maurergroup / dfttoolkit / 15077298886

from os.path import join

import numpy as np

from dfttoolkit.geometry import AimsGeometry

class FrictionTensor:

    def __init__(self, directroy):

        self.geometry = AimsGeometry(join(directroy, "geometry.in"))

        self.friction_tensor_raw = self.read_friction_tensor(

    @property

    def friction_tensor(self):

        return self.friction_tensor_raw

    @friction_tensor.setter

    def friction_tensor(self, friction_tensor_raw) -> None:

        self.friction_tensor_raw = friction_tensor_raw

    def read_friction_tensor(self, filename: str):

        atom_indices = []

        friction_tensor_0 = []

        with open(filename) as f:

            lines = f.readlines()

        for line in lines:

            if "# n_atom" in line:

                line = line.strip().split(" ")

                line_1 = []

                for i in line:

                    if i != "":

                        line_1.append(i)

                atom_index = 3 * (int(line_1[2]) - 1) + int(line_1[4]) - 1

                atom_indices.append(atom_index)

            elif "#" not in line:

                friction_tensor_line = [float(i) for i in line.split(" ") if i != ""]

                friction_tensor_0.append(friction_tensor_line)

        friction_tensor_0 = np.array(friction_tensor_0)

        n = len(self.geometry)

        friction_tensor = np.zeros((3 * n, 3 * n))

        for ind_0, atom_index_0 in enumerate(atom_indices):

            for ind_1, atom_index_1 in enumerate(atom_indices):

                friction_tensor[atom_index_0, atom_index_1] = friction_tensor_0[

        return friction_tensor

    def get_life_time(self, vibration):

        vibration /= np.linalg.norm(vibration)

        force = self.friction_tensor_raw.dot(vibration)

        eta = vibration.dot(force)

        return 1 / eta