thermoIntegration/liquid/water.md

#ifndef _WATER_MD_
#define _WATER_MD_

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_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 = "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);
  }

  
  cutoffGroup{
    
    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);
  }

  
  cutoffGroup{
    
    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);
  }

  
  cutoffGroup{
    
    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);
  }

  
  cutoffGroup{
    
    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);
  }

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

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

#endif
Revision:	2489
Committed:	Tue Dec 6 16:49:59 2005 UTC (18 years, 7 months ago) by tim
File size:	2710 byte(s)
Log Message:	remove deprecated keywords from samples
#	User	Rev	Content
1	chrisfen	2121	#ifndef _WATER_MD_
2			#define _WATER_MD_
3
4			molecule{
5			name = "SSD_E";
6	tim	2489
7	chrisfen	2121	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	tim	2489
17	chrisfen	2121	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	tim	2489
27	chrisfen	2121	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	tim	2489
37	chrisfen	2121	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	tim	2489
47	chrisfen	2121	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	tim	2489
61	chrisfen	2121	rigidBody[0]{
62	tim	2489
63	chrisfen	2121	members(0, 1, 2);
64			}
65
66	tim	2489
67			cutoffGroup{
68
69	chrisfen	2121	members(0, 1, 2);
70			}
71			}
72
73			molecule{
74			name = "TIP4P";
75	tim	2489
76	chrisfen	2121	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	tim	2489
93	chrisfen	2121	rigidBody[0]{
94	tim	2489
95	chrisfen	2121	members(0, 1, 2, 3);
96			}
97
98	tim	2489
99			cutoffGroup{
100
101	chrisfen	2121	members(0, 1, 2, 3);
102			}
103			}
104
105			molecule{
106			name = "TIP5P";
107	tim	2489
108	chrisfen	2121	atom[0]{
109			type = "O_TIP5P";
110			position( 0.0, 0.0, -0.06556 );
111			}
112			atom[1]{
113			type = "H_TIP5P";
114			position( 0.0, 0.75695, 0.52032 );
115			}
116			atom[2]{
117			type = "H_TIP5P";
118			position( 0.0, -0.75695, 0.52032 );
119			}
120			atom[3]{
121			type = "EP_TIP5P";
122			position( 0.57154, 0.0, -0.46971 );
123			}
124			atom[4]{
125			type = "EP_TIP5P";
126			position( -0.57154, 0.0, -0.46971 );
127			}
128	tim	2489
129	chrisfen	2121	rigidBody[0]{
130	tim	2489
131	chrisfen	2121	members(0, 1, 2, 3, 4);
132			}
133
134	tim	2489
135			cutoffGroup{
136
137	chrisfen	2121	members(0, 1, 2, 3, 4);
138			}
139			}
140
141			molecule{
142			name = "SPCE";
143	tim	2489
144	chrisfen	2121	atom[0]{
145			type = "O_SPCE";
146			position( 0.0, 0.0, -0.06461 );
147			}
148			atom[1]{
149			type = "H_SPCE";
150			position( 0.0, 0.81649, 0.51275 );
151			}
152			atom[2]{
153			type = "H_SPCE";
154			position( 0.0, -0.81649, 0.51275 );
155			}
156	tim	2489
157	chrisfen	2121	rigidBody[0]{
158	tim	2489
159	chrisfen	2121	members(0, 1, 2);
160			}
161
162	tim	2489
163			cutoffGroup{
164
165	chrisfen	2121	members(0, 1, 2);
166			}
167			}
168
169			molecule{
170			name = "SPC";
171	tim	2489
172	chrisfen	2121	atom[0]{
173			type = "O_SPC";
174			position( 0.0, 0.0, -0.06461 );
175			}
176			atom[1]{
177			type = "H_SPC";
178			position( 0.0, 0.81649, 0.51275 );
179			}
180			atom[2]{
181			type = "H_SPC";
182			position( 0.0, -0.81649, 0.51275 );
183			}
184	tim	2489
185	chrisfen	2121	rigidBody[0]{
186	tim	2489
187	chrisfen	2121	members(0, 1, 2);
188			}
189
190	tim	2489
191			cutoffGroup{
192
193	chrisfen	2121	members(0, 1, 2);
194			}
195			}
196
197			molecule{
198			name = "DPD";
199	tim	2489
200	chrisfen	2121	atom[0]{
201			type = "DPD";
202			position(0.0, 0.0, 0.0);
203			}
204			}
205
206			#endif