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sample/input/descriptor_vectors/H-W/DV_creator.py

+####################################################################################################
+## Copyright (C) 2020 Udo von Toussaint, F. J. Dominguez-Gutierrez, Michele Compostella, Markus Rampp
+##
+## This program is free software; you can redistribute it and/or modify
+## it under the terms of the GNU General Public License as published by
+## the Free Software Foundation; either version 2, or (at your option)
+## any later version.
+##
+## This program 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 General Public License for more details.
+##
+## You should have received a copy of the GNU General Public License
+## along with this program; if not, write to the Free Software
+## Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
+## 02110-1301, USA.
+##
+#####################################################################################################
+##
+## General Notes:
+## FaVaD: Fingerprint And VisuAlization of Defects. Version: 1.0
+## Python script to generate the set of standard descriptor vectors
+## Please modify the code to create the chosen reference descriptor vector of the standard defect
+## The geometry of the standard defect is defined in a xyz file
+##
+#####################################################################################################
+
+import numpy as np
+from numpy import *
+import matplotlib.pyplot as plt
+import linecache
+import subprocess
+import sys
+#########################################################
+num_lines = sum(1 for line in open('interstitial_geometry.xyz'))
+num_atom = int(linecache.getline('interstitial_geometry.xyz',1))
+print('checking xyz file')
+num_lines = num_lines-2
+if ( num_lines== num_atom): 
+   print('xyz is in good shape')
+else:
+   sys.exit("xyz file corrupted, please check its format")
+##### computing descriptor vectors of damaged sample ####
+print('computing standard descriptor vector')
+# command line for hundreds to thousands of atoms
+cmd = 'quip atoms_filename=interstitial_geometry.xyz descriptor_str="soap cutoff=3.0 l_max=4 n_max=4 atom_sigma=0.5 n_Z=2 Z={74 1} n_species=2 species_Z={74 1}" > vectors.dat'
+#
+subprocess.call(cmd,shell=True)
+
+i = 0
+arr = []
+# Cleaning quip output file
+# Start reading DV at line 11
+for i in range(11,11+num_atom):
+     dv_1 = np.array(linecache.getline('vectors.dat',i)[7::].split())
+     dv = dv_1.astype(np.float)
+     arr.append(dv)
+
+arr = np.array(arr)
+DV_length = len(arr[0,:])
+print('The number of DV components is: {0}'.format(DV_length))
+#### Printing out results
+#### bcc DV ##################################
+print('Results are given in: bcc_vector.dat')
+file_1 = open('bcc_vector.dat','w')
+for i in range(0,DV_length):
+    file_1.write("{0} \n".format(arr[0,i]))
+
+
+#### interstitial DV ##################################
+print('Results are given in: interstitial_vector.dat')
+file_1 = open('interstitial_vector.dat','w')
+for i in range(0,DV_length):
+    file_1.write("{0} \n".format(arr[432,i]))
+
+#### W(first NN) DV ##################################
+print('Results are given in: W_first_NN_vector.dat')
+file_1 = open('W_first_NN_vector.dat','w')
+for i in range(0,DV_length):
+    file_1.write("{0} \n".format(arr[54,i]))
+
+#### W(second NN) DV ##################################
+print('Results are given in: W_second_NN_vector.dat')
+file_1 = open('W_second_NN_vector.dat','w')
+for i in range(0,DV_length):
+    file_1.write("{0} \n".format(arr[361,i]))
+
+
+#cleaning files
+print('cleaning...')
+cmd1 = 'rm vectors.dat'
+subprocess.call(cmd1,shell=True)
+print('Done!')