mirror of https://github.com/phonopy/phono3py.git
Merge phonopy PR #178 (not PR of phono3py)
This commit is contained in:
Atsushi Togo
parent
435669e50e
commit
42a23c8230
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@ -0,0 +1,233 @@
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"""Velocity operator of Simoncelli, Marzari, and Mauri."""
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# Copyright (C) 2013 Atsushi Togo
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# All rights reserved.
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#
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# This file is part of phonopy.
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#
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# Redistribution and use in source and binary forms, with or without
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# modification, are permitted provided that the following conditions
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# are met:
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#
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# * Redistributions of source code must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# * Redistributions in binary form must reproduce the above copyright
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# notice, this list of conditions and the following disclaimer in
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# the documentation and/or other materials provided with the
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# distribution.
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#
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# * Neither the name of the phonopy project nor the names of its
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# contributors may be used to endorse or promote products derived
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# from this software without specific prior written permission.
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#
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
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# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
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# COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
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# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
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# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
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# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
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# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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# POSSIBILITY OF SUCH DAMAGE.
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import numpy as np
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from phonopy.phonon.group_velocity import GroupVelocity
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from phonopy.units import VaspToTHz
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class VelocityOperator(GroupVelocity):
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"""Class to calculate velocity operator of phonons."""
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def __init__(
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self,
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dynamical_matrix,
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q_length=None,
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symmetry=None,
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frequency_factor_to_THz=VaspToTHz,
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cutoff_frequency=1e-4,
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):
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"""Init method.
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dynamical_matrix : DynamicalMatrix or DynamicalMatrixNAC
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Dynamical matrix class instance.
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q_length : float
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This is used such as D(q + q_length) - D(q - q_length) for
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calculating finite difference of dynamical matrix.
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Default is None, which gives 1e-5.
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symmetry : Symmetry
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This is used to symmetrize group velocity at each q-points.
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Default is None, which means no symmetrization.
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frequency_factor_to_THz : float
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Unit conversion factor to convert to THz. Default is VaspToTHz.
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cutoff_frequency : float
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Group velocity is set zero if phonon frequency is below this value.
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"""
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self._dynmat = dynamical_matrix
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primitive = dynamical_matrix.primitive
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self._reciprocal_lattice_inv = primitive.cell
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self._reciprocal_lattice = np.linalg.inv(self._reciprocal_lattice_inv)
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self._q_length = q_length
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if self._q_length is None:
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self._q_length = 5e-6
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self._symmetry = symmetry
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self._factor = frequency_factor_to_THz
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self._cutoff_frequency = cutoff_frequency
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self._directions = np.array(
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[
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[
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1,
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2,
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3,
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],
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# this is a random direction, not used and left here for historical
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# reasons.
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[1, 0, 0], # x
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[0, 1, 0], # y
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[0, 0, 1],
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],
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dtype="double",
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) # z
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self._directions[0] /= np.linalg.norm(
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self._directions[0]
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) # normalize the random direction
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self._q_points = None
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self._velocity_operators = None
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self._perturbation = None
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def run(self, q_points, perturbation=None):
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"""Velocity operators are computed at q-points.
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q_points : Array-like
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List of q-points such as [[0, 0, 0], [0.1, 0.2, 0.3], ...].
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perturbation : Array-like
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Direction in fractional coordinates of reciprocal space.
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"""
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self._q_points = q_points
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self._perturbation = perturbation
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if perturbation is None:
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# Give a random direction to break symmetry
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self._directions[0] = np.array([1, 0, 0]) # normalized later
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else:
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self._directions[0] = np.dot(self._reciprocal_lattice, perturbation)
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self._directions[0] /= np.linalg.norm(self._directions[0])
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gv_operator = [
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self._calculate_velocity_operator_at_q(q) for q in self._q_points
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]
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self._velocity_operators = np.array(gv_operator, dtype="complex", order="C")
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@property
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def velocity_operators(self):
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"""Return velocity operators."""
