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connect_edgetonode.py
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connect_edgetonode.py
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#################
#
# This file is part of
# ToBaCCo - Topologically-Based Crystal Constructor
#
# Copyright 2017 Yamil J. Colon <yamilcolon2015@u.northwestern.edu>
# Diego Gomez-Gualdron <dgomezgualdron@mines.edu>
# Ben Bucior <ben.bucior@gmail.com>
#
# ToBaCCo is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ToBaCCo is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
#################
import os
import numpy as np
import re
import fnmatch
import itertools
from neighbors import neighbor_edges, neighbor_vertices
from nodes import __node_properties
from transformations import superimposition_matrix
from placing_bb_func import __place_bb
from operator import itemgetter
from edges import __edge_properties
from placing_edge import __place_edge
import sys
import contextlib
#Connect edge to two nodes of the same type
def __edge_to_node(unit_cell, e1_coord, v11_nbors_for_e1, node_1_elements, edge_elements, node_1_frac_coord, edge_frac_coord, node_1_connectivity, edge_connectivity):
elements=[]
frac_coords=[]
#Update indexes of atoms in structure, node first, then edge.
for j in range(len(node_1_elements)):
if len(node_1_elements[j])==1:
index = re.split('(\d+)', node_1_elements[j][0][0])
index_number = int(index[1])+len(node_1_elements[0])*j
index_number = str(index_number)
updated_index = index[0]+index_number
elements.append(index[0]+index_number + ' ' + node_1_elements[j][0][1])
frac_coords.append(node_1_frac_coord[j])
elif not len(node_1_elements[j])==1:
for i in range(len(node_1_elements[j])):
index = re.split('(\d+)', node_1_elements[j][i][0])
index_number = int(index[1])+len(node_1_elements[0])*j
index_number = str(index_number)
updated_index = index[0]+index_number
elements.append(index[0]+index_number + ' ' + node_1_elements[j][i][1])
frac_coords.append(node_1_frac_coord[j][i])
for j in range(len(edge_elements)):
for i in range(len(edge_elements[j])):
index = re.split('(\d+)', edge_elements[j][i][0])
index_number = int(index[1])+len(edge_elements[0])*j + len(node_1_elements)*len(node_1_elements[0]) #+ len(node_2_elements)*len(node_2_elements[0])
index_number = str(index_number)
updated_index = index[0]+index_number
elements.append(str(index[0]+index_number + ' ' + edge_elements[j][i][1]))
frac_coords.append(edge_frac_coord[j][i])
#Update indexes of atoms in connectivity
connectivity=[]
for j in range(len(node_1_connectivity)):
for i in range(len(node_1_connectivity[j])):
index_1 = re.split('(\d+)', node_1_connectivity[j][i][0])
index_number_one = int(index_1[1])+len(node_1_elements[0])*j
index_number_one = str(index_number_one)
updated_index_one = index_1[0]+index_number_one
index_2 = re.split('(\d+)', node_1_connectivity[j][i][1])
index_number_two = int(index_2[1])+len(node_1_elements[0])*j
index_number_two = str(index_number_two)
updated_index_two = index_2[0]+index_number_two
connectivity.append(updated_index_one + ' ' + updated_index_two + ' ' + node_1_connectivity[j][i][2] + ' ' + node_1_connectivity[j][i][3] + ' ' + node_1_connectivity[j][i][4])
for j in range(len(edge_connectivity)):
for i in range(len(edge_connectivity[j])):
index_1 = re.split('(\d+)', edge_connectivity[j][i][0])
