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root/group/trunk/OOPSE/libmdtools/AtomVisitor.cpp
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Comparing trunk/OOPSE/libmdtools/AtomVisitor.cpp (file contents):
Revision 1126 by tim, Tue Apr 20 05:39:38 2004 UTC vs.
Revision 1252 by gezelter, Mon Jun 7 14:26:33 2004 UTC

# Line 44 | Line 44 | void SSDAtomVisitor::visit(DirectionalAtom* datom){
44    double ox[3] = {0.0, 0.0, -0.0654};
45    double u[3] = {0, 0, 1};
46    double rotMatrix[3][3];
47 +  double rotTrans[3][3];
48    AtomInfo* atomInfo;
49    double pos[3];
49 –  double vel[3];
50    double newVec[3];
51    double q[4];
52    AtomData* atomData;
# Line 78 | Line 78 | void SSDAtomVisitor::visit(DirectionalAtom* datom){
78    datom->getPos(pos);
79    datom->getQ(q);
80    datom->getA(rotMatrix);
81 +
82 +  // We need A^T to convert from body-fixed to space-fixed:
83 +  transposeMat3(rotMatrix, rotTrans);
84    
85    //center of mass of the water molecule
86 <  matVecMul3(rotMatrix, u, newVec);
86 >  matVecMul3(rotTrans, u, newVec);
87    atomInfo = new AtomInfo;
88    atomInfo->AtomType = "X";
89    atomInfo->pos[0] = pos[0];
# Line 93 | Line 96 | void SSDAtomVisitor::visit(DirectionalAtom* datom){
96    atomData->addAtomInfo(atomInfo);
97  
98    //oxygen
99 <  matVecMul3(rotMatrix, ox, newVec);
99 >  matVecMul3(rotTrans, ox, newVec);
100    atomInfo = new AtomInfo;
101    atomInfo->AtomType = "O";
102    atomInfo->pos[0] = pos[0] + newVec[0];
# Line 106 | Line 109 | void SSDAtomVisitor::visit(DirectionalAtom* datom){
109  
110  
111    //hydrogen1
112 <    matVecMul3(rotMatrix, h1, newVec);
112 >    matVecMul3(rotTrans, h1, newVec);
113    atomInfo = new AtomInfo;
114    atomInfo->AtomType = "H";
115    atomInfo->pos[0] = pos[0] + newVec[0];
# Line 118 | Line 121 | void SSDAtomVisitor::visit(DirectionalAtom* datom){
121    atomData->addAtomInfo(atomInfo);
122  
123    //hydrogen2
124 <  matVecMul3(rotMatrix, h2, newVec);
124 >  matVecMul3(rotTrans, h2, newVec);
125    atomInfo = new AtomInfo;
126    atomInfo->AtomType = "H";
127    atomInfo->pos[0] = pos[0] + newVec[0];
# Line 150 | Line 153 | const string SSDAtomVisitor::toString(){
153    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
154    result += buffer;
155  
156 <  sprintf(buffer , "Visitor Description: Convert SSD into 4 differnet atoms\n");
156 >  sprintf(buffer , "Visitor Description: Convert SSD into 4 different atoms\n");
157    result += buffer;
158  
159    sprintf(buffer ,"------------------------------------------------------------------\n");

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