water/ssde/water.md

#ifndef _WATER_MD_
#define _WATER_MD_

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

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

molecule{
  name = "SSD_E";
  
  atom[0]{
    type = "SSD_E";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}
molecule{
  name = "SSD_Q";
  
  atom[0]{
    type = "SSD_Q";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

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

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

molecule{
  name = "SSD1";
  
  atom[0]{
    type = "SSD1";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "TRED";
  
  atom[0]{
    type = "TRED";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
  atom[1]{
    type = "EP_TRED";
    position( 0.0, 0.0, 0.5 );
  }

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

molecule{
  name = "TIP3P";
  
  atom[0]{
    type = "O_TIP3P";
    position( 0.0, 0.0, -0.06556 );
  }
  atom[1]{
    type = "H_TIP3P";
    position( 0.0, 0.75695, 0.52032 );
  }
  atom[2]{
    type = "H_TIP3P";
    position( 0.0, -0.75695, 0.52032 );
  }
  
  rigidBody[0]{     
    members(0, 1, 2);
  }  
}

molecule{
  name = "TIP4P";
  
  atom[0]{
    type = "O_TIP4P";
    position( 0.0, 0.0, -0.06556 );
  }
  atom[1]{
    type = "H_TIP4P";
    position( 0.0, 0.75695, 0.52032 );
  }
  atom[2]{
    type = "H_TIP4P";
    position( 0.0, -0.75695, 0.52032 );
  }
  atom[3]{
    type = "EP_TIP4P";
    position( 0.0, 0.0, 0.08444 );
  }
  
  rigidBody[0]{    
    members(0, 1, 2, 3);
  }  
}

molecule{
  name = "TIP4P-Ew";
  
  atom[0]{
    type = "O_TIP4P-Ew";
    position( 0.0, 0.0, -0.06556 );
  }
  atom[1]{
    type = "H_TIP4P-Ew";
    position( 0.0, 0.75695, 0.52032 );
  }
  atom[2]{
    type = "H_TIP4P-Ew";
    position( 0.0, -0.75695, 0.52032 );
  }
  atom[3]{
    type = "EP_TIP4P-Ew";
    position( 0.0, 0.0, 0.05944 );
  }
  
  rigidBody[0]{    
    members(0, 1, 2, 3);
  }
}

molecule{
  name = "TIP5P";
  
  atom[0]{
    type = "O_TIP5P";
    position( 0.0, 0.0, -0.06556 );
  }
  atom[1]{
    type = "H_TIP5P";
    position( 0.0, 0.75695, 0.52032 );
  }
  atom[2]{
    type = "H_TIP5P";
    position( 0.0, -0.75695, 0.52032 );
  }
  atom[3]{
    type = "EP_TIP5P";
    position( 0.57154, 0.0, -0.46971 );
  }
  atom[4]{
    type = "EP_TIP5P";
    position( -0.57154, 0.0, -0.46971 );
  }
  
  rigidBody[0]{
    members(0, 1, 2, 3, 4);
  }
}

molecule{
  name = "TIP5P-E";
  
  atom[0]{
    type = "O_TIP5P-E";
    position( 0.0, 0.0, -0.06556 );
  }
  atom[1]{
    type = "H_TIP5P";
    position( 0.0, 0.75695, 0.52032 );
  }
  atom[2]{
    type = "H_TIP5P";
    position( 0.0, -0.75695, 0.52032 );
  }
  atom[3]{
    type = "EP_TIP5P";
    position( 0.57154, 0.0, -0.46971 );
  }
  atom[4]{
    type = "EP_TIP5P";
    position( -0.57154, 0.0, -0.46971 );
  }
  
  rigidBody[0]{    
    members(0, 1, 2, 3, 4);
  }
}

molecule{
  name = "SPCE";
  
  atom[0]{
    type = "O_SPCE";
    position( 0.0, 0.0, -0.06461 );
  }
  atom[1]{
    type = "H_SPCE";
    position( 0.0, 0.81649, 0.51275 );
  }
  atom[2]{
    type = "H_SPCE";
    position( 0.0, -0.81649, 0.51275 );
  }
  
  rigidBody[0]{    
    members(0, 1, 2);
  }
}

molecule{
  name = "SPC";
  
  atom[0]{
    type = "O_SPC";
    position( 0.0, 0.0, -0.06461 );
  }
  atom[1]{
    type = "H_SPC";
    position( 0.0, 0.81649, 0.51275 );
  }
  atom[2]{
    type = "H_SPC";
    position( 0.0, -0.81649, 0.51275 );
  }
  
