water/ssdrf/water.md

#ifndef _WATER_MD_
#define _WATER_MD_

molecule{
  name = "SSD_E";
  nAtoms = 1;
  atom[0]{
    type = "SSD_E";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "SSD_RF";
  nAtoms = 1;
  atom[0]{
    type = "SSD_RF";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "SSD";
  nAtoms = 1;
  atom[0]{
    type = "SSD";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "SSD1";
  nAtoms = 1;
  atom[0]{
    type = "SSD1";
    position( 0.0, 0.0, 0.0 );
    orientation( 0.0, 0.0, 0.0 );
  }
}

molecule{
  name = "TIP3P";
  nAtoms = 3;
  atom[0]{
    type = "O_TIP3P";
    position( 0.0, 0.0, -0.06556 );
  }
  atom[1]{
    type = "H_TIP3P";
    position( 0.0, 0.75695, 0.52032 );
  }
  atom[2]{
    type = "H_TIP3P";
    position( 0.0, -0.75695, 0.52032 );
  }

  nRigidBodies = 1;
  rigidBody[0]{ 
    nMembers = 3;
    members(0, 1, 2);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 3;
    members(0, 1, 2);
  }
}

molecule{
  name = "TIP4P";
  nAtoms = 4;
  atom[0]{
    type = "O_TIP4P";
    position( 0.0, 0.0, -0.06556 );
  }
  atom[1]{
    type = "H_TIP4P";
    position( 0.0, 0.75695, 0.52032 );
  }
  atom[2]{
    type = "H_TIP4P";
    position( 0.0, -0.75695, 0.52032 );
  }
  atom[3]{
    type = "EP_TIP4P";
    position( 0.0, 0.0, 0.08444 );
  }
  nRigidBodies = 1;
  rigidBody[0]{
    nMembers = 4;
    members(0, 1, 2, 3);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 4;
    members(0, 1, 2, 3);
  }
}

molecule{
  name = "TIP5P";
  nAtoms = 5;
  atom[0]{
    type = "O_TIP5P";
    position( 0.0, 0.0, -0.06556 );
  }
  atom[1]{
    type = "H_TIP5P";
    position( 0.0, 0.75695, 0.52032 );
  }
  atom[2]{
    type = "H_TIP5P";
    position( 0.0, -0.75695, 0.52032 );
  }
  atom[3]{
    type = "EP_TIP5P";
    position( 0.57154, 0.0, -0.46971 );
  }
  atom[4]{
    type = "EP_TIP5P";
    position( -0.57154, 0.0, -0.46971 );
  }
  nRigidBodies = 1;
  rigidBody[0]{
    nMembers = 5;
    members(0, 1, 2, 3, 4);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 5;
    members(0, 1, 2, 3, 4);
  }
}

molecule{
  name = "SPCE";
  nAtoms = 3;
  atom[0]{
    type = "O_SPCE";
    position( 0.0, 0.0, -0.06461 );
  }
  atom[1]{
    type = "H_SPCE";
    position( 0.0, 0.81649, 0.51275 );
  }
  atom[2]{
    type = "H_SPCE";
    position( 0.0, -0.81649, 0.51275 );
  }
  nRigidBodies = 1;
  rigidBody[0]{
    nMembers = 3;
    members(0, 1, 2);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 3;
    members(0, 1, 2);
  }
}

molecule{
  name = "SPC";
  nAtoms = 3;
  atom[0]{
    type = "O_SPC";
    position( 0.0, 0.0, -0.06461 );
  }
  atom[1]{
    type = "H_SPC";
    position( 0.0, 0.81649, 0.51275 );
  }
  atom[2]{
    type = "H_SPC";
    position( 0.0, -0.81649, 0.51275 );
  }
  nRigidBodies = 1;
  rigidBody[0]{
    nMembers = 3;
    members(0, 1, 2);
  }

  nCutoffGroups = 1;
  cutoffGroup[0]{
    nMembers = 3;
    members(0, 1, 2);
  }
}

molecule{
  name = "DPD";
  nAtoms = 1;
  atom[0]{
    type = "DPD";
    position(0.0, 0.0, 0.0);
  }
}