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return self._velocity_operators
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def _calculate_velocity_operator_at_q(self, q):
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self._dynmat.set_dynamical_matrix(q)
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dm = self._dynmat.get_dynamical_matrix()
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eigvals, eigvecs = np.linalg.eigh(dm)
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eigvals = eigvals.real
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freqs = np.sqrt(abs(eigvals)) * np.sign(eigvals) * self._factor
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nat3 = len(freqs)
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gv_operator = np.zeros((nat3, nat3, 3), dtype="complex", order="C")
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#
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# compute the finite differences along several directions
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# ddms is a list of FD derivatives of the dynamical matrix
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# computed along several directions
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ddms = self._get_dsqrtD_FD(np.array(q))
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#
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# ddms[0] cointains the FD derivative in the direction in which the velocity
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# operator is diagonalized
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for id_dir in range(0, 3):
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gv_operator[:, :, id_dir] = (
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np.matmul(eigvecs.T.conj(), np.matmul(ddms[id_dir + 1], eigvecs))
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* self._factor
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)
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#
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# enforce the velocity operator to be Hermitian
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gv_operator[:, :, id_dir] = (
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gv_operator[:, :, id_dir].T.conj() + gv_operator[:, :, id_dir]
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) / 2.0
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return gv_operator
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def _get_dsqrtD_FD(self, q):
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"""Compute finite difference of sqrt of dynamical matrices."""
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#
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ddm = []
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# _q_length is a float specifying the modulus of the q-vector displacement
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# used to compute the finite differences
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for dqc in self._directions * self._q_length:
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dq = np.dot(self._reciprocal_lattice_inv, dqc)
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ddm.append(
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self._delta_sqrt_dynamical_matrix(q, dq, self._dynmat)
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/ self._q_length
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/ 2
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)
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return np.array(ddm)
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def _sqrt_dynamical_matrix(self, flag_gamma, dm):
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# returns the sqrt of the dynamical matrix in the cartesian basis
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eigvals, eigvecs = np.linalg.eigh(dm)
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eigvals = eigvals.real
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# will give NaN in case of negative frequencies
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freqs = np.sign(eigvals) * np.sqrt(abs(eigvals))
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# print('raw=',freqs)
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#
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# enforce eigenvalues and eigenvectors to zero for acoustic modes at Gamma point
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if flag_gamma:
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freqs[0] = 0.0
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eigvecs[:, 0] = 0.0
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freqs[1] = 0.0
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eigvecs[:, 1] = 0.0
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freqs[2] = 0.0
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eigvecs[:, 2] = 0.0
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#
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if any(f < 0.0 for f in freqs):
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print("ERROR: negative frequency=", freqs)
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# this is a diagonal matrix containing the frequencies on the diagonal
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# we take the element-wise sqrt of a diagonal matrix, in eigenmodes basis
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omega_matrix = np.sqrt(np.matmul(eigvecs.T.conj(), np.matmul(dm, eigvecs)))
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# now we go back to the Cartesian basis
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sqrt_dm = np.matmul(eigvecs, np.matmul(omega_matrix, eigvecs.T.conj()))
