Calculate interatomic distances.
Requirement: tkcrystalbase.py

Download script from .\crystal_distance.py

import sys
import os
from numpy import sin, cos, tan, arcsin, arccos, arctan, exp, log, sqrt
import numpy as np
from numpy import linalg as la
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt

from tkcrystalbase import *


"""
Calculate interatomic distances.
  Requirement: tkcrystalbase.py
"""


# Lattice parameters (angstrom and degree)
#lattice_parameters = [ 5.62, 5.62, 5.62, 60.0, 60.0, 60.0]
lattice_parameters = [ 5.62, 5.62, 5.62, 90.0, 90.0, 90.0]

# Site information (atom name, site label, atomic number, atomic mass, charge, radius, color, position)
sites = [
         ['Na', 'Na1', 11, 22.98997, +1.0, 0.7, 'red', np.array([0.0, 0.0, 0.0])]
        ,['Na', 'Na2', 11, 22.98997, +1.0, 0.7, 'red', np.array([0.0, 0.5, 0.5])]
        ,['Na', 'Na3', 11, 22.98997, +1.0, 0.7, 'red', np.array([0.5, 0.0, 0.5])]
        ,['Na', 'Na4', 11, 22.98997, +1.0, 0.7, 'red', np.array([0.5, 0.5, 0.0])]
        ,['Cl', 'Cl1', 17, 35.4527, -1.0, 1.4, 'blue', np.array([0.5, 0.0, 0.0])]
        ,['Cl', 'Cl2', 17, 35.4527, -1.0, 1.4, 'blue', np.array([0.5, 0.5, 0.5])]
        ,['Cl', 'Cl3', 17, 35.4527, -1.0, 1.4, 'blue', np.array([0.0, 0.0, 0.5])]
        ,['Cl', 'Cl4', 17, 35.4527, -1.0, 1.4, 'blue', np.array([0.0, 0.5, 0.0])]
        ]

# Distance range
rmin = 0.1 # angstrom. used to judge identical site
rmax = 4.5 # angstrom.


def main():
    print("")
    print("Lattice parameters:", lattice_parameters)
    aij = cal_lattice_vectors(lattice_parameters)
    print("Lattice vectors:")
    print(" ax: ({:10.4g}, {:10.4g}, {:10.4g}) A".format(aij[0][0], aij[0][1], aij[0][2]))
    print(" ay: ({:10.4g}, {:10.4g}, {:10.4g}) A".format(aij[1][0], aij[1][1], aij[1][2]))
    print(" az: ({:10.4g}, {:10.4g}, {:10.4g}) A".format(aij[2][0], aij[2][1], aij[2][2]))
    inf = cal_metrics(lattice_parameters)
    gij = inf['gij']
    print("Metric tensor:")
    print(" gij: ({:10.4g}, {:10.4g}, {:10.4g}) A".format(*gij[0]))
    print(" ({:10.4g}, {:10.4g}, {:10.4g}) A".format(*gij[1]))
    print(" ({:10.4g}, {:10.4g}, {:10.4g}) A".format(*gij[2]))
    print("")
    volume = cal_volume(aij)
    print("Volume: {:12.4g} A^3".format(volume))

    print("")
    print("Unit cell volume: {:12.4g} A^3".format(volume))
    Raij = cal_reciprocal_lattice_vectors(aij)
    Rlatt = cal_reciprocal_lattice_parameters(Raij)
    Rinf = cal_metrics(Rlatt)
    Rgij = Rinf['gij']
    print("Reciprocal lattice parameters:", Rlatt)
    print("Reciprocal lattice vectors:")
    print(" Rax: ({:10.4g}, {:10.4g}, {:10.4g}) A^-1".format(*Raij[0]))
    print(" Ray: ({:10.4g}, {:10.4g}, {:10.4g}) A^-1".format(*Raij[1]))
    print(" Raz: ({:10.4g}, {:10.4g}, {:10.4g}) A^-1".format(*Raij[2]))
    print("Reciprocal lattice metric tensor:")
    print(" Rgij: ({:10.4g}, {:10.4g}, {:10.4g}) A^-1".format(*Rgij[0]))
    print(" ({:10.4g}, {:10.4g}, {:10.4g}) A^-1".format(*Rgij[1]))
    print(" ({:10.4g}, {:10.4g}, {:10.4g}) A^-1".format(*Rgij[2]))
    Rvolume = cal_volume(Raij)
    print("Reciprocal unit cell volume: {:12.4g} A^-3".format(Rvolume))

# Calculate the range of unit cells
    nxmax = int(rmax / lattice_parameters[0]) + 1
    nymax = int(rmax / lattice_parameters[1]) + 1
    nzmax = int(rmax / lattice_parameters[2]) + 1
    print("")
    print("nmax:", nxmax, nymax, nzmax)

# Calculate interatomic distances and store them in rlist list variable
    rlist = []
    for isite0 in range(len(sites)):
        site0 = sites[isite0]
        name0, label0, z0, M0, q0, r0, color0, pos0 = site0
        for isite1 in range(len(sites)):
            site1 = sites[isite1]
            name1, label1, z1, M1, q1, r1, color1, pos1 = site1
            for iz in range(-nzmax, nzmax+1):
             for iy in range(-nymax, nymax+1):
              for ix in range(-nxmax, nxmax+1):
                dis = distance(pos0, pos1 + np.array([ix, iy, iz]), gij)
                if dis < rmin or rmax < dis:
                    continue

                rlist.append([dis, site0, site1, ix, iy, iz])

#                print(" {:4} ({:8.4g}, {:8.4g}, {:8.4g}) - {:4} ({:8.4g}, {:8.4g}, {:8.4g}) + ({:2d}, {:2d}, {:2d}): dis = {:10.4g} A"
#                    .format(label0, pos0[0], pos0[1], pos0[2], label1, pos1[0], pos1[1], pos1[2], ix, iy, iz, dis))

# Sort rlist by distance (x[0] priority)
    rlist.sort(key = lambda x: (x[0], x[1], x[3], x[4], x[5], x[2]))

    print("")
    print("Interatomic distances:")
    for rinf in rlist:
        dis, site0, site1, ix, iy, iz = rinf
        name0, label0, z0, M0, q0, r0, color0, pos0 = site0
        name1, label1, z1, M1, q1, r1, color1, pos1 = site1
        print(" {:4} ({:8.4g}, {:8.4g}, {:8.4g}) - {:4} ({:8.4g}, {:8.4g}, {:8.4g}) + ({:2d}, {:2d}, {:2d}): dis = {:10.4g} A"
            .format(label0, pos0[0], pos0[1], pos0[2], label1, pos1[0], pos1[1], pos1[2], ix, iy, iz, dis))

    print("")
    exit()


if __name__ == '__main__':
    main()