water/tip3p_ice/water.md

#ifndef _WATER_MD_
#define _WATER_MD_

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

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

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

molecule{
  name = "SSD1";
  nAtoms = 1;
  atom[0]{
    type = "SSD1";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "TIP3P";
  nAtoms = 3;
  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 );
  }

  nRigidBodies = 1;
  rigidBody[0]{ 
    nMembers = 3;
    members(0, 1, 2);
  }

//  nCutoffGroups = 1;
//  cutoffGroup[0]{
//    nMembers = 3;
//    members(0, 1, 2);
//  }
}

molecule{
  name = "TIP4P";
  nAtoms = 4;
  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 );
  }
  nRigidBodies = 1;
  rigidBody[0]{
    nMembers = 4;
    members(0, 1, 2, 3);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 4;
    members(0, 1, 2, 3);
  }
}

molecule{
  name = "TIP4P-Ew";
  nAtoms = 4;
  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 );
  }
  nRigidBodies = 1;
  rigidBody[0]{
    nMembers = 4;
    members(0, 1, 2, 3);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 4;
    members(0, 1, 2, 3);
  }
}

molecule{
  name = "TIP5P";
  nAtoms = 5;
  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 );
  }
  nRigidBodies = 1;
  rigidBody[0]{
    nMembers = 5;
    members(0, 1, 2, 3, 4);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 5;
    members(0, 1, 2, 3, 4);
  }
}

molecule{
  name = "SPCE";
  nAtoms = 3;
  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 );
  }
  nRigidBodies = 1;
  rigidBody[0]{
    nMembers = 3;
    members(0, 1, 2);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 3;
    members(0, 1, 2);
  }
}

molecule{
  name = "SPC";
  nAtoms = 3;
  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 );
  }
  nRigidBodies = 1;
  rigidBody[0]{
    nMembers = 3;
    members(0, 1, 2);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 3;
    members(0, 1, 2);
  }
}