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#
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return sqrt_dm
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def _delta_sqrt_dynamical_matrix(self, q, delta_q, dynmat):
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#
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flag_gamma = False
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if np.linalg.norm(q) < np.linalg.norm(delta_q):
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flag_gamma = True
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if (
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(self._dynmat.is_nac())
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and (self._dynmat.nac_method == "gonze")
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and flag_gamma
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):
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dynmat.set_dynamical_matrix(
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q - delta_q, q_direction=(q - delta_q) / np.linalg.norm(q - delta_q)
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)
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dm1 = dynmat.get_dynamical_matrix()
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sqrt_dm1 = self._sqrt_dynamical_matrix(flag_gamma, dm1)
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dynmat.set_dynamical_matrix(
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q + delta_q, q_direction=(q + delta_q) / np.linalg.norm(q + delta_q)
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)
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dm2 = dynmat.get_dynamical_matrix()
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sqrt_dm2 = self._sqrt_dynamical_matrix(flag_gamma, dm2)
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else:
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dynmat.set_dynamical_matrix(q - delta_q)
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dm1 = dynmat.get_dynamical_matrix()
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sqrt_dm1 = self._sqrt_dynamical_matrix(flag_gamma, dm1)
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dynmat.set_dynamical_matrix(q + delta_q)
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dm2 = dynmat.get_dynamical_matrix()
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sqrt_dm2 = self._sqrt_dynamical_matrix(flag_gamma, dm2)
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#
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#
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return sqrt_dm2 - sqrt_dm1
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@ -0,0 +1,4 @@
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14.400
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2.43533967 0 0 0 2.43533967 0 0 0 2.43533967
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1.086875 0 0 0 1.086875 0 0 0 1.086875
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-1.086875 0 0 0 -1.086875 0 0 0 -1.086875
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|
|
@ -0,0 +1,136 @@
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64
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2
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1
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||||
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|
||||
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|
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||||
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|
||||
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|
||||
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|
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0.0005170500 0.0000010700 0.0000010700
|
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|
||||
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|
||||
-0.0000146100 0.0000000000 0.0001925900
|
||||
-0.0000113300 0.0000000000 -0.0001898400
|
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|
||||
-0.0000146100 0.0000000000 -0.0001925900
|
||||
-0.0000113300 0.0000000000 0.0001898400
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||||
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|
||||
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|
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|
||||
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|
||||
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|
||||
-0.0000113300 0.0001898400 0.0000000000
|
||||
|
|
@ -3,6 +3,7 @@ import os
|
|||
|
||||
import phonopy
|
||||
import pytest
|
||||
from phonopy import Phonopy
|
||||
from phonopy.interface.phonopy_yaml import read_cell_yaml
|
||||
|
||||
import phono3py
|
||||
|
|
@ -253,3 +254,19 @@ def aln_lda(request):
|
|||
store_dense_svecs=enable_v2,
|
||||
log_level=1,
|
||||
)
|
||||
|
||||
|
||||
@pytest.fixture(scope="session")
|
||||
def ph_nacl() -> Phonopy:
|
||||
"""Return Phonopy class instance of NaCl 2x2x2."""
|
||||
yaml_filename = os.path.join(current_dir, "phonopy_disp_NaCl.yaml")
|
||||
force_sets_filename = os.path.join(current_dir, "FORCE_SETS_NaCl")
|
||||
born_filename = os.path.join(current_dir, "BORN_NaCl")
|
||||
return phonopy.load(
|
||||
yaml_filename,
|
||||
force_sets_filename=force_sets_filename,
|
||||
born_filename=born_filename,
|
||||
is_compact_fc=False,
|
||||
log_level=1,
|
||||
produce_fc=True,
|
||||
)
|
||||
|
|
|
|||
|
|
@ -0,0 +1,363 @@
|
|||
"""Tests for velocity operator."""
|
||||
import numpy as np
|
||||
from phonopy import Phonopy
|
||||
|
||||
from phono3py.phonon.velocity_operator import VelocityOperator
|
||||
|
||||
|
||||
def test_gv_operator_nacl(ph_nacl: Phonopy):
|
||||
"""Test of GroupVelocity by NaCl."""
