LatticeGreenFunction_new/setup.py at master · aztan2/LatticeGreenFunction_new · GitHub

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import numpy as np
import numpy.linalg as la
from collections import namedtuple


def readinputs(f):

    """
    Reads in information from input file:
    parameters related to the material and crystal structure,
    followed by information related to setting up the dislocation slab geometry.

    Parameters
    ----------
    f : filename to read data from e.g. input_bccscrew

    Returns
    -------
    crystalclass: crystal class (0=isotropic; 1=cubic; 2=hexagonal)
    a0          : lattice constant in angstroms
    Cijs        : list of Cijs

    M           : 3x3 matrix for rotating from mnt basis to cartesian basis
                  (columns are normalized m,n,t vectors)
    t_mag       : magnitude of the periodic vector along the dislocation threading direction

    """

    ## read in lines from input file and ignore blank lines and comment lines
    lines = [line.rstrip() for line in f if line.rstrip() if line[0] != '#']

    # first line is the crystal class
    crystalclass = int(lines[0].split()[0])

    # a1,a2,a3
#    A = np.array([[float(lines[1].split()[0]),float(lines[1].split()[1]),float(lines[1].split()[2])],
#                  [float(lines[2].split()[0]),float(lines[2].split()[1]),float(lines[2].split()[2])],
#                  [float(lines[3].split()[0]),float(lines[3].split()[1]),float(lines[3].split()[2])]]).T

    # number of basis atoms
#    num_basis = int(lines[4].split()[0])

    # basis atom positions in unit cell
#    unitcell_pos = []
#    for i in range(num_basis):
#        unitcell_pos.append([float(lines[5+i].split()[0]),float(lines[5+i].split()[1]),float(lines[5+i].split()[2])])

    # lattice constant (Angstroms)
    a0 = float(lines[-6].split()[0])

    # elastic constants (GPa)
    Cijs = [float(entry) for entry in lines[-5].split()]

    # m,n,t
    m = np.array([float(lines[-4].split()[0]),float(lines[-4].split()[1]),float(lines[-4].split()[2])])
    n = np.array([float(lines[-3].split()[0]),float(lines[-3].split()[1]),float(lines[-3].split()[2])])
    t = np.array([float(lines[-2].split()[0]),float(lines[-2].split()[1]),float(lines[-2].split()[2])])
    M = np.array([m/la.norm(m),n/la.norm(n),t/la.norm(t)]).T

    # t_mag
    t_mag = np.sqrt(float(lines[-1].split()[0]))


    return (crystalclass,a0,Cijs,M,t_mag)


def readprimitive(f):

    """
    Reads in information from primitive input file.
    This file is only needed if using the bulk FCs method for seeting up D.

    Parameters
    ----------
    f : filename to read data from e.g. input_bccscrew

    Returns
    -------
    A  : 3x3 matrix for rotating from primitive basis to cubic cartesian basis
         (columns are a1,a2,a3 vectors)
    unitcell_pos: positions of the basis atoms within the primitive unit cell

    """

    ## read in lines from input file and ignore blank lines and comment lines
    lines = [line.rstrip() for line in f if line.rstrip() if line[0] != '#']

    # a1,a2,a3
    A = np.array([[float(lines[0].split()[0]),float(lines[0].split()[1]),float(lines[0].split()[2])],
                  [float(lines[1].split()[0]),float(lines[1].split()[1]),float(lines[1].split()[2])],
                  [float(lines[2].split()[0]),float(lines[2].split()[1]),float(lines[2].split()[2])]]).T

    # number of basis atoms
    num_basis = int(lines[3].split()[0])

    # basis atom positions in unit cell
    unitcell_pos = []
    for i in range(num_basis):
        unitcell_pos.append([float(lines[4+i].split()[0]),float(lines[4+i].split()[1]),float(lines[4+i].split()[2])])

    return (A,unitcell_pos)