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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 2065 by tim, Tue Mar 1 14:45:45 2005 UTC vs.
Revision 2240 by tim, Thu May 26 22:45:00 2005 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 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();
104 –  
105 –  //creat ignore visitor
106 –  if(args_info.ignore_given ||args_info.water_flag){
105      
106 <    IgnoreVisitor* ignoreVisitor = new IgnoreVisitor(info);
109 <    
110 <    for(int i = 0; i < args_info.ignore_given; i++)
111 <      ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
112 <    
113 <    //ignore water
114 <    if(args_info.water_flag){
115 <      ignoreVisitor->addIgnoreType("SSD");
116 <      ignoreVisitor->addIgnoreType("SSD1");
117 <      ignoreVisitor->addIgnoreType("SSD_E");
118 <      ignoreVisitor->addIgnoreType("SSD_RF");
119 <      ignoreVisitor->addIgnoreType("TIP3P_RB_0");
120 <      ignoreVisitor->addIgnoreType("TIP4P_RB_0");
121 <      ignoreVisitor->addIgnoreType("TIP5P_RB_0");
122 <      ignoreVisitor->addIgnoreType("SPCE_RB_0");      
123 <      ignoreVisitor->addIgnoreType("DPD_RB_0");
124 <    }
125 <    
126 <    compositeVisitor->addVisitor(ignoreVisitor, 1000);
127 <  }
128 <  
129 <  //creat RigidBody Visitor
106 >  //create RigidBody Visitor
107    if(args_info.rigidbody_flag){
108      RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
109      compositeVisitor->addVisitor(rbCOMVisitor, 900);
133 –  }
134 –  
135 –  //create selection visitor
136 –  //if (args_info.selection_given){
137 –  //  SelectionVisitor* selectionVisitor = new SelectionVisitor(info, args_info.selection_arg);
138 –  //  compositeVisitor->addVisitor(selectionVisitor, 850);
139 –  //}
140 –
141 –  SelectionEvaluator* evaluator = NULL;
142 –  if (args_info.selection_given) {
143 –    evaluator = new SelectionEvaluator(info);
144 –    assert(evaluator);
145 –    evaluator->loadScriptString( args_info.selection_arg);
146 –          
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    
119 <  //creat default atom visitor
119 >  //create default atom visitor
120    DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
121    compositeVisitor->addVisitor(defaultAtomVisitor, 700);
122    
123 <  //creat waterType visitor
123 >  //create waterType visitor
124    if(args_info.watertype_flag){
125      WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
126      compositeVisitor->addVisitor(waterTypeVisitor, 600);
127    }
128 +
129 +  if (args_info.basetype_flag) {
130 +      AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
131 +      compositeVisitor->addVisitor(atomNameVisitor, 550);
132 +
133 +  }
134    
135    //create ZconsVisitor
136    if(args_info.zconstraint_flag){
# Line 175 | Line 144 | int main(int argc, char* argv[]){
144      }
145    }
146    
147 <  //creat wrapping visitor
147 >  //create wrapping visitor
148    
149    if(args_info.periodicBox_flag){
150      WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
151      compositeVisitor->addVisitor(wrappingVisitor, 400);
152    }
153  
154 <  //creat replicate visitor
154 >  //create replicate visitor
155    if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
156      Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
157      ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
# Line 198 | Line 167 | int main(int argc, char* argv[]){
167      exit(1);
168    }
169      
170 <  //creat xyzVisitor
171 <  XYZVisitor* xyzVisitor = new XYZVisitor(info);
170 >  //create xyzVisitor
171 >  XYZVisitor* xyzVisitor;
172 >  if (args_info.selection_given) {
173 >    xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
174 >  } else {
175 >    xyzVisitor = new XYZVisitor(info);
176 >  }
177    compositeVisitor->addVisitor(xyzVisitor, 200);
178    
179    std::cout << compositeVisitor->toString();
180    
181 <  //creat prepareVisitor
181 >  //create prepareVisitor
182    PrepareVisitor* prepareVisitor = new PrepareVisitor();
183    
184    //open dump file
# Line 222 | Line 196 | int main(int argc, char* argv[]){
196    Molecule* mol;
197    StuntDouble* integrableObject;
198    RigidBody* rb;
199 <
226 <  if (evaluator && !evaluator->isDynamic()) {
227 <    info->getSelectionManager()->setSelectionSet(evaluator->evaluate());
228 <  }
229 <  
199 >      
200    for (int i = 0; i < nframes; i += args_info.frame_arg){
201      dumpReader->readFrame(i);
202      
# Line 250 | Line 220 | int main(int argc, char* argv[]){
220      //update visitor
221      compositeVisitor->update();
222  
223 <    //if dynamic, we need to re-evaluate the selection
254 <    if (evaluator && evaluator->isDynamic()) {
255 <      info->getSelectionManager()->setSelectionSet(evaluator->evaluate());
256 <    }
257 <    
223 >
224      //visit stuntdouble
225      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
226        for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
# Line 270 | Line 236 | int main(int argc, char* argv[]){
236    
237    xyzStream.close();
238    
239 <  
239 >  delete prepareVisitor;
240    delete compositeVisitor;
241    delete info;
242    

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