|
||||
gv_operator_square_modulus_ref = {}
|
||||
# direction 0
|
||||
gv_operator_square_modulus_ref[0] = np.array(
|
||||
[
|
||||
[
|
||||
2.42970100e02,
|
||||
-6.20236119e00,
|
||||
-1.82999046e-01,
|
||||
-2.09295390e-01,
|
||||
4.07782967e01,
|
||||
2.10142118e-01,
|
||||
],
|
||||
[
|
||||
-6.20236119e00,
|
||||
2.73261377e02,
|
||||
-3.71620328e02,
|
||||
8.44686890e-01,
|
||||
-1.61985084e00,
|
||||
-5.01748557e00,
|
||||
],
|
||||
[
|
||||
-1.82999046e-01,
|
||||
-3.71620328e02,
|
||||
1.03489135e03,
|
||||
-2.58482318e01,
|
||||
1.88975807e-02,
|
||||
1.33902037e01,
|
||||
],
|
||||
[
|
||||
-2.09295390e-01,
|
||||
8.44686890e-01,
|
||||
-2.58482318e01,
|
||||
1.30173952e00,
|
||||
-1.56714339e-01,
|
||||
3.74138211e00,
|
||||
],
|
||||
[
|
||||
4.07782967e01,
|
||||
-1.61985084e00,
|
||||
1.88975807e-02,
|
||||
-1.56714339e-01,
|
||||
1.07994337e01,
|
||||
-2.56681660e00,
|
||||
],
|
||||
[
|
||||
2.10142118e-01,
|
||||
-5.01748557e00,
|
||||
1.33902037e01,
|
||||
3.74138211e00,
|
||||
-2.56681660e00,
|
||||
5.34677654e02,
|
||||
],
|
||||
]
|
||||
)
|
||||
|
||||
# direction 1
|
||||
gv_operator_square_modulus_ref[1] = np.array(
|
||||
[
|
||||
[190.26961913, 24.42080327, 18.66103712, 3.499692, 17.12151154, 7.82170714],
|
||||
[
|
||||
24.42080327,
|
||||
753.95642101,
|
||||
449.00523399,
|
||||
56.90864201,
|
||||
-3.00513131,
|
||||
178.25703584,
|
||||
],
|
||||
[
|
||||
18.66103712,
|
||||
449.00523399,
|
||||
282.90229148,
|
||||
124.96202594,
|
||||
-3.1864197,
|
||||
46.43438272,
|
||||
],
|
||||
[
|
||||
3.499692,
|
||||
56.90864201,
|
||||
124.96202594,
|
||||
628.61784617,
|
||||
-13.41223828,
|
||||
-240.42545741,
|
||||
],
|
||||
[
|
||||
17.12151154,
|
||||
-3.00513131,
|
||||
-3.1864197,
|
||||
-13.41223828,
|
||||
4.49707039,
|
||||
2.33350832,
|
||||
],
|
||||
[
|
||||
7.82170714,
|
||||
178.25703584,
|
||||
46.43438272,
|
||||
-240.42545741,
|
||||
2.33350832,
|
||||
394.18935848,
|
||||
],
|
||||
]
|
||||
)
|
||||
# direction 2
|
||||
gv_operator_square_modulus_ref[2] = np.array(
|
||||
[
|
||||
[
|
||||
3.21847047e02,
|
||||
-2.87032091e01,
|
||||
-2.45808366e01,
|
||||
-1.57578343e00,
|
||||
-1.32856444e02,
|
||||
-1.34389001e01,
|
||||
],
|
||||
[
|
||||
-2.87032091e01,
|
||||
5.54329513e01,
|
||||
1.16917174e02,
|
||||
-3.18740464e00,
|
||||
8.04928014e00,
|
||||
6.19917390e01,
|
||||
],
|
||||
[
|
||||
-2.45808366e01,
|
||||
1.16917174e02,
|
||||
2.55127746e02,
|
||||
5.66979440e-01,
|
||||
9.79228317e00,
|
||||
7.96414618e01,
|
||||
],
|
||||
[
|
||||
-1.57578343e00,
|
||||
-3.18740464e00,
|
||||
5.66979440e-01,
|
||||
1.61522304e01,
|
||||
1.98704126e01,
|
||||
-1.14635470e02,
|
||||
],
|
||||
[
|
||||
-1.32856444e02,
|
||||
8.04928014e00,
|
||||
9.79228317e00,
|
||||
1.98704126e01,
|
||||
8.60482934e02,
|
||||
-1.68196151e01,
|
||||
],
|
||||
[
|
||||
-1.34389001e01,
|
||||
6.19917390e01,
|
||||
7.96414618e01,
|
||||
-1.14635470e02,
|
||||
-1.68196151e01,
|
||||
8.58940749e02,
|
||||
],
|
||||
]
|
||||
)
|
||||
|
||||
gv_operator = VelocityOperator(
|
||||
ph_nacl.dynamical_matrix, symmetry=ph_nacl.primitive_symmetry
|
||||
)