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

#endif
Revision:	2342
Committed:	Tue Oct 4 19:32:58 2005 UTC (18 years, 9 months ago) by chrisfen
File size:	3679 byte(s)
Log Message:	just some random changes when testing
#	Content
1	#ifndef _WATER_MD_
2	#define _WATER_MD_
3
4	molecule{
5	name = "SSD_E";
6	nAtoms = 1;
7	atom[0]{
8	type = "SSD_E";
9	position( 0.0, 0.0, 0.0 );
10	orientation( 0.0, 0.0, 0.0 );
11	}
12	}
13
14	molecule{
15	name = "SSD_RF";
16	nAtoms = 1;
17	atom[0]{
18	type = "SSD_RF";
19	position( 0.0, 0.0, 0.0 );
20	orientation( 0.0, 0.0, 0.0 );
21	}
22	}
23
24	molecule{
25	name = "SSD";
26	nAtoms = 1;
27	atom[0]{
28	type = "SSD";
29	position( 0.0, 0.0, 0.0 );
30	orientation( 0.0, 0.0, 0.0 );
31	}
32	}
33
34	molecule{
35	name = "SSD1";
36	nAtoms = 1;
37	atom[0]{
38	type = "SSD1";
39	position( 0.0, 0.0, 0.0 );
40	orientation( 0.0, 0.0, 0.0 );
41	}
42	}
43
44	molecule{
45	name = "TIP3P";
46	nAtoms = 3;
47	atom[0]{
48	type = "O_TIP3P";
49	position( 0.0, 0.0, -0.06556 );
50	}
51	atom[1]{
52	type = "H_TIP3P";
53	position( 0.0, 0.75695, 0.52032 );
54	}
55	atom[2]{
56	type = "H_TIP3P";
57	position( 0.0, -0.75695, 0.52032 );
58	}
59
60	nRigidBodies = 1;
61	rigidBody[0]{
62	nMembers = 3;
63	members(0, 1, 2);
64	}
65
66	// nCutoffGroups = 1;
67	// cutoffGroup[0]{
68	// nMembers = 3;
69	// members(0, 1, 2);
70	// }
71	}
72
73	molecule{
74	name = "TIP4P";
75	nAtoms = 4;
76	atom[0]{
77	type = "O_TIP4P";
78	position( 0.0, 0.0, -0.06556 );
79	}
80	atom[1]{
81	type = "H_TIP4P";
82	position( 0.0, 0.75695, 0.52032 );
83	}
84	atom[2]{
85	type = "H_TIP4P";
86	position( 0.0, -0.75695, 0.52032 );
87	}
88	atom[3]{
89	type = "EP_TIP4P";
90	position( 0.0, 0.0, 0.08444 );
91	}
92	nRigidBodies = 1;
93	rigidBody[0]{
94	nMembers = 4;
95	members(0, 1, 2, 3);
96	}
97
98	nCutoffGroups = 1;
99	cutoffGroup[0]{
100	nMembers = 4;
101	members(0, 1, 2, 3);
102	}
103	}
104
105	molecule{
106	name = "TIP4P-Ew";
107	nAtoms = 4;
108	atom[0]{
109	type = "O_TIP4P-Ew";
110	position( 0.0, 0.0, -0.06556 );
111	}
112	atom[1]{
113	type = "H_TIP4P-Ew";
114	position( 0.0, 0.75695, 0.52032 );
115	}
116	atom[2]{
117	type = "H_TIP4P-Ew";
118	position( 0.0, -0.75695, 0.52032 );
119	}
120	atom[3]{
121	type = "EP_TIP4P-Ew";
122	position( 0.0, 0.0, 0.05944 );
123	}
124	nRigidBodies = 1;
125	rigidBody[0]{
126	nMembers = 4;
127	members(0, 1, 2, 3);
128	}
129
130	nCutoffGroups = 1;
131	cutoffGroup[0]{
132	nMembers = 4;
133	members(0, 1, 2, 3);
134	}
135	}
136
137	molecule{
138	name = "TIP5P";
139	nAtoms = 5;
140	atom[0]{
141	type = "O_TIP5P";
142	position( 0.0, 0.0, -0.06556 );
143	}
144	atom[1]{
145	type = "H_TIP5P";
146	position( 0.0, 0.75695, 0.52032 );
147	}
148	atom[2]{
149	type = "H_TIP5P";
150	position( 0.0, -0.75695, 0.52032 );
151	}
152	atom[3]{
153	type = "EP_TIP5P";
154	position( 0.57154, 0.0, -0.46971 );
155	}
156	atom[4]{
157	type = "EP_TIP5P";
158	position( -0.57154, 0.0, -0.46971 );
159	}
160	nRigidBodies = 1;
161	rigidBody[0]{
162	nMembers = 5;
163	members(0, 1, 2, 3, 4);
164	}
165
166	nCutoffGroups = 1;
167	cutoffGroup[0]{
168	nMembers = 5;
169	members(0, 1, 2, 3, 4);
170	}
171	}
172
173	molecule{
174	name = "SPCE";
175	nAtoms = 3;
176	atom[0]{
177	type = "O_SPCE";
178	position( 0.0, 0.0, -0.06461 );
179	}
180	atom[1]{
181	type = "H_SPCE";
182	position( 0.0, 0.81649, 0.51275 );
183	}
184	atom[2]{
185	type = "H_SPCE";
186	position( 0.0, -0.81649, 0.51275 );
187	}
188	nRigidBodies = 1;
189	rigidBody[0]{
190	nMembers = 3;
191	members(0, 1, 2);
192	}
193
194	nCutoffGroups = 1;
195	cutoffGroup[0]{
196	nMembers = 3;
197	members(0, 1, 2);
198	}
199	}
200
201	molecule{
202	name = "SPC";
203	nAtoms = 3;
204	atom[0]{
205	type = "O_SPC";
206	position( 0.0, 0.0, -0.06461 );
207	}
208	atom[1]{
209	type = "H_SPC";
210	position( 0.0, 0.81649, 0.51275 );
211	}
212	atom[2]{
213	type = "H_SPC";
214	position( 0.0, -0.81649, 0.51275 );
215	}
216	nRigidBodies = 1;
217	rigidBody[0]{
218	nMembers = 3;
219	members(0, 1, 2);
220	}
221
222	nCutoffGroups = 1;
223	cutoffGroup[0]{
224	nMembers = 3;
225	members(0, 1, 2);
226	}
227	}
228
229	molecule{
230	name = "DPD";
231	nAtoms = 1;
232	atom[0]{
233	type = "DPD";
234	position(0.0, 0.0, 0.0);
235	}
236	}
237
238	#endif