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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 1455 by gezelter, Thu Jun 24 20:44:18 2010 UTC vs.
Revision 1474 by gezelter, Wed Jul 21 14:29:14 2010 UTC

# Line 47 | Line 47
47   #include "brains/Register.hpp"
48   #include "brains/SimCreator.hpp"
49   #include "brains/SimInfo.hpp"
50 + #include "brains/ForceManager.hpp"
51   #include "io/DumpReader.hpp"
52   #include "utils/simError.h"
53   #include "visitors/AtomVisitor.hpp"
# Line 70 | Line 71 | int main(int argc, char* argv[]){
71    gengetopt_args_info args_info;
72    std::string dumpFileName;
73    std::string xyzFileName;
74 +  bool printVel;
75 +  bool printFrc;
76 +  bool printVec;
77 +  bool printChrg;
78    
79    //parse the command line option
80    if (cmdline_parser (argc, argv, &args_info) != 0) {
# Line 94 | Line 99 | int main(int argc, char* argv[]){
99    //parse md file and set up the system
100    SimCreator creator;
101    SimInfo* info = creator.createSim(dumpFileName, false);
102 +  ForceManager* forceMan = new ForceManager(info);
103    
104    //create visitor list
105    CompositeVisitor* compositeVisitor = new CompositeVisitor();
# Line 107 | Line 113 | int main(int argc, char* argv[]){
113    //create SSD atom visitor
114    SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
115    compositeVisitor->addVisitor(ssdVisitor, 800);
116 +
117 +  //create GBtail atom visitor
118 +  GBtailVisitor* gbtVisitor = new GBtailVisitor(info);
119 +  compositeVisitor->addVisitor(gbtVisitor, 790);
120 +
121 +  //create GBhead atom visitor
122 +  GBheadVisitor* gbhVisitor = new GBheadVisitor(info);
123 +  compositeVisitor->addVisitor(gbhVisitor, 789);
124    
125    //create default atom visitor
126    DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
# Line 147 | Line 161 | int main(int argc, char* argv[]){
161    //}
162  
163    //create replicate visitor
164 <  if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
165 <    Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
166 <    ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
164 >  if(args_info.repeatX_given > 0 ||
165 >     args_info.repeatY_given > 0 ||
166 >     args_info.repeatY_given > 0) {
167 >    Vector3i replicateOpt(args_info.repeatX_arg,
168 >                          args_info.repeatY_arg,
169 >                          args_info.repeatZ_arg);
170 >    ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info,
171 >                                                              replicateOpt);
172      compositeVisitor->addVisitor(replicateVisitor, 300);
173    }
174  
175  
176    //create rotation visitor
177    if (args_info.refsele_given&& args_info.originsele_given) {
178 <    compositeVisitor->addVisitor(new LipidTransVisitor(info, args_info.originsele_arg, args_info.refsele_arg), 250);
178 >    compositeVisitor->addVisitor(new LipidTransVisitor(info,
179 >                                                       args_info.originsele_arg,
180 >                                                       args_info.refsele_arg),
181 >                                 250);
182    } else if (args_info.refsele_given || args_info.originsele_given) {
183 <    std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
183 >    std::cerr << "Both of --refsele and --originsele should appear by pair"
184 >              << std::endl;
185      exit(1);
186    }
187 <    
187 >  
188    //create xyzVisitor
189    XYZVisitor* xyzVisitor;
190  
# Line 171 | Line 194 | int main(int argc, char* argv[]){
194      xyzVisitor = new XYZVisitor(info);
195    }
196  
197 <  if(args_info.printPosOnly_flag){
198 <    bool posOnly = true;
199 <    xyzVisitor->setPosOnly(posOnly);
197 >  if(args_info.velocities_flag){
198 >    printVel = true;
199 >    xyzVisitor->doVelocities(printVel);
200    }
201 <
201 >  if(args_info.forces_flag){
202 >    printFrc = true;
203 >    xyzVisitor->doForces(printFrc);
204 >  }
205 >  if(args_info.vectors_flag){
206 >    printVec = true;
207 >    xyzVisitor->doVectors(printVec);
208 >  }
209 >  if(args_info.charges_flag){
210 >    printChrg = true;
211 >    xyzVisitor->doCharges(printChrg);
212 >  }
213 >  
214    compositeVisitor->addVisitor(xyzVisitor, 200);
215    
216    //create prepareVisitor
# Line 185 | Line 220 | int main(int argc, char* argv[]){
220    DumpReader* dumpReader = new DumpReader(info, dumpFileName);
221    int nframes = dumpReader->getNFrames();
222    
188 –  
223    std::ofstream xyzStream(xyzFileName.c_str());
224    
225    SimInfo::MoleculeIterator miter;
# Line 202 | Line 236 | int main(int argc, char* argv[]){
236        
237    for (int i = 0; i < nframes; i += args_info.frame_arg){
238      dumpReader->readFrame(i);
239 <
239 >    
240 >    if (printFrc) forceMan->calcForces();
241 >    
242      //wrapping the molecule
243      if(args_info.periodicBox_flag) {
244        currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();    
245 <      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
245 >      for (mol = info->beginMolecule(miter); mol != NULL;
246 >           mol = info->nextMolecule(miter)) {
247            molCom = mol->getCom();
248            newMolCom = molCom;
249            currentSnapshot->wrapVector(newMolCom);
250            displacement = newMolCom - molCom;
251 <        for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
251 >        for (integrableObject = mol->beginIntegrableObject(iiter);
252 >             integrableObject != NULL;
253               integrableObject = mol->nextIntegrableObject(iiter)) {  
254            integrableObject->setPos(integrableObject->getPos() + displacement);
255          }
256        }    
257      }
258      //update atoms of rigidbody
259 <    for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
259 >    for (mol = info->beginMolecule(miter); mol != NULL;
260 >         mol = info->nextMolecule(miter)) {
261        
262        //change the positions of atoms which belong to the rigidbodies
263 <      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
263 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
264 >           rb = mol->nextRigidBody(rbIter)) {
265          rb->updateAtoms();
266 +        if (printVel) rb->updateAtomVel();
267        }
268      }
269      
270      //prepare visit
271 <    for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
272 <      for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
271 >    for (mol = info->beginMolecule(miter); mol != NULL;
272 >         mol = info->nextMolecule(miter)) {
273 >      for (integrableObject = mol->beginIntegrableObject(iiter);
274 >           integrableObject != NULL;
275             integrableObject = mol->nextIntegrableObject(iiter)) {
276          integrableObject->accept(prepareVisitor);
277        }
# Line 239 | Line 282 | int main(int argc, char* argv[]){
282  
283  
284      //visit stuntdouble
285 <    for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
286 <      for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
285 >    for (mol = info->beginMolecule(miter); mol != NULL;
286 >         mol = info->nextMolecule(miter)) {
287 >      for (integrableObject = mol->beginIntegrableObject(iiter);
288 >           integrableObject != NULL;
289             integrableObject = mol->nextIntegrableObject(iiter)) {
290          integrableObject->accept(compositeVisitor);
291        }

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