|
||||
# we chose an 'ugly' q-point because we want to avoid degeneracies.
|
||||
# degeneracies are tested in phono3py
|
||||
gv_operator.run([[0.1, 0.22, 0.33]])
|
||||
square_modulus = np.zeros((6, 6, 3))
|
||||
for direction in range(2, 3):
|
||||
square_modulus[:, :, direction] = np.matmul(
|
||||
gv_operator.velocity_operators[0][:, :, direction],
|
||||
gv_operator.velocity_operators[0][:, :, direction].conjugate().T,
|
||||
).real
|
||||
np.testing.assert_allclose(
|
||||
square_modulus[:, :, direction].ravel(),
|
||||
gv_operator_square_modulus_ref[direction].ravel(),
|
||||
atol=1e-4,
|
||||
)
|
||||
|
||||
|
||||
def test_gv_operator_si(ph_si: Phonopy):
|
||||
"""Test of GroupVelocity by Si."""
|
||||
gv_operator_square_modulus_ref = {}
|
||||
# direction 0
|
||||
gv_operator_square_modulus_ref[0] = np.array(
|
||||
[
|
||||
[
|
||||
2.73572808e03,
|
||||
-4.06210738e00,
|
||||
1.33571471e03,
|
||||
-1.11264018e00,
|
||||
-2.72825378e02,
|
||||
3.23442510e-01,
|
||||
],
|
||||
[
|
||||
-4.06210738e00,
|
||||
2.72065300e03,
|
||||
-3.20535769e01,
|
||||
-4.41527949e02,
|
||||
-1.29661972e01,
|
||||
5.12752451e02,
|
||||
],
|
||||
[
|
||||
1.33571471e03,
|
||||
-3.20535769e01,
|
||||
4.16058788e03,
|
||||
-1.19524446e00,
|
||||
-1.26829836e01,
|
||||
-1.15732958e00,
|
||||
],
|
||||
[
|
||||
-1.11264018e00,
|
||||
-4.41527949e02,
|
||||
-1.19524446e00,
|
||||
1.45914531e03,
|
||||
1.90180987e00,
|
||||
-8.45069100e02,
|
||||
],
|
||||
[
|
||||
-2.72825378e02,
|
||||
-1.29661972e01,
|
||||
-1.26829836e01,
|
||||
1.90180987e00,
|
||||
1.78584698e03,
|
||||
-2.25355370e-01,
|
||||
],
|
||||
[
|
||||
3.23442510e-01,
|
||||
5.12752451e02,
|
||||
-1.15732958e00,
|
||||
-8.45069100e02,
|
||||
-2.25355370e-01,
|
||||
7.25820137e02,
|
||||
],
|
||||
]
|
||||
)
|
||||
|
||||
# direction 1
|
||||
gv_operator_square_modulus_ref[1] = np.array(
|
||||
[
|
||||
[
|
||||
1.95698890e03,
|
||||
-8.55308045e00,
|
||||
-6.97133428e02,
|
||||
8.21442883e-01,
|
||||
-1.08587694e03,
|
||||
-9.83370396e-02,
|
||||
],
|
||||
[
|
||||
-8.55308045e00,
|
||||
2.20579768e03,
|
||||
4.90281444e00,
|
||||
-2.83807879e02,
|
||||
3.01470115e00,
|
||||
-7.45274905e02,
|
||||
],
|
||||
[
|
||||
-6.97133428e02,
|
||||
4.90281444e00,
|
||||
2.96863421e03,
|
||||
-2.26085394e-01,
|
||||
-7.66976692e00,
|
||||
2.51720167e-01,
|
||||
],
|
||||
[
|
||||
