/
Modify.py
172 lines (159 loc) · 7.33 KB
/
Modify.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
# -*- coding: utf-8 -*-
"""
Created on Mon Dec 17 19:25:56 2018
@author: HP ElifeBook
"""
import numpy as np
#import numpy.random as nr
import pandas as pd
#from scipy.optimize import root,fsolve
import Init,Random,Rebuild,Dummy,Build
import random
class Box_locate(Init.Box):
def __init__(self,x,y,z):
super(Box_locate,self).__init__(x,y,z)
atomlist=[]
self.atomlist=Init.Atomlist(atomlist)
def locate(self,lx,ly,lz):self.lx,self.ly,self.lz=float(lx),float(ly),float(lz)
def make_box(self,ux,uy,uz,mv):
_,atomlist=Build_one()
self.atomlist=atomlist
for atom in atomlist.value:
atom.x,atom.y,atom.z=(atom.x*self.x+self.lx)/ux,(atom.y*self.y+self.ly-mv[0])/uy,(atom.z*self.z+self.lz-mv[1])/uz
def add_atom(self,atomlist,ux,uy,uz):
dx=np.random.random(1)[0]
self.dx=dx
#atom=Init.Atom(0.5,0.5,0.5,'O',0)
#atom.flag=0
#atomlist.value=[atom]
for atom in atomlist.value:
atom.x=((atom.x)*15+self.lx)/ux
atom.y=(atom.y*15+self.ly)/uy
atom.z=(atom.z*15+self.lz)/uz
#for atom in atomlist.value:
# atom.x,atom.y,atom.z=(atom.x*self.x+self.lx)/ux,(atom.y*self.y+self.ly)/uy,(atom.z*self.z+self.lz)/uz
self.atomlist=atomlist
self.flag=1
def addmore_atom(self,atomlist,ux,uy,uz):
#dx=np.random.random(1)[0]/3
#self.dx=self.dx+dx
for atom in atomlist.value:
atom.x=((atom.x+self.dx)*15+15*self.flag+self.lx)/ux
atom.y=(atom.y*15+self.ly)/uy
atom.z=(atom.z*15+self.lz)/uz
self.atomlist.value=self.atomlist.value+atomlist.value
self.flag=self.flag+1
class Modbox(object):
def __init__(self,x,y,z,num=1,dm=0):
self.x,self.y,self.z=float(x),float(y),float(z)
self.num=int(num)
self.ux,self.uy,self.uz=x,num*y+dm*num,num*z+dm*num
self.dm=dm
self.otherboxlist=[]
def divide_box(self,mv):
boxlist=[]
for j in range(self.num):
for k in range(self.num):
box_locate=Box_locate(self.x,self.y,self.z)
box_locate.locate(0,j*self.y+self.dm*j,k*self.z+self.dm*k)#changed
box_locate.make_box(self.ux,self.uy,self.uz,mv)
boxlist.append(box_locate)
print('\n######## Finish Initializing Supercell ########\n')
emptyboxlist=[]
ir=int(self.ux/(self.dm+0.1))
for i in range(ir):
for j in range(self.num):
for k in range(self.num):
box_locate1=Box_locate(self.x,self.dm,self.z)
box_locate1.locate(i*self.dm,(j+1)*self.y+j*self.dm,k*self.z+k*self.dm)
box_locate2=Box_locate(self.x,self.y,self.dm)
box_locate2.locate(i*self.dm,j*self.y+j*self.dm,(k+1)*self.z+k*self.dm)
box_locate3=Box_locate(self.x,self.dm,self.dm)
box_locate3.locate(i*self.dm,(j+1)*self.y+(j+1)*self.dm,(k+1)*self.z+(1+k)*self.dm)
emptyboxlist=emptyboxlist+[box_locate1,box_locate2,box_locate3]
self.boxlist=boxlist
self.emptyboxlist=emptyboxlist
def add_atomlist(self):
atomlist_tot1=[]
atomlist_tot2=[]
for box in self.boxlist:
atomlist_tot1=atomlist_tot1+box.atomlist.value
for box in self.otherboxlist:
atomlist_tot2=atomlist_tot2+box.atomlist.value
self.atomlist1=Init.Atomlist(atomlist_tot1)
self.atomlist1.reindex()
self.atomlist2=Init.Atomlist(atomlist_tot2)
self.atomlist2.reindex()
class Superbox(Modbox):
def __init__(self,x,y,z):
super(Superbox,self).__init__(x,y,z)
self.atomlist=Init.Atomlist([])
self.flag=0
def add_modbox(self,modbox):
for atom in modbox.atomlist.value:
atom.x=(atom.x*modbox.ux+self.flag*modbox.ux)/self.x
self.atomlist.value=self.atomlist.value+modbox.atomlist.value
self.flag=self.flag+1
def Build_one(inputfile='PVDF-model.cif'):
box,atomlist=Init.Split_file(inputfile)
#oldatomlist=atomlist
#print('A Good Thing is that We Successfully Initialize the File!')
