mirror of https://github.com/phonopy/phonopy.git
q-point modes are re-written using class
This commit is contained in:
Atsushi Togo
parent
24234c4332
commit
d070cc5535
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@ -51,7 +51,7 @@ from phonopy.phonon.thermal_displacement import ThermalDisplacements, \
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ThermalDistances, ThermalDisplacementMatrices
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from phonopy.phonon.animation import Animation
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from phonopy.phonon.modulation import Modulation
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from phonopy.phonon.qpoints_mode import write_yaml as write_yaml_qpoints
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from phonopy.phonon.qpoints_mode import QpointsPhonon
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from phonopy.phonon.irreps import IrReps
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from phonopy.phonon.group_velocity import GroupVelocity
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from phonopy.phonon.tetrahedron_mesh import TetrahedronMesh
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@ -765,13 +765,16 @@ class Phonopy:
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write_dynamical_matrices=False,
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factor=VaspToTHz):
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self._set_dynamical_matrix()
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write_yaml_qpoints(q_points,
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self._dynamical_matrix,
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nac_q_direction=nac_q_direction,
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is_eigenvectors=is_eigenvectors,
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group_velocity=self._group_velocity,
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write_dynamical_matrices=write_dynamical_matrices,
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factor=self._factor)
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self._qpoints_phonon = QpointsPhonon(
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q_points,
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self._dynamical_matrix,
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nac_q_direction=nac_q_direction,
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is_eigenvectors=is_eigenvectors,
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group_velocity=self._group_velocity,
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write_dynamical_matrices=write_dynamical_matrices,
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factor=self._factor)
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self._qpoints_phonon.write_yaml()
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# Animation
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def write_animation(self,
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@ -1424,7 +1424,7 @@ class PhonopyConfParser(ConfParser):
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# q-vector direction at q->0 for non-analytical term correction
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if params.has_key('q_direction'):
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self._settings.set_q_direction(params['q_direction'])
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self._settings.set_nac_q_direction(params['q_direction'])
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# Anime mode
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if params.has_key('anime_type'):
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@ -36,109 +36,124 @@ import numpy as np
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import cmath
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from phonopy.units import VaspToTHz
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def write_yaml(qpoints,
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dynamical_matrix,
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nac_q_direction=None,
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is_eigenvectors=False,
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group_velocity=None,
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write_dynamical_matrices=False,
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factor=VaspToTHz):
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cell = dynamical_matrix.get_primitive()
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num_atom = cell.get_number_of_atoms()
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m = cell.get_masses()
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names = cell.get_chemical_symbols()
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positions = cell.get_scaled_positions()
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lattice = cell.get_cell()
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class QpointsPhonon:
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def __init__(self,
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qpoints,
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dynamical_matrix,
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nac_q_direction=None,
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is_eigenvectors=False,
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group_velocity=None,
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write_dynamical_matrices=False,
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factor=VaspToTHz):
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cell = dynamical_matrix.get_primitive()
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self._natom = cell.get_number_of_atoms()
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self._masses = cell.get_masses()
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self._symbols = cell.get_chemical_symbols()
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self._positions = cell.get_scaled_positions()
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self._lattice = cell.get_cell()
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self._qpoints = qpoints
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self._dynamical_matrix = dynamical_matrix
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self._nac_q_direction = nac_q_direction
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self._is_eigenvectors = is_eigenvectors
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self._group_velocity = group_velocity
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self._write_dynamical_matrix = write_dynamical_matrices
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self._factor = factor
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if group_velocity is not None:
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group_velocity.set_q_points(qpoints, perturbation=nac_q_direction)
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group_velocities = group_velocity.get_group_velocity()
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self._gv = None
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self._dm = None
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self._eigenvectors = None
