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root/group/trunk/OOPSE-4/src/applications/dump2Xyz/Dump2XYZ.cpp
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Comparing trunk/OOPSE-4/src/applications/dump2Xyz/Dump2XYZ.cpp (file contents):
Revision 2097 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 2984 by gezelter, Wed Aug 30 21:04:04 2006 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# 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 67 | Line 68 | int main(int argc, char* argv[]){
68    
69    gengetopt_args_info args_info;
70    std::string dumpFileName;
70 –  std::string mdFileName;
71    std::string xyzFileName;
72    
73    //parse the command line option
# Line 83 | Line 83 | int main(int argc, char* argv[]){
83      exit(1);
84    }
85    
86 –  mdFileName = dumpFileName;
87 –  mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
88 –
86    if (args_info.output_given){
87      xyzFileName = args_info.output_arg;
88    } else {
# Line 95 | 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 <  
98 <  
102 <  //creat visitor list
97 >
98 >  //create visitor list
99    CompositeVisitor* compositeVisitor = new CompositeVisitor();
100      
101 <  //creat RigidBody Visitor
101 >  //create RigidBody Visitor
102    if(args_info.rigidbody_flag){
103      RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
104      compositeVisitor->addVisitor(rbCOMVisitor, 900);
105    }
106    
107 <  //creat SSD atom visitor
107 >  //create SSD atom visitor
108    SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
109    compositeVisitor->addVisitor(ssdVisitor, 800);
110    
111    LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
112    compositeVisitor->addVisitor(linearVisitor, 750);
113 +  if (args_info.gb_given) {
114 +    linearVisitor->addGayBerneAtomType(args_info.gb_arg);
115 +  }
116    
117 <  //creat default atom visitor
117 >  GBLipidAtomVisitor* gbLipidVisitor = new GBLipidAtomVisitor(info);
118 >  compositeVisitor->addVisitor(gbLipidVisitor, 740);
119 >
120 >  //create default atom visitor
121    DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
122    compositeVisitor->addVisitor(defaultAtomVisitor, 700);
123    
124 <  //creat waterType visitor
124 >  //create waterType visitor
125    if(args_info.watertype_flag){
126      WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
127      compositeVisitor->addVisitor(waterTypeVisitor, 600);
128    }
129 +
130 +  if (args_info.basetype_flag) {
131 +      AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
132 +      compositeVisitor->addVisitor(atomNameVisitor, 550);
133 +
134 +  }
135    
136    //create ZconsVisitor
137    if(args_info.zconstraint_flag){
# Line 137 | Line 145 | int main(int argc, char* argv[]){
145      }
146    }
147    
148 <  //creat wrapping visitor
148 >  //create wrapping visitor
149    
150 <  if(args_info.periodicBox_flag){
151 <    WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
152 <    compositeVisitor->addVisitor(wrappingVisitor, 400);
153 <  }
150 >  //if(args_info.periodicBox_flag){
151 >  //  WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
152 >  //  compositeVisitor->addVisitor(wrappingVisitor, 400);
153 >  //}
154  
155 <  //creat replicate visitor
155 >  //create replicate visitor
156    if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
157      Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
158      ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
# Line 160 | Line 168 | int main(int argc, char* argv[]){
168      exit(1);
169    }
170      
171 <  //creat xyzVisitor
171 >  //create xyzVisitor
172    XYZVisitor* xyzVisitor;
173    if (args_info.selection_given) {
174      xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
# Line 171 | Line 179 | int main(int argc, char* argv[]){
179    
180    std::cout << compositeVisitor->toString();
181    
182 <  //creat prepareVisitor
182 >  //create prepareVisitor
183    PrepareVisitor* prepareVisitor = new PrepareVisitor();
184    
185    //open dump file
# Line 189 | Line 197 | int main(int argc, char* argv[]){
197    Molecule* mol;
198    StuntDouble* integrableObject;
199    RigidBody* rb;
200 +  Vector3d molCom;
201 +  Vector3d newMolCom;
202 +  Vector3d displacement;
203 +  Mat3x3d hmat;
204 +  Snapshot* currentSnapshot;
205        
206    for (int i = 0; i < nframes; i += args_info.frame_arg){
207      dumpReader->readFrame(i);
208 <    
208 >
209 >    //wrapping the molecule
210 >    if(args_info.periodicBox_flag) {
211 >      currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();    
212 >      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
213 >          molCom = mol->getCom();
214 >          newMolCom = molCom;
215 >          currentSnapshot->wrapVector(newMolCom);
216 >          displacement = newMolCom - molCom;
217 >        for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
218 >             integrableObject = mol->nextIntegrableObject(iiter)) {  
219 >          integrableObject->setPos(integrableObject->getPos() + displacement);
220 >        }
221 >      }    
222 >    }
223      //update atoms of rigidbody
224      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
225        
# Line 229 | Line 256 | int main(int argc, char* argv[]){
256    
257    xyzStream.close();
258    
259 <  
259 >  delete prepareVisitor;
260    delete compositeVisitor;
261    delete info;
262    

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