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root/OpenMD/branches/development/src/visitors/ReplacementVisitor.cpp
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trunk/src/visitors/ReplacementVisitor.cpp (file contents), Revision 1456 by gezelter, Fri Jun 25 17:40:24 2010 UTC vs.
branches/development/src/visitors/ReplacementVisitor.cpp (file contents), Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

# Line 35 | Line 35
35   *                                                                      
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).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
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   #include <cstring>
# Line 55 | Line 56 | namespace OpenMD {
56      myTypes_.clear();
57    }
58    
59 <  bool ReplacementVisitor::isReplacedAtom(const std::string& atomType) {
59 >  bool ReplacementVisitor::isReplacedAtom(const std::string &atomType) {
60      std::set<std::string>::iterator strIter;
61      strIter = myTypes_.find(atomType);
62      return strIter != myTypes_.end() ? true : false;
63    }
64  
65 <  void ReplacementVisitor::addSite(const std::string& name,
66 <                                   const Vector3d refPos) {
65 >  void ReplacementVisitor::addSite(const std::string &name,
66 >                                   const Vector3d &refPos) {
67      AtomInfo* atomInfo = new AtomInfo();
68      atomInfo->atomTypeName = name;
69      atomInfo->pos = refPos;
70      sites_->addAtomInfo(atomInfo);
71    }
72 <  void ReplacementVisitor::addSite(const std::string& name,
73 <                                   const Vector3d refPos,
74 <                                   const Vector3d refVec) {
72 >  void ReplacementVisitor::addSite(const std::string &name,
73 >                                   const Vector3d &refPos,
74 >                                   const Vector3d &refVec) {
75      AtomInfo* atomInfo = new AtomInfo();
76      atomInfo->atomTypeName = name;
77      atomInfo->pos = refPos;
# Line 80 | Line 81 | namespace OpenMD {
81    }
82    
83    void ReplacementVisitor::visit(DirectionalAtom *datom) {
83 –    std::vector<AtomInfo*>atoms;
84      
85      RotMat3x3d   A;
86      RotMat3x3d   Atrans;
# Line 120 | Line 120 | namespace OpenMD {
120          
121      pos = datom->getPos();
122      vel = datom->getVel();
123 <    frc = datom->getFrc();
124 <    trq = datom->getTrq();
123 >
124      j   = datom->getJ();
125      I   = datom->getI();
126      A   = datom->getA();
127 +
128      skewMat(0, 0) =  0;
129      skewMat(0, 1) =  j[2] / I(2, 2);
130      skewMat(0, 2) = -j[1] / I(1, 1);    
# Line 134 | Line 134 | namespace OpenMD {
134      skewMat(2, 0) =  j[1] / I(1, 1);
135      skewMat(2, 1) = -j[0] / I(0, 0);
136      skewMat(2, 2) =  0;
137 –
137      Mat3x3d mat = (A * skewMat).transpose();
138      
139      // We need A^T to convert from body-fixed to space-fixed:

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