-
Notifications
You must be signed in to change notification settings - Fork 4
/
genxyz_gui.py
155 lines (147 loc) · 7.23 KB
/
genxyz_gui.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
import numpy as np
import pandas as pd
import math
from tkinter import *
from tkinter import messagebox
from tkinter import filedialog
def select_file1():
selected_file_path = filedialog.askopenfilename() # 使用askopenfilename函数选择单个文件
select_path1.set(selected_file_path)
def select_file2():
selected_file_path = filedialog.askopenfilename() # 使用askopenfilename函数选择单个文件
select_path2.set(selected_file_path)
def calc():
try:
with open(Entry1.get()) as f1:
m1=f1.readlines()
xyz1=list(filter(None,[ l.split() for l in m1[2:] if not l.startswith('\n') ]))
with open(Entry2.get()) as f2:
m2=f2.readlines()
xyz2=list(filter(None,[ l.split() for l in m2[2:] if not l.startswith('\n') ]))
df1=pd.DataFrame(xyz1,columns=["atom","x","y","z"])
df2=pd.DataFrame(xyz2,columns=["atom","x","y","z"])
data1=df1[["x","y","z"]].values.astype(np.float64)
data2=df2[["x","y","z"]].values.astype(np.float64)
vec=data1[int(Entry3.get())-1]-data2[int(Entry4.get())-1]
proc_data=data2
for i in range(1,int(Entry6.get())+1):
proc_data=np.append(proc_data,data2+vec*float(Entry5.get())*i/math.sqrt(np.square(vec).sum()),axis=0)
mm=pd.DataFrame(proc_data,columns=["x","y","z"])
mm.insert(0,"atom",np.tile(df2["atom"].values,int(Entry6.get())+1))
# -------------------------------------------------------------------------------- #
# 输出轨迹
fp=open("traj.xyz","w")
for m in range(int(Entry6.get())+1):
print("{}".format(data1.shape[0]+data2.shape[0]),file=fp)
print("{}".format(m*float(Entry5.get())),file=fp)
for i in range(data1.shape[0]):
print ("{} {} {} {}".format(df1.iloc[i]["atom"],df1.iloc[i]["x"],df1.iloc[i]["y"],df1.iloc[i]["z"]),file=fp)
for j in range(data2.shape[0]):
print ("{} {:.8f} {:.8f} {:.8f}".format(mm.iloc[(m*(data2.shape[0])+j)]["atom"],mm.iloc[(m*(data2.shape[0])+j)]["x"],mm.iloc[(m*(data2.shape[0])+j)]["y"],mm.iloc[(m*(data2.shape[0])+j)]["z"]),file=fp)
fp.close()
#-------------------------------------------------------------------------------#
# 输出gaussian文件
fg=open("traj.gjf","w")
for m in range(int(Entry6.get())+1):
chkname="%chk="+"traj_"+str(m)+".chk"
print("{}".format(chkname),file=fg)
print("{}".format("%nproc="+str(Entry9.get())),file=fg)
print("{}".format("%mem="+str(Entry10.get())),file=fg)
print("{}".format("#p "+str(Entry11.get())+"/"+str(Entry12.get())+" "+str(Entry14.get())),file=fg)
print("{}".format(" "),file=fg)
print("{}".format("traj_"+str(m)+" Structure"),file=fg)
print("{}".format(" "),file=fg)
print("{}".format(str(Entry7.get())+" "+str(Entry8.get())),file=fg)
for i in range(data1.shape[0]):
print ("{} {} {} {}".format(df1.iloc[i]["atom"],df1.iloc[i]["x"],df1.iloc[i]["y"],df1.iloc[i]["z"]),file=fg)
for j in range(data2.shape[0]):
print ("{} {:.8f} {:.8f} {:.8f}".format(mm.iloc[(m*(data2.shape[0])+j)]["atom"],mm.iloc[(m*(data2.shape[0])+j)]["x"],mm.iloc[(m*(data2.shape[0])+j)]["y"],mm.iloc[(m*(data2.shape[0])+j)]["z"]),file=fg)
print("{}".format(" "),file=fg)
# print("{}".format("{}".format("notatoms="+str(Entry13.get()))),file=fg)
print("{}".format(" "),file=fg)
if m!=int(Entry6.get()):
print("{}".format("--link1--"),file=fg)
else:
continue
fg.close()
messagebox.showinfo("congratulation!","Generating done")
except :
messagebox.showerror("Waring!!!!","please check your input!")
