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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 2749 by tim, Wed May 10 01:44:48 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 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);
110    }
111    
112 <  //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 <          
147 <  }
148 <  
149 <  //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 175 | 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    }
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 198 | Line 173 | int main(int argc, char* argv[]){
173      exit(1);
174    }
175      
176 <  //creat xyzVisitor
177 <  XYZVisitor* xyzVisitor = new XYZVisitor(info);
176 >  //create xyzVisitor
177 >  XYZVisitor* xyzVisitor;
178 >  if (args_info.selection_given) {
179 >    xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
180 >  } else {
181 >    xyzVisitor = new XYZVisitor(info);
182 >  }
183    compositeVisitor->addVisitor(xyzVisitor, 200);
184    
185    std::cout << compositeVisitor->toString();
186    
187 <  //creat prepareVisitor
187 >  //create prepareVisitor
188    PrepareVisitor* prepareVisitor = new PrepareVisitor();
189    
190    //open dump file
# Line 222 | Line 202 | int main(int argc, char* argv[]){
202    Molecule* mol;
203    StuntDouble* integrableObject;
204    RigidBody* rb;
205 <
226 <  if (evaluator && !evaluator->isDynamic()) {
227 <    info->getSelectionManager()->setSelectionSet(evaluator->evaluate());
228 <  }
229 <  
205 >      
206    for (int i = 0; i < nframes; i += args_info.frame_arg){
207      dumpReader->readFrame(i);
208      
# Line 250 | Line 226 | int main(int argc, char* argv[]){
226      //update visitor
227      compositeVisitor->update();
228  
229 <    //if dynamic, we need to re-evaluate the selection
254 <    if (evaluator && evaluator->isDynamic()) {
255 <      info->getSelectionManager()->setSelectionSet(evaluator->evaluate());
256 <    }
257 <    
229 >
230      //visit stuntdouble
231      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
232        for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
# Line 270 | Line 242 | int main(int argc, char* argv[]){
242    
243    xyzStream.close();
244    
245 <  
245 >  delete prepareVisitor;
246    delete compositeVisitor;
247    delete info;
248    

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