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placing_edge_1node.py
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#################
#
# This file is part of
# ToBaCCo - Topologically-Based Crystal Constructor
#
# Copyright 2017 Yamil J. Colon <[email protected]>
# Diego Gomez-Gualdron <[email protected]>
# Ben Bucior <[email protected]>
#
# 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 sys
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 connect_nodetonode import __node_to_node
from edges import __edge_properties
from operator import itemgetter
##Placing edge building block when topology contains one node.
np.set_printoptions(threshold = sys.maxint)
def __place_edge_1node(arg, unit_cell, edge_coord, node_1_coord, v11_nbors_for_e1):
edge= __edge_properties(arg)
connection_site_edge = edge[0]
distance_connection_site = edge[1]
angle_connection_site_pair = edge[2]
connectivity = edge[3]
elements = edge[4]
element_coord = edge[5]
bb_elements=[]
bb_frac_coordinates=[]
bb_connectivity=[]
for j in range(len(edge_coord)):
node_1_vector =[]
node_2_vector =[]
##Get coordinates of neighboring nodes to find connection vectors
node_1_vector.append(node_1_coord[v11_nbors_for_e1[j][0]])
node_2_vector.append(node_1_coord[v11_nbors_for_e1[j][1]])
node_1_vector=np.asarray(node_1_vector) # fract. coord. of neigboring nodes
node_2_vector=np.asarray(node_2_vector)
edge_node_1_vector=[]
for i in range(len(node_1_vector)):
diffa = node_1_vector[i][0]-edge_coord[j][0]
diffb = node_1_vector[i][1]-edge_coord[j][1]
diffc = node_1_vector[i][2]-edge_coord[j][2]
### PERIODIC BOUNDARY CONDITIONS
if diffa > 0.5:
node_1_vector[i][0] = node_1_vector[i][0] - 1
elif diffa < -0.5:
node_1_vector[i][0] = node_1_vector[i][0] + 1
if diffb > 0.5:
node_1_vector[i][1] = node_1_vector[i][1] - 1
elif diffb < -0.5:
node_1_vector[i][1] = node_1_vector[i][1] + 1
if diffc > 0.5:
node_1_vector[i][2] = node_1_vector[i][2] - 1
elif diffc < -0.5:
node_1_vector[i][2] = node_1_vector[i][2] + 1
edge_node_1_vector.append(node_1_vector[i] - edge_coord[j])
edge_node_1_vector =np.asarray(edge_node_1_vector) ## fract vectors edge to node adjusted for PBCs
node_1_vector_real=[]
for i in range(len(edge_node_1_vector)):
vector_1_real = np.dot(np.transpose(unit_cell), edge_node_1_vector[i])
node_1_vector_real.append(vector_1_real)
node_1_vector_real = np.asarray(node_1_vector_real) # real (not fractional) coord vector of network
edge_node_2_vector=[]
for i in range(len(node_2_vector)):
diffa = node_2_vector[i][0]-edge_coord[j][0]
diffb = node_2_vector[i][1]-edge_coord[j][1]
diffc = node_2_vector[i][2]-edge_coord[j][2]
### PERIODIC BOUNDARY CONDITIONS
if diffa > 0.5:
node_2_vector[i][0] = node_2_vector[i][0] - 1
elif diffa < -0.5:
node_2_vector[i][0] = node_2_vector[i][0] + 1
if diffb > 0.5:
node_2_vector[i][1] = node_2_vector[i][1] - 1
elif diffb < -0.5:
node_2_vector[i][1] = node_2_vector[i][1] + 1
if diffc > 0.5:
node_2_vector[i][2] = node_2_vector[i][2] - 1
elif diffc < -0.5:
node_2_vector[i][2] = node_2_vector[i][2] + 1
edge_node_2_vector.append(node_2_vector[i] - edge_coord[j])
edge_node_2_vector =np.asarray(edge_node_2_vector) ## fract vectors from edge to node 2 adjusted for PBCs
node_2_vector_real=[]
for i in range(len(edge_node_2_vector)):
vector_2_real = np.dot(np.transpose(unit_cell), edge_node_2_vector[i])
node_2_vector_real.append(vector_2_real)
node_2_vector_real = np.asarray(node_2_vector_real) # real (not fractional) coord vector of network
edge_coord_real = np.dot(np.transpose(unit_cell), edge_coord[j]) # real coord of network edge (centroid of edge)
norm_node_1_vector_real=[]
for i in range(len(node_1_vector_real)):
norm = node_1_vector_real[i]/np.linalg.norm(node_1_vector_real[i])
norm_node_1_vector_real.append(norm)
norm_node_1_vector_real = np.asarray(norm_node_1_vector_real) # normalized network vectors
norm_node_2_vector_real=[]
for i in range(len(node_2_vector_real)):
norm = node_2_vector_real[i]/np.linalg.norm(node_2_vector_real[i])
norm_node_2_vector_real.append(norm)
norm_node_2_vector_real = np.asarray(norm_node_2_vector_real) # normalized network vectors
connection_edge=[]
connection_1 = norm_node_1_vector_real[0]*distance_connection_site[0]
connection_2 = norm_node_2_vector_real[0]*distance_connection_site[1] ##coordinates to where edge connection sites should be placed
connection_edge.append(connection_1)
connection_edge.append(connection_2)
connection_edge.append(np.cross(connection_1, connection_2))
connection_edge = np.asarray(connection_edge)
connection_site=[]
connection_site.append(connection_site_edge[0])
connection_site.append(connection_site_edge[1])
connection_site.append(np.cross(connection_site_edge[0], connection_site_edge[1]))
connection_site = np.asarray(connection_site)
##Calculate transformation matrix, using quaternions, to map building block vectors onto network vectors
tfmatrix = superimposition_matrix(np.transpose(connection_site), np.transpose(connection_edge), usesvd=False)
connection_site_plusone = np.append(connection_site, np.ones([len(connection_site),1]),1) # add a column of ones for dimension agreement
tf_connection_site =[]
for i in range(len(connection_site)):
new_sites = np.dot(tfmatrix, connection_site_plusone[i]) #apply transformation matrix to each building block vector
tf_connection_site.append(new_sites)
tf_connection_site = np.asarray(tf_connection_site) #coordinates of building block connection sites, mapped onto network node sites
tf_connection_site = tf_connection_site[:, :-1] #remove the column of ones, to obtain final set of coordinates
###Apply transformation matrix to all atoms in building block
element_coord_plusone = np.append(element_coord, np.ones([len(element_coord),1]),1)
tf_element_coord=[]
for i in range(len(element_coord)):
new_element= np.dot(tfmatrix, element_coord_plusone[i])
tf_element_coord.append(new_element)
tf_element_coord = np.asarray(tf_element_coord)
tf_element_coord = tf_element_coord[:, :-1]
tf_frac_element_coord=[]
for i in range(len(tf_element_coord)):
frac_element_coord = np.dot(np.transpose(np.linalg.inv(unit_cell)), tf_element_coord[i])
frac_element_coord = frac_element_coord + edge_coord[j]
tf_frac_element_coord.append(frac_element_coord)
tf_frac_element_coord = np.asarray(tf_frac_element_coord) #edge after transformation, in frac coords
bb_elements.append(elements)
bb_frac_coordinates.append(tf_frac_element_coord)
bb_connectivity.append(connectivity)
bb_elements = np.asarray(bb_elements)
bb_frac_coordinates = np.asarray(bb_frac_coordinates)
bb_connectivity=np.asarray(bb_connectivity)
return bb_elements, bb_frac_coordinates, bb_connectivity