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Comparing trunk/OOPSE-3.0/samples/water/spce/water.md (file contents):
Revision 2435 by chrisfen, Tue Nov 15 16:37:51 2005 UTC vs.
Revision 2777 by chrisfen, Thu May 25 21:40:57 2006 UTC

# Line 3 | Line 3 | molecule{
3  
4   molecule{
5    name = "Cl-";
6 <  nAtoms = 1;
6 >  
7    atom[0]{
8      type = "Cl-";
9      position(0.0, 0.0, 0.0);
# Line 12 | Line 12 | molecule{
12  
13   molecule{
14    name = "Na+";
15 <  nAtoms = 1;
15 >  
16    atom[0]{
17      type = "Na+";
18      position(0.0, 0.0, 0.0);
# Line 21 | Line 21 | molecule{
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 31 | 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 41 | 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 51 | 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 61 | Line 61 | molecule{
61  
62   molecule{
63    name = "TIP3P";
64 <  nAtoms = 3;
64 >  
65    atom[0]{
66      type = "O_TIP3P";
67      position( 0.0, 0.0, -0.06556 );
# Line 75 | Line 75 | molecule{
75      position( 0.0, -0.75695, 0.52032 );
76    }
77  
78 <  nRigidBodies = 1;
78 >  
79    rigidBody[0]{
80 <    nMembers = 3;
80 >    
81      members(0, 1, 2);
82    }
83  
84 <  nCutoffGroups = 1;
85 <  cutoffGroup[0]{
86 <    nMembers = 3;
84 >  
85 >  cutoffGroup{
86 >    
87      members(0, 1, 2);
88    }
89   }
90  
91   molecule{
92    name = "TIP4P";
93 <  nAtoms = 4;
93 >  
94    atom[0]{
95      type = "O_TIP4P";
96      position( 0.0, 0.0, -0.06556 );
# Line 107 | Line 107 | molecule{
107      type = "EP_TIP4P";
108      position( 0.0, 0.0, 0.08444 );
109    }
110 <  nRigidBodies = 1;
110 >  
111    rigidBody[0]{
112 <    nMembers = 4;
112 >    
113      members(0, 1, 2, 3);
114    }
115  
116 <  nCutoffGroups = 1;
117 <  cutoffGroup[0]{
118 <    nMembers = 4;
116 >  
117 >  cutoffGroup{
118 >    
119      members(0, 1, 2, 3);
120    }
121   }
122  
123   molecule{
124    name = "TIP4P-Ew";
125 <  nAtoms = 4;
125 >  
126    atom[0]{
127      type = "O_TIP4P-Ew";
128      position( 0.0, 0.0, -0.06556 );
# Line 139 | Line 139 | molecule{
139      type = "EP_TIP4P-Ew";
140      position( 0.0, 0.0, 0.05944 );
141    }
142 <  nRigidBodies = 1;
142 >  
143    rigidBody[0]{
144 <    nMembers = 4;
144 >    
145      members(0, 1, 2, 3);
146    }
147  
148 <  nCutoffGroups = 1;
149 <  cutoffGroup[0]{
150 <    nMembers = 4;
148 >  
149 >  cutoffGroup{
150 >    
151      members(0, 1, 2, 3);
152    }
153   }
154  
155   molecule{
156    name = "TIP5P";
157 <  nAtoms = 5;
157 >  
158    atom[0]{
159      type = "O_TIP5P";
160      position( 0.0, 0.0, -0.06556 );
# Line 175 | Line 175 | molecule{
175      type = "EP_TIP5P";
176      position( -0.57154, 0.0, -0.46971 );
177    }
178 <  nRigidBodies = 1;
178 >  
179    rigidBody[0]{
180 <    nMembers = 5;
180 >    
181      members(0, 1, 2, 3, 4);
182    }
183  
184 <  nCutoffGroups = 1;
185 <  cutoffGroup[0]{
186 <    nMembers = 5;
184 >  
185 >  cutoffGroup{
186 >    
187 >    members(0, 1, 2, 3, 4);
188 >  }
189 > }
190 >
191 > molecule{
192 >  name = "TIP5P-E";
193 >  
194 >  atom[0]{
195 >    type = "O_TIP5P-E";
196 >    position( 0.0, 0.0, -0.06556 );
197 >  }
198 >  atom[1]{
199 >    type = "H_TIP5P";
200 >    position( 0.0, 0.75695, 0.52032 );
201 >  }
202 >  atom[2]{
203 >    type = "H_TIP5P";
204 >    position( 0.0, -0.75695, 0.52032 );
205 >  }
206 >  atom[3]{
207 >    type = "EP_TIP5P";
208 >    position( 0.57154, 0.0, -0.46971 );
209 >  }
210 >  atom[4]{
211 >    type = "EP_TIP5P";
212 >    position( -0.57154, 0.0, -0.46971 );
213 >  }
214 >  
215 >  rigidBody[0]{
216 >    
217      members(0, 1, 2, 3, 4);
218    }
219 +
220 +  
221 +  cutoffGroup{
222 +    
223 +    members(0, 1, 2, 3, 4);
224 +  }
225   }
226  
227   molecule{
228    name = "SPCE";
229 <  nAtoms = 3;
229 >  
230    atom[0]{
231      type = "O_SPCE";
232      position( 0.0, 0.0, -0.06461 );
# Line 203 | Line 239 | molecule{
239      type = "H_SPCE";
240      position( 0.0, -0.81649, 0.51275 );
241    }
242 <  nRigidBodies = 1;
242 >  
243    rigidBody[0]{
244 <    nMembers = 3;
244 >    
245      members(0, 1, 2);
246    }
247  
248 < //  nCutoffGroups = 1;
249 < //  cutoffGroup[0]{
250 < //    nMembers = 3;
251 < //    members(0, 1, 2);
252 < //  }
248 >  
249 >  cutoffGroup{
250 >    
251 >    members(0, 1, 2);
252 >  }
253   }
254  
255   molecule{
256    name = "SPC";
257 <  nAtoms = 3;
257 >  
258    atom[0]{
259      type = "O_SPC";
260      position( 0.0, 0.0, -0.06461 );
# Line 231 | Line 267 | molecule{
267      type = "H_SPC";
268      position( 0.0, -0.81649, 0.51275 );
269    }
270 <  nRigidBodies = 1;
270 >  
271    rigidBody[0]{
272 <    nMembers = 3;
272 >    
273      members(0, 1, 2);
274    }
275  
276 <  nCutoffGroups = 1;
277 <  cutoffGroup[0]{
278 <    nMembers = 3;
276 >  
277 >  cutoffGroup{
278 >    
279      members(0, 1, 2);
280    }
281   }
282  
283   molecule{
284    name = "DPD";
285 <  nAtoms = 1;
285 >  
286    atom[0]{
287      type = "DPD";
288      position(0.0, 0.0, 0.0);

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