#endif
Revision:	375
Committed:	Tue Feb 22 19:26:05 2005 UTC (20 years, 8 months ago) by chrisfen
Original Path:	*trunk/samples/water/ssdrf/water.md*
File size:	3140 byte(s)
Log Message:	Added ssdrf sample
#	User	Rev	Content
1	chrisfen	375	#ifndef _WATER_MD_
2			#define _WATER_MD_
3
4			molecule{
5			name = "SSD_E";
6			nAtoms = 1;
7			atom[0]{
8			type = "SSD_E";
9			position( 0.0, 0.0, 0.0 );
10			orientation( 0.0, 0.0, 0.0 );
11			}
12			}
13
14			molecule{
15			name = "SSD_RF";
16			nAtoms = 1;
17			atom[0]{
18			type = "SSD_RF";
19			position( 0.0, 0.0, 0.0 );
20			orientation( 0.0, 0.0, 0.0 );
21			}
22			}
23
24			molecule{
25			name = "SSD";
26			nAtoms = 1;
27			atom[0]{
28			type = "SSD";
29			position( 0.0, 0.0, 0.0 );
30			orientation( 0.0, 0.0, 0.0 );
31			}
32			}
33
34			molecule{
35			name = "SSD1";
36			nAtoms = 1;
37			atom[0]{
38			type = "SSD1";
39			position( 0.0, 0.0, 0.0 );
40			orientation( 0.0, 0.0, 0.0 );
41			}
42			}
43
44			molecule{
45			name = "TIP3P";
46			nAtoms = 3;
47			atom[0]{
48			type = "O_TIP3P";
49			position( 0.0, 0.0, -0.06556 );
50			}
51			atom[1]{
52			type = "H_TIP3P";
53			position( 0.0, 0.75695, 0.52032 );
54			}
55			atom[2]{
56			type = "H_TIP3P";
57			position( 0.0, -0.75695, 0.52032 );
58			}
59
60			nRigidBodies = 1;
61			rigidBody[0]{
62			nMembers = 3;
63			members(0, 1, 2);
64			}
65
66			nCutoffGroups = 1;
67			cutoffGroup[0]{
68			nMembers = 3;
69			members(0, 1, 2);
70			}
71			}
72
73			molecule{
74			name = "TIP4P";
75			nAtoms = 4;
76			atom[0]{
77			type = "O_TIP4P";
78			position( 0.0, 0.0, -0.06556 );
79			}
80			atom[1]{
81			type = "H_TIP4P";
82			position( 0.0, 0.75695, 0.52032 );
83			}
84			atom[2]{
85			type = "H_TIP4P";
86			position( 0.0, -0.75695, 0.52032 );
87			}
88			atom[3]{
89			type = "EP_TIP4P";
90			position( 0.0, 0.0, 0.08444 );
91			}
92			nRigidBodies = 1;
93			rigidBody[0]{
94			nMembers = 4;
95			members(0, 1, 2, 3);
96			}
97
98			nCutoffGroups = 1;
99			cutoffGroup[0]{
100			nMembers = 4;
101			members(0, 1, 2, 3);
102			}
103			}
104
105			molecule{
106			name = "TIP5P";
107			nAtoms = 5;
108			atom[0]{
109			type = "O_TIP5P";
110			position( 0.0, 0.0, -0.06556 );
111			}
112			atom[1]{
113			type = "H_TIP5P";
114			position( 0.0, 0.75695, 0.52032 );
115			}
116			atom[2]{
117			type = "H_TIP5P";
118			position( 0.0, -0.75695, 0.52032 );
119			}
120			atom[3]{
121			type = "EP_TIP5P";
122			position( 0.57154, 0.0, -0.46971 );
123			}
124			atom[4]{
125			type = "EP_TIP5P";
126			position( -0.57154, 0.0, -0.46971 );
127			}
128			nRigidBodies = 1;
129			rigidBody[0]{
130			nMembers = 5;
131			members(0, 1, 2, 3, 4);
132			}
133
134			nCutoffGroups = 1;
135			cutoffGroup[0]{
136			nMembers = 5;
137			members(0, 1, 2, 3, 4);
138			}
139			}
140
141			molecule{
142			name = "SPCE";
143			nAtoms = 3;
144			atom[0]{
145			type = "O_SPCE";
146			position( 0.0, 0.0, -0.06461 );
147			}
148			atom[1]{
149			type = "H_SPCE";
150			position( 0.0, 0.81649, 0.51275 );
151			}
152			atom[2]{
153			type = "H_SPCE";
154			position( 0.0, -0.81649, 0.51275 );
155			}
156			nRigidBodies = 1;
157			rigidBody[0]{
158			nMembers = 3;
159			members(0, 1, 2);
160			}
161
162			nCutoffGroups = 1;
163			cutoffGroup[0]{
164			nMembers = 3;
165			members(0, 1, 2);
166			}
167			}
168
169			molecule{
170			name = "SPC";
171			nAtoms = 3;
172			atom[0]{
173			type = "O_SPC";
174			position( 0.0, 0.0, -0.06461 );
175			}
176			atom[1]{
177			type = "H_SPC";
178			position( 0.0, 0.81649, 0.51275 );
179			}
180			atom[2]{
181			type = "H_SPC";
182			position( 0.0, -0.81649, 0.51275 );
183			}
184			nRigidBodies = 1;
185			rigidBody[0]{
186			nMembers = 3;
187			members(0, 1, 2);
188			}
189
190			nCutoffGroups = 1;
191			cutoffGroup[0]{
192			nMembers = 3;
193			members(0, 1, 2);
194			}
195			}
196
197			molecule{
198			name = "DPD";
199			nAtoms = 1;
200			atom[0]{
201			type = "DPD";
202			position(0.0, 0.0, 0.0);
203			}
204			}
205
206			#endif