordinates: [ 0.1666666666666667, 0.0000000000000000, 0.2277389082314037 ]
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- symbol: Ag # 86 -> 86
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||||
coordinates: [ 0.5000000000000000, 0.0000000000000000, 0.2277389082314037 ]
|
||||
- symbol: Ag # 87 -> 87
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||||
coordinates: [ 0.8333333333333334, 0.0000000000000000, 0.2277389082314037 ]
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||||
- symbol: Ag # 88 -> 88
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||||
coordinates: [ 0.1666666666666667, 0.5000000000000000, 0.2277389082314037 ]
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- symbol: Ag # 89 -> 89
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||||
coordinates: [ 0.5000000000000000, 0.5000000000000000, 0.2277389082314037 ]
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||||
- symbol: Ag # 90 -> 90
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||||
coordinates: [ 0.8333333333333334, 0.5000000000000000, 0.2277389082314037 ]
|
||||
- symbol: Ag # 91 -> 91
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||||
coordinates: [ 0.1666666666666667, 0.0000000000000000, 0.7277389082314037 ]
|
||||
- symbol: Ag # 92 -> 92
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||||
coordinates: [ 0.5000000000000000, 0.0000000000000000, 0.7277389082314037 ]
|
||||
- symbol: Ag # 93 -> 93
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||||
coordinates: [ 0.8333333333333334, 0.0000000000000000, 0.7277389082314037 ]
|
||||
- symbol: Ag # 94 -> 94
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||||
coordinates: [ 0.1666666666666667, 0.5000000000000000, 0.7277389082314037 ]
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||||
- symbol: Ag # 95 -> 95
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||||
coordinates: [ 0.5000000000000000, 0.5000000000000000, 0.7277389082314037 ]
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- symbol: Ag # 96 -> 96
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||||
coordinates: [ 0.8333333333333334, 0.5000000000000000, 0.7277389082314037 ]
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- symbol: N # 1
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coordinates: [ 0.5000000000000000, 0.5000000000000000, 0.1095444300000000 ]
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mass: 14.006700
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- symbol: N # 2
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coordinates: [ 0.0000000000000000, 0.0000000000000000, 0.6095444300000000 ]
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mass: 14.006700
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- symbol: O # 3
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coordinates: [ 0.5000000000000000, 0.6654353800000000, 0.9730617300000000 ]
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mass: 15.999400
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- symbol: O # 4
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coordinates: [ 0.5000000000000000, 0.3345646200000000, 0.9730617300000000 ]
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mass: 15.999400
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||||
- symbol: O # 5
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coordinates: [ 0.0000000000000000, 0.1654353800000000, 0.4730617300000000 ]
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mass: 15.999400
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- symbol: O # 6
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coordinates: [ 0.0000000000000000, 0.8345646200000000, 0.4730617300000000 ]
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mass: 15.999400
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- symbol: Ag # 7
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||||
coordinates: [ 0.5000000000000000, 0.5000000000000000, 0.5443321400000000 ]
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||||
mass: 107.868200
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||||
- symbol: Ag # 8
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||||
coordinates: [ 0.0000000000000000, 0.0000000000000000, 0.0443321400000000 ]
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mass: 107.868200
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poscar_order:
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- 1
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- 2
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@ -204,91 +36,3 @@ poscar_order:
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- 6
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- 7
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- 8
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- 9
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- 10
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- 11
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- 12
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- 49
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- 50
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- 51
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- 52
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- 53
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- 47
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- 48
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Loading…
Reference in New Issue