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Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (file contents):
Revision 1474 by gezelter, Wed Jul 21 14:29:14 2010 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 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 <iostream>
# Line 63 | Line 64 | using namespace OpenMD;
64  
65   using namespace OpenMD;
66  
67 + using namespace std;
68   int main(int argc, char* argv[]){
69    
68 –  //register force fields
69 –  registerForceFields();
70 –  
70    gengetopt_args_info args_info;
71 <  std::string dumpFileName;
72 <  std::string xyzFileName;
73 <  bool printVel;
74 <  bool printFrc;
75 <  bool printVec;
76 <  bool printChrg;
71 >  string dumpFileName;
72 >  string xyzFileName;
73 >
74 >  bool printVel(false);
75 >  bool printFrc(false);
76 >  bool printVec(false);
77 >  bool printChrg(false);
78 >  bool printField(false);
79    
80    //parse the command line option
81    if (cmdline_parser (argc, argv, &args_info) != 0) {
# Line 85 | Line 86 | int main(int argc, char* argv[]){
86    if (args_info.input_given){
87      dumpFileName = args_info.input_arg;
88    } else {
89 <    std::cerr << "Does not have input file name" << std::endl;
89 >    cerr << "Does not have input file name" << endl;
90      exit(1);
91    }
92    
# Line 138 | Line 139 | int main(int argc, char* argv[]){
139    if (args_info.basetype_flag) {
140      AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
141      compositeVisitor->addVisitor(atomNameVisitor, 550);    
142 <    std::cout << compositeVisitor->toString();
142 >    cout << compositeVisitor->toString();
143    }
144    
145    //create ZconsVisitor
# Line 163 | Line 164 | int main(int argc, char* argv[]){
164    //create replicate visitor
165    if(args_info.repeatX_given > 0 ||
166       args_info.repeatY_given > 0 ||
167 <     args_info.repeatY_given > 0) {
167 >     args_info.repeatZ_given > 0) {
168      Vector3i replicateOpt(args_info.repeatX_arg,
169                            args_info.repeatY_arg,
170                            args_info.repeatZ_arg);
# Line 180 | Line 181 | int main(int argc, char* argv[]){
181                                                         args_info.refsele_arg),
182                                   250);
183    } else if (args_info.refsele_given || args_info.originsele_given) {
184 <    std::cerr << "Both of --refsele and --originsele should appear by pair"
185 <              << std::endl;
184 >    cerr << "Both of --refsele and --originsele should appear by pair"
185 >         << endl;
186      exit(1);
187    }
188    
# Line 210 | Line 211 | int main(int argc, char* argv[]){
211      printChrg = true;
212      xyzVisitor->doCharges(printChrg);
213    }
214 +  if(args_info.efield_flag){
215 +    printField = true;
216 +    xyzVisitor->doElectricFields(printField);
217 +  }
218    
219    compositeVisitor->addVisitor(xyzVisitor, 200);
220    
# Line 220 | Line 225 | int main(int argc, char* argv[]){
225    DumpReader* dumpReader = new DumpReader(info, dumpFileName);
226    int nframes = dumpReader->getNFrames();
227    
228 <  std::ofstream xyzStream(xyzFileName.c_str());
228 >  ofstream xyzStream(xyzFileName.c_str());
229    
230    SimInfo::MoleculeIterator miter;
231    Molecule::IntegrableObjectIterator  iiter;
232    Molecule::RigidBodyIterator rbIter;
233    Molecule* mol;
234 <  StuntDouble* integrableObject;
234 >  StuntDouble* sd;
235    RigidBody* rb;
236    Vector3d molCom;
237    Vector3d newMolCom;
# Line 244 | Line 249 | int main(int argc, char* argv[]){
249        currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();    
250        for (mol = info->beginMolecule(miter); mol != NULL;
251             mol = info->nextMolecule(miter)) {
252 <          molCom = mol->getCom();
253 <          newMolCom = molCom;
254 <          currentSnapshot->wrapVector(newMolCom);
255 <          displacement = newMolCom - molCom;
256 <        for (integrableObject = mol->beginIntegrableObject(iiter);
257 <             integrableObject != NULL;
258 <             integrableObject = mol->nextIntegrableObject(iiter)) {  
259 <          integrableObject->setPos(integrableObject->getPos() + displacement);
252 >        
253 >        molCom = mol->getCom();
254 >        newMolCom = molCom;
255 >        currentSnapshot->wrapVector(newMolCom);
256 >        displacement = newMolCom - molCom;
257 >
258 >        for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
259 >             sd = mol->nextIntegrableObject(iiter)) {  
260 >
261 >          sd->setPos(sd->getPos() + displacement);
262 >          
263          }
264        }    
265      }
266 +
267      //update atoms of rigidbody
268      for (mol = info->beginMolecule(miter); mol != NULL;
269           mol = info->nextMolecule(miter)) {
# Line 262 | Line 271 | int main(int argc, char* argv[]){
271        //change the positions of atoms which belong to the rigidbodies
272        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
273             rb = mol->nextRigidBody(rbIter)) {
274 +
275          rb->updateAtoms();
276          if (printVel) rb->updateAtomVel();
277 +
278        }
279      }
280      
281      //prepare visit
282      for (mol = info->beginMolecule(miter); mol != NULL;
283           mol = info->nextMolecule(miter)) {
284 <      for (integrableObject = mol->beginIntegrableObject(iiter);
285 <           integrableObject != NULL;
286 <           integrableObject = mol->nextIntegrableObject(iiter)) {
287 <        integrableObject->accept(prepareVisitor);
284 >
285 >      for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
286 >           sd = mol->nextIntegrableObject(iiter)) {
287 >
288 >        sd->accept(prepareVisitor);
289 >
290        }
291      }
292      
# Line 284 | Line 297 | int main(int argc, char* argv[]){
297      //visit stuntdouble
298      for (mol = info->beginMolecule(miter); mol != NULL;
299           mol = info->nextMolecule(miter)) {
300 <      for (integrableObject = mol->beginIntegrableObject(iiter);
301 <           integrableObject != NULL;
302 <           integrableObject = mol->nextIntegrableObject(iiter)) {
303 <        integrableObject->accept(compositeVisitor);
300 >
301 >      for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
302 >           sd = mol->nextIntegrableObject(iiter)) {
303 >
304 >        sd->accept(compositeVisitor);
305 >
306        }
307      }
308      

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