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root/OpenMD/trunk/src/applications/dump2Xyz/Dump2XYZ.cpp
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Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (file contents):
Revision 369 by tim, Fri Feb 18 23:07:32 2005 UTC vs.
Revision 1303 by cli2, Mon Oct 13 21:35:22 2008 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 >  Ring5gbAtomVisitor* ring5Visitor = new Ring5gbAtomVisitor(info);
121 >  compositeVisitor->addVisitor(ring5Visitor, 730);
122 >
123 >  HeadAtomVisitor* headVisitor = new HeadAtomVisitor(info);
124 >  compositeVisitor->addVisitor(headVisitor, 720);
125 >
126 >  //create default atom visitor
127    DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
128    compositeVisitor->addVisitor(defaultAtomVisitor, 700);
129    
130 <  //creat waterType visitor
131 <  if(args_info.watertype_flag){
132 <    WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
133 <    compositeVisitor->addVisitor(waterTypeVisitor, 600);
130 >  // if we gave the -w option, we want to skip the waters:
131 >  std::cerr << "-w flag was set to:" << args_info.water_given << "\n";
132 >  if (!args_info.water_given) {
133 >    //create waterType visitor
134 >    if(args_info.watertype_flag){
135 >      WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
136 >      compositeVisitor->addVisitor(waterTypeVisitor, 600);
137 >    }
138    }
139 +
140 +  if (args_info.basetype_flag) {
141 +      AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
142 +      compositeVisitor->addVisitor(atomNameVisitor, 550);
143 +
144 +  }
145    
146    //create ZconsVisitor
147    if(args_info.zconstraint_flag){
# Line 175 | Line 155 | int main(int argc, char* argv[]){
155      }
156    }
157    
158 <  //creat wrapping visitor
158 >  //create wrapping visitor
159    
160 <  if(args_info.periodicBox_flag){
161 <    WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
162 <    compositeVisitor->addVisitor(wrappingVisitor, 400);
163 <  }
160 >  //if(args_info.periodicBox_flag){
161 >  //  WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
162 >  //  compositeVisitor->addVisitor(wrappingVisitor, 400);
163 >  //}
164  
165 <  //creat replicate visitor
165 >  //create replicate visitor
166    if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
167      Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
168      ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
# Line 194 | Line 174 | int main(int argc, char* argv[]){
174    if (args_info.refsele_given&& args_info.originsele_given) {
175      compositeVisitor->addVisitor(new LipidTransVisitor(info, args_info.originsele_arg, args_info.refsele_arg), 250);
176    } else if (args_info.refsele_given || args_info.originsele_given) {
177 <    std::cerr << "Both of --refsele and --originselc should appear by pair" << std::endl;
177 >    std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
178      exit(1);
179    }
180      
181 <  //creat xyzVisitor
182 <  XYZVisitor* xyzVisitor = new XYZVisitor(info);
181 >  //create xyzVisitor
182 >  XYZVisitor* xyzVisitor;
183 >
184 >  if (args_info.selection_given) {
185 >    xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
186 >  } else {
187 >    xyzVisitor = new XYZVisitor(info);
188 >  }
189 >
190 >  if(args_info.printPosOnly_flag){
191 >    bool posOnly = true;
192 >    xyzVisitor->setPosOnly(posOnly);
193 >  }
194 >
195    compositeVisitor->addVisitor(xyzVisitor, 200);
196    
197    std::cout << compositeVisitor->toString();
198    
199 <  //creat prepareVisitor
199 >  //create prepareVisitor
200    PrepareVisitor* prepareVisitor = new PrepareVisitor();
201    
202    //open dump file
# Line 212 | Line 204 | int main(int argc, char* argv[]){
204    int nframes = dumpReader->getNFrames();
205    
206    
207 <  std::ofstream xyzStream;    
216 <  xyzStream .open(xyzFileName.c_str());
207 >  std::ofstream xyzStream(xyzFileName.c_str());
208    
218 –  
209    SimInfo::MoleculeIterator miter;
210    Molecule::IntegrableObjectIterator  iiter;
211    Molecule::RigidBodyIterator rbIter;
212    Molecule* mol;
213    StuntDouble* integrableObject;
214    RigidBody* rb;
215 <
216 <  if (evaluator && !evaluator->isDynamic()) {
217 <    info->getSelectionManager()->setSelectionSet(evaluator->evaluate());
218 <  }
219 <  
215 >  Vector3d molCom;
216 >  Vector3d newMolCom;
217 >  Vector3d displacement;
218 >  Mat3x3d hmat;
219 >  Snapshot* currentSnapshot;
220 >      
221    for (int i = 0; i < nframes; i += args_info.frame_arg){
222      dumpReader->readFrame(i);
223 <    
223 >
224 >    //wrapping the molecule
225 >    if(args_info.periodicBox_flag) {
226 >      currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();    
227 >      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
228 >          molCom = mol->getCom();
229 >          newMolCom = molCom;
230 >          currentSnapshot->wrapVector(newMolCom);
231 >          displacement = newMolCom - molCom;
232 >        for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
233 >             integrableObject = mol->nextIntegrableObject(iiter)) {  
234 >          integrableObject->setPos(integrableObject->getPos() + displacement);
235 >        }
236 >      }    
237 >    }
238      //update atoms of rigidbody
239      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
240        
# Line 250 | Line 255 | int main(int argc, char* argv[]){
255      //update visitor
256      compositeVisitor->update();
257  
258 <    //if dynamic, we need to re-evaluate the selection
254 <    if (evaluator && evaluator->isDynamic()) {
255 <      info->getSelectionManager()->setSelectionSet(evaluator->evaluate());
256 <    }
257 <    
258 >
259      //visit stuntdouble
260      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
261        for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
# Line 267 | Line 268 | int main(int argc, char* argv[]){
268      xyzVisitor->clear();
269      
270    }//end for (int i = 0; i < nframes; i += args_info.frame_arg)
271 <  
271 >
272    xyzStream.close();
273 <  
273 <  
273 >  delete prepareVisitor;
274    delete compositeVisitor;
275    delete info;
276 –  
276   }

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