8.21442883e-01,
|
||||
-2.83807879e02,
|
||||
-2.26085394e-01,
|
||||
4.24208287e02,
|
||||
6.40518671e-03,
|
||||
4.96247028e02,
|
||||
],
|
||||
[
|
||||
-1.08587694e03,
|
||||
3.01470115e00,
|
||||
-7.66976692e00,
|
||||
6.40518671e-03,
|
||||
8.39180146e02,
|
||||
-8.39817213e-01,
|
||||
],
|
||||
[
|
||||
-9.83370396e-02,
|
||||
-7.45274905e02,
|
||||
2.51720167e-01,
|
||||
4.96247028e02,
|
||||
-8.39817213e-01,
|
||||
7.45082308e02,
|
||||
],
|
||||
]
|
||||
)
|
||||
|
||||
# direction 2
|
||||
gv_operator_square_modulus_ref[2] = np.array(
|
||||
[
|
||||
[
|
||||
1.53807537e03,
|
||||
-3.89302418e00,
|
||||
-1.75424484e02,
|
||||
-1.65219640e00,
|
||||
1.31051315e02,
|
||||
2.03331851e-02,
|
||||
],
|
||||
[
|
||||
-3.89302418e00,
|
||||
2.57583012e03,
|
||||
1.04592533e01,
|
||||
-9.42612420e02,
|
||||
-1.42765014e01,
|
||||
3.33706787e01,
|
||||
],
|
||||
[
|
||||
-1.75424484e02,
|
||||
1.04592533e01,
|
||||
2.92924900e03,
|
||||
-8.53691987e-02,
|
||||
-2.44376137e02,
|
||||
-1.00559293e00,
|
||||
],
|
||||
[
|
||||
-1.65219640e00,
|
||||
-9.42612420e02,
|
||||
-8.53691987e-02,
|
||||
4.18562364e02,
|
||||
-3.54778535e-01,
|
||||
-1.90266774e02,
|
||||
],
|
||||
[
|
||||
1.31051315e02,
|
||||
-1.42765014e01,
|
||||
-2.44376137e02,
|
||||
-3.54778535e-01,
|
||||
4.36890621e01,
|
||||
6.82908650e-01,
|
||||
],
|
||||
[
|
||||
2.03331851e-02,
|
||||
3.33706787e01,
|
||||
-1.00559293e00,
|
||||
-1.90266774e02,
|
||||
6.82908650e-01,
|
||||
1.51072731e03,
|
||||
],
|
||||
]
|
||||
)
|
||||
|
||||
gv_operator = VelocityOperator(
|
||||
ph_si.dynamical_matrix, symmetry=ph_si.primitive_symmetry
|
||||
)
|
||||
gv_operator.run([[0.1, 0.22, 0.33]])
|
||||
square_modulus = np.zeros((6, 6, 3))
|
||||
for direction in range(2, 3):
|
||||
square_modulus[:, :, direction] = np.matmul(
|
||||
gv_operator.velocity_operators[0][:, :, direction],
|
||||
gv_operator.velocity_operators[0][:, :, direction].conj().T,
|
||||
)
|
||||
np.testing.assert_allclose(
|
||||
square_modulus[:, :, direction].ravel(),
|
||||
gv_operator_square_modulus_ref[direction].ravel(),
|
||||
atol=1e-5,
|
||||
)
|
||||
|
|
@ -0,0 +1,356 @@
|
|||
phonopy:
|
||||
version: 2.7.0
|
||||
frequency_unit_conversion_factor: 15.633302
|
||||
symmetry_tolerance: 1.00000e-05
|
||||
configuration:
|
||||
cell_filename: "POSCAR-unitcell"
|
||||
create_displacements: ".true."
