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root/group/trunk/OOPSE/libmdtools/OtherVisitor.cpp
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Comparing trunk/OOPSE/libmdtools/OtherVisitor.cpp (file contents):
Revision 1118 by tim, Mon Apr 19 03:52:27 2004 UTC vs.
Revision 1129 by tim, Thu Apr 22 03:29:30 2004 UTC

# Line 15 | Line 15 | void IgnoreVisitor::visit(RigidBody* rb){
15   }
16  
17   void IgnoreVisitor::visit(RigidBody* rb){
18 <  if(isIgnoreType(rb->getType()))
18 >  vector<Atom*> myAtoms;
19 >  vector<Atom*>::iterator atomIter;
20 >  AtomInfo* atomInfo;
21 >  
22 >  if(isIgnoreType(rb->getType())){
23 >    
24      internalVisit(rb);
25 +
26 +    myAtoms = rb->getAtoms();    
27 +    
28 +    for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
29 +      internalVisit(*atomIter);
30 +
31 +  }
32 +  
33   }
34  
35   bool IgnoreVisitor::isIgnoreType(const string& name){
# Line 38 | Line 51 | const string IgnoreVisitor::toString(){
51  
52   const string IgnoreVisitor::toString(){
53    char buffer[65535];
54 +  string result;
55    set<string>::iterator i;
56    
57 <  sprintf(buffer,"------------------------------------------------------------------\n");
58 <  sprintf(buffer,"Visitor name: %s", visitorName.c_str());
57 >  sprintf(buffer ,"------------------------------------------------------------------\n");
58 >  result += buffer;
59  
60 +  sprintf(buffer ,"Visitor name: %s", visitorName.c_str());
61 +  result += buffer;
62 +
63 +  sprintf(buffer ,"Visitor Description: ignore  stuntdoubles\n");
64 +  result += buffer;
65 +
66    //print the ignore type list
67 <  sprintf(buffer, "Ignore type list contains below types:\n");
68 <  for(i = itList.begin(); i != itList.end(); ++i)
49 <    sprintf(buffer,"%s,\t", i->c_str());
50 <  sprintf(buffer,"\n");
67 >  sprintf(buffer , "Ignore type list contains below types:\n");
68 >  result += buffer;
69  
70 <  sprintf(buffer,"------------------------------------------------------------------\n");
70 >  for(i = itList.begin(); i != itList.end(); ++i){
71 >    sprintf(buffer ,"%s\t", i->c_str());
72 >    result += buffer;
73  
74 <  return buffer;
74 >  }
75 >  sprintf(buffer ,"\n");
76 >  result += buffer;
77 >
78 >  sprintf(buffer ,"------------------------------------------------------------------\n");
79 >  result += buffer;
80 >
81 >  return result;
82   }
83  
84   //----------------------------------------------------------------------------//
# Line 71 | Line 98 | void WrappingVisitor::internalVisit(StuntDouble* sd){
98    GenericData* data;
99    AtomData* atomData;
100    AtomInfo* atomInfo;
74 –  double pos[3];
101    vector<AtomInfo*>::iterator i;
102  
103    data = sd->getProperty("ATOMDATA");
104 <  if(data != NULL)
104 >  if(data != NULL){
105      atomData = dynamic_cast<AtomData*>(data);  
106      if(atomData == NULL)
107        return;
108 +  }
109    else
110      return;
111  
112 <  for(atomInfo = atomData->beginAtomInfo(i); atomInfo != NULL; atomData->nextAtomInfo(i))
112 >  for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i))
113      info->wrapVector(atomInfo->pos);
114 +
115    
116 + }
117 +
118 + const string WrappingVisitor::toString(){
119 +  char buffer[65535];
120 +  string result;
121 +  
122 +  sprintf(buffer ,"------------------------------------------------------------------\n");
123 +  result += buffer;
124 +
125 +  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
126 +  result += buffer;
127 +
128 +  sprintf(buffer ,"Visitor Description: wrapping atoms back to periodic box\n");
129 +  result += buffer;
130 +
131 +  sprintf(buffer,"------------------------------------------------------------------\n");
132 +  result += buffer;
133 +
134 +  return result;
135   }
136  
137   //----------------------------------------------------------------------------//
138  
139 < ReplicateVisitor::ReplicateVisitor(SimInfo* info, IntVec3 replicateOpt) : BaseVisitor(){
139 > ReplicateVisitor::ReplicateVisitor(SimInfo* info, IntVec3 opt) : BaseVisitor(){
140    this->info = info;
141    visitorName = "ReplicateVisitor";
142 <  this->replicateOpt = replicateOpt;
142 >  this->replicateOpt = opt;
143    //generate the replicate directions
144 <  for(int i = 0; i < replicateOpt[0]; i ++)
145 <    for(int j = 0; i < replicateOpt[1]; j ++)
146 <      for(int k = 0; i < replicateOpt[2]; k ++)
