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Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 UTC vs.
Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #ifndef VISITORS_REPLACEMENTVISITOR_HPP
# Line 82 | Line 83 | namespace OpenMD {
83    public:
84      SSDAtomVisitor(SimInfo* info) : ReplacementVisitor(info) {
85        visitorName = "SSDAtomVisitor";
86 <
86 >      
87        /// these are the atom names we can replace with a fixed structure
88        addReplacedAtomName("SSD");
89        addReplacedAtomName("SSD_E");
# Line 90 | Line 91 | namespace OpenMD {
91        addReplacedAtomName("SSD1");
92        addReplacedAtomName("TAP");
93        addReplacedAtomName("TRED");
94 <
94 >      
95        // this is the reference structure we'll use for the replacement:
96        addSite("H", Vector3d(0.0, -0.75695, 0.5206));
97        addSite("H", Vector3d(0.0,  0.75695, 0.5206));
# Line 98 | Line 99 | namespace OpenMD {
99        addSite("X", Vector3d(0.0,  0.0,     0.0   ), Vector3d(0,0,1));
100      }
101    };
102 <
102 >  
103    class GBtailVisitor : public ReplacementVisitor{
104    public:
105      GBtailVisitor(SimInfo* info) : ReplacementVisitor(info) {
# Line 106 | Line 107 | namespace OpenMD {
107        
108        
109        /// these are the atom names we can replace with a fixed structure
110 <        addReplacedAtomName("GBtail");
111 <        
112 <        // this is the reference structure we'll use for the replacement:
113 <        addSite("C", Vector3d(0.0, 0.0, 9.0));
114 <        addSite("C", Vector3d(0.0, 0.0, 0.0));
115 <        addSite("C", Vector3d(0.0, 0.0, -9.0));
110 >      addReplacedAtomName("GBtail");
111 >      
112 >      // this is the reference structure we'll use for the replacement:
113 >      addSite("C", Vector3d(0.0, 0.0, 9.0));
114 >      addSite("C", Vector3d(0.0, 0.0, 0.0));
115 >      addSite("C", Vector3d(0.0, 0.0, -9.0));
116      }
117    };  
118    
# Line 121 | Line 122 | namespace OpenMD {
122        visitorName = "GBheadVisitor";
123        
124        /// these are the atom names we can replace with a fixed structure
125 <        addReplacedAtomName("GBhead");
126 <        
127 <        // this is the reference structure we'll use for the replacement:
128 <        addSite("N", Vector3d(0.0, 0.0, 3.5));
129 <        addSite("C", Vector3d(0.0, 0.0, 0.0));
130 <        addSite("P", Vector3d(0.0, 0.0, -3.5));
125 >      addReplacedAtomName("GBhead");
126 >      
127 >      // this is the reference structure we'll use for the replacement:
128 >      addSite("N", Vector3d(0.0, 0.0, 3.5));
129 >      addSite("C", Vector3d(0.0, 0.0, 0.0));
130 >      addSite("P", Vector3d(0.0, 0.0, -3.5));
131      }
132 <  };  
132 <
133 <  
132 >  };      
133   }//namespace OpenMD
134   #endif

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