|
||||
primitive_axes: "auto"
|
||||
dim: "2 2 2"
|
||||
|
||||
physical_unit:
|
||||
atomic_mass: "AMU"
|
||||
length: "angstrom"
|
||||
force_constants: "eV/angstrom^2"
|
||||
|
||||
space_group:
|
||||
type: "Fm-3m"
|
||||
number: 225
|
||||
Hall_symbol: "-F 4 2 3"
|
||||
|
||||
primitive_matrix:
|
||||
- [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
|
||||
- [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
|
||||
- [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
|
||||
|
||||
supercell_matrix:
|
||||
- [ 2, 0, 0 ]
|
||||
- [ 0, 2, 0 ]
|
||||
- [ 0, 0, 2 ]
|
||||
|
||||
primitive_cell:
|
||||
lattice:
|
||||
- [ 0.000000000000000, 2.845150738087836, 2.845150738087836 ] # a
|
||||
- [ 2.845150738087836, 0.000000000000000, 2.845150738087836 ] # b
|
||||
- [ 2.845150738087836, 2.845150738087836, 0.000000000000000 ] # c
|
||||
points:
|
||||
- symbol: Na # 1
|
||||
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
|
||||
mass: 22.989769
|
||||
- symbol: Cl # 2
|
||||
coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ]
|
||||
mass: 35.453000
|
||||
reciprocal_lattice: # without 2pi
|
||||
- [ -0.175737613233118, 0.175737613233118, 0.175737613233118 ] # a*
|
||||
- [ 0.175737613233118, -0.175737613233118, 0.175737613233118 ] # b*
|
||||
- [ 0.175737613233118, 0.175737613233118, -0.175737613233118 ] # c*
|
||||
|
||||
unit_cell:
|
||||
lattice:
|
||||
- [ 5.690301476175671, 0.000000000000000, 0.000000000000000 ] # a
|
||||
- [ 0.000000000000000, 5.690301476175671, 0.000000000000000 ] # b
|
||||
- [ 0.000000000000000, 0.000000000000000, 5.690301476175671 ] # c
|
||||
points:
|
||||
- symbol: Na # 1
|
||||
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 2
|
||||
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 3
|
||||
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 4
|
||||
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Cl # 5
|
||||
coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 5
|
||||
- symbol: Cl # 6
|
||||
coordinates: [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 5
|
||||
- symbol: Cl # 7
|
||||
coordinates: [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 5
|
||||
- symbol: Cl # 8
|
||||
coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 5
|
||||
|
||||
supercell:
|
||||
lattice:
|
||||
- [ 11.380602952351342, 0.000000000000000, 0.000000000000000 ] # a
|
||||
- [ 0.000000000000000, 11.380602952351342, 0.000000000000000 ] # b
|
||||
- [ 0.000000000000000, 0.000000000000000, 11.380602952351342 ] # c
|
||||
points:
|
||||
- symbol: Na # 1
|
||||
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 2
|
||||
coordinates: [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 3
|
||||
coordinates: [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 4
|
||||
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 5
|
||||
coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 6
|
||||
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 7
|
||||
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 8
|
||||
coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 9
|
||||
coordinates: [ 0.000000000000000, 0.250000000000000, 0.250000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 10
|
||||
coordinates: [ 0.500000000000000, 0.250000000000000, 0.250000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 11
|
||||
coordinates: [ 0.000000000000000, 0.750000000000000, 0.250000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 12
|
||||
coordinates: [ 0.500000000000000, 0.750000000000000, 0.250000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 13
|
||||
coordinates: [ 0.000000000000000, 0.250000000000000, 0.750000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 14
|
||||
coordinates: [ 0.500000000000000, 0.250000000000000, 0.750000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 15
|
||||
coordinates: [ 0.000000000000000, 0.750000000000000, 0.750000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 16
|
||||
coordinates: [ 0.500000000000000, 0.750000000000000, 0.750000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 17
|
||||
coordinates: [ 0.250000000000000, 0.000000000000000, 0.250000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 18
|
||||
coordinates: [ 0.750000000000000, 0.000000000000000, 0.250000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 19
|
||||
coordinates: [ 0.250000000000000, 0.500000000000000, 0.250000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 20
|
||||
coordinates: [ 0.750000000000000, 0.500000000000000, 0.250000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 21
|
||||
coordinates: [ 0.250000000000000, 0.000000000000000, 0.750000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 22
|
||||
coordinates: [ 0.750000000000000, 0.000000000000000, 0.750000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 23
|
||||
coordinates: [ 0.250000000000000, 0.500000000000000, 0.750000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 24
|
||||
coordinates: [ 0.750000000000000, 0.500000000000000, 0.750000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 25
|
||||
coordinates: [ 0.250000000000000, 0.250000000000000, 0.000000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 26
