mirror of https://github.com/phonopy/phonopy.git
Improve performance by changing order of iteration loops
This commit is contained in:
Atsushi Togo
parent
ca260565a6
commit
752ff7e9c3
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@ -45,11 +45,12 @@ class Unfolding:
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atom_mapping,
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bands):
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self._phonon = phonon
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self._supercell_matrix = supercell_matrix
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self._supercell_matrix = np.array(supercell_matrix, dtype='intc')
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self._ideal_positions = ideal_positions
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self._atom_mapping = atom_mapping
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self._bands = bands
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self._symprec = self._phonon.get_symmetry().get_symmetry_tolerance()
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self._translations = None
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self._index_set = None
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self._qpoints = None
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@ -127,20 +128,21 @@ class Unfolding:
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weights = np.zeros((eigvecs.shape[0], len(self._comm_points)),
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dtype='complex128')
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N = len(self._comm_points)
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for i, G in enumerate(self._comm_points):
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for shift, indices in zip(trans, self._index_set):
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for shift, indices in zip(trans, self._index_set):
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dot_eigs = np.einsum(
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'ij,ij->j', eigvecs.conj(), eigvecs[indices, :]) / N
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for i, G in enumerate(self._comm_points):
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phase = np.exp(2j * np.pi * np.dot(G, shift))
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eigvecs_shifted = eigvecs[indices, :]
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weights[:, i] += np.einsum(
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'ij,ij->j', eigvecs.conj(), eigvecs_shifted) * phase / N
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weights[:, i] += dot_eigs * phase
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## Strainghtforward norm calculation (equivalent speed)
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# eigvecs_shifted = np.zeros_like(eigvecs)
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# for shift, indices in zip(trans, self._index_set):
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# phase = np.exp(2j * np.pi * np.dot(G, shift))
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# eigvecs_shifted += eigvecs[indices, :] * phase
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# weights[:, i] = np.einsum(
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# 'ij,ij->j', eigvecs_shifted.conj(), eigvecs_shifted) / N**2
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# # Strainghtforward norm calculation (equivalent speed)
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# for i, G in enumerate(self._comm_points):
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# eigvecs_shifted = np.zeros_like(eigvecs)
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# for shift, indices in zip(trans, self._index_set):
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# phase = np.exp(2j * np.pi * np.dot(G, shift))
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# eigvecs_shifted += eigvecs[indices, :] * phase
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# weights[:, i] = np.einsum(
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# 'ij,ij->j', eigvecs_shifted.conj(), eigvecs_shifted) / N**2
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if (weights.imag > 1e-5).any():
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print("Phonopy warning: Encountered imaginary values.")
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@ -20,36 +20,37 @@ class TestUnfolding(unittest.TestCase):
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def tearDown(self):
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pass
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def test_Unfolding(self):
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nd = 10
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# def test_Unfolding_NaCl(self):
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# self._run_unfolding()
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def test_Unfolding_SC(self):
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self._run_unfolding(unfolding_supercell_matrix=np.diag([4, 4, 4]))
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def _run_unfolding(self, unfolding_supercell_matrix=[[-2, 2, 2],
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[2, -2, 2],
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[2, 2, -2]]):
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nd = 50
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band = [np.array([[i - nd, 0, 0] for i in range(2 * nd + 1)],
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dtype='double') / nd / 2]
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smat = np.diag([2, 2, 2])
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pmat = [[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]]
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phonon_ideal = self._get_phonon(smat, pmat, self._cell)
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self._set_nac_params(phonon_ideal)
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supercell = phonon_ideal.get_supercell()
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primitive = phonon_ideal.get_primitive()
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smat = np.linalg.inv(primitive.get_primitive_matrix())
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supercell_matrix = np.rint(smat).astype('intc')
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phonon = self._get_phonon(np.eye(3, dtype='intc'), np.eye(3), supercell)
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self._set_nac_params(phonon, primitive)
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# self._set_nac_params(phonon, primitive)
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mapping = range(phonon.get_supercell().get_number_of_atoms())
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unfolding = Unfolding(phonon,
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supercell_matrix,
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supercell.get_scaled_positions(),
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unfolding_supercell_matrix,
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supercell.get_scaled_positions(),
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mapping,
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band)
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unfolding.run()
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comm_points = unfolding.get_commensurate_points()
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print(comm_points)
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# (nd + 1, num_atom_super / num_atom_prim, num_atom_super * 3)
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weights = unfolding.get_unfolding_weights()
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freqs = unfolding.get_frequencies()
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P = primitive.get_primitive_matrix()
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P = np.linalg.inv(unfolding_supercell_matrix)
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print(weights.shape)
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self._write_wieghts(band, freqs, comm_points, weights, P)
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@ -61,17 +62,25 @@ class TestUnfolding(unittest.TestCase):
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for j, f in enumerate(freqs[i]):
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for k, G in enumerate(comm_points_super):
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q_ext = q + G
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if (np.abs(q_ext[1:]) > 1e-5).any():
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continue
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uw = weights[i, j, k]
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q_k = np.dot(P.T, q_ext)
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lines.append("%f %f %f %f %f" %
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(q_k[0], q_k[1], q_k[2], f, uw))
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q_k -= np.rint(q_k)
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q_q = np.dot(P.T, q)
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q_g = np.dot(P.T, G)
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# if (np.abs(q_k[1] - q_k[2]) > 1e-5 or
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# np.abs(q_k[0]) > 1e-5):
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# continue
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if (np.abs(q_k[1]) > 1e-5 or
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np.abs(q_k[2]) > 1e-5):
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continue
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lines.append("%f %f %f %f %f %f %f %f %f %f %f" %
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(q_k[0], q_k[1], q_k[2],
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q_q[0], q_q[1], q_q[2],
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q_g[0], q_g[1], q_g[2],
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f, uw))
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w.write("\n".join(lines))
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def _get_phonon(self, smat, pmat, cell):
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print smat
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print pmat
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phonon = Phonopy(cell,
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smat,
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primitive_matrix=pmat,
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