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self._frequencies = None
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w = open('qpoints.yaml', 'w')
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w.write("nqpoint: %-7d\n" % len(qpoints))
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w.write("natom: %-7d\n" % num_atom)
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w.write("atom-info:\n")
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for mass, name in zip(m, names):
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w.write("- { name: %2s, mass: %10.5f }\n" % (name, mass))
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self._run()
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def write_yaml(self):
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w = open('qpoints.yaml', 'w')
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w.write("nqpoint: %-7d\n" % len(self._qpoints))
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w.write("natom: %-7d\n" % self._natom)
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w.write("atom-info:\n")
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for mass, name in zip(self._masses, self._symbols):
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w.write("- { name: %2s, mass: %10.5f }\n" % (name, mass))
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w.write("real-basis:\n")
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for vec in self._lattice:
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w.write("- [ %20.15f, %20.15f, %20.15f ]\n" % tuple(vec))
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w.write("real-basis:\n")
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w.write("- [ %20.15f, %20.15f, %20.15f ]\n" % (tuple(lattice[0])))
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w.write("- [ %20.15f, %20.15f, %20.15f ]\n" % (tuple(lattice[1])))
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w.write("- [ %20.15f, %20.15f, %20.15f ]\n" % (tuple(lattice[2])))
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rec_lattice = np.linalg.inv(lattice).T
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w.write("reciprocal-basis: # q point is multiplied from rhs.\n")
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w.write("- [ %20.15f, %20.15f, %20.15f ]\n" % (tuple(rec_lattice[0])))
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w.write("- [ %20.15f, %20.15f, %20.15f ]\n" % (tuple(rec_lattice[1])))
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w.write("- [ %20.15f, %20.15f, %20.15f ]\n" % (tuple(rec_lattice[2])))
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w.write("position:\n")
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for pos in positions:
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w.write("- [ %20.15f, %20.15f, %20.15f ]\n" % (tuple(pos)))
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w.write("phonon:\n")
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for i, q in enumerate(qpoints):
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if nac_q_direction is not None and (np.abs(q) < 1e-5).all():
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dynamical_matrix.set_dynamical_matrix(q, q_direction=nac_q_direction)
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else:
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dynamical_matrix.set_dynamical_matrix(q)
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dm = dynamical_matrix.get_dynamical_matrix()
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w.write("- q-position: [ %12.7f, %12.7f, %12.7f ]\n" % tuple(q))
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if write_dynamical_matrices:
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w.write(" dynamical_matrix:\n")
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for row in dm:
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w.write(" - [ ")
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for j, elem in enumerate(row):
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w.write("%15.10f, %15.10f" % (elem.real, elem.imag))
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if j == len(row) - 1:
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w.write(" ]\n")
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else:
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w.write(", ")
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w.write(" band:\n")
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rec_lattice = np.linalg.inv(self._lattice).T
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w.write("reciprocal-basis: # column vectors\n")
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for vec in rec_lattice:
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w.write("- [ %20.15f, %20.15f, %20.15f ]\n" % tuple(vec))
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w.write("position:\n")
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for pos in self._positions:
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w.write("- [ %20.15f, %20.15f, %20.15f ]\n" % tuple(pos))
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if is_eigenvectors:
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eigenvalues, eigenvectors = np.linalg.eigh(dm)
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else:
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eigenvalues = np.linalg.eigvalsh(dm)
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w.write("phonon:\n")
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for i, q in enumerate(self._qpoints):
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w.write("- q-position: [ %12.7f, %12.7f, %12.7f ]\n" % tuple(q))
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if self._write_dynamical_matrix:
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w.write(" dynamical_matrix:\n")
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for row in self._dm[i]:
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w.write(" - [ ")
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for j, elem in enumerate(row):
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w.write("%15.10f, %15.10f" % (elem.real, elem.imag))
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if j == len(row) - 1:
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w.write(" ]\n")
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else:
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w.write(", ")
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w.write(" band:\n")
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for j, freq in enumerate(self._frequencies[i]):
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w.write(" - # %d\n" % (j + 1))
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w.write(" frequency: %15.10f\n" % freq)
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if self._gv is not None:
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w.write(" group_velocity: [ %13.7f, %13.7f, %13.7f ]\n" %
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tuple(self._gv[i, j]))
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if self._is_eigenvectors:
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w.write(" eigenvector:\n")
