ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/applications/dump2Xyz/Dump2XYZ.cpp
(Generate patch)

Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (file contents):
Revision 968 by tim, Tue May 23 18:46:11 2006 UTC vs.
Revision 1283 by gezelter, Wed Jul 30 18:48:01 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 121 | Line 116 | int main(int argc, char* argv[]){
116    
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);
# Line 175 | Line 176 | int main(int argc, char* argv[]){
176      
177    //create xyzVisitor
178    XYZVisitor* xyzVisitor;
179 +
180    if (args_info.selection_given) {
181      xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
182    } else {
183      xyzVisitor = new XYZVisitor(info);
184    }
185 +
186 +  if(args_info.printPosOnly_flag){
187 +    bool posOnly = true;
188 +    xyzVisitor->setPosOnly(posOnly);
189 +  }
190 +
191    compositeVisitor->addVisitor(xyzVisitor, 200);
192    
193    std::cout << compositeVisitor->toString();
# Line 192 | Line 200 | int main(int argc, char* argv[]){
200    int nframes = dumpReader->getNFrames();
201    
202    
203 <  std::ofstream xyzStream;    
196 <  xyzStream .open(xyzFileName.c_str());
203 >  std::ofstream xyzStream(xyzFileName.c_str());
204    
198 –  
205    SimInfo::MoleculeIterator miter;
206    Molecule::IntegrableObjectIterator  iiter;
207    Molecule::RigidBodyIterator rbIter;
# Line 258 | Line 264 | int main(int argc, char* argv[]){
264      xyzVisitor->clear();
265      
266    }//end for (int i = 0; i < nframes; i += args_info.frame_arg)
267 <  
267 >
268    xyzStream.close();
263 –  
269    delete prepareVisitor;
270    delete compositeVisitor;
271    delete info;
267 –  
272   }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines