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root/OpenMD/trunk/src/applications/dump2Xyz/Dump2XYZ.cpp
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Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (file contents):
Revision 954 by tim, Wed May 10 01:44:48 2006 UTC vs.
Revision 1303 by cli2, Mon Oct 13 21:35:22 2008 UTC

# Line 68 | Line 68 | int main(int argc, char* argv[]){
68    
69    gengetopt_args_info args_info;
70    std::string dumpFileName;
71 –  std::string mdFileName;
71    std::string xyzFileName;
72    
73    //parse the command line option
# Line 84 | Line 83 | int main(int argc, char* argv[]){
83      exit(1);
84    }
85    
87 –  mdFileName = dumpFileName;
88 –  mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
89 –
86    if (args_info.output_given){
87      xyzFileName = args_info.output_arg;
88    } else {
# Line 96 | Line 92 | int main(int argc, char* argv[]){
92    
93    //parse md file and set up the system
94    SimCreator creator;
95 <  SimInfo* info = creator.createSim(mdFileName, false);
95 >  SimInfo* info = creator.createSim(dumpFileName, false);
96    
97 <  
102 <  
97 >
98    //create visitor list
99    CompositeVisitor* compositeVisitor = new CompositeVisitor();
100      
# Line 122 | Line 117 | int main(int argc, char* argv[]){
117    GBLipidAtomVisitor* gbLipidVisitor = new GBLipidAtomVisitor(info);
118    compositeVisitor->addVisitor(gbLipidVisitor, 740);
119  
120 +  Ring5gbAtomVisitor* ring5Visitor = new Ring5gbAtomVisitor(info);
121 +  compositeVisitor->addVisitor(ring5Visitor, 730);
122 +
123 +  HeadAtomVisitor* headVisitor = new HeadAtomVisitor(info);
124 +  compositeVisitor->addVisitor(headVisitor, 720);
125 +
126    //create default atom visitor
127    DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
128    compositeVisitor->addVisitor(defaultAtomVisitor, 700);
129    
130 <  //create waterType visitor
131 <  if(args_info.watertype_flag){
132 <    WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
133 <    compositeVisitor->addVisitor(waterTypeVisitor, 600);
130 >  // if we gave the -w option, we want to skip the waters:
131 >  std::cerr << "-w flag was set to:" << args_info.water_given << "\n";
132 >  if (!args_info.water_given) {
133 >    //create waterType visitor
134 >    if(args_info.watertype_flag){
135 >      WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
136 >      compositeVisitor->addVisitor(waterTypeVisitor, 600);
137 >    }
138    }
139  
140    if (args_info.basetype_flag) {
# Line 152 | Line 157 | int main(int argc, char* argv[]){
157    
158    //create wrapping visitor
159    
160 <  if(args_info.periodicBox_flag){
161 <    WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
162 <    compositeVisitor->addVisitor(wrappingVisitor, 400);
163 <  }
160 >  //if(args_info.periodicBox_flag){
161 >  //  WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
162 >  //  compositeVisitor->addVisitor(wrappingVisitor, 400);
163 >  //}
164  
165    //create replicate visitor
166    if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
# Line 175 | Line 180 | int main(int argc, char* argv[]){
180      
181    //create xyzVisitor
182    XYZVisitor* xyzVisitor;
183 +
184    if (args_info.selection_given) {
185      xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
186    } else {
187      xyzVisitor = new XYZVisitor(info);
188    }
189 +
190 +  if(args_info.printPosOnly_flag){
191 +    bool posOnly = true;
192 +    xyzVisitor->setPosOnly(posOnly);
193 +  }
194 +
195    compositeVisitor->addVisitor(xyzVisitor, 200);
196    
197    std::cout << compositeVisitor->toString();
# Line 192 | Line 204 | int main(int argc, char* argv[]){
204    int nframes = dumpReader->getNFrames();
205    
206    
207 <  std::ofstream xyzStream;    
196 <  xyzStream .open(xyzFileName.c_str());
207 >  std::ofstream xyzStream(xyzFileName.c_str());
208    
198 –  
209    SimInfo::MoleculeIterator miter;
210    Molecule::IntegrableObjectIterator  iiter;
211    Molecule::RigidBodyIterator rbIter;
212    Molecule* mol;
213    StuntDouble* integrableObject;
214    RigidBody* rb;
215 +  Vector3d molCom;
216 +  Vector3d newMolCom;
217 +  Vector3d displacement;
218 +  Mat3x3d hmat;
219 +  Snapshot* currentSnapshot;
220        
221    for (int i = 0; i < nframes; i += args_info.frame_arg){
222      dumpReader->readFrame(i);
223 <    
223 >
224 >    //wrapping the molecule
225 >    if(args_info.periodicBox_flag) {
226 >      currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();    
227 >      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
228 >          molCom = mol->getCom();
229 >          newMolCom = molCom;
230 >          currentSnapshot->wrapVector(newMolCom);
231 >          displacement = newMolCom - molCom;
232 >        for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
233 >             integrableObject = mol->nextIntegrableObject(iiter)) {  
234 >          integrableObject->setPos(integrableObject->getPos() + displacement);
235 >        }
236 >      }    
237 >    }
238      //update atoms of rigidbody
239      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
240        
# Line 239 | Line 268 | int main(int argc, char* argv[]){
268      xyzVisitor->clear();
269      
270    }//end for (int i = 0; i < nframes; i += args_info.frame_arg)
271 <  
271 >
272    xyzStream.close();
244 –  
273    delete prepareVisitor;
274    delete compositeVisitor;
275    delete info;
248 –  
276   }

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