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
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
|
#!/usr/bin/python
#*******************************************************************************
# *
# Viewmol *
# *
# D E M O . P Y *
# *
# Copyright (c) Joerg-R. Hill, October 2003 *
# *
#*******************************************************************************
#
# $Id: demo.py,v 1.2 2003/11/07 13:19:53 jrh Exp $
# $Log: demo.py,v $
# Revision 1.2 2003/11/07 13:19:53 jrh
# Release 2.4
#
# Revision 1.1 2000/12/10 15:04:03 jrh
# Initial revision
#
#
import os
import viewmol
import molecule
import spectrum
import atom
import element
import energylevels
import history
import label
import light
ON=viewmol.__dict__['ON']
OFF=viewmol.__dict__['OFF']
WIREMODEL=viewmol.__dict__['WIREMODEL']
STICKMODEL=viewmol.__dict__['STICKMODEL']
BALLMODEL=viewmol.__dict__['BALLMODEL']
CPKMODEL=viewmol.__dict__['CPKMODEL']
PERSPECTIVE=viewmol.__dict__['PERSPECTIVE']
LINE=viewmol.__dict__['LINE']
SURFACE=viewmol.__dict__['SURFACE']
ORTHO=viewmol.__dict__['ORTHO']
MO=molecule.__dict__['MO']
DENSITY=molecule.__dict__['DENSITY']
IP_LOG=molecule.__dict__['IP_LOG']
REACTANT=molecule.__dict__['REACTANT']
PRODUCT=molecule.__dict__['PRODUCT']
REACTION=viewmol.__dict__['REACTION']
ANIMATE=spectrum.__dict__['ANIMATE']
ARROWS=spectrum.__dict__['ARROWS']
GAUSSIANS=spectrum.__dict__['GAUSSIANS']
class demo:
def rotate(self, mol, axis, speed):
n=0
fps=viewmol.getFramesPerSecond()
if fps>50.0:
increment=2*speed
else:
increment=5*speed
while n<180:
mol.rotate(n*axis[0], n*axis[1], n*axis[2])
viewmol.redraw()
n=n+increment
def translate(self, mol, direction):
n=0.0
while n<10.0:
mol.translate(n*direction[0], n*direction[1], n*direction[2])
viewmol.redraw()
n=n+0.5
def drawingModes(self, molecule):
size=viewmol.getWindowSize()
label1=label.label()
label1.translate(20, size[1]-20, 0)
label1.text('Viewmol supports different representations')
label2=label.label()
label2.translate(20, size[1]-40, 0)
label2.text('such as wire frame models ...')
viewmol.model(WIREMODEL)
self.rotate(molecule, (1.0, 0.0, 0.0), 1.0)
label2.text('... stick models ...')
viewmol.model(STICKMODEL)
self.rotate(molecule, (0.0, 1.0, 1.0), 1.0)
label2.text('... ball-and-stick models ...')
viewmol.model(BALLMODEL)
self.rotate(molecule, (0.0, 0.0, 1.0), 1.0)
label2.text('... or CPK models.')
viewmol.model(CPKMODEL)
self.rotate(molecule, (1.0, 1.0, 0.0), 1.0)
label2.delete()
label1.text('There is also a perspective mode.')
viewmol.projection(PERSPECTIVE)
self.rotate(molecule, (0.0, 1.0, 1.0), 10.0)
label1.text('And you can turn lights on and off and move them.')
lights=viewmol.getLights()
lights[0].switch(OFF)
self.rotate(lights[1], (0.0, 1.0, 0.0), 10.0)
lights[1].rotate(0, 0, 0)
lights[0].switch(ON)
label1.text('You can also change drawing style and resolution.')
viewmol.drawingMode(LINE)
n=10
while n<30:
viewmol.sphereResolution(n)
viewmol.redraw()
n=n+4
viewmol.drawingMode(SURFACE)
viewmol.sphereResolution(20)
label1.delete()
viewmol.projection(ORTHO)
viewmol.model(WIREMODEL)
def vibrations(self, molecule):
size=viewmol.getWindowSize()
label1=label.label()
label1.translate(20, size[1]-20, 0)
label1.text('Viewmol can also show vibrational spectra.')
viewmol.model(STICKMODEL)
spectrum1=molecule.getSpectrum()
spectrum1.show()
spectrum1.mode(27)
spectrum1.display(ANIMATE)
self.rotate(molecule, (1.0, 0.0, 1.0), 1.0)
label1.text('Of course, it doesn\'t have to be animated.')
spectrum1.display(ARROWS)
spectrum1.style(GAUSSIANS)
self.rotate(molecule, (0.0, 1.0, 0.0), 1.0)
spectrum1.deselect()
del spectrum1
label1.delete()
def MOs(self, molecule):
size=viewmol.getWindowSize()
label1=label.label()
label1.translate(20, size[1]-50, 0)
label1.text('Viewmol can show energy levels and MOs ...')
