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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 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1212 by xsun, Wed Jan 23 21:21:13 2008 UTC

# 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();
100      
101 <  //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 <  //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
130 >  //create waterType visitor
131    if(args_info.watertype_flag){
132      WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
133      compositeVisitor->addVisitor(waterTypeVisitor, 600);
134    }
135 +
136 +  if (args_info.basetype_flag) {
137 +      AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
138 +      compositeVisitor->addVisitor(atomNameVisitor, 550);
139 +
140 +  }
141    
142    //create ZconsVisitor
143    if(args_info.zconstraint_flag){
# Line 137 | Line 151 | int main(int argc, char* argv[]){
151      }
152    }
153    
154 <  //creat wrapping visitor
154 >  //create wrapping visitor
155    
156 <  if(args_info.periodicBox_flag){
157 <    WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
158 <    compositeVisitor->addVisitor(wrappingVisitor, 400);
159 <  }
156 >  //if(args_info.periodicBox_flag){
157 >  //  WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
158 >  //  compositeVisitor->addVisitor(wrappingVisitor, 400);
159 >  //}
160  
161 <  //creat replicate visitor
161 >  //create replicate visitor
162    if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
163      Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
164      ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
# Line 160 | Line 174 | int main(int argc, char* argv[]){
174      exit(1);
175    }
176      
177 <  //creat xyzVisitor
177 >  //create xyzVisitor
178    XYZVisitor* xyzVisitor;
179 +
180    if (args_info.selection_given) {
181      xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
182    } else {
183      xyzVisitor = new XYZVisitor(info);
184    }
185 +
186 +  if(args_info.printPosOnly_flag){
187 +    bool posOnly = true;
188 +    xyzVisitor->setPosOnly(posOnly);
189 +  }
190 +
191    compositeVisitor->addVisitor(xyzVisitor, 200);
192    
193    std::cout << compositeVisitor->toString();
194    
195 <  //creat prepareVisitor
195 >  //create prepareVisitor
196    PrepareVisitor* prepareVisitor = new PrepareVisitor();
197    
198    //open dump file
# Line 189 | Line 210 | int main(int argc, char* argv[]){
210    Molecule* mol;
211    StuntDouble* integrableObject;
212    RigidBody* rb;
213 +  Vector3d molCom;
214 +  Vector3d newMolCom;
215 +  Vector3d displacement;
216 +  Mat3x3d hmat;
217 +  Snapshot* currentSnapshot;
218        
219    for (int i = 0; i < nframes; i += args_info.frame_arg){
220      dumpReader->readFrame(i);
221 <    
221 >
222 >    //wrapping the molecule
223 >    if(args_info.periodicBox_flag) {
224 >      currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();    
225 >      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
226 >          molCom = mol->getCom();
227 >          newMolCom = molCom;
228 >          currentSnapshot->wrapVector(newMolCom);
229 >          displacement = newMolCom - molCom;
230 >        for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
231 >             integrableObject = mol->nextIntegrableObject(iiter)) {  
232 >          integrableObject->setPos(integrableObject->getPos() + displacement);
233 >        }
234 >      }    
235 >    }
236      //update atoms of rigidbody
237      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
238        

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