index_number_one = int(index_1[1])+len(edge_elements[0])*j + len(node_1_elements)*len(node_1_elements[0])# + len(node_2_elements)*len(node_2_elements[0])
index_number_one = str(index_number_one)
updated_index_one = index_1[0]+index_number_one
index_2 = re.split('(\d+)', edge_connectivity[j][i][1])
index_number_two = int(index_2[1])+len(edge_elements[0])*j + len(node_1_elements)*len(node_1_elements[0])# + len(node_2_elements)*len(node_2_elements[0])
index_number_two = str(index_number_two)
updated_index_two = index_2[0]+index_number_two
connectivity.append(updated_index_one + ' ' + updated_index_two + ' ' + edge_connectivity[j][i][2] + ' ' + edge_connectivity[j][i][3] + ' ' + edge_connectivity[j][i][4])
####Establishing a connection between edge and node
for k in range(len(v11_nbors_for_e1)):
node_1_connection = node_1_elements[v11_nbors_for_e1[k][0]]
node_2_connection = node_1_elements[v11_nbors_for_e1[k][1]]
edge_connection = edge_elements[k]
location_1=[]
connection_frac_coord_1=[]
location_2=[]
connection_frac_coord_2=[]
for i in [i for i, x in enumerate(node_1_connection) if x[0][0][0] == 'X']:
location_1.append(i)
if len(node_1_connection)==1:
connection_frac_coord_1.append(node_1_frac_coord[v11_nbors_for_e1[k][0]])
elif not len(node_1_connection)==1:
connection_frac_coord_1.append(node_1_frac_coord[v11_nbors_for_e1[k][0]][i]) # grab connection coord of first node
for i in [i for i, x in enumerate(node_2_connection) if x[0][0][0] == 'X']:
location_2.append(i)
if len(node_2_connection)==1:
connection_frac_coord_2.append(node_1_frac_coord[v11_nbors_for_e1[k][1]])
elif not len(node_2_connection)==1:
connection_frac_coord_2.append(node_1_frac_coord[v11_nbors_for_e1[k][1]][i]) # grab connection coord of second node
location_edge=[]
edge_conn_frac_coord=[]
for i in [i for i, x in enumerate(edge_connection) if x[0][0][0] == 'X']:
location_edge.append(i)
edge_conn_frac_coord.append(edge_frac_coord[k][i])
###Calculate vectors from node to edge, and from node to connection points
centroid_x_1=[]
centroid_y_1=[]
centroid_z_1=[]
for j in range(len(connection_frac_coord_1)):
centroid_x_1.append(connection_frac_coord_1[j][0])
centroid_y_1.append(connection_frac_coord_1[j][1])
centroid_z_1.append(connection_frac_coord_1[j][2])
centroid_x_1 = sum(centroid_x_1)/len(connection_frac_coord_1)
centroid_y_1 = sum(centroid_y_1)/len(connection_frac_coord_1)
centroid_z_1 = sum(centroid_z_1)/len(connection_frac_coord_1)
centroid_x_2=[]
centroid_y_2=[]
centroid_z_2=[]
for j in range(len(connection_frac_coord_2)):
centroid_x_2.append(connection_frac_coord_2[j][0])
centroid_y_2.append(connection_frac_coord_2[j][1])
centroid_z_2.append(connection_frac_coord_2[j][2])
centroid_x_2 = sum(centroid_x_2)/len(connection_frac_coord_2)
centroid_y_2 = sum(centroid_y_2)/len(connection_frac_coord_2)
centroid_z_2 = sum(centroid_z_2)/len(connection_frac_coord_2)
centroid_1 = [centroid_x_1, centroid_y_1, centroid_z_1]
centroid_2 = [centroid_x_2, centroid_y_2, centroid_z_2]
##Adjust edge_coord for PBCs, node_1
edge_pos_1 = e1_coord[k]
diffa = edge_pos_1[0]-centroid_1[0]
diffb = edge_pos_1[1]-centroid_1[1]
diffc = edge_pos_1[2]-centroid_1[2]
### PERIODIC BOUNDARY CONDITIONS
if diffa > 0.5:
edge_pos_1[0] = edge_pos_1[0] - 1
elif diffa < -0.5:
edge_pos_1[0] = edge_pos_1[0] + 1
if diffb > 0.5:
edge_pos_1[1] = edge_pos_1[1] - 1
elif diffb < -0.5:
edge_pos_1[1] = edge_pos_1[1] + 1
if diffc > 0.5:
edge_pos_1[2] = edge_pos_1[2] - 1
elif diffc < -0.5:
edge_pos_1[2] = edge_pos_1[2] + 1