if __name__ == '__main__':
root=Tk()
root.title("genxyz")
root.geometry("500x500")
root.configure(background="#C6DBEF")
select_path1=StringVar()
select_path2=StringVar()
Label1=Label(root,text="xyz1文件路径：").grid(row=0,column=1,padx=10,pady=5)
Entry1=Entry(root,textvariable=select_path1)
Entry1.grid(row=0,column=2)
Button1=Button(root,text="选择xyz文件",command=select_file1).grid(row=0,column=3,padx=10,pady=5)
Label2=Label(root,text="xyz2文件路径：").grid(row=1,column=1)
Entry2=Entry(root,textvariable=select_path2)
Entry2.grid(row=1,column=2)
Button2=Button(root,text="选择xyz文件",command=select_file2).grid(row=1,column=3)
atx1=StringVar()
atx1.set("163")
Label3=Label(root,text="atomidx1=").grid(row=2,column=1,ipadx=0)
Entry3=Entry(root,textvariable=atx1)
Entry3.grid(row=2,column=2,padx=0,pady=5)
atx2=StringVar()
atx2.set("1")
Label4=Label(root,text="atomidx2=").grid(row=2,column=3,padx=0)
Entry4=Entry(root,textvariable=atx2)
Entry4.grid(row=2,column=4,padx=0,pady=5)
stepsize=StringVar()
stepsize.set("0.05")
Label5=Label(root,text="stepsize=").grid(row=3,column=1,ipadx=0)
Entry5=Entry(root,textvariable=stepsize)
Entry5.grid(row=3,column=2,padx=0,pady=5)
step=StringVar()
step.set("50")
Label6=Label(root,text="step=").grid(row=3,column=3,padx=0)
Entry6=Entry(root,textvariable=step)
Entry6.grid(row=3,column=4,padx=0,pady=5)
charge=StringVar()
charge.set("0")
Label7=Label(root,text="charge=").grid(row=4,column=1,ipadx=0)
Entry7=Entry(root,textvariable=charge)
Entry7.grid(row=4,column=2,padx=0,pady=5)
spin=StringVar()
spin.set("1")
Label8=Label(root,text="spin=").grid(row=4,column=3,padx=0)
Entry8=Entry(root,textvariable=spin)
Entry8.grid(row=4,column=4,padx=0,pady=5)
nproc=StringVar()
nproc.set("32")
Label9=Label(root,text="nproc=").grid(row=5,column=1,ipadx=0)
Entry9=Entry(root,textvariable=nproc)
Entry9.grid(row=5,column=2,padx=0,pady=5)
mem=StringVar()
mem.set("12GB")
Label10=Label(root,text="mem=").grid(row=5,column=3,padx=0)
Entry10=Entry(root,textvariable=mem)
Entry10.grid(row=5,column=4,padx=0,pady=5)
method=StringVar()
method.set("b3lyp")
Label11=Label(root,text="method=").grid(row=6,column=1,ipadx=0)
Entry11=Entry(root,textvariable=method)
Entry11.grid(row=6,column=2,padx=0,pady=5)
basis=StringVar()
basis.set("6-31G(d,p)")
Label12=Label(root,text="basis=").grid(row=6,column=3,padx=0)
Entry12=Entry(root,textvariable=basis)
Entry12.grid(row=6,column=4,padx=0,pady=5)
#fixatom=StringVar()
#fixatom.set("1,2,16,17,33,34,52,71,78,86,97,111,113,129,130,156,145")
#Label13=Label(root,text="fixatoms=").grid(row=7,column=1,ipadx=0)
#Entry13=Entry(root,textvariable=fixatom,width=50)
#Entry13.grid(row=7,column=2,padx=0,pady=5,columnspan=3)
other=StringVar()
other.set("")
Label14=Label(root,text="other=").grid(row=8,column=1,padx=0)
Entry14=Entry(root,textvariable=other)
Entry14.grid(row=8,column=2,padx=0,pady=5)
Button3=Button(text="generator",command=calc)
Button3.grid(row=9,column=1)
root.mainloop()