144 >  for(int i = 0; i <= replicateOpt[0]; i ++)
145 >    for(int j = 0; j <= replicateOpt[1]; j ++)
146 >      for(int k = 0; k <= replicateOpt[2]; k ++)
147          //skip original frame
148          if(i == 0 && j ==0 && k ==0)
149            continue;
# Line 125 | Line 172 | void ReplicateVisitor::internalVisit(StuntDouble* sd){
172    
173    //if there is not atom data, just skip it
174    data = sd->getProperty("ATOMDATA");
175 <  if(data != NULL)
175 >  if(data != NULL){
176      atomData = dynamic_cast<AtomData*>(data);  
177      if(atomData == NULL)
178        return;
179 +  }
180    else
181      return;
182  
# Line 161 | Line 209 | const string ReplicateVisitor::toString(){
209  
210   const string ReplicateVisitor::toString(){
211    char buffer[65535];
212 +  string result;
213    set<string>::iterator i;
214    
215 <  sprintf(buffer,"------------------------------------------------------------------\n");
216 <  sprintf(buffer,"Visitor name: %s", visitorName.c_str());
215 >  sprintf(buffer ,"------------------------------------------------------------------\n");
216 >  result += buffer;
217  
218 +  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
219 +  result += buffer;
220 +
221 +  sprintf(buffer ,"Visitor Description: replicate the atoms in different direction\n");
222 +  result += buffer;
223 +  
224    //print the replicate direction
225 <  sprintf(buffer, "repeatX = %d:\n", replicateOpt[0]);
226 <  sprintf(buffer, "repeatY = %d:\n", replicateOpt[1]);
172 <  sprintf(buffer, "repeatZ = %d:\n", replicateOpt[2]);
225 >  sprintf(buffer , "repeatX = %d:\n", replicateOpt[0]);
226 >  result += buffer;
227  
228 +  sprintf(buffer , "repeatY = %d:\n", replicateOpt[1]);
229 +  result += buffer;
230  
231 +  sprintf(buffer , "repeatZ = %d:\n", replicateOpt[2]);
232 +  result += buffer;
233 +
234 +
235    sprintf(buffer,"------------------------------------------------------------------\n");
236 +  result += buffer;
237  
238 <  return buffer;
238 >  return result;
239   }
240  
241   //----------------------------------------------------------------------------//
# Line 210 | Line 271 | void XYZVisitor::internalVisit(StuntDouble* sd){
271    
272    //if there is not atom data, just skip it
273    data = sd->getProperty("ATOMDATA");
274 <  if(data != NULL)
274 >  if(data != NULL){
275      atomData = dynamic_cast<AtomData*>(data);  
276      if(atomData == NULL)
277        return;
278 +  }
279    else
280      return;
281  
# Line 221 | Line 283 | void XYZVisitor::internalVisit(StuntDouble* sd){
283  
284      if(printDipole)
285        sprintf(buffer, "%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
286 <                  atomInfo->AtomType,
286 >                  atomInfo->AtomType.c_str(),
287                    atomInfo->pos[0],
288                    atomInfo->pos[1],
289                    atomInfo->pos[2],
# Line 230 | Line 292 | void XYZVisitor::internalVisit(StuntDouble* sd){
292                    atomInfo->dipole[2]);
293      else
294        sprintf(buffer, "%s%15.8f%15.8f%15.8f",
295 <                  atomInfo->AtomType,
295 >                  atomInfo->AtomType.c_str(),
296                    atomInfo->pos[0],
297                    atomInfo->pos[1],
298 <                  atomInfo->pos[2]);        
298 >                  atomInfo->pos[2]);  
299 >
300 >    frame.push_back(buffer);
301 >              
302    }
303  
239 –  frame.push_back(buffer);
240 –          
304   }
305  
306   bool XYZVisitor::isIgnore(StuntDouble* sd){
# Line 270 | Line 333 | void XYZVisitor::writeFrame(ostream& outStream){
333  
334    for(i = frame.begin(); i != frame.end(); ++i)
335      outStream << *i << endl;
336 + }
337 +
338 + const string XYZVisitor::toString(){
339 +  char buffer[65535];
340 +  string result;
341 +  
342 +  sprintf(buffer ,"------------------------------------------------------------------\n");
343 +  result += buffer;
344 +
345 +  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
346 +  result += buffer;
347 +
348 +  sprintf(buffer ,"Visitor Description: assemble the atom data and output xyz file\n");
349 +  result += buffer;
350 +
351 +  sprintf(buffer,"------------------------------------------------------------------\n");
352 +  result += buffer;
353 +
354 +  return result;
355   }
356  
357   //----------------------------------------------------------------------------//
