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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 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 968 by tim, Tue May 23 18:46:11 2006 UTC

# Line 57 | Line 57
57   #include "selection/SelectionEvaluator.hpp"
58   #include "selection/SelectionManager.hpp"
59   #include "visitors/LipidTransVisitor.hpp"
60 + #include "visitors/AtomNameVisitor.hpp"
61  
62   using namespace oopse;
63  
# Line 99 | Line 100 | int main(int argc, char* argv[]){
100    
101    
102    
103 <  //creat visitor list
103 >  //create visitor list
104    CompositeVisitor* compositeVisitor = new CompositeVisitor();
105      
106 <  //creat RigidBody Visitor
106 >  //create RigidBody Visitor
107    if(args_info.rigidbody_flag){
108      RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
109      compositeVisitor->addVisitor(rbCOMVisitor, 900);
110    }
111    
112 <  //creat SSD atom visitor
112 >  //create SSD atom visitor
113    SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
114    compositeVisitor->addVisitor(ssdVisitor, 800);
115    
116    LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
117    compositeVisitor->addVisitor(linearVisitor, 750);
118 +  if (args_info.gb_given) {
119 +    linearVisitor->addGayBerneAtomType(args_info.gb_arg);
120 +  }
121    
122 <  //creat default atom visitor
122 >  GBLipidAtomVisitor* gbLipidVisitor = new GBLipidAtomVisitor(info);
123 >  compositeVisitor->addVisitor(gbLipidVisitor, 740);
124 >
125 >  //create default atom visitor
126    DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
127    compositeVisitor->addVisitor(defaultAtomVisitor, 700);
128    
129 <  //creat waterType visitor
129 >  //create waterType visitor
130    if(args_info.watertype_flag){
131      WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
132      compositeVisitor->addVisitor(waterTypeVisitor, 600);
133    }
134 +
135 +  if (args_info.basetype_flag) {
136 +      AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
137 +      compositeVisitor->addVisitor(atomNameVisitor, 550);
138 +
139 +  }
140    
141    //create ZconsVisitor
142    if(args_info.zconstraint_flag){
# Line 137 | Line 150 | int main(int argc, char* argv[]){
150      }
151    }
152    
153 <  //creat wrapping visitor
153 >  //create wrapping visitor
154    
155 <  if(args_info.periodicBox_flag){
156 <    WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
157 <    compositeVisitor->addVisitor(wrappingVisitor, 400);
158 <  }
155 >  //if(args_info.periodicBox_flag){
156 >  //  WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
157 >  //  compositeVisitor->addVisitor(wrappingVisitor, 400);
158 >  //}
159  
160 <  //creat replicate visitor
160 >  //create replicate visitor
161    if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
162      Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
163      ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
# Line 160 | Line 173 | int main(int argc, char* argv[]){
173      exit(1);
174    }
175      
176 <  //creat xyzVisitor
176 >  //create xyzVisitor
177    XYZVisitor* xyzVisitor;
178    if (args_info.selection_given) {
179      xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
# Line 171 | Line 184 | int main(int argc, char* argv[]){
184    
185    std::cout << compositeVisitor->toString();
186    
187 <  //creat prepareVisitor
187 >  //create prepareVisitor
188    PrepareVisitor* prepareVisitor = new PrepareVisitor();
189    
190    //open dump file
# Line 189 | Line 202 | int main(int argc, char* argv[]){
202    Molecule* mol;
203    StuntDouble* integrableObject;
204    RigidBody* rb;
205 +  Vector3d molCom;
206 +  Vector3d newMolCom;
207 +  Vector3d displacement;
208 +  Mat3x3d hmat;
209 +  Snapshot* currentSnapshot;
210        
211    for (int i = 0; i < nframes; i += args_info.frame_arg){
212      dumpReader->readFrame(i);
213 <    
213 >
214 >    //wrapping the molecule
215 >    if(args_info.periodicBox_flag) {
216 >      currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();    
217 >      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
218 >          molCom = mol->getCom();
219 >          newMolCom = molCom;
220 >          currentSnapshot->wrapVector(newMolCom);
221 >          displacement = newMolCom - molCom;
222 >        for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
223 >             integrableObject = mol->nextIntegrableObject(iiter)) {  
224 >          integrableObject->setPos(integrableObject->getPos() + displacement);
225 >        }
226 >      }    
227 >    }
228      //update atoms of rigidbody
229      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
230        

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