samples/minimizer/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 = "DPD";
  
  atom[0]{
    type = "DPD";
    position(0.0, 0.0, 0.0);
  }
}

molecule{
  name = "OFAKE";
  
  atom[0]{
    type = "O_TIP3P";
    position( 0.0, 0.0, -0.06556 );
  }
}

molecule{
  name = "HFAKE";
  
  atom[0]{
    type = "H_FAKE";
    position( 0.0, 0.0, -0.06556 );
  }
}


Revision:	790
Committed:	Tue Dec 6 16:49:59 2005 UTC (19 years, 5 months ago) by tim
File size:	2530 byte(s)
Log Message:	remove deprecated keywords from samples
#	User	Rev	Content
1	gezelter	2	molecule{
2			name = "SSD_E";
3	tim	790
4	gezelter	2	atom[0]{
5			type = "SSD_E";
6			position( 0.0, 0.0, 0.0 );
7			orientation( 0.0, 0.0, 0.0 );
8			}
9			}
10
11			molecule{
12			name = "SSD_RF";
13	tim	790
14	gezelter	2	atom[0]{
15			type = "SSD_RF";
16			position( 0.0, 0.0, 0.0 );
17			orientation( 0.0, 0.0, 0.0 );
18			}
19			}
20
21			molecule{
22			name = "SSD";
23	tim	790
24	gezelter	2	atom[0]{
25			type = "SSD";
26			position( 0.0, 0.0, 0.0 );
27			orientation( 0.0, 0.0, 0.0 );
28			}
29			}
30
31			molecule{
32			name = "SSD1";
33	tim	790
34	gezelter	2	atom[0]{
35			type = "SSD1";
36			position( 0.0, 0.0, 0.0 );
37			orientation( 0.0, 0.0, 0.0 );
38			}
39			}
40
41			molecule{
42			name = "TIP3P";
43	tim	790
44	gezelter	2	atom[0]{
45			type = "O_TIP3P";
46			position( 0.0, 0.0, -0.06556 );
47			}
48			atom[1]{
49			type = "H_TIP3P";
50			position( 0.0, 0.75695, 0.52032 );
51			}
52			atom[2]{
53			type = "H_TIP3P";
54			position( 0.0, -0.75695, 0.52032 );
55			}
56
57	tim	790
58	gezelter	2	rigidBody[0]{
59	tim	790
60	gezelter	2	members(0, 1, 2);
61			}
62
63	tim	790
64			cutoffGroup{
65
66	gezelter	2	members(0, 1, 2);
67			}
68
69			}
70
71			molecule{
72			name = "TIP4P";
73	tim	790
74	gezelter	2	atom[0]{
75			type = "O_TIP4P";
76			position( 0.0, 0.0, -0.06556 );
77			}
78			atom[1]{
79			type = "H_TIP4P";
80			position( 0.0, 0.75695, 0.52032 );
81			}
82			atom[2]{
83			type = "H_TIP4P";
84			position( 0.0, -0.75695, 0.52032 );
85			}
86			atom[3]{
87			type = "EP_TIP4P";
88			position( 0.0, 0.0, 0.08444 );
89			}
90	tim	790
91	gezelter	2	rigidBody[0]{
92	tim	790
93	gezelter	2	members(0, 1, 2, 3);
94			}
95
96	tim	790
97			cutoffGroup{
98
99	gezelter	2	members(0, 1, 2, 3);
100			}
101
102			}
103
104			molecule{
105			name = "TIP5P";
106	tim	790
107	gezelter	2	atom[0]{
108			type = "O_TIP5P";
109			position( 0.0, 0.0, -0.06556 );
110			}
111			atom[1]{
112			type = "H_TIP5P";
113			position( 0.0, 0.75695, 0.52032 );
114			}
115			atom[2]{
116			type = "H_TIP5P";
117			position( 0.0, -0.75695, 0.52032 );
118			}
119			atom[3]{
120			type = "EP_TIP5P";
121			position( 0.57154, 0.0, -0.46971 );
122			}
123			atom[4]{
124			type = "EP_TIP5P";
125			position( -0.57154, 0.0, -0.46971 );
126			}
127	tim	790
128	gezelter	2	rigidBody[0]{
129	tim	790
130	gezelter	2	members(0, 1, 2, 3, 4);
131			}
132
133	tim	790
134			cutoffGroup{
135
136	gezelter	2	members(0, 1, 2, 3, 4);
137			}
138
139			}
140
141			molecule{
142			name = "SPCE";
143	tim	790
144	gezelter	2	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	790
157	gezelter	2	rigidBody[0]{
158	tim	790
159	gezelter	2	members(0, 1, 2);
160			}
161
162	tim	790
163			cutoffGroup{
164
165	gezelter	2	members(0, 1, 2);
166			}
167
168			}
169
170			molecule{
171			name = "DPD";
172	tim	790
173	gezelter	2	atom[0]{
174			type = "DPD";
175			position(0.0, 0.0, 0.0);
176			}
177			}
178
179			molecule{
180			name = "OFAKE";
181	tim	790
182	gezelter	2	atom[0]{
183			type = "O_TIP3P";
184			position( 0.0, 0.0, -0.06556 );
185			}
186			}
187
188			molecule{
189			name = "HFAKE";
190	tim	790
191	gezelter	2	atom[0]{
192			type = "H_FAKE";
193			position( 0.0, 0.0, -0.06556 );
194			}
195			}
196
197