|
||||
coordinates: [ 0.750000000000000, 0.250000000000000, 0.000000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 27
|
||||
coordinates: [ 0.250000000000000, 0.750000000000000, 0.000000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 28
|
||||
coordinates: [ 0.750000000000000, 0.750000000000000, 0.000000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 29
|
||||
coordinates: [ 0.250000000000000, 0.250000000000000, 0.500000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 30
|
||||
coordinates: [ 0.750000000000000, 0.250000000000000, 0.500000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 31
|
||||
coordinates: [ 0.250000000000000, 0.750000000000000, 0.500000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Na # 32
|
||||
coordinates: [ 0.750000000000000, 0.750000000000000, 0.500000000000000 ]
|
||||
mass: 22.989769
|
||||
reduced_to: 1
|
||||
- symbol: Cl # 33
|
||||
coordinates: [ 0.250000000000000, 0.250000000000000, 0.250000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 34
|
||||
coordinates: [ 0.750000000000000, 0.250000000000000, 0.250000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 35
|
||||
coordinates: [ 0.250000000000000, 0.750000000000000, 0.250000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 36
|
||||
coordinates: [ 0.750000000000000, 0.750000000000000, 0.250000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 37
|
||||
coordinates: [ 0.250000000000000, 0.250000000000000, 0.750000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 38
|
||||
coordinates: [ 0.750000000000000, 0.250000000000000, 0.750000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 39
|
||||
coordinates: [ 0.250000000000000, 0.750000000000000, 0.750000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 40
|
||||
coordinates: [ 0.750000000000000, 0.750000000000000, 0.750000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 41
|
||||
coordinates: [ 0.250000000000000, 0.000000000000000, 0.000000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 42
|
||||
coordinates: [ 0.750000000000000, 0.000000000000000, 0.000000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 43
|
||||
coordinates: [ 0.250000000000000, 0.500000000000000, 0.000000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 44
|
||||
coordinates: [ 0.750000000000000, 0.500000000000000, 0.000000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 45
|
||||
coordinates: [ 0.250000000000000, 0.000000000000000, 0.500000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 46
|
||||
coordinates: [ 0.750000000000000, 0.000000000000000, 0.500000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 47
|
||||
coordinates: [ 0.250000000000000, 0.500000000000000, 0.500000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 48
|
||||
coordinates: [ 0.750000000000000, 0.500000000000000, 0.500000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 49
|
||||
coordinates: [ 0.000000000000000, 0.250000000000000, 0.000000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 50
|
||||
coordinates: [ 0.500000000000000, 0.250000000000000, 0.000000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 51
|
||||
coordinates: [ 0.000000000000000, 0.750000000000000, 0.000000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 52
|
||||
coordinates: [ 0.500000000000000, 0.750000000000000, 0.000000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 53
|
||||
coordinates: [ 0.000000000000000, 0.250000000000000, 0.500000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 54
|
||||
coordinates: [ 0.500000000000000, 0.250000000000000, 0.500000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 55
|
||||
coordinates: [ 0.000000000000000, 0.750000000000000, 0.500000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 56
|
||||
coordinates: [ 0.500000000000000, 0.750000000000000, 0.500000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 57
|
||||
coordinates: [ 0.000000000000000, 0.000000000000000, 0.250000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 58
|
||||
coordinates: [ 0.500000000000000, 0.000000000000000, 0.250000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 59
|
||||
coordinates: [ 0.000000000000000, 0.500000000000000, 0.250000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 60
|
||||
coordinates: [ 0.500000000000000, 0.500000000000000, 0.250000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 61
|
||||
coordinates: [ 0.000000000000000, 0.000000000000000, 0.750000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 62
|
||||
coordinates: [ 0.500000000000000, 0.000000000000000, 0.750000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 63
|
||||
coordinates: [ 0.000000000000000, 0.500000000000000, 0.750000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
- symbol: Cl # 64
|
||||
coordinates: [ 0.500000000000000, 0.500000000000000, 0.750000000000000 ]
|
||||
mass: 35.453000
|
||||
reduced_to: 33
|
||||
|
||||
displacements:
|
||||
- atom: 1
|
||||
displacement:
|
||||
[ 0.0100000000000000, 0.0000000000000000, 0.0000000000000000 ]
|
||||
- atom: 33
|
||||
displacement:
|
||||
[ 0.0100000000000000, 0.0000000000000000, 0.0000000000000000 ]
|
||||
Loading…
Reference in New Issue