samples/alkane/alkanes.md

#ifndef __ALKANES_MD__
#define __ALKANES_MD__

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

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

  
  bond{
    members( 0, 1 );
  }
}

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

  
  bond{
    members( 0, 1 );
  }
}


molecule{

  name = "propane";
  
  
  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 );
  }

  
  bond{
    members( 0, 1 );
  }

  bond{
    members( 1, 2 );
  }

  
  bend{
    members( 0, 1, 2 );
  }
}

molecule{

  name = "butane";
  
  
  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 );
  }
  

  bond{
    members( 0, 1 );
  }

  bond{
    members( 1, 2 );
  }

  bond{
    members( 2, 3 );
  }

  
  bend{
    members( 0, 1, 2 );
  }

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

  
  torsion{
    members( 0, 1, 2, 3 );
  }
}

molecule{

  name = "pentane";
  
  
  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 );
  }
  

  bond{
    members( 0, 1 );
  }

  bond{
    members( 1, 2 );
  }

  bond{
    members( 2, 3 );
  }

  bond{
    members( 3, 4 );
  }

  
  bend{
    members( 0, 1, 2 );
  }

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

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

  
  torsion{
    members( 0, 1, 2, 3 );
  }

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

molecule{

  name = "pseudoButane";
  
  
  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 );
  }
  

  bond{
    members( 0, 1 );
  }

  bond{
    members( 1, 2 );
  }

  bond{
    members( 2, 3 );
  }

  
  bend{
    members( 0, 1, 2 );
  }

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

  
  torsion{
    members( 0, 1, 2, 3 );
  }

  
  rigidBody[0]{
    
    members(0);
  }
  rigidBody[1]{
    
    members(1);
  }

  rigidBody[2]{
    
    members(2);
  }

  rigidBody[3]{
    
    members(3);
  }


}
#endif
Revision:	2489
Committed:	Tue Dec 6 16:49:59 2005 UTC (18 years, 7 months ago) by tim
File size:	2894 byte(s)
Log Message:	remove deprecated keywords from samples
#	User	Rev	Content
1	gezelter	1490	#ifndef __ALKANES_MD__
2			#define __ALKANES_MD__
3
4			molecule{
5			name = "methane";
6	tim	2489
7	gezelter	1490	atom[0]{
8			type="CH4";
9			position( 0.0, 0.0, 0.0 );
10			}
11			}
12
13			molecule{
14			name = "ethane";
15	tim	2489
16	gezelter	1490	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	tim	2489
26			bond{
27	gezelter	1490	members( 0, 1 );
28			}
29			}
30
31			molecule{
32			name = "ethane2";
33	tim	2489
34	gezelter	1490	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	tim	2489
44			bond{
45	gezelter	1490	members( 0, 1 );
46			}
47			}
48
49
50
51			molecule{
52
53			name = "propane";
54
55	tim	2489
56	gezelter	1490	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	tim	2489
72	gezelter	1490
73	tim	2489	bond{
74	gezelter	1490	members( 0, 1 );
75			}
76
77	tim	2489	bond{
78	gezelter	1490	members( 1, 2 );
79			}
80
81	tim	2489
82			bend{
83	gezelter	1490	members( 0, 1, 2 );
84			}
85			}
86
87			molecule{
88
89			name = "butane";
90
91	tim	2489
92	gezelter	1490	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	tim	2489
114	gezelter	1490
115	tim	2489	bond{
116	gezelter	1490	members( 0, 1 );
117			}
118
119	tim	2489	bond{
120	gezelter	1490	members( 1, 2 );
121			}
122
123	tim	2489	bond{
124	gezelter	1490	members( 2, 3 );
125			}
126
127	tim	2489
128			bend{
129	gezelter	1490	members( 0, 1, 2 );
130			}
131
132	tim	2489	bend{
133	gezelter	1490	members( 1, 2, 3 );
134			}
135
136	tim	2489
137			torsion{
138	gezelter	1490	members( 0, 1, 2, 3 );
139			}
140			}
141
142			molecule{
143
144			name = "pentane";
145
146	tim	2489
147	gezelter	1490	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	tim	2489
174	gezelter	1490
175	tim	2489	bond{
176	gezelter	1490	members( 0, 1 );
177			}
178
179	tim	2489	bond{
180	gezelter	1490	members( 1, 2 );
181			}
182
183	tim	2489	bond{
184	gezelter	1490	members( 2, 3 );
185			}
186
187	tim	2489	bond{
188	gezelter	1490	members( 3, 4 );
189			}
190
191	tim	2489
192			bend{
193	gezelter	1490	members( 0, 1, 2 );
194			}
195
196	tim	2489	bend{
197	gezelter	1490	members( 1, 2, 3 );
198			}
199
200	tim	2489	bend{
201	gezelter	1490	members( 2, 3, 4 );
202			}
203
204	tim	2489
205			torsion{
206	gezelter	1490	members( 0, 1, 2, 3 );
207			}
208
209	tim	2489	torsion{
210	gezelter	1490	members( 1, 2, 3, 4 );
211			}
212			}
213
214			molecule{
215
216			name = "pseudoButane";
217
218	tim	2489
219	gezelter	1490	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	tim	2489
241	gezelter	1490
242	tim	2489	bond{
243	gezelter	1490	members( 0, 1 );
244			}
245
246	tim	2489	bond{
247	gezelter	1490	members( 1, 2 );
248			}
249
250	tim	2489	bond{
251	gezelter	1490	members( 2, 3 );
252			}
253
254	tim	2489
255			bend{
256	gezelter	1490	members( 0, 1, 2 );
257			}
258
259	tim	2489	bend{
260	gezelter	1490	members( 1, 2, 3 );
261			}
262
263	tim	2489
264			torsion{
265	gezelter	1490	members( 0, 1, 2, 3 );
266			}
267
268	tim	2489
269	gezelter	1490	rigidBody[0]{
270	tim	2489
271	gezelter	1490	members(0);
272			}
273			rigidBody[1]{
274	tim	2489
275	gezelter	1490	members(1);
276			}
277
278			rigidBody[2]{
279	tim	2489
280	gezelter	1490	members(2);
281			}
282
283			rigidBody[3]{
284	tim	2489
285	gezelter	1490	members(3);
286			}
287
288
289			}
290			#endif