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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 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 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 + #include "visitors/AtomNameVisitor.hpp"
61 +
62   using namespace oopse;
63  
64   int main(int argc, char* argv[]){
# Line 81 | Line 86 | int main(int argc, char* argv[]){
86    
87    mdFileName = dumpFileName;
88    mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
89 <  
89 >
90    if (args_info.output_given){
91      xyzFileName = args_info.output_arg;
92    } else {
# Line 91 | Line 96 | int main(int argc, char* argv[]){
96    
97    //parse md file and set up the system
98    SimCreator creator;
99 <  SimInfo* info = creator.createSim(mdFileName);
99 >  SimInfo* info = creator.createSim(mdFileName, false);
100    
101    
102    
103 <  //creat visitor list
103 >  //create visitor list
104    CompositeVisitor* compositeVisitor = new CompositeVisitor();
100 –  
101 –  //creat ignore visitor
102 –  if(args_info.ignore_given ||args_info.water_flag){
105      
106 <    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
106 >  //create RigidBody Visitor
107    if(args_info.rigidbody_flag){
108      RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
109      compositeVisitor->addVisitor(rbCOMVisitor, 900);
110    }
111    
112 <  //compositeVisitor->addVisitor(lipidVisitor, 900);
132 <  
133 <  //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 159 | 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
156 >
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);
161      compositeVisitor->addVisitor(replicateVisitor, 300);
162    }
163 <  
164 <  //creat xyzVisitor
165 <  XYZVisitor* xyzVisitor = new XYZVisitor(info);
163 >
164 >
165 >  //create rotation visitor
166 >  if (args_info.refsele_given&& args_info.originsele_given) {
167 >    compositeVisitor->addVisitor(new LipidTransVisitor(info, args_info.originsele_arg, args_info.refsele_arg), 250);
168 >  } else if (args_info.refsele_given || args_info.originsele_given) {
169 >    std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
170 >    exit(1);
171 >  }
172 >    
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 197 | Line 199 | int main(int argc, char* argv[]){
199    Molecule* mol;
200    StuntDouble* integrableObject;
201    RigidBody* rb;
202 <  
202 >      
203    for (int i = 0; i < nframes; i += args_info.frame_arg){
204      dumpReader->readFrame(i);
205      
# Line 220 | Line 222 | int main(int argc, char* argv[]){
222      
223      //update visitor
224      compositeVisitor->update();
225 <    
225 >
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 236 | Line 239 | int main(int argc, char* argv[]){
239    
240    xyzStream.close();
241    
242 <  
242 >  delete prepareVisitor;
243    delete compositeVisitor;
244    delete info;
245    

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