##Vector node to edge, node_1
node_1_to_edge = edge_pos_1-centroid_1
##Vector edge to node 1
edge_to_node_1 = -node_1_to_edge
##Adjust edge_coord for PBCs, node_2
edge_pos_2 = e1_coord[k]
diffa = edge_pos_2[0]-centroid_2[0]
diffb = edge_pos_2[1]-centroid_2[1]
diffc = edge_pos_2[2]-centroid_2[2]
### PERIODIC BOUNDARY CONDITIONS
if diffa > 0.5:
edge_pos_2[0] = edge_pos_2[0] - 1
elif diffa < -0.5:
edge_pos_2[0] = edge_pos_2[0] + 1
if diffb > 0.5:
edge_pos_2[1] = edge_pos_2[1] - 1
elif diffb < -0.5:
edge_pos_2[1] = edge_pos_2[1] + 1
if diffc > 0.5:
edge_pos_2[2] = edge_pos_2[2] - 1
elif diffc < -0.5:
edge_pos_2[2] = edge_pos_2[2] + 1
##Vector node to edge, node_2
node_2_to_edge = edge_pos_2-centroid_2
##Vector edge to node 2
edge_to_node_2 = -node_2_to_edge
##Vectors node to connection_site, node_1
connection_1_vector=[]
for i in range(len(connection_frac_coord_1)):
connection_1_vector.append(connection_frac_coord_1[i]-centroid_1)
connection_2_vector=[]
for i in range(len(connection_frac_coord_2)):
connection_2_vector.append(connection_frac_coord_2[i]-centroid_2)
##Calculate angle between node-connection site and node-edge vectors, the smallest angles correspond to the sites to be connected
angle_1=[]
if len(node_1_connection)==1:
angle_1.append(0)
elif not len(node_1_connection)==1:
for i in range(len(connection_1_vector)):
angle=np.arccos(np.dot(node_1_to_edge, connection_1_vector[i])/(np.linalg.norm(node_1_to_edge)*np.linalg.norm(connection_1_vector[i])))*180/np.pi
if np.isnan(angle)==True:
angle= np.arccos(round(np.dot(node_1_to_edge, connection_1_vector[i])/(np.linalg.norm(node_1_to_edge)*np.linalg.norm(connection_1_vector[i]))))*180/np.pi
angle_1.append(angle)
angle_2=[]
if len(node_2_connection)==1:
angle_2.append(0)
elif not len(node_2_connection)==1:
for i in range(len(connection_2_vector)):
angle=np.arccos(np.dot(node_2_to_edge, connection_2_vector[i])/(np.linalg.norm(node_2_to_edge)*np.linalg.norm(connection_2_vector[i])))*180/np.pi
if np.isnan(angle)==True:
angle= np.arccos(round(np.dot(node_2_to_edge, connection_2_vector[i])/(np.linalg.norm(node_2_to_edge)*np.linalg.norm(connection_2_vector[i]))))*180/np.pi
angle_2.append(angle)
edge_connection_vector=[]
#Vectors edge to connection site
xi_plus=[]##positions to return connection sites back to their original positions after connection
xi_minus=[]
yi_plus=[]
yi_minus=[]
zi_plus=[]
zi_minus=[]
for i in range(len(edge_conn_frac_coord)):
diffa_edge = edge_conn_frac_coord[i][0] - e1_coord[k][0]
diffb_edge = edge_conn_frac_coord[i][1] - e1_coord[k][1]
diffc_edge = edge_conn_frac_coord[i][2] - e1_coord[k][2]
if diffa_edge > 0.5:
edge_conn_frac_coord[i][0] = edge_conn_frac_coord[i][0] - 1
xi_plus.append(i)
elif diffa_edge < -0.5:
edge_conn_frac_coord[i][0] = edge_conn_frac_coord[i][0] + 1
xi_minus.append(i)
if diffb_edge > 0.5:
edge_conn_frac_coord[i][1] = edge_conn_frac_coord[i][1] - 1
yi_plus.append(i)
elif diffb_edge < -0.5:
edge_conn_frac_coord[i][1] = edge_conn_frac_coord[i][1] + 1
yi_minus.append(i)
if diffc_edge > 0.5:
edge_conn_frac_coord[i][2] = edge_conn_frac_coord[i][2] - 1
zi_plus.append(i)
elif diffc_edge < -0.5:
edge_conn_frac_coord[i][2] = edge_conn_frac_coord[i][2] + 1
zi_minus.append(i)
edge_connection_vector.append(edge_conn_frac_coord[i] - e1_coord[k])
index_of_connection_1 = min(enumerate(angle_1), key=itemgetter(1))[0] #connection site of node_1
