ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE-4/src/applications/dump2Xyz/Dump2XYZ.cpp
(Generate patch)

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 2581 by xsun, Thu Feb 2 15:49:42 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    
119 <  //creat default atom visitor
119 >  GBLipidAtomVisitor* gbLipidVisitor = new GBLipidAtomVisitor(info);
120 >  compositeVisitor->addVisitor(gbLipidVisitor, 740);
121 >
122 >  //create default atom visitor
123    DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
124    compositeVisitor->addVisitor(defaultAtomVisitor, 700);
125    
126 <  //creat waterType visitor
126 >  //create waterType visitor
127    if(args_info.watertype_flag){
128      WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
129      compositeVisitor->addVisitor(waterTypeVisitor, 600);
130    }
131 +
132 +  if (args_info.basetype_flag) {
133 +      AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
134 +      compositeVisitor->addVisitor(atomNameVisitor, 550);
135 +
136 +  }
137    
138    //create ZconsVisitor
139    if(args_info.zconstraint_flag){
# Line 175 | Line 147 | int main(int argc, char* argv[]){
147      }
148    }
149    
150 <  //creat wrapping visitor
150 >  //create wrapping visitor
151    
152    if(args_info.periodicBox_flag){
153      WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
154      compositeVisitor->addVisitor(wrappingVisitor, 400);
155    }
156  
157 <  //creat replicate visitor
157 >  //create replicate visitor
158    if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
159      Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
160      ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
# Line 198 | Line 170 | int main(int argc, char* argv[]){
170      exit(1);
171    }
172      
173 <  //creat xyzVisitor
174 <  XYZVisitor* xyzVisitor = new XYZVisitor(info);
173 >  //create xyzVisitor
174 >  XYZVisitor* xyzVisitor;
175 >  if (args_info.selection_given) {
176 >    xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
177 >  } else {
178 >    xyzVisitor = new XYZVisitor(info);
179 >  }
180    compositeVisitor->addVisitor(xyzVisitor, 200);
181    
182    std::cout << compositeVisitor->toString();
183    
184 <  //creat prepareVisitor
184 >  //create prepareVisitor
185    PrepareVisitor* prepareVisitor = new PrepareVisitor();
186    
187    //open dump file
# Line 222 | Line 199 | int main(int argc, char* argv[]){
199    Molecule* mol;
200    StuntDouble* integrableObject;
201    RigidBody* rb;
202 <
226 <  if (evaluator && !evaluator->isDynamic()) {
227 <    info->getSelectionManager()->setSelectionSet(evaluator->evaluate());
228 <  }
229 <  
202 >      
203    for (int i = 0; i < nframes; i += args_info.frame_arg){
204      dumpReader->readFrame(i);
205      
# Line 250 | Line 223 | int main(int argc, char* argv[]){
223      //update visitor
224      compositeVisitor->update();
225  
226 <    //if dynamic, we need to re-evaluate the selection
254 <    if (evaluator && evaluator->isDynamic()) {
255 <      info->getSelectionManager()->setSelectionSet(evaluator->evaluate());
256 <    }
257 <    
226 >
227      //visit stuntdouble
228      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
229        for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
# Line 270 | Line 239 | int main(int argc, char* argv[]){
239    
240    xyzStream.close();
241    
242 <  
242 >  delete prepareVisitor;
243    delete compositeVisitor;
244    delete info;
245    

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines