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:	1618
Committed:	Mon Sep 12 17:09:26 2011 UTC (13 years, 9 months ago) by gezelter
File size:	2895 byte(s)
Log Message:	Build fixes for qhull 2011, fixes for compilation with PGI.
#	Content
1	#ifndef __ALKANES_MD__
2	#define __ALKANES_MD__
3
4	molecule{
5	name = "methane";
6
7	atom[0]{
8	type="CH4";
9	position( 0.0, 0.0, 0.0 );
10	}
11	}
12
13	molecule{
14	name = "ethane";
15
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
26	bond{
27	members( 0, 1 );
28	}
29	}
30
31	molecule{
32	name = "ethane2";
33
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
44	bond{
45	members( 0, 1 );
46	}
47	}
48
49
50
51	molecule{
52
53	name = "propane";
54
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
72
73	bond{
74	members( 0, 1 );
75	}
76
77	bond{
78	members( 1, 2 );
79	}
80
81
82	bend{
83	members( 0, 1, 2 );
84	}
85	}
86
87	molecule{
88
89	name = "butane";
90
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
114
115	bond{
116	members( 0, 1 );
117	}
118
119	bond{
120	members( 1, 2 );
121	}
122
123	bond{
124	members( 2, 3 );
125	}
126
127
128	bend{
129	members( 0, 1, 2 );
130	}
131
132	bend{
133	members( 1, 2, 3 );
134	}
135
136
137	torsion{
138	members( 0, 1, 2, 3 );
139	}
140
141	}
142
143	molecule{
144
145	name = "pentane";
146
147
148	atom[0]{
149	type = "CH3";
150	position( -0.626, 1.407, 0.0 );
151	}
152
153	atom[1]{
154	type = "CH2";
155	position( 0.0, 0.0, 0.0 );
156	}
157
158	atom[2]{
159	type = "CH2";
160	position( 1.54, 0.0, 0.0 );
161	}
162
163	atom[3]{
164	type = "CH2";
165	position( 2.166, -1.407, 0.0 );
166	}
167
168	atom[4]{
169	type = "CH3";
170	position( 3.706, -1.407, 0.0 );
171	}
172
173
174
175
176	bond{
177	members( 0, 1 );
178	}
179
180	bond{
181	members( 1, 2 );
182	}
183
184	bond{
185	members( 2, 3 );
186	}
187
188	bond{
189	members( 3, 4 );
190	}
191
192
193	bend{
194	members( 0, 1, 2 );
195	}
196
197	bend{
198	members( 1, 2, 3 );
199	}
200
201	bend{
202	members( 2, 3, 4 );
203	}
204
205
206	torsion{
207	members( 0, 1, 2, 3 );
208	}
209
210	torsion{
211	members( 1, 2, 3, 4 );
212	}
213	}
214
215	molecule{
216
217	name = "pseudoButane";
218
219
220	atom[0]{
221	type = "CH3";
222	position( -0.626, 1.407, 0.0 );
223	}
224
225	atom[1]{
226	type = "CH2";
227	position( 0.0, 0.0, 0.0 );
228	}
229
230	atom[2]{
231	type = "CH2";
232	position( 1.54, 0.0, 0.0 );
233	}
234
235	atom[3]{
236	type = "CH3";
237	position( 2.166, -1.407, 0.0 );
238	}
239
240
241
242
243	bond{
244	members( 0, 1 );
245	}
246
247	bond{
248	members( 1, 2 );
249	}
250
251	bond{
252	members( 2, 3 );
253	}
254
255
256	bend{
257	members( 0, 1, 2 );
258	}
259
260	bend{
261	members( 1, 2, 3 );
262	}
263
264
265	torsion{
266	members( 0, 1, 2, 3 );
267	}
268
269
270	rigidBody[0]{
271
272	members(0);
273	}
274	rigidBody[1]{
275
276	members(1);
277	}
278
279	rigidBody[2]{
280
281	members(2);
282	}
283
284	rigidBody[3]{
285
286	members(3);
287	}
288
289
290	}
291	#endif