index_of_connection_2 = min(enumerate(angle_2), key=itemgetter(1))[0] #connection site of node_2
angle_edge_1 = []
for i in range(len(edge_connection_vector)):
angle_edge_1.append(round(np.arccos(round(np.dot(edge_to_node_1, edge_connection_vector[i])/(np.linalg.norm(edge_to_node_1)*np.linalg.norm(edge_connection_vector[i]))))*180/np.pi))
angle_edge_2 = []
for i in range(len(edge_connection_vector)):
angle_edge_2.append(round(np.arccos(round(np.dot(edge_to_node_2, edge_connection_vector[i])/(np.linalg.norm(edge_to_node_2)*np.linalg.norm(edge_connection_vector[i]))))*180/np.pi))
index_conn_edge_1 = min(enumerate(angle_edge_1), key=itemgetter(1))[0]
index_conn_edge_2 = min(enumerate(angle_edge_2), key=itemgetter(1))[0]
##After connection sites have been identified, return connection sites to original position
for i in range(len(xi_plus)):
edge_frac_coord[k][location_edge[xi_plus[i]]][0] = edge_frac_coord[k][location_edge[xi_plus[i]]][0] +1
for i in range(len(xi_minus)):
edge_frac_coord[k][location_edge[xi_minus[i]]][0] = edge_frac_coord[k][location_edge[xi_minus[i]]][0] -1
for i in range(len(yi_plus)):
edge_frac_coord[k][location_edge[yi_plus[i]]][1] = edge_frac_coord[k][location_edge[yi_plus[i]]][1] +1
for i in range(len(yi_minus)):
edge_frac_coord[k][location_edge[yi_minus[i]]][1] = edge_frac_coord[k][location_edge[yi_minus[i]]][1] -1
for i in range(len(zi_plus)):
edge_frac_coord[k][location_edge[zi_plus[i]]][2] = edge_frac_coord[k][location_edge[zi_plus[i]]][2] +1
for i in range(len(zi_minus)):
edge_frac_coord[k][location_edge[zi_minus[i]]][2] = edge_frac_coord[k][location_edge[zi_minus[i]]][2] -1
##Coordinates of connection sites to be connected
if len(node_1_connection)==1:
connection_node_1_coord = node_1_frac_coord[v11_nbors_for_e1[k][0]]
elif not len(node_1_connection)==1:
connection_node_1_coord = node_1_frac_coord[v11_nbors_for_e1[k][0]][location_1[index_of_connection_1]]
if len(node_2_connection)==1:
connection_node_2_coord = node_1_frac_coord[v11_nbors_for_e1[k][1]]
elif not len(node_2_connection)==1:
connection_node_2_coord = node_1_frac_coord[v11_nbors_for_e1[k][1]][location_2[index_of_connection_2]]
edge_conn_to_node_1 = edge_frac_coord[k][location_edge[index_conn_edge_1]]
edge_conn_to_node_2 = edge_frac_coord[k][location_edge[index_conn_edge_2]]
PBC_1 = edge_conn_to_node_1
PBC_2 = connection_node_1_coord
connection_bond_EtoN1 = np.linalg.norm(np.dot(np.transpose(unit_cell), connection_node_1_coord) - np.dot(np.transpose(unit_cell), edge_conn_to_node_1))
diffa_conn = PBC_2[0]-PBC_1[0]
diffb_conn = PBC_2[1]-PBC_1[1]
diffc_conn = PBC_2[2]-PBC_1[2]
symm = [5,5,5]
symm_alt = [5,5,5]
#### PERIODIC BOUNDARY CONDITIONS
if diffa_conn > 0.5:
symm[0]=4
symm_alt[0]=6
elif diffa_conn < -0.5:
symm[0]=6
symm_alt[0]=4
if diffb_conn > 0.5:
symm[1]=4
symm_alt[1]=6
elif diffb_conn < -0.5:
symm[1]=6
symm_alt[1]=4
if diffc_conn > 0.5:
symm[2]=4
symm_alt[2]=6
elif diffc_conn < -0.5:
symm[2]=6
symm_alt[2]=4
index_conn_1 = location_edge[index_conn_edge_1] + 1
atom_index_conn_1 = index_conn_1 + len(edge_elements[0])*k + len(node_1_elements)*len(node_1_elements[0])
index_conn_2 = location_1[index_of_connection_1] + 1
atom_index_conn_2 = index_conn_2 + len(node_1_elements[0])*v11_nbors_for_e1[k][0]
##Add connection to connectivity information, taking into account periodic boundary conditions
if all(x==5 for x in symm):