energylevel1=molecule.getEnergyLevels()
energylevel1.show()
energylevel1.selectMO(21)
viewmol.isosurface(0.05)
molecule.showElectrons(MO, 20, IP_LOG)
self.rotate(molecule, (1.0, 1.0, 1.0), 1.0)
label1.text('... or the electron density.')
del energylevel1
molecule.showElectrons(DENSITY, 20, IP_LOG)
self.rotate(molecule, (0.0, 1.0, 1.0), 1.0)
n=0.05
while n>0.001:
viewmol.isosurface(n)
viewmol.redraw()
n=n-0.001
molecule.showElectrons(OFF)
label1.delete()
def history(self, molecule):
size=viewmol.getWindowSize()
label1=label.label()
label1.translate(20, size[1]-20, 0)
label1.text('Viewmol can show the history of an optimization.')
history1=molecule.getHistory()
history1.show()
molecule.showForces(ON)
n=1
while n < 9:
history1.iteration(n)
viewmol.redraw()
n=n+1
molecule.showForces(OFF)
del history1
label1.delete()
def buildMolecule(self, molecule1):
size=viewmol.getWindowSize()
label1=label.label()
label1.translate(20, size[1]-20, 0)
label1.text('Viewmol can also be used to build molecules.')
viewmol.model(STICKMODEL)
atoms=molecule1.getAtoms()
atoms[11].replace('C')
viewmol.redraw()
molecule1.addAtom('H', atoms[11])
molecule1.addAtom('C', atoms[11])
viewmol.redraw()
molecule1.addAtom('C', atoms[11])
viewmol.redraw()
del atoms
atoms=molecule1.getAtoms()
molecule1.addAtom('O', atoms[14])
viewmol.redraw()
molecule1.addAtom('N', atoms[14])
viewmol.redraw()
del atoms
atoms=molecule1.getAtoms()
molecule1.addAtom('H', atoms[16])
molecule1.addAtom('H', atoms[16])
viewmol.redraw()
molecule1.addAtom('H', atoms[13])
molecule1.addAtom('H', atoms[13])
self.rotate(molecule1, (0.0, 1.0, 0.0), 1.0)
del atoms
label1.delete()
def thermodynamics(self):
size=viewmol.getWindowSize()
label1=label.label()
label1.translate(20, size[1]-20, 0)
label1.text('Viewmol can handle reaction thermodynamics.')
viewmol.showWarnings(OFF)
viewmolpath=os.getenv("VIEWMOLPATH")
molecule1=viewmol.load(viewmolpath + '/examples/reaction/hio3.outmol')
molecule1.reaction(PRODUCT)
text='Lets load a number of molecules: ' + molecule1.title()
label2=label.label()
label2.translate(20, 40, 0)
label2.text(text)
self.translate(molecule1, (-1.0, 1.0, 0.0))
molecule2=viewmol.load(viewmolpath + '/examples/reaction/i2.outmol')
molecule2.reaction(REACTANT)
molecule2.rotate(90.0, 0.0, 0.0)
text=text + ', ' + molecule2.title()
label2.text(text)
self.translate(molecule2, (1.0, 1.0, 0.0))
molecule3=viewmol.load(viewmolpath + '/examples/reaction/hno3.outmol')
molecule3.reaction(REACTANT)
text=text + ', ' + molecule3.title()
label2.text(text)
self.translate(molecule3, (-1.0, -1.0, 0.0))
molecule4=viewmol.load(viewmolpath + '/examples/reaction/no.outmol')
molecule4.reaction(PRODUCT)
text=text + ', ' + molecule4.title()
label2.text(text)
molecule4.rotate(90.0, 0.0, 0.0)
self.translate(molecule4, (1.0, -1.0, 0.0))
molecule5=viewmol.load(viewmolpath + '/examples/reaction/h2o.outmol')
molecule5.reaction(PRODUCT)
text=text + ', ' + molecule5.title()
label2.text(text)
viewmol.showThermodynamics(REACTION)
def run(self):
viewmolpath=os.getenv("VIEWMOLPATH")
molecule1=viewmol.load(viewmolpath + '/examples/turbomole/control')
self.drawingModes(molecule1)
self.vibrations(molecule1)
self.MOs(molecule1)
self.history(molecule1)
self.buildMolecule(molecule1)
viewmol.delete(molecule1)
self.thermodynamics()
def register(self, language):
viewmol.registerMenuItem("Demonstration")
#-------------------------
if __name__ == '__main__':
demonstration=demo()
demo.run(demonstration)
|