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for k in range(self._natom):
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w.write(" - # atom %d\n" % (k + 1))
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for l in (0, 1, 2):
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w.write(" - [ %17.14f, %17.14f ]\n" %
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(self._eigenvectors[i][k * 3 + l, j].real,
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self._eigenvectors[i][k * 3 + l, j].imag))
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w.write("\n")
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for j, eig in enumerate(eigenvalues.real):
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if eig < 0:
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freq = -np.sqrt(-eig)
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def _run(self):
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if self._group_velocity is not None:
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self._group_velocity.set_q_points(
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self._qpoints, perturbation=self._nac_q_direction)
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self._gv = self._group_velocity.get_group_velocity()
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if self._write_dynamical_matrix:
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self._dm = []
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self._frequencies = []
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if self._is_eigenvectors:
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self._eigenvectors = []
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for q in self._qpoints:
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dm = self._get_dynamical_matrix(q)
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if self._write_dynamical_matrix:
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self._dm.append(dm)
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if self._is_eigenvectors:
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eigvals, eigvecs = np.linalg.eigh(dm)
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self._eigenvectors.append(eigvecs)
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else:
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freq = np.sqrt(eig)
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w.write(" - # %d\n" % (j+1))
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w.write(" frequency: %15.10f\n" % (freq * factor))
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if group_velocity is not None:
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w.write(" group_velocity: ")
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w.write("[ %13.7f, %13.7f, %13.7f ]\n" %
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tuple(group_velocities[i, j]))
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if is_eigenvectors:
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w.write(" eigenvector:\n")
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for k in range(num_atom):
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w.write(" - # atom %d\n" % (k+1))
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for l in (0,1,2):
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w.write(" - [ %17.14f, %17.14f ]\n" %
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(eigenvectors[k*3+l,j].real,
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eigenvectors[k*3+l,j].imag))
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w.write(" eigenvector_time_aligned:\n")
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for k in range(num_atom):
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w.write(" - # atom %d, freq*sqrt(m) %f, [%f %f %f]\n" %
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((k+1, freq * factor * np.sqrt(m[k])) +
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tuple(positions[k])))
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phase_shift = np.exp(2j * np.pi * np.dot(positions[k], q))
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eig_aligned = eigenvectors[k*3:(k+1)*3, j] * phase_shift
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for l in (0, 1, 2):
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w.write(
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" - [ %17.14f, %17.14f ] # %7.2f, %7.4f\n" %
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(eig_aligned[l].real, eig_aligned[l].imag,
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np.angle(eig_aligned[l], deg=True),
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abs(eig_aligned[l])))
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w.write("\n")
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eigvals = np.linalg.eigvalsh(dm)
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eigvals = eigvals.real
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self._frequencies.append(np.sqrt(np.abs(eigvals)) *
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np.sign(eigvals) * self._factor)
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def _get_dynamical_matrix(self, q):
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if self._nac_q_direction is not None and (np.abs(q) < 1e-5).all():
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self._dynamical_matrix.set_dynamical_matrix(
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q, q_direction=self._nac_q_direction)
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else:
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self._dynamical_matrix.set_dynamical_matrix(q)
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return self._dynamical_matrix.get_dynamical_matrix()
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@ -850,7 +850,7 @@ if run_mode == 'qpoints':
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print "Frequencies at q-points given by QPOINTS:"
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phonon.write_yaml_qpoints(
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q_points,
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nac_q_direction=settings.get_q_direction(),
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nac_q_direction=settings.get_nac_q_direction(),
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is_eigenvectors=settings.get_is_eigenvectors(),
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write_dynamical_matrices=settings.get_write_dynamical_matrices(),
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factor=factor)
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@ -922,7 +922,7 @@ elif run_mode=='modulation':
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phonon_modes,
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delta_q=delta_q,
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derivative_order=derivative_order,
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nac_q_direction=settings.get_q_direction())
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nac_q_direction=settings.get_nac_q_direction())
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phonon.write_modulations()
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phonon.write_yaml_modulations()
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