connectivity.append(edge_connection[location_edge[index_conn_edge_1]][0][0] + str(atom_index_conn_1) + ' ' + node_1_connection[location_1[index_of_connection_1]][0][0] + str(atom_index_conn_2) + ' ' + str(connection_bond_EtoN1) + ' ' + '.' + ' ' + 'S')
elif not all(x==5 for x in symm):#For when connection crosses boundaries
connectivity.append(edge_connection[location_edge[index_conn_edge_1]][0][0] + str(atom_index_conn_1) + ' ' + node_1_connection[location_1[index_of_connection_1]][0][0] + str(atom_index_conn_2) + ' ' + str(connection_bond_EtoN1) + ' ' + '1_' + str(symm[0])+str(symm[1]) + str(symm[2]) + ' ' + 'S')
connectivity.append(node_1_connection[location_1[index_of_connection_1]][0][0] + str(atom_index_conn_2) + ' ' + edge_connection[location_edge[index_conn_edge_1]][0][0] + str(atom_index_conn_1) + ' ' + str(connection_bond_EtoN1) + ' ' + '1_' + str(symm_alt[0])+str(symm_alt[1]) + str(symm_alt[2]) + ' ' + 'S')
PBC_1 = edge_conn_to_node_2
PBC_2 = connection_node_2_coord
connection_bond_EtoN2 = np.linalg.norm(np.dot(np.transpose(unit_cell), connection_node_2_coord) - np.dot(np.transpose(unit_cell), edge_conn_to_node_2))
diffa_conn = PBC_2[0]-PBC_1[0]
diffb_conn = PBC_2[1]-PBC_1[1]
diffc_conn = PBC_2[2]-PBC_1[2]
symm = [5,5,5]
symm_alt = [5,5,5]
#### PERIODIC BOUNDARY CONDITIONS
if diffa_conn > 0.5:
symm[0]=4
symm_alt[0] = 6
elif diffa_conn < -0.5:
symm[0]=6
symm_alt[0] = 4
if diffb_conn > 0.5:
symm[1]=4
symm_alt[1]=6
elif diffb_conn < -0.5:
symm[1]=6
symm_alt[1]=4
if diffc_conn > 0.5:
symm[2]=4
symm_alt[2]=6
elif diffc_conn < -0.5:
symm[2]=6
symm_alt[2]=4
index_conn_1 = location_edge[index_conn_edge_2] + 1
atom_index_conn_1 = index_conn_1 + len(edge_elements[0])*k + len(node_1_elements)*len(node_1_elements[0])
index_conn_2 = location_2[index_of_connection_2] + 1
atom_index_conn_2 = index_conn_2 + len(node_1_elements[0])*v11_nbors_for_e1[k][1]
##Add connection to connectivity information, taking into account periodic boundary conditions
if all(x==5 for x in symm):
connectivity.append(edge_connection[location_edge[index_conn_edge_2]][0][0] + str(atom_index_conn_1) + ' ' + node_2_connection[location_2[index_of_connection_2]][0][0] + str(atom_index_conn_2) + ' ' + str(connection_bond_EtoN2) + ' ' + '.' + ' ' + 'S')
elif not all(x==5 for x in symm):#For when connection crosses boundaries
connectivity.append(edge_connection[location_edge[index_conn_edge_2]][0][0] + str(atom_index_conn_1) + ' ' + node_2_connection[location_2[index_of_connection_2]][0][0] + str(atom_index_conn_2) + ' ' + str(connection_bond_EtoN2) + ' ' + '1_' + str(symm[0])+str(symm[1]) + str(symm[2]) + ' ' + 'S')
connectivity.append(node_2_connection[location_2[index_of_connection_2]][0][0] + str(atom_index_conn_2) + ' ' + edge_connection[location_edge[index_conn_edge_2]][0][0] + str(atom_index_conn_1) + ' ' + str(connection_bond_EtoN2) + ' ' + '1_' + str(symm_alt[0])+str(symm_alt[1]) + str(symm_alt[2]) + ' ' + 'S')
#Change to .cif format
new_frac_coords=[]
for j in range(len(frac_coords)):
for i in range(len(frac_coords[j])):
new_frac_coords.append('{:f}'.format(float(frac_coords[j][i])))
new_frac_coords = np.asarray(new_frac_coords)
new_frac_coords = np.asarray(np.split(new_frac_coords, len(elements)))
element_and_frac_coord = np.asarray(np.column_stack((elements, new_frac_coords)))
def fmtcols(mylist, cols):
lines = ("\t".join(mylist[i:i+cols]) for i in xrange(0,len(mylist),cols))
return '\n'.join(lines)
new_connectivity = fmtcols(connectivity, 1)
return element_and_frac_coord, new_connectivity