build_index=Random.Randomlize(atomlist)
atomlist,Good_random,count=Rebuild.Rebuild_H_to_CF3(atomlist,build_index,box)
if not Good_random:
while Good_random!=True:
print('Starting Regeneration, this would be time-consuming')
box,atomlist=Init.Split_file(inputfile)
#atomlist=oldatomlist
build_index=Random.Randomlize(atomlist)
atomlist,Good_random,count=Rebuild.Rebuild_H_to_CF3(atomlist,build_index,box)
print('Luckily We have a Good Random Number! Though Still '+ str(count)+' Warning was Made. Forget it.')
return box,atomlist
def Add_plastic(modbox,numplast):
#print(len(modbox.emptyboxlist+modbox.emptyboxlist))
boxchoice=random.sample(modbox.emptyboxlist,numplast)
#boxchoice=modbox.emptyboxlist+modbox.emptyboxlist
for box in boxchoice:
index=np.random.randint(7)+1
_,atomlist=Init.Split_file('DBP-'+str(index)+'.cif')
if len(box.atomlist.value)==0:
box.add_atom(atomlist,modbox.ux,modbox.uy,modbox.uz)
else:
#print('REUSE!')
box.addmore_atom(atomlist,modbox.ux,modbox.uy,modbox.uz)
modbox.otherboxlist=boxchoice
def Start(inputfile='PVDF-model.cif',size=2000,dm=15,mv=[0,0]):
size=size/2
box,atomlist=Init.Split_file(inputfile)
num=int(pow(size/len(atomlist.value),1/2)+1)
print('Now Generating a Supercell of ',1,'*',num,'*',num,'\n')
print('######## Now Initializing Supercell ########\n')
modbox=Modbox(box.x,box.y,box.z,num,dm)
modbox.divide_box(mv)
modbox.add_atomlist()
#print('Though required size was ',size,', in total we make ',len(modbox.atomlist.value),' atoms\n')
print('######## Now Generating Plasticizer ########\n')
numplast=Dummy.Calc_dummy(modbox.atomlist1)
Add_plastic(modbox,numplast)
modbox.add_atomlist()
print('Though required size was ',size*2,', in total we make ',len(modbox.atomlist1.value+modbox.atomlist2.value),' atoms, including ',len(modbox.atomlist2.value),' atoms from plasticizers\n')
mass1=Dummy.Calc_mass(modbox.atomlist1)
mass2=Dummy.Calc_mass(modbox.atomlist2)
print('The actual Mass Ratio is ',mass2/(mass1+mass2)*100,'\n')
Build.build_poscar(modbox.atomlist1,modbox,filename='Polymer')
Build.build_poscar(modbox.atomlist2,modbox,filename='Plastic')
Build.build_poscar(Init.Atomlist(modbox.atomlist1.value+modbox.atomlist2.value),modbox,filename='Combine')
#modbox.uy,modbox.uz=modbox.uy+modbox.num*10,modbox.uz+modbox.num*10
#return modbox
def get_key(value,modboxdict):return list (modboxdict.keys()) [list (modboxdict.values()).index (value)]
def Continue(num):
modboxlist=[]
for i in range(num):
modbox=Start()
modboxlist.append(modbox)
numlist=np.arange(num).tolist()
modboxdict=dict(zip(numlist,modboxlist))
superbox=Superbox(modboxlist[0].ux*num,modboxlist[0].uy,modboxlist[0].uz)
for modbox in modboxlist:
superbox.add_modbox(modbox)
Build.build_data(superbox.atomlist,superbox)