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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 2053 by tim, Fri Feb 18 23:07:32 2005 UTC vs.
Revision 3115 by chuckv, Tue Jan 16 22:17:27 2007 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 67 | Line 68 | int main(int argc, char* argv[]){
68    
69    gengetopt_args_info args_info;
70    std::string dumpFileName;
70 –  std::string mdFileName;
71    std::string xyzFileName;
72    
73    //parse the command line option
# Line 83 | Line 83 | int main(int argc, char* argv[]){
83      exit(1);
84    }
85    
86 –  mdFileName = dumpFileName;
87 –  mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
88 –
86    if (args_info.output_given){
87      xyzFileName = args_info.output_arg;
88    } else {
# Line 95 | Line 92 | int main(int argc, char* argv[]){
92    
93    //parse md file and set up the system
94    SimCreator creator;
95 <  SimInfo* info = creator.createSim(mdFileName, false);
95 >  SimInfo* info = creator.createSim(dumpFileName, false);
96    
97 <  
98 <  
102 <  //creat visitor list
97 >
98 >  //create visitor list
99    CompositeVisitor* compositeVisitor = new CompositeVisitor();
104 –  
105 –  //creat ignore visitor
106 –  if(args_info.ignore_given ||args_info.water_flag){
100      
101 <    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
101 >  //create RigidBody Visitor
102    if(args_info.rigidbody_flag){
103      RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
104      compositeVisitor->addVisitor(rbCOMVisitor, 900);
105    }
106    
107 <  //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
107 >  //create SSD atom visitor
108    SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
109    compositeVisitor->addVisitor(ssdVisitor, 800);
110    
111    LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
112    compositeVisitor->addVisitor(linearVisitor, 750);
113 +  if (args_info.gb_given) {
114 +    linearVisitor->addGayBerneAtomType(args_info.gb_arg);
115 +  }
116    
117 <  //creat default atom visitor
117 >  GBLipidAtomVisitor* gbLipidVisitor = new GBLipidAtomVisitor(info);
118 >  compositeVisitor->addVisitor(gbLipidVisitor, 740);
119 >
120 >  //create default atom visitor
121    DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
122    compositeVisitor->addVisitor(defaultAtomVisitor, 700);
123    
124 <  //creat waterType visitor
124 >  //create waterType visitor
125    if(args_info.watertype_flag){
126      WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
127      compositeVisitor->addVisitor(waterTypeVisitor, 600);
128    }
129 +
130 +  if (args_info.basetype_flag) {
131 +      AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
132 +      compositeVisitor->addVisitor(atomNameVisitor, 550);
133 +
134 +  }
135    
136    //create ZconsVisitor
137    if(args_info.zconstraint_flag){
# Line 175 | Line 145 | int main(int argc, char* argv[]){
145      }
146    }
147    
148 <  //creat wrapping visitor
148 >  //create wrapping visitor
149    
150 <  if(args_info.periodicBox_flag){
151 <    WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
152 <    compositeVisitor->addVisitor(wrappingVisitor, 400);
153 <  }
150 >  //if(args_info.periodicBox_flag){
151 >  //  WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
152 >  //  compositeVisitor->addVisitor(wrappingVisitor, 400);
153 >  //}
154  
155 <  //creat replicate visitor
155 >  //create replicate visitor
156    if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
157      Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
158      ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
# Line 194 | Line 164 | int main(int argc, char* argv[]){
164    if (args_info.refsele_given&& args_info.originsele_given) {
165      compositeVisitor->addVisitor(new LipidTransVisitor(info, args_info.originsele_arg, args_info.refsele_arg), 250);
166    } else if (args_info.refsele_given || args_info.originsele_given) {
167 <    std::cerr << "Both of --refsele and --originselc should appear by pair" << std::endl;
167 >    std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
168      exit(1);
169    }
170      
171 <  //creat xyzVisitor
172 <  XYZVisitor* xyzVisitor = new XYZVisitor(info);
171 >  //create xyzVisitor
172 >  XYZVisitor* xyzVisitor;
173 >
174 >  if (args_info.selection_given) {
175 >    xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
176 >  } else {
177 >    xyzVisitor = new XYZVisitor(info);
178 >  }
179 >
180 >  if(args_info.printPosOnly_flag){
181 >    bool posOnly = true;
182 >    xyzVisitor->setPosOnly(posOnly);
183 >  }
184 >
185    compositeVisitor->addVisitor(xyzVisitor, 200);
186    
187    std::cout << compositeVisitor->toString();
188    
189 <  //creat prepareVisitor
189 >  //create prepareVisitor
190    PrepareVisitor* prepareVisitor = new PrepareVisitor();
191    
192    //open dump file
# Line 222 | Line 204 | int main(int argc, char* argv[]){
204    Molecule* mol;
205    StuntDouble* integrableObject;
206    RigidBody* rb;
207 <
208 <  if (evaluator && !evaluator->isDynamic()) {
209 <    info->getSelectionManager()->setSelectionSet(evaluator->evaluate());
210 <  }
211 <  
207 >  Vector3d molCom;
208 >  Vector3d newMolCom;
209 >  Vector3d displacement;
210 >  Mat3x3d hmat;
211 >  Snapshot* currentSnapshot;
212 >      
213    for (int i = 0; i < nframes; i += args_info.frame_arg){
214      dumpReader->readFrame(i);
215 <    
215 >
216 >    //wrapping the molecule
217 >    if(args_info.periodicBox_flag) {
218 >      currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();    
219 >      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
220 >          molCom = mol->getCom();
221 >          newMolCom = molCom;
222 >          currentSnapshot->wrapVector(newMolCom);
223 >          displacement = newMolCom - molCom;
224 >        for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
225 >             integrableObject = mol->nextIntegrableObject(iiter)) {  
226 >          integrableObject->setPos(integrableObject->getPos() + displacement);
227 >        }
228 >      }    
229 >    }
230      //update atoms of rigidbody
231      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
232        
# Line 250 | Line 247 | int main(int argc, char* argv[]){
247      //update visitor
248      compositeVisitor->update();
249  
250 <    //if dynamic, we need to re-evaluate the selection
254 <    if (evaluator && evaluator->isDynamic()) {
255 <      info->getSelectionManager()->setSelectionSet(evaluator->evaluate());
256 <    }
257 <    
250 >
251      //visit stuntdouble
252      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
253        for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
# Line 270 | Line 263 | int main(int argc, char* argv[]){
263    
264    xyzStream.close();
265    
266 <  
266 >  delete prepareVisitor;
267    delete compositeVisitor;
268    delete info;
269    

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