ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE-4/samples/water/tip4p/water.md
(Generate patch)

Comparing trunk/OOPSE-4/samples/water/tip4p/water.md (file contents):
Revision 2216 by chrisfen, Fri Apr 29 16:26:27 2005 UTC vs.
Revision 2777 by chrisfen, Thu May 25 21:40:57 2006 UTC

# Line 2 | Line 2 | molecule{
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 13 | 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 23 | 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 33 | 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 43 | 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 57 | 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 89 | 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 121 | 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 157 | 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 185 | 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;
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 213 | 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);

Diff Legend

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