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.
#	User	Rev	Content
1	gezelter	2	#ifndef __ALKANES_MD__
2			#define __ALKANES_MD__
3
4			molecule{
5			name = "methane";
6	tim	790
7	gezelter	2	atom[0]{
8			type="CH4";
9			position( 0.0, 0.0, 0.0 );
10			}
11			}
12
13			molecule{
14			name = "ethane";
15	tim	790
16	gezelter	2	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	790
26			bond{
27	gezelter	2	members( 0, 1 );
28			}
29			}
30
31			molecule{
32			name = "ethane2";
33	tim	790
34	gezelter	2	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	790
44			bond{
45	gezelter	2	members( 0, 1 );
46			}
47			}
48
49
50
51			molecule{
52
53			name = "propane";
54
55	tim	790
56	gezelter	2	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	790
72	gezelter	2
73	tim	790	bond{
74	gezelter	2	members( 0, 1 );
75			}
76
77	tim	790	bond{
78	gezelter	2	members( 1, 2 );
79			}
80
81	tim	790
82			bend{
83	gezelter	2	members( 0, 1, 2 );
84			}
85			}
86
87			molecule{
88
89			name = "butane";
90
91	tim	790
92	gezelter	2	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	790
114	gezelter	2
115	tim	790	bond{
116	gezelter	2	members( 0, 1 );
117			}
118
119	tim	790	bond{
120	gezelter	2	members( 1, 2 );
121			}
122
123	tim	790	bond{
124	gezelter	2	members( 2, 3 );
125			}
126
127	tim	790
128			bend{
129	gezelter	2	members( 0, 1, 2 );
130			}
131
132	tim	790	bend{
133	gezelter	2	members( 1, 2, 3 );
134			}
135
136	tim	790
137			torsion{
138	gezelter	2	members( 0, 1, 2, 3 );
139			}
140	gezelter	1618
141	gezelter	2	}
142
143			molecule{
144
145			name = "pentane";
146
147	tim	790
148	gezelter	2	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	tim	790
175	gezelter	2
176	tim	790	bond{
177	gezelter	2	members( 0, 1 );
178			}
179
180	tim	790	bond{
181	gezelter	2	members( 1, 2 );
182			}
183
184	tim	790	bond{
185	gezelter	2	members( 2, 3 );
186			}
187
188	tim	790	bond{
189	gezelter	2	members( 3, 4 );
190			}
191
192	tim	790
193			bend{
194	gezelter	2	members( 0, 1, 2 );
195			}
196
197	tim	790	bend{
198	gezelter	2	members( 1, 2, 3 );
199			}
200
201	tim	790	bend{
202	gezelter	2	members( 2, 3, 4 );
203			}
204
205	tim	790
206			torsion{
207	gezelter	2	members( 0, 1, 2, 3 );
208			}
209
210	tim	790	torsion{
211	gezelter	2	members( 1, 2, 3, 4 );
212			}
213			}
214
215			molecule{
216
217			name = "pseudoButane";
218
219	tim	790
220	gezelter	2	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	tim	790
242	gezelter	2
243	tim	790	bond{
244	gezelter	2	members( 0, 1 );
245			}
246
247	tim	790	bond{
248	gezelter	2	members( 1, 2 );
249			}
250
251	tim	790	bond{
252	gezelter	2	members( 2, 3 );
253			}
254
255	tim	790
256			bend{
257	gezelter	2	members( 0, 1, 2 );
258			}
259
260	tim	790	bend{
261	gezelter	2	members( 1, 2, 3 );
262			}
263
264	tim	790
265			torsion{
266	gezelter	2	members( 0, 1, 2, 3 );
267			}
268
269	tim	790
270	gezelter	2	rigidBody[0]{
271	tim	790
272	gezelter	2	members(0);
273			}
274			rigidBody[1]{
275	tim	790
276	gezelter	2	members(1);
277			}
278
279			rigidBody[2]{
280	tim	790
281	gezelter	2	members(2);
282			}
283
284			rigidBody[3]{
285	tim	790
286	gezelter	2	members(3);
287			}
288
289
290			}
291			#endif