358  
359 < void PrepareVisitor::internalVisit(StuntDouble * sd){
359 > void PrepareVisitor::internalVisit(Atom * atom){
360    GenericData* data;
361    AtomData* atomData;
362  
363    //if visited property is  existed, remove it
364 <  data = sd->getProperty("VISITED");
364 >  data = atom->getProperty("VISITED");
365    if(data != NULL){
366 <    sd->removeProperty("VISITED");  
366 >    atom->removeProperty("VISITED");  
367    }
368  
369    //remove atomdata
370 <  data = sd->getProperty("ATOMDATA");
371 <  if(data != NULL)
370 >  data = atom->getProperty("ATOMDATA");
371 >  if(data != NULL){
372      atomData = dynamic_cast<AtomData*>(data);  
373      if(atomData != NULL)
374 <      sd->removeProperty("ATOMDATA");
374 >      atom->removeProperty("ATOMDATA");
375 >  }
376 >  
377   }
378  
379 + void PrepareVisitor::internalVisit(RigidBody * rb){
380 +  GenericData* data;
381 +  AtomData* atomData;
382 +  vector<Atom*> myAtoms;
383 +  vector<Atom*>::iterator atomIter;
384 +  
385 +  //if visited property is  existed, remove it
386 +  data = rb->getProperty("VISITED");
387 +  if(data != NULL){
388 +    rb->removeProperty("VISITED");  
389 +  }
390 +
391 +  //remove atomdata
392 +  data = rb->getProperty("ATOMDATA");
393 +  if(data != NULL){
394 +    atomData = dynamic_cast<AtomData*>(data);  
395 +    if(atomData != NULL)
396 +      rb->removeProperty("ATOMDATA");
397 +  }
398 +
399 +  myAtoms = rb->getAtoms();
400 +    
401 +  for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
402 +   internalVisit (*atomIter);  
403 + }
404 +
405 + const string PrepareVisitor::toString(){
406 +  char buffer[65535];
407 +  string result;
408 +  
409 +  sprintf(buffer ,"------------------------------------------------------------------\n");
410 +  result += buffer;
411 +
412 +  sprintf(buffer ,"Visitor name: %s", visitorName.c_str());
413 +  result += buffer;
414 +
415 +  sprintf(buffer ,"Visitor Description: prepare for operation of other vistors\n");
416 +  result += buffer;
417 +
418 +  sprintf(buffer ,"------------------------------------------------------------------\n");
419 +  result += buffer;
420 +
421 +  return result;
422 + }
423 +
424 + //----------------------------------------------------------------------------//
425 +
426 + WaterTypeVisitor:: WaterTypeVisitor(){
427 +  visitorName = "WaterTypeVisitor";
428 +  waterTypeList.insert("TIP3P_RB_0");
429 +  waterTypeList.insert("TIP4P_RB_0");
430 +  waterTypeList.insert("TIP5P_RB_0");
431 +  waterTypeList.insert("SPCE_RB_0");  
432 + }
433 +
434 +
435 + void WaterTypeVisitor:: visit(RigidBody* rb){
436 +  string rbName;
437 +  vector<Atom*> myAtoms;
438 +  vector<Atom*>::iterator atomIter;
439 +  GenericData* data;
440 +  AtomData* atomData;
441 +  AtomInfo* atomInfo;
442 +  vector<AtomInfo*>::iterator i;
443 +  
444 +  rbName = rb->getType();
445 +
446 +  if(waterTypeList.find(rbName) != waterTypeList.end()){
447 +
448 +    myAtoms = rb->getAtoms();    
449 +    for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter){
450 +
451 +      data = (*atomIter)->getProperty("ATOMDATA");
452 +      if(data != NULL){
453 +        atomData = dynamic_cast<AtomData*>(data);  
454 +        if(atomData == NULL)
455 +          continue;
456 +      }
457 +      else
458 +        continue;
459 +      
460 +      for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)){
461 +        replaceType(atomInfo->AtomType);
462 +      }//end for(atomInfo)
463 +
464 +    }//end for(atomIter)
465 +      
466 +  }//end if (waterTypeList.find(rbName) != waterTypeList.end())
467 +  
468 + }
469 +
470 + void WaterTypeVisitor:: replaceType(string& atomType){
471 +  atomType = atomType.substr(0, atomType.find('_'));
472 + }
473 +
474 + const string WaterTypeVisitor:: toString(){
475 +  char buffer[65535];
476 +  string result;
477 +  
478 +  sprintf(buffer ,"------------------------------------------------------------------\n");
479 +  result += buffer;
480 +
481 +  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
482 +  result += buffer;
483 +
484 +  sprintf(buffer ,"Visitor Description: Replace the atom type in water model\n");
485 +  result += buffer;
486 +
487 +  sprintf(buffer ,"------------------------------------------------------------------\n");
488 +  result += buffer;
489 +
490 +  return result;
491 + }
492 +

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