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Comparing:
trunk/samples/minimizer/water.md (file contents), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/samples/minimizer/water.md (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

# Line 1 | Line 1
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 <  nAtoms = 1;
24 >  
25    atom[0]{
26      type = "SSD_E";
27      position( 0.0, 0.0, 0.0 );
# Line 10 | Line 31 | molecule{
31  
32   molecule{
33    name = "SSD_RF";
34 <  nAtoms = 1;
34 >  
35    atom[0]{
36      type = "SSD_RF";
37      position( 0.0, 0.0, 0.0 );
# Line 20 | Line 41 | molecule{
41  
42   molecule{
43    name = "SSD";
44 <  nAtoms = 1;
44 >  
45    atom[0]{
46      type = "SSD";
47      position( 0.0, 0.0, 0.0 );
# Line 30 | Line 51 | molecule{
51  
52   molecule{
53    name = "SSD1";
54 <  nAtoms = 1;
54 >  
55    atom[0]{
56      type = "SSD1";
57      position( 0.0, 0.0, 0.0 );
# Line 39 | Line 60 | molecule{
60   }
61  
62   molecule{
63 +  name = "TRED";
64 +  
65 +  atom[0]{
66 +    type = "TRED";
67 +    position( 0.0, 0.0, 0.0 );
68 +    orientation( 0.0, 0.0, 0.0 );
69 +  }
70 +  atom[1]{
71 +    type = "EP_TRED";
72 +    position( 0.0, 0.0, 0.5 );
73 +  }
74 +
75 +  rigidBody[0]{
76 +    members(0, 1);
77 +  }
78 + }
79 +
80 + molecule{
81    name = "TIP3P";
82 <  nAtoms = 3;
82 >  
83    atom[0]{
84      type = "O_TIP3P";
85      position( 0.0, 0.0, -0.06556 );
# Line 53 | Line 92 | molecule{
92      type = "H_TIP3P";
93      position( 0.0, -0.75695, 0.52032 );
94    }
95 <
96 <  nRigidBodies = 1;
58 <  rigidBody[0]{
59 <    nMembers = 3;
95 >  
96 >  rigidBody[0]{    
97      members(0, 1, 2);
98 <  }
62 <
63 <  nCutoffGroups = 1;
64 <  cutoffGroup[0]{
65 <    nMembers = 3;
66 <    members(0, 1, 2);
67 <  }
68 <
98 >  }  
99   }
100  
101   molecule{
102    name = "TIP4P";
103 <  nAtoms = 4;
103 >  
104    atom[0]{
105      type = "O_TIP4P";
106      position( 0.0, 0.0, -0.06556 );
# Line 87 | Line 117 | molecule{
117      type = "EP_TIP4P";
118      position( 0.0, 0.0, 0.08444 );
119    }
120 <  nRigidBodies = 1;
121 <  rigidBody[0]{
92 <    nMembers = 4;
120 >  
121 >  rigidBody[0]{    
122      members(0, 1, 2, 3);
123 <  }
123 >  }  
124 > }
125  
126 <  nCutoffGroups = 1;
127 <  cutoffGroup[0]{
128 <    nMembers = 4;
126 > molecule{
127 >  name = "TIP4P-Ew";
128 >  
129 >  atom[0]{
130 >    type = "O_TIP4P-Ew";
131 >    position( 0.0, 0.0, -0.06556 );
132 >  }
133 >  atom[1]{
134 >    type = "H_TIP4P-Ew";
135 >    position( 0.0, 0.75695, 0.52032 );
136 >  }
137 >  atom[2]{
138 >    type = "H_TIP4P-Ew";
139 >    position( 0.0, -0.75695, 0.52032 );
140 >  }
141 >  atom[3]{
142 >    type = "EP_TIP4P-Ew";
143 >    position( 0.0, 0.0, 0.05944 );
144 >  }
145 >  
146 >  rigidBody[0]{    
147      members(0, 1, 2, 3);
148    }
101 –
149   }
150  
151   molecule{
152    name = "TIP5P";
153 <  nAtoms = 5;
153 >  
154    atom[0]{
155      type = "O_TIP5P";
156      position( 0.0, 0.0, -0.06556 );
# Line 124 | Line 171 | molecule{
171      type = "EP_TIP5P";
172      position( -0.57154, 0.0, -0.46971 );
173    }
174 <  nRigidBodies = 1;
174 >  
175    rigidBody[0]{
129 –    nMembers = 5;
176      members(0, 1, 2, 3, 4);
177    }
178 + }
179  
180 <  nCutoffGroups = 1;
181 <  cutoffGroup[0]{
182 <    nMembers = 5;
180 > molecule{
181 >  name = "TIP5P-E";
182 >  
183 >  atom[0]{
184 >    type = "O_TIP5P-E";
185 >    position( 0.0, 0.0, -0.06556 );
186 >  }
187 >  atom[1]{
188 >    type = "H_TIP5P";
189 >    position( 0.0, 0.75695, 0.52032 );
190 >  }
191 >  atom[2]{
192 >    type = "H_TIP5P";
193 >    position( 0.0, -0.75695, 0.52032 );
194 >  }
195 >  atom[3]{
196 >    type = "EP_TIP5P";
197 >    position( 0.57154, 0.0, -0.46971 );
198 >  }
199 >  atom[4]{
200 >    type = "EP_TIP5P";
201 >    position( -0.57154, 0.0, -0.46971 );
202 >  }
203 >  
204 >  rigidBody[0]{    
205      members(0, 1, 2, 3, 4);
206    }
138 –
207   }
208  
209   molecule{
210    name = "SPCE";
211 <  nAtoms = 3;
211 >  
212    atom[0]{
213      type = "O_SPCE";
214      position( 0.0, 0.0, -0.06461 );
# Line 153 | Line 221 | molecule{
221      type = "H_SPCE";
222      position( 0.0, -0.81649, 0.51275 );
223    }
224 <  nRigidBodies = 1;
225 <  rigidBody[0]{
158 <    nMembers = 3;
224 >  
225 >  rigidBody[0]{    
226      members(0, 1, 2);
227    }
228 + }
229  
230 <  nCutoffGroups = 1;
231 <  cutoffGroup[0]{
232 <    nMembers = 3;
230 > molecule{
231 >  name = "SPC";
232 >  
233 >  atom[0]{
234 >    type = "O_SPC";
235 >    position( 0.0, 0.0, -0.06461 );
236 >  }
237 >  atom[1]{
238 >    type = "H_SPC";
239 >    position( 0.0, 0.81649, 0.51275 );
240 >  }
241 >  atom[2]{
242 >    type = "H_SPC";
243 >    position( 0.0, -0.81649, 0.51275 );
244 >  }
245 >  
246 >  rigidBody[0]{    
247      members(0, 1, 2);
248    }
167 –
249   }
250  
251   molecule{
252    name = "DPD";
253 <  nAtoms = 1;
253 >  
254    atom[0]{
255      type = "DPD";
256      position(0.0, 0.0, 0.0);
257    }
258   }
259  
260 < molecule{
180 <  name = "OFAKE";
181 <  nAtoms = 1;
182 <  atom[0]{
183 <    type = "O_TIP3P";
184 <    position( 0.0, 0.0, -0.06556 );
185 <  }
186 < }
187 <
188 < molecule{
189 <  name = "HFAKE";
190 <  nAtoms = 1;
191 <  atom[0]{
192 <    type = "H_FAKE";
193 <    position( 0.0, 0.0, -0.06556 );
194 <  }
195 < }
196 <
197 <
260 > #endif

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