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root/group/trunk/OOPSE/libmdtools/AtomVisitor.cpp
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Comparing trunk/OOPSE/libmdtools/AtomVisitor.cpp (file contents):
Revision 1118 by tim, Mon Apr 19 03:52:27 2004 UTC vs.
Revision 1129 by tim, Thu Apr 22 03:29:30 2004 UTC

# Line 2 | Line 2
2   #include "AtomVisitor.hpp"
3   #include "DirectionalAtom.hpp"
4   #include "MatVec3.h"
5 + #include "RigidBody.hpp"
6  
7 + void BaseAtomVisitor::visit(RigidBody* rb){
8 +  //vector<Atom*> myAtoms;
9 +  //vector<Atom*>::iterator atomIter;
10 +
11 +  //myAtoms = rb->getAtoms();
12 +  
13 +  //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
14 +  //  (*atomIter)->accept(this);
15 + }
16 +
17   void BaseAtomVisitor::setVisited(Atom* atom){
18    GenericData* data;
19    data = atom->getProperty("VISITED");
# Line 33 | 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];
50    double vel[3];
# Line 43 | Line 55 | void SSDAtomVisitor::visit(DirectionalAtom* datom){
55    bool haveAtomData;
56    
57    //if atom is not SSD atom, just skip it
58 <  if(!strcmp(datom->getType(), "SSD"))
58 >  if(strcmp(datom->getType(), "SSD"))
59      return;
60  
61    data = datom->getProperty("ATOMDATA");
# Line 67 | Line 79 | void SSDAtomVisitor::visit(DirectionalAtom* datom){
79    datom->getPos(pos);
80    datom->getQ(q);
81    datom->getA(rotMatrix);
82 +
83 +  // We need A^T to convert from body-fixed to space-fixed:
84 +  transposeMat3(rotMatrix, rotTrans);
85    
86    //center of mass of the water molecule
87 <  matVecMul3(rotMatrix, u, newVec);
87 >  matVecMul3(rotTrans, u, newVec);
88    atomInfo = new AtomInfo;
89    atomInfo->AtomType = "X";
90    atomInfo->pos[0] = pos[0];
# Line 82 | Line 97 | void SSDAtomVisitor::visit(DirectionalAtom* datom){
97    atomData->addAtomInfo(atomInfo);
98  
99    //oxygen
100 <  matVecMul3(rotMatrix, ox, newVec);
100 >  matVecMul3(rotTrans, ox, newVec);
101    atomInfo = new AtomInfo;
102    atomInfo->AtomType = "O";
103    atomInfo->pos[0] = pos[0] + newVec[0];
# Line 95 | Line 110 | void SSDAtomVisitor::visit(DirectionalAtom* datom){
110  
111  
112    //hydrogen1
113 <    matVecMul3(rotMatrix, h1, newVec);
113 >    matVecMul3(rotTrans, h1, newVec);
114    atomInfo = new AtomInfo;
115    atomInfo->AtomType = "H";
116    atomInfo->pos[0] = pos[0] + newVec[0];
# Line 107 | Line 122 | void SSDAtomVisitor::visit(DirectionalAtom* datom){
122    atomData->addAtomInfo(atomInfo);
123  
124    //hydrogen2
125 <  matVecMul3(rotMatrix, h2, newVec);
125 >  matVecMul3(rotTrans, h2, newVec);
126    atomInfo = new AtomInfo;
127    atomInfo->AtomType = "H";
128    atomInfo->pos[0] = pos[0] + newVec[0];
# Line 129 | Line 144 | void DefaultAtomVisitor::visit(Atom* atom){
144  
145   }
146  
147 + const string SSDAtomVisitor::toString(){
148 +  char buffer[65535];
149 +  string result;
150 +  
151 +  sprintf(buffer ,"------------------------------------------------------------------\n");
152 +  result += buffer;
153 +
154 +  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
155 +  result += buffer;
156 +
157 +  sprintf(buffer , "Visitor Description: Convert SSD into 4 differnet atoms\n");
158 +  result += buffer;
159 +
160 +  sprintf(buffer ,"------------------------------------------------------------------\n");
161 +  result += buffer;
162 +
163 +  return result;
164 + }
165 +
166 + //----------------------------------------------------------------------------//
167 +
168   void DefaultAtomVisitor::visit(Atom* atom){
169    AtomData* atomData;
170    AtomInfo* atomInfo;
# Line 138 | Line 174 | void DefaultAtomVisitor::visit(Atom* atom){
174      return;
175  
176   atomInfo =new AtomInfo;
177 +
178 +  atomData = new AtomData;
179 +  atomData->setID("ATOMDATA");
180  
181    atom->getPos(pos);
182    atomInfo->AtomType = atom->getType();
# Line 148 | Line 187 | void DefaultAtomVisitor::visit(Atom* atom){
187    atomInfo->dipole[1] = 0.0;
188    atomInfo->dipole[2] = 0.0;
189  
190 <  atomData = new AtomData;
191 <  atomData->setID("ATOMDATA");
190 >
191 >  atomData->addAtomInfo(atomInfo);
192 >  
193    atom->addProperty(atomData);
194  
195    setVisited(atom);
# Line 166 | Line 206 | void DefaultAtomVisitor::visit(DirectionalAtom* datom)
206    datom->getPos(pos);
207    datom->getU(u);
208  
209 +  atomData = new AtomData;
210 +  atomData->setID("ATOMDATA");
211    atomInfo =new AtomInfo;
212    
213    atomInfo->AtomType = datom->getType();
# Line 176 | Line 218 | void DefaultAtomVisitor::visit(DirectionalAtom* datom)
218    atomInfo->dipole[1] = u[1];
219    atomInfo->dipole[2] = u[2];  
220  
221 <  atomData = new AtomData;
222 <  atomData->setID("ATOMDATA");
221 >  atomData->addAtomInfo(atomInfo);
222 >
223    datom->addProperty(atomData);
224  
225    setVisited(datom);
226   }
227 <    
227 >
228 >
229 > const string DefaultAtomVisitor::toString(){
230 >  char buffer[65535];
231 >  string result;
232 >  
233 >  sprintf(buffer ,"------------------------------------------------------------------\n");
234 >  result += buffer;
235 >
236 >  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
237 >  result += buffer;
238 >
239 >  sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n");
240 >  result += buffer;
241 >
242 >  sprintf(buffer ,"------------------------------------------------------------------\n");
243 >  result += buffer;
244 >
245 >  return result;
246 > }    

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