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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 1934 by tim, Wed Jan 12 23:21:42 2005 UTC vs.
Revision 2224 by chrisfen, Thu May 12 19:43:48 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 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    
102 <  //creat visitor list
102 >  //create visitor list
103    CompositeVisitor* compositeVisitor = new CompositeVisitor();
100 –  
101 –  //creat ignore visitor
102 –  if(args_info.ignore_given ||args_info.water_flag){
104      
105 <    IgnoreVisitor* ignoreVisitor = new IgnoreVisitor();
105 <    
106 <    for(int i = 0; i < args_info.ignore_given; i++)
107 <      ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
108 <    
109 <    //ignore water
110 <    if(args_info.water_flag){
111 <      ignoreVisitor->addIgnoreType("SSD");
112 <      ignoreVisitor->addIgnoreType("SSD1");
113 <      ignoreVisitor->addIgnoreType("SSD_E");
114 <      ignoreVisitor->addIgnoreType("SSD_RF");
115 <      ignoreVisitor->addIgnoreType("TIP3P_RB_0");
116 <      ignoreVisitor->addIgnoreType("TIP4P_RB_0");
117 <      ignoreVisitor->addIgnoreType("TIP5P_RB_0");
118 <      ignoreVisitor->addIgnoreType("SPCE_RB_0");      
119 <      ignoreVisitor->addIgnoreType("DPD_RB_0");
120 <    }
121 <    
122 <    compositeVisitor->addVisitor(ignoreVisitor, 1000);
123 <  }
124 <  
125 <  //creat RigidBody Visitor
105 >  //create RigidBody Visitor
106    if(args_info.rigidbody_flag){
107      RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
108      compositeVisitor->addVisitor(rbCOMVisitor, 900);
109    }
110    
111 <  //compositeVisitor->addVisitor(lipidVisitor, 900);
132 <  
133 <  //creat SSD atom visitor
111 >  //create SSD atom visitor
112    SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
113    compositeVisitor->addVisitor(ssdVisitor, 800);
114    
115    LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
116    compositeVisitor->addVisitor(linearVisitor, 750);
117    
118 <  //creat default atom visitor
118 >  //create default atom visitor
119    DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
120    compositeVisitor->addVisitor(defaultAtomVisitor, 700);
121    
122 <  //creat waterType visitor
122 >  //create waterType visitor
123    if(args_info.watertype_flag){
124      WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
125      compositeVisitor->addVisitor(waterTypeVisitor, 600);
# Line 159 | Line 137 | int main(int argc, char* argv[]){
137      }
138    }
139    
140 <  //creat wrapping visitor
140 >  //create wrapping visitor
141    
142    if(args_info.periodicBox_flag){
143      WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
144      compositeVisitor->addVisitor(wrappingVisitor, 400);
145    }
146 <  
147 <  //creat replicate visitor
146 >
147 >  //create replicate visitor
148    if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
149      Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
150      ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
151      compositeVisitor->addVisitor(replicateVisitor, 300);
152    }
153 <  
154 <  //creat xyzVisitor
155 <  XYZVisitor* xyzVisitor = new XYZVisitor(info);
153 >
154 >
155 >  //create rotation visitor
156 >  if (args_info.refsele_given&& args_info.originsele_given) {
157 >    compositeVisitor->addVisitor(new LipidTransVisitor(info, args_info.originsele_arg, args_info.refsele_arg), 250);
158 >  } else if (args_info.refsele_given || args_info.originsele_given) {
159 >    std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
160 >    exit(1);
161 >  }
162 >    
163 >  //create xyzVisitor
164 >  XYZVisitor* xyzVisitor;
165 >  if (args_info.selection_given) {
166 >    xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
167 >  } else {
168 >    xyzVisitor = new XYZVisitor(info);
169 >  }
170    compositeVisitor->addVisitor(xyzVisitor, 200);
171    
172    std::cout << compositeVisitor->toString();
173    
174 <  //creat prepareVisitor
174 >  //create prepareVisitor
175    PrepareVisitor* prepareVisitor = new PrepareVisitor();
176    
177    //open dump file
# Line 197 | Line 189 | int main(int argc, char* argv[]){
189    Molecule* mol;
190    StuntDouble* integrableObject;
191    RigidBody* rb;
192 <  
192 >      
193    for (int i = 0; i < nframes; i += args_info.frame_arg){
194      dumpReader->readFrame(i);
195      
# Line 220 | Line 212 | int main(int argc, char* argv[]){
212      
213      //update visitor
214      compositeVisitor->update();
215 <    
215 >
216 >
217      //visit stuntdouble
218      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
219        for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
# Line 236 | Line 229 | int main(int argc, char* argv[]){
229    
230    xyzStream.close();
231    
232 <  
232 >  delete prepareVisitor;
233    delete compositeVisitor;
234    delete info;
235    

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