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root/OpenMD/branches/development/samples/minimizer/water.md
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Comparing:
trunk/samples/minimizer/water.md (file contents), Revision 790 by tim, Tue Dec 6 16:49:59 2005 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    
25    atom[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    
83    atom[0]{
# Line 53 | Line 92 | molecule{
92      type = "H_TIP3P";
93      position( 0.0, -0.75695, 0.52032 );
94    }
56 –
95    
96 <  rigidBody[0]{
59 <    
96 >  rigidBody[0]{    
97      members(0, 1, 2);
98 <  }
62 <
63 <  
64 <  cutoffGroup{
65 <    
66 <    members(0, 1, 2);
67 <  }
68 <
98 >  }  
99   }
100  
101   molecule{
# Line 88 | Line 118 | molecule{
118      position( 0.0, 0.0, 0.08444 );
119    }
120    
121 <  rigidBody[0]{
92 <    
121 >  rigidBody[0]{    
122      members(0, 1, 2, 3);
123 <  }
123 >  }  
124 > }
125  
126 + molecule{
127 +  name = "TIP4P-Ew";
128    
129 <  cutoffGroup{
130 <    
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{
# Line 126 | Line 173 | molecule{
173    }
174    
175    rigidBody[0]{
129 –    
176      members(0, 1, 2, 3, 4);
177    }
178 + }
179  
180 + molecule{
181 +  name = "TIP5P-E";
182    
183 <  cutoffGroup{
184 <    
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{
# Line 154 | Line 222 | molecule{
222      position( 0.0, -0.81649, 0.51275 );
223    }
224    
225 <  rigidBody[0]{
158 <    
225 >  rigidBody[0]{    
226      members(0, 1, 2);
227    }
161 –
162 –  
163 –  cutoffGroup{
164 –    
165 –    members(0, 1, 2);
166 –  }
167 –
228   }
229  
230   molecule{
231 <  name = "DPD";
231 >  name = "SPC";
232    
233    atom[0]{
234 <    type = "DPD";
235 <    position(0.0, 0.0, 0.0);
234 >    type = "O_SPC";
235 >    position( 0.0, 0.0, -0.06461 );
236    }
237 < }
238 <
239 < molecule{
240 <  name = "OFAKE";
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 <  atom[0]{
247 <    type = "O_TIP3P";
184 <    position( 0.0, 0.0, -0.06556 );
246 >  rigidBody[0]{    
247 >    members(0, 1, 2);
248    }
249   }
250  
251   molecule{
252 <  name = "HFAKE";
252 >  name = "DPD";
253    
254    atom[0]{
255 <    type = "H_FAKE";
256 <    position( 0.0, 0.0, -0.06556 );
255 >    type = "DPD";
256 >    position(0.0, 0.0, 0.0);
257    }
258   }
259  
260 <
260 > #endif

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