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Comparing trunk/OOPSE-4/samples/water/ssdrf/water.md (file contents):
Revision 2397 by chrisfen, Wed Oct 26 23:30:52 2005 UTC vs.
Revision 2489 by tim, Tue Dec 6 16:49:59 2005 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 = "PAIR";
24 <  nAtoms = 3;
24 >  
25    atom[0]{
26      type = "Pchg+";
27      position(0.0, 1, 1.0);
# Line 35 | Line 35 | molecule{
35      position(0.0, 0.0, -1.0);
36    }
37  
38 <  nRigidBodies = 1;
38 >  
39    rigidBody[0]{
40 <    nMembers = 3;
40 >    
41      members(0, 1, 2);
42    }
43  
44 <  nCutoffGroups = 1;
45 <  cutoffGroup[0]{
46 <    nMembers = 3;
44 >  
45 >  cutoffGroup{
46 >    
47      members(0, 1, 2);
48    }
49   }
50  
51   molecule{
52    name = "PDIP";
53 <  nAtoms = 1;
53 >  
54    atom[0]{
55      type = "PDIP";
56      position( 0.0, 0.0, 0.0 );
# Line 60 | Line 60 | molecule{
60  
61   molecule{
62    name = "SSD_E";
63 <  nAtoms = 1;
63 >  
64    atom[0]{
65      type = "SSD_E";
66      position( 0.0, 0.0, 0.0 );
# Line 70 | Line 70 | molecule{
70  
71   molecule{
72    name = "SSD_RF";
73 <  nAtoms = 1;
73 >  
74    atom[0]{
75      type = "SSD_RF";
76      position( 0.0, 0.0, 0.0 );
# Line 80 | Line 80 | molecule{
80  
81   molecule{
82    name = "SSD";
83 <  nAtoms = 1;
83 >  
84    atom[0]{
85      type = "SSD";
86      position( 0.0, 0.0, 0.0 );
# Line 90 | Line 90 | molecule{
90  
91   molecule{
92    name = "SSD1";
93 <  nAtoms = 1;
93 >  
94    atom[0]{
95      type = "SSD1";
96      position( 0.0, 0.0, 0.0 );
# Line 100 | Line 100 | molecule{
100  
101   molecule{
102    name = "TIP3P";
103 <  nAtoms = 3;
103 >  
104    atom[0]{
105      type = "O_TIP3P";
106      position( 0.0, 0.0, -0.06556 );
# Line 114 | Line 114 | molecule{
114      position( 0.0, -0.75695, 0.52032 );
115    }
116  
117 <  nRigidBodies = 1;
117 >  
118    rigidBody[0]{
119 <    nMembers = 3;
119 >    
120      members(0, 1, 2);
121    }
122  
123 <  nCutoffGroups = 1;
124 <  cutoffGroup[0]{
125 <    nMembers = 3;
123 >  
124 >  cutoffGroup{
125 >    
126      members(0, 1, 2);
127    }
128   }
129  
130   molecule{
131    name = "TIP4P";
132 <  nAtoms = 4;
132 >  
133    atom[0]{
134      type = "O_TIP4P";
135      position( 0.0, 0.0, -0.06556 );
# Line 146 | Line 146 | molecule{
146      type = "EP_TIP4P";
147      position( 0.0, 0.0, 0.08444 );
148    }
149 <  nRigidBodies = 1;
149 >  
150    rigidBody[0]{
151 <    nMembers = 4;
151 >    
152      members(0, 1, 2, 3);
153    }
154  
155 <  nCutoffGroups = 1;
156 <  cutoffGroup[0]{
157 <    nMembers = 4;
155 >  
156 >  cutoffGroup{
157 >    
158      members(0, 1, 2, 3);
159    }
160   }
161  
162   molecule{
163    name = "TIP4P-Ew";
164 <  nAtoms = 4;
164 >  
165    atom[0]{
166      type = "O_TIP4P-Ew";
167      position( 0.0, 0.0, -0.06556 );
# Line 178 | Line 178 | molecule{
178      type = "EP_TIP4P-Ew";
179      position( 0.0, 0.0, 0.05944 );
180    }
181 <  nRigidBodies = 1;
181 >  
182    rigidBody[0]{
183 <    nMembers = 4;
183 >    
184      members(0, 1, 2, 3);
185    }
186  
187 <  nCutoffGroups = 1;
188 <  cutoffGroup[0]{
189 <    nMembers = 4;
187 >  
188 >  cutoffGroup{
189 >    
190      members(0, 1, 2, 3);
191    }
192   }
193  
194   molecule{
195    name = "TIP5P";
196 <  nAtoms = 5;
196 >  
197    atom[0]{
198      type = "O_TIP5P";
199      position( 0.0, 0.0, -0.06556 );
# Line 214 | Line 214 | molecule{
214      type = "EP_TIP5P";
215      position( -0.57154, 0.0, -0.46971 );
216    }
217 <  nRigidBodies = 1;
217 >  
218    rigidBody[0]{
219 <    nMembers = 5;
219 >    
220      members(0, 1, 2, 3, 4);
221    }
222  
223 <  nCutoffGroups = 1;
224 <  cutoffGroup[0]{
225 <    nMembers = 5;
223 >  
224 >  cutoffGroup{
225 >    
226      members(0, 1, 2, 3, 4);
227    }
228   }
229  
230   molecule{
231    name = "SPCE";
232 <  nAtoms = 3;
232 >  
233    atom[0]{
234      type = "O_SPCE";
235      position( 0.0, 0.0, -0.06461 );
# Line 242 | Line 242 | molecule{
242      type = "H_SPCE";
243      position( 0.0, -0.81649, 0.51275 );
244    }
245 <  nRigidBodies = 1;
245 >  
246    rigidBody[0]{
247 <    nMembers = 3;
247 >    
248      members(0, 1, 2);
249    }
250  
251 <  nCutoffGroups = 1;
252 <  cutoffGroup[0]{
253 <    nMembers = 3;
251 >  
252 >  cutoffGroup{
253 >    
254      members(0, 1, 2);
255    }
256   }
257  
258   molecule{
259    name = "SPC";
260 <  nAtoms = 3;
260 >  
261    atom[0]{
262      type = "O_SPC";
263      position( 0.0, 0.0, -0.06461 );
# Line 270 | Line 270 | molecule{
270      type = "H_SPC";
271      position( 0.0, -0.81649, 0.51275 );
272    }
273 <  nRigidBodies = 1;
273 >  
274    rigidBody[0]{
275 <    nMembers = 3;
275 >    
276      members(0, 1, 2);
277    }
278  
279 <  nCutoffGroups = 1;
280 <  cutoffGroup[0]{
281 <    nMembers = 3;
279 >  
280 >  cutoffGroup{
281 >    
282      members(0, 1, 2);
283    }
284   }
285  
286   molecule{
287    name = "DPD";
288 <  nAtoms = 1;
288 >  
289    atom[0]{
290      type = "DPD";
291      position(0.0, 0.0, 0.0);

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