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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 1930 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 2065 by tim, Tue Mar 1 14:45:45 2005 UTC

# Line 54 | Line 54 | using namespace oopse;
54   #include "visitors/RigidBodyVisitor.hpp"
55   #include "visitors/OtherVisitor.hpp"
56   #include "visitors/ZconsVisitor.hpp"
57 + #include "selection/SelectionEvaluator.hpp"
58 + #include "selection/SelectionManager.hpp"
59 + #include "visitors/LipidTransVisitor.hpp"
60 +
61   using namespace oopse;
62  
63   int main(int argc, char* argv[]){
# Line 81 | Line 85 | int main(int argc, char* argv[]){
85    
86    mdFileName = dumpFileName;
87    mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
88 <  
88 >
89    if (args_info.output_given){
90      xyzFileName = args_info.output_arg;
91    } else {
# Line 91 | Line 95 | int main(int argc, char* argv[]){
95    
96    //parse md file and set up the system
97    SimCreator creator;
98 <  SimInfo* info = creator.createSim(mdFileName);
98 >  SimInfo* info = creator.createSim(mdFileName, false);
99    
100    
101    
# Line 101 | Line 105 | int main(int argc, char* argv[]){
105    //creat ignore visitor
106    if(args_info.ignore_given ||args_info.water_flag){
107      
108 <    IgnoreVisitor* ignoreVisitor = new IgnoreVisitor();
108 >    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]);
# Line 128 | Line 132 | int main(int argc, char* argv[]){
132      compositeVisitor->addVisitor(rbCOMVisitor, 900);
133    }
134    
135 <  //compositeVisitor->addVisitor(lipidVisitor, 900);
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 >          
147 >  }
148    
149    //creat SSD atom visitor
150    SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
151    compositeVisitor->addVisitor(ssdVisitor, 800);
152    
153 <  LinearVisitor* linearVisitor = new LinearAtomVisitor(info);
153 >  LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
154    compositeVisitor->addVisitor(linearVisitor, 750);
155    
156    //creat default atom visitor
# Line 165 | Line 181 | int main(int argc, char* argv[]){
181      WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
182      compositeVisitor->addVisitor(wrappingVisitor, 400);
183    }
184 <  
184 >
185    //creat replicate visitor
186    if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
187      Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
188      ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
189      compositeVisitor->addVisitor(replicateVisitor, 300);
190    }
191 <  
191 >
192 >
193 >  //create rotation visitor
194 >  if (args_info.refsele_given&& args_info.originsele_given) {
195 >    compositeVisitor->addVisitor(new LipidTransVisitor(info, args_info.originsele_arg, args_info.refsele_arg), 250);
196 >  } else if (args_info.refsele_given || args_info.originsele_given) {
197 >    std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
198 >    exit(1);
199 >  }
200 >    
201    //creat xyzVisitor
202    XYZVisitor* xyzVisitor = new XYZVisitor(info);
203    compositeVisitor->addVisitor(xyzVisitor, 200);
# Line 197 | Line 222 | int main(int argc, char* argv[]){
222    Molecule* mol;
223    StuntDouble* integrableObject;
224    RigidBody* rb;
225 +
226 +  if (evaluator && !evaluator->isDynamic()) {
227 +    info->getSelectionManager()->setSelectionSet(evaluator->evaluate());
228 +  }
229    
230    for (int i = 0; i < nframes; i += args_info.frame_arg){
231      dumpReader->readFrame(i);
# Line 220 | Line 249 | int main(int argc, char* argv[]){
249      
250      //update visitor
251      compositeVisitor->update();
252 +
253 +    //if dynamic, we need to re-evaluate the selection
254 +    if (evaluator && evaluator->isDynamic()) {
255 +      info->getSelectionManager()->setSelectionSet(evaluator->evaluate());
256 +    }
257      
258      //visit stuntdouble
259      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {

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