samples/alkane/alkanes.md

#ifndef __ALKANES_MD__
#define __ALKANES_MD__

molecule{
  name = "methane";
  nAtoms = 1;
  atom[0]{
    type="CH4";
    position( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "ethane";
  nAtoms = 2;
  atom[0]{
    type = "CH3";
    position( 0.0, 0.0, 0.0 );
  }
  atom[1]{
    type = "CH3";
    position( 0.0, 1.54, 0.0 );
  }

  nBonds = 1;
  bond[0]{
    members( 0, 1 );
  }
}

molecule{
  name = "ethane2";
  nAtoms = 2;
  atom[0]{
    type = "CH3";
    position( 0.0, 0.0, 0.0 );
  }
  atom[1]{
    type = "CH3";
    position( 0.0, 1.54, 0.0 );
  }

  nBonds = 1;
  bond[0]{
    members( 0, 1 );
  }
}


molecule{

  name = "propane";
  nAtoms = 3;
  
  atom[0]{
    type = "CH3";
    position( -0.626, 1.407, 0.0 );
  }

  atom[1]{
    type = "CH2";
    position( 0.0, 0.0, 0.0 );
  }

  atom[2]{
    type = "CH3";
    position( 1.54, 0.0, 0.0 );
  }

  nBonds = 2;

  bond[0]{
    members( 0, 1 );
  }

  bond[1]{
    members( 1, 2 );
  }

  nBends = 1;
  bend[0]{
    members( 0, 1, 2 );
  }
}

molecule{

  name = "butane";
  nAtoms = 4;
  
  atom[0]{
    type = "CH3";
    position( -0.626, 1.407, 0.0 );
  }

  atom[1]{
    type = "CH2";
    position( 0.0, 0.0, 0.0 );
  }

  atom[2]{
    type = "CH2";
    position( 1.54, 0.0, 0.0 );
  }

  atom[3]{
    type = "CH3";
    position( 2.166, -1.407, 0.0 );
  }
  

  nBonds = 3;

  bond[0]{
    members( 0, 1 );
  }

  bond[1]{
    members( 1, 2 );
  }

  bond[2]{
    members( 2, 3 );
  }

  nBends = 2;
  bend[0]{
    members( 0, 1, 2 );
  }

  bend[1]{
    members( 1, 2, 3 );
  }

  nTorsions = 1;
  torsion[0]{
    members( 0, 1, 2, 3 );
  }
}

molecule{

  name = "pentane";
  nAtoms = 5;
  
  atom[0]{
    type = "CH3";
    position( -0.626, 1.407, 0.0 );
  }

  atom[1]{
    type = "CH2";
    position( 0.0, 0.0, 0.0 );
  }

  atom[2]{
    type = "CH2";
    position( 1.54, 0.0, 0.0 );
  }

  atom[3]{
    type = "CH2";
    position( 2.166, -1.407, 0.0 );
  }

  atom[4]{
    type = "CH3";
    position( 3.706, -1.407, 0.0 );
  }
  

  nBonds = 4;

  bond[0]{
    members( 0, 1 );
  }

  bond[1]{
    members( 1, 2 );
  }

  bond[2]{
    members( 2, 3 );
  }

  bond[3]{
    members( 3, 4 );
  }

  nBends = 3;
  bend[0]{
    members( 0, 1, 2 );
  }

  bend[1]{
    members( 1, 2, 3 );
  }

  bend[2]{
    members( 2, 3, 4 );
  }

  nTorsions = 2;
  torsion[0]{
    members( 0, 1, 2, 3 );
  }

  torsion[1]{
    members( 1, 2, 3, 4 );
  }
}

molecule{

  name = "pseudoButane";
  nAtoms = 4;
  
  atom[0]{
    type = "CH3";
    position( -0.626, 1.407, 0.0 );
  }

  atom[1]{
    type = "CH2";
    position( 0.0, 0.0, 0.0 );
  }

  atom[2]{
    type = "CH2";
    position( 1.54, 0.0, 0.0 );
  }

  atom[3]{
    type = "CH3";
    position( 2.166, -1.407, 0.0 );
  }
  

  nBonds = 3;

  bond[0]{
    members( 0, 1 );
  }

  bond[1]{
    members( 1, 2 );
  }

  bond[2]{
    members( 2, 3 );
  }

  nBends = 2;
  bend[0]{
    members( 0, 1, 2 );
  }

  bend[1]{
    members( 1, 2, 3 );
  }

  nTorsions = 1;
  torsion[0]{
    members( 0, 1, 2, 3 );
  }

  nRigidBodies = 4;
  rigidBody[0]{
    nMembers = 1;
    members(0);
  }
  rigidBody[1]{
    nMembers = 1;
    members(1);
  }

