ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE-3.0/samples/water/spce/water.md
(Generate patch)

Comparing trunk/OOPSE-3.0/samples/water/spce/water.md (file contents):
Revision 2437 by chrisfen, Tue Nov 15 19:03:39 2005 UTC vs.
Revision 2955 by chrisfen, Wed Jul 19 12:46:20 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 60 | 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 +  cutoffGroup{
80 +    members(0, 1);
81 +  }
82 + }
83 +
84 + molecule{
85    name = "TIP3P";
86 <  nAtoms = 3;
86 >  
87    atom[0]{
88      type = "O_TIP3P";
89      position( 0.0, 0.0, -0.06556 );
# Line 75 | Line 97 | molecule{
97      position( 0.0, -0.75695, 0.52032 );
98    }
99  
100 <  nRigidBodies = 1;
100 >  
101    rigidBody[0]{
102 <    nMembers = 3;
102 >    
103      members(0, 1, 2);
104    }
105  
106 <  nCutoffGroups = 1;
107 <  cutoffGroup[0]{
108 <    nMembers = 3;
106 >  
107 >  cutoffGroup{
108 >    
109      members(0, 1, 2);
110    }
111   }
112  
113   molecule{
114    name = "TIP4P";
115 <  nAtoms = 4;
115 >  
116    atom[0]{
117      type = "O_TIP4P";
118      position( 0.0, 0.0, -0.06556 );
# Line 107 | Line 129 | molecule{
129      type = "EP_TIP4P";
130      position( 0.0, 0.0, 0.08444 );
131    }
132 <  nRigidBodies = 1;
132 >  
133    rigidBody[0]{
134 <    nMembers = 4;
134 >    
135      members(0, 1, 2, 3);
136    }
137  
138 <  nCutoffGroups = 1;
139 <  cutoffGroup[0]{
140 <    nMembers = 4;
138 >  
139 >  cutoffGroup{
140 >    
141      members(0, 1, 2, 3);
142    }
143   }
144  
145   molecule{
146    name = "TIP4P-Ew";
147 <  nAtoms = 4;
147 >  
148    atom[0]{
149      type = "O_TIP4P-Ew";
150      position( 0.0, 0.0, -0.06556 );
# Line 139 | Line 161 | molecule{
161      type = "EP_TIP4P-Ew";
162      position( 0.0, 0.0, 0.05944 );
163    }
164 <  nRigidBodies = 1;
164 >  
165    rigidBody[0]{
166 <    nMembers = 4;
166 >    
167      members(0, 1, 2, 3);
168    }
169  
170 <  nCutoffGroups = 1;
171 <  cutoffGroup[0]{
172 <    nMembers = 4;
170 >  
171 >  cutoffGroup{
172 >    
173      members(0, 1, 2, 3);
174    }
175   }
176  
177   molecule{
178    name = "TIP5P";
179 <  nAtoms = 5;
179 >  
180    atom[0]{
181      type = "O_TIP5P";
182      position( 0.0, 0.0, -0.06556 );
# Line 175 | Line 197 | molecule{
197      type = "EP_TIP5P";
198      position( -0.57154, 0.0, -0.46971 );
199    }
200 <  nRigidBodies = 1;
200 >  
201 >  rigidBody[0]{
202 >    
203 >    members(0, 1, 2, 3, 4);
204 >  }
205 >
206 >  
207 >  cutoffGroup{
208 >    
209 >    members(0, 1, 2, 3, 4);
210 >  }
211 > }
212 >
213 > molecule{
214 >  name = "TIP5P-E";
215 >  
216 >  atom[0]{
217 >    type = "O_TIP5P-E";
218 >    position( 0.0, 0.0, -0.06556 );
219 >  }
220 >  atom[1]{
221 >    type = "H_TIP5P";
222 >    position( 0.0, 0.75695, 0.52032 );
223 >  }
224 >  atom[2]{
225 >    type = "H_TIP5P";
226 >    position( 0.0, -0.75695, 0.52032 );
227 >  }
228 >  atom[3]{
229 >    type = "EP_TIP5P";
230 >    position( 0.57154, 0.0, -0.46971 );
231 >  }
232 >  atom[4]{
233 >    type = "EP_TIP5P";
234 >    position( -0.57154, 0.0, -0.46971 );
235 >  }
236 >  
237    rigidBody[0]{
238 <    nMembers = 5;
238 >    
239      members(0, 1, 2, 3, 4);
240    }
241  
242 <  nCutoffGroups = 1;
243 <  cutoffGroup[0]{
244 <    nMembers = 5;
242 >  
243 >  cutoffGroup{
244 >    
245      members(0, 1, 2, 3, 4);
246    }
247   }
248  
249   molecule{
250    name = "SPCE";
251 <  nAtoms = 3;
251 >  
252    atom[0]{
253      type = "O_SPCE";
254      position( 0.0, 0.0, -0.06461 );
# Line 203 | Line 261 | molecule{
261      type = "H_SPCE";
262      position( 0.0, -0.81649, 0.51275 );
263    }
264 <  nRigidBodies = 1;
264 >  
265    rigidBody[0]{
266 <    nMembers = 3;
266 >    
267      members(0, 1, 2);
268    }
269  
270 <  nCutoffGroups = 1;
271 <  cutoffGroup[0]{
272 <    nMembers = 3;
270 >  
271 >  cutoffGroup{
272 >    
273      members(0, 1, 2);
274    }
275   }
276  
277   molecule{
278    name = "SPC";
279 <  nAtoms = 3;
279 >  
280    atom[0]{
281      type = "O_SPC";
282      position( 0.0, 0.0, -0.06461 );
# Line 231 | Line 289 | molecule{
289      type = "H_SPC";
290      position( 0.0, -0.81649, 0.51275 );
291    }
292 <  nRigidBodies = 1;
292 >  
293    rigidBody[0]{
294 <    nMembers = 3;
294 >    
295      members(0, 1, 2);
296    }
297  
298 <  nCutoffGroups = 1;
299 <  cutoffGroup[0]{
300 <    nMembers = 3;
298 >  
299 >  cutoffGroup{
300 >    
301      members(0, 1, 2);
302    }
303   }
304  
305   molecule{
306    name = "DPD";
307 <  nAtoms = 1;
307 >  
308    atom[0]{
309      type = "DPD";
310      position(0.0, 0.0, 0.0);

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines