Create Bonds and Angles for LAMMPS's input
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1 #!/usr/bin/python 2 #python 2.7 3 text_all = [] 4 xatom_tmp = [] 5 xatom = [] 6 bond = [] 7 double_bond = [] 8 i = 0 9 j = 0 10 dd = 0.0 11 #lattice constant 12 a = 10.86 13 b = 10.86 14 c = 10.86 15 16 def isBond(list1, list2): 17 #i = -1 0 1, j = -1 0 1 18 for i in range(-1,2): 19 for j in range(-1,2): 20 for k in range(-1,2): 21 dd_tmp = 0.0 22 dd_tmp += (list1[0] - list2[0] + a * i) ** 2 23 dd_tmp += (list1[1] - list2[1] + b * j) ** 2 24 dd_tmp += (list1[2] - list2[2] + c * k) ** 2 25 dd_tmp = dd_tmp ** 0.5 26 if dd_tmp < 3.0: 27 return 1 28 29 return 0 30 31 def contain_same_point(list1, list2): 32 list3 = [0, 0.0, 0.0, 0.0] 33 for i in range(0,2): 34 for j in range(0,2): 35 if(list1[i] == list2[j]): 36 list3[0] = 1 37 list3[1] = list1[1-i] 38 list3[2] = list1[i] 39 list3[3] = list2[1-j] 40 return list3 41 42 43 file_in = open('data.lammps') 44 text_all = file_in.readlines() 45 file_in.close() 46 47 num_lines = len(text_all) 48 #(0:5) means a[0], a[1], a[2], a[3], a[4], a[5], totally 5 elements 49 for i in range(19,83): 50 xatom_tmp.append(text_all[i].split()) 51 xatom.append([xatom_tmp[i-19][2], xatom_tmp[i-19][3], xatom_tmp[i-19][4]]) 52 53 #initialize xatom_f as a 5x3 float matrix 54 xatom_f = [[0.0 for col in range(3)] for row in range(num_lines)] 55 56 for i in range(0,64): 57 xatom_f[i][0] = float(xatom[i][0]) 58 xatom_f[i][1] = float(xatom[i][1]) 59 xatom_f[i][2] = float(xatom[i][2]) 60 61 #bonds, A-B and B-A, same bond, count 1. 62 for i in range(0,64): 63 for j in range(i+1,64): 64 if (isBond(xatom_f[i], xatom_f[j]) == 1): 65 bond.append([i,j]) 66 k = 0 67 print "Bonds: " 68 print "\n" 69 for i in bond: 70 k += 1 71 print k, 1, i[0], i[1] 72 73 top = bond[0][0] 74 angle = [] 75 print "Angles: " 76 print "\n" 77 for i in range(0,len(bond)): 78 for j in range(i+1,len(bond)): 79 tmp = contain_same_point(bond[i],bond[j]) 80 if (tmp[0] == 1): 81 print tmp[1],tmp[2],tmp[3]