  rigidBody[2]{
    nMembers = 1;
    members(2);
  }

  rigidBody[3]{
    nMembers = 1;
    members(3);
  }


}
#endif
Revision:	1447
Committed:	Fri Jul 30 21:01:35 2004 UTC (21 years, 3 months ago) by gezelter
File size:	3270 byte(s)
Log Message:	Initial import of OOPSE sources into cvs tree
#	User	Rev	Content
1	gezelter	1447	#ifndef __ALKANES_MD__
2			#define __ALKANES_MD__
3
4			molecule{
5			name = "methane";
6			nAtoms = 1;
7			atom[0]{
8			type="CH4";
9			position( 0.0, 0.0, 0.0 );
10			}
11			}
12
13			molecule{
14			name = "ethane";
15			nAtoms = 2;
16			atom[0]{
17			type = "CH3";
18			position( 0.0, 0.0, 0.0 );
19			}
20			atom[1]{
21			type = "CH3";
22			position( 0.0, 1.54, 0.0 );
23			}
24
25			nBonds = 1;
26			bond[0]{
27			members( 0, 1 );
28			}
29			}
30
31			molecule{
32			name = "ethane2";
33			nAtoms = 2;
34			atom[0]{
35			type = "CH3";
36			position( 0.0, 0.0, 0.0 );
37			}
38			atom[1]{
39			type = "CH3";
40			position( 0.0, 1.54, 0.0 );
41			}
42
43			nBonds = 1;
44			bond[0]{
45			members( 0, 1 );
46			}
47			}
48
49
50
51			molecule{
52
53			name = "propane";
54			nAtoms = 3;
55
56			atom[0]{
57			type = "CH3";
58			position( -0.626, 1.407, 0.0 );
59			}
60
61			atom[1]{
62			type = "CH2";
63			position( 0.0, 0.0, 0.0 );
64			}
65
66			atom[2]{
67			type = "CH3";
68			position( 1.54, 0.0, 0.0 );
69			}
70
71			nBonds = 2;
72
73			bond[0]{
74			members( 0, 1 );
75			}
76
77			bond[1]{
78			members( 1, 2 );
79			}
80
81			nBends = 1;
82			bend[0]{
83			members( 0, 1, 2 );
84			}
85			}
86
87			molecule{
88
89			name = "butane";
90			nAtoms = 4;
91
92			atom[0]{
93			type = "CH3";
94			position( -0.626, 1.407, 0.0 );
95			}
96
97			atom[1]{
98			type = "CH2";
99			position( 0.0, 0.0, 0.0 );
100			}
101
102			atom[2]{
103			type = "CH2";
104			position( 1.54, 0.0, 0.0 );
105			}
106
107			atom[3]{
108			type = "CH3";
109			position( 2.166, -1.407, 0.0 );
110			}
111
112
113			nBonds = 3;
114
115			bond[0]{
116			members( 0, 1 );
117			}
118
119			bond[1]{
120			members( 1, 2 );
121			}
122
123			bond[2]{
124			members( 2, 3 );
125			}
126
127			nBends = 2;
128			bend[0]{
129			members( 0, 1, 2 );
130			}
131
132			bend[1]{
133			members( 1, 2, 3 );
134			}
135
136			nTorsions = 1;
137			torsion[0]{
138			members( 0, 1, 2, 3 );
139			}
140			}
141
142			molecule{
143
144			name = "pentane";
145			nAtoms = 5;
146
147			atom[0]{
148			type = "CH3";
149			position( -0.626, 1.407, 0.0 );
150			}
151
152			atom[1]{
153			type = "CH2";
154			position( 0.0, 0.0, 0.0 );
155			}
156
157			atom[2]{
158			type = "CH2";
159			position( 1.54, 0.0, 0.0 );
160			}
161
162			atom[3]{
163			type = "CH2";
164			position( 2.166, -1.407, 0.0 );
165			}
166
167			atom[4]{
168			type = "CH3";
169			position( 3.706, -1.407, 0.0 );
170			}
171
172
173			nBonds = 4;
174
175			bond[0]{
176			members( 0, 1 );
177			}
178
179			bond[1]{
180			members( 1, 2 );
181			}
182
183			bond[2]{
184			members( 2, 3 );
185			}
186
187			bond[3]{
188			members( 3, 4 );
189			}
190
191			nBends = 3;
192			bend[0]{
193			members( 0, 1, 2 );
194			}
195
196			bend[1]{
197			members( 1, 2, 3 );
198			}
199
200			bend[2]{
201			members( 2, 3, 4 );
202			}
203
204			nTorsions = 2;
205			torsion[0]{
206			members( 0, 1, 2, 3 );
207			}
208
209			torsion[1]{
210			members( 1, 2, 3, 4 );
211			}
212			}
213
214			molecule{
215
216			name = "pseudoButane";
217			nAtoms = 4;
218
219			atom[0]{
220			type = "CH3";
221			position( -0.626, 1.407, 0.0 );
222			}
223
224			atom[1]{
225			type = "CH2";
226			position( 0.0, 0.0, 0.0 );
227			}
228
229			atom[2]{
230			type = "CH2";
231			position( 1.54, 0.0, 0.0 );
232			}
233
234			atom[3]{
235			type = "CH3";
236			position( 2.166, -1.407, 0.0 );
237			}
238
239
240			nBonds = 3;
241
242			bond[0]{
243			members( 0, 1 );
244			}
245
246			bond[1]{
247			members( 1, 2 );
248			}
249
250			bond[2]{
251			members( 2, 3 );
252			}
253
254			nBends = 2;
255			bend[0]{
256			members( 0, 1, 2 );
257			}
258
259			bend[1]{
260			members( 1, 2, 3 );
261			}
262
263			nTorsions = 1;
264			torsion[0]{
265			members( 0, 1, 2, 3 );
266			}
267
268			nRigidBodies = 4;
269			rigidBody[0]{
270			nMembers = 1;
271			members(0);
272			}
273			rigidBody[1]{
274			nMembers = 1;
275			members(1);
276			}
277
278			rigidBody[2]{
279			nMembers = 1;
280			members(2);
281			}
282
283			rigidBody[3]{
284			nMembers = 1;
285			members(3);
286			}
287
288
289			}
290			#endif