  rigidBody[0]{    
    members(0, 1, 2);
  }
}

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

#endif
Revision:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (12 years, 2 months ago) by gezelter
File size:	3882 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	Content
1	#ifndef _WATER_MD_
2	#define _WATER_MD_
3
4	molecule{
5	name = "Cl-";
6
7	atom[0]{
8	type = "Cl-";
9	position(0.0, 0.0, 0.0);
10	}
11	}
12
13	molecule{
14	name = "Na+";
15
16	atom[0]{
17	type = "Na+";
18	position(0.0, 0.0, 0.0);
19	}
20	}
21
22	molecule{
23	name = "SSD_E";
24
25	atom[0]{
26	type = "SSD_E";
27	position( 0.0, 0.0, 0.0 );
28	orientation( 0.0, 0.0, 0.0 );
29	}
30	}
31	molecule{
32	name = "SSD_Q";
33
34	atom[0]{
35	type = "SSD_Q";
36	position( 0.0, 0.0, 0.0 );
37	orientation( 0.0, 0.0, 0.0 );
38	}
39	}
40
41	molecule{
42	name = "SSD_RF";
43
44	atom[0]{
45	type = "SSD_RF";
46	position( 0.0, 0.0, 0.0 );
47	orientation( 0.0, 0.0, 0.0 );
48	}
49	}
50
51	molecule{
52	name = "SSD";
53
54	atom[0]{
55	type = "SSD";
56	position( 0.0, 0.0, 0.0 );
57	orientation( 0.0, 0.0, 0.0 );
58	}
59	}
60
61	molecule{
62	name = "SSD1";
63
64	atom[0]{
65	type = "SSD1";
66	position( 0.0, 0.0, 0.0 );
67	orientation( 0.0, 0.0, 0.0 );
68	}
69	}
70
71	molecule{
72	name = "TRED";
73
74	atom[0]{
75	type = "TRED";
76	position( 0.0, 0.0, 0.0 );
77	orientation( 0.0, 0.0, 0.0 );
78	}
79	atom[1]{
80	type = "EP_TRED";
81	position( 0.0, 0.0, 0.5 );
82	}
83
84	rigidBody[0]{
85	members(0, 1);
86	}
87	}
88
89	molecule{
90	name = "TIP3P";
91
92	atom[0]{
93	type = "O_TIP3P";
94	position( 0.0, 0.0, -0.06556 );
95	}
96	atom[1]{
97	type = "H_TIP3P";
98	position( 0.0, 0.75695, 0.52032 );
99	}
100	atom[2]{
101	type = "H_TIP3P";
102	position( 0.0, -0.75695, 0.52032 );
103	}
104
105	rigidBody[0]{
106	members(0, 1, 2);
107	}
108	}
109
110	molecule{
111	name = "TIP4P";
112
113	atom[0]{
114	type = "O_TIP4P";
115	position( 0.0, 0.0, -0.06556 );
116	}
117	atom[1]{
118	type = "H_TIP4P";
119	position( 0.0, 0.75695, 0.52032 );
120	}
121	atom[2]{
122	type = "H_TIP4P";
123	position( 0.0, -0.75695, 0.52032 );
124	}
125	atom[3]{
126	type = "EP_TIP4P";
127	position( 0.0, 0.0, 0.08444 );
128	}
129
130	rigidBody[0]{
131	members(0, 1, 2, 3);
132	}
133	}
134
135	molecule{
136	name = "TIP4P-Ew";
137
138	atom[0]{
139	type = "O_TIP4P-Ew";
140	position( 0.0, 0.0, -0.06556 );
141	}
142	atom[1]{
143	type = "H_TIP4P-Ew";
144	position( 0.0, 0.75695, 0.52032 );
145	}
146	atom[2]{
147	type = "H_TIP4P-Ew";
148	position( 0.0, -0.75695, 0.52032 );
149	}
150	atom[3]{
151	type = "EP_TIP4P-Ew";
152	position( 0.0, 0.0, 0.05944 );
153	}
154
155	rigidBody[0]{
156	members(0, 1, 2, 3);
157	}
158	}
159
160	molecule{
161	name = "TIP5P";
162
163	atom[0]{
164	type = "O_TIP5P";
165	position( 0.0, 0.0, -0.06556 );
166	}
167	atom[1]{
168	type = "H_TIP5P";
169	position( 0.0, 0.75695, 0.52032 );
170	}
171	atom[2]{
172	type = "H_TIP5P";
173	position( 0.0, -0.75695, 0.52032 );
174	}
175	atom[3]{
176	type = "EP_TIP5P";
177	position( 0.57154, 0.0, -0.46971 );
178	}
179	atom[4]{
180	type = "EP_TIP5P";
181	position( -0.57154, 0.0, -0.46971 );
182	}
183
184	rigidBody[0]{
185	members(0, 1, 2, 3, 4);
186	}
187	}
188
189	molecule{
190	name = "TIP5P-E";
191
192	atom[0]{
193	type = "O_TIP5P-E";
194	position( 0.0, 0.0, -0.06556 );
195	}
196	atom[1]{
197	type = "H_TIP5P";
198	position( 0.0, 0.75695, 0.52032 );
199	}
200	atom[2]{
201	type = "H_TIP5P";
202	position( 0.0, -0.75695, 0.52032 );
203	}
204	atom[3]{
205	type = "EP_TIP5P";
206	position( 0.57154, 0.0, -0.46971 );
207	}
208	atom[4]{
209	type = "EP_TIP5P";
210	position( -0.57154, 0.0, -0.46971 );
211	}
212
213	rigidBody[0]{
214	members(0, 1, 2, 3, 4);
215	}
216	}
217
218	molecule{
219	name = "SPCE";
220
221	atom[0]{
222	type = "O_SPCE";
223	position( 0.0, 0.0, -0.06461 );
224	}
225	atom[1]{
226	type = "H_SPCE";
227	position( 0.0, 0.81649, 0.51275 );
228	}
229	atom[2]{
230	type = "H_SPCE";
231	position( 0.0, -0.81649, 0.51275 );
232	}
233
234	rigidBody[0]{
235	members(0, 1, 2);
236	}
237	}
238
239	molecule{
240	name = "SPC";
241
242	atom[0]{
243	type = "O_SPC";
244	position( 0.0, 0.0, -0.06461 );
245	}
246	atom[1]{
247	type = "H_SPC";
248	position( 0.0, 0.81649, 0.51275 );
249	}
250	atom[2]{
251	type = "H_SPC";
252	position( 0.0, -0.81649, 0.51275 );
253	}
254
255	rigidBody[0]{
256	members(0, 1, 2);
257	}
258	}
259
260	molecule{
261	name = "DPD";
262
263	atom[0]{
264	type = "DPD";
265	position(0.0, 0.0, 0.0);
266	}
267	}
268
269	#endif