OOPSE/libmdtools/OtherVisitor.cpp

#include "OtherVisitor.hpp"
#include "DirectionalAtom.hpp"
#include "RigidBody.hpp"
#include "Molecule.hpp"
#include "SimInfo.hpp"
//----------------------------------------------------------------------------//
void IgnoreVisitor::visit(Atom* atom){
  if(isIgnoreType(atom->getType()))
    internalVisit(atom);
}

void IgnoreVisitor::visit(DirectionalAtom* datom){
  if(isIgnoreType(datom->getType()))
    internalVisit(datom);
}

void IgnoreVisitor::visit(RigidBody* rb){
  vector<Atom*> myAtoms;
  vector<Atom*>::iterator atomIter;
  AtomInfo* atomInfo;
  
  if(isIgnoreType(rb->getType())){
    
    internalVisit(rb);

    myAtoms = rb->getAtoms();    
    
    for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
      internalVisit(*atomIter);

  }
  
}

bool IgnoreVisitor::isIgnoreType(const string& name){
  return itList.find(name) != itList.end() ? true : false;
}

void IgnoreVisitor::internalVisit(StuntDouble* sd){
  GenericData* data;
  data = sd->getProperty("IGNORE");

  //if this stuntdoulbe is already marked as ignore just skip it
  if (data == NULL){
    data = new GenericData;
    data->setID("IGNORE");
    sd->addProperty(data);
  }
    
}

const string IgnoreVisitor::toString(){
  char buffer[65535];
  string result;
  set<string>::iterator i;
  
  sprintf(buffer ,"------------------------------------------------------------------\n");
  result += buffer;

  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
  result += buffer;

  sprintf(buffer ,"Visitor Description: ignore  stuntdoubles\n");
  result += buffer;

  //print the ignore type list
  sprintf(buffer , "Ignore type list contains below types:\n");
  result += buffer;

  for(i = itList.begin(); i != itList.end(); ++i){
    sprintf(buffer ,"%s\t", i->c_str());
    result += buffer;

  }
  sprintf(buffer ,"\n");
  result += buffer;

  sprintf(buffer ,"------------------------------------------------------------------\n");
  result += buffer;

  return result;
}

//----------------------------------------------------------------------------//

void WrappingVisitor::visit(Atom* atom){
  internalVisit(atom);
}
void WrappingVisitor::visit(DirectionalAtom* datom){
  internalVisit(datom);
}

void WrappingVisitor::visit(RigidBody* rb){
  internalVisit(rb);
}

void WrappingVisitor::internalVisit(StuntDouble* sd){
  GenericData* data;
  AtomData* atomData;
  AtomInfo* atomInfo;
  vector<AtomInfo*>::iterator i;

  data = sd->getProperty("ATOMDATA");
  if(data != NULL){
    atomData = dynamic_cast<AtomData*>(data);  
    if(atomData == NULL)
      return;
  }
  else
    return;

  for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i))
    info->wrapVector(atomInfo->pos);

   
}

const string WrappingVisitor::toString(){
  char buffer[65535];
  string result;
  
  sprintf(buffer ,"------------------------------------------------------------------\n");
  result += buffer;

  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
  result += buffer;

  sprintf(buffer ,"Visitor Description: wrapping atoms back to periodic box\n");
  result += buffer;
 
  sprintf(buffer,"------------------------------------------------------------------\n");
  result += buffer;

  return result;
}

//----------------------------------------------------------------------------//

ReplicateVisitor::ReplicateVisitor(SimInfo* info, IntVec3 opt) : BaseVisitor(){
  this->info = info;
  visitorName = "ReplicateVisitor";
  this->replicateOpt = opt;
  //generate the replicate directions
  for(int i = 0; i <= replicateOpt[0]; i ++)
    for(int j = 0; j <= replicateOpt[1]; j ++)
      for(int k = 0; k <= replicateOpt[2]; k ++)
        //skip original frame
        if(i == 0 && j ==0 && k ==0)
          continue;
        else
          dir.push_back(IntVec3(i, j, k));
  
}
void ReplicateVisitor::visit(Atom* atom){
  internalVisit(atom);
}
void ReplicateVisitor::visit(DirectionalAtom* datom){
  internalVisit(datom);
}

void ReplicateVisitor::visit(RigidBody* rb){
  internalVisit(rb);
}

void ReplicateVisitor::internalVisit(StuntDouble* sd){
  GenericData* data;
  AtomData* atomData;
  AtomInfo* atomInfo;
  double box[3][3];
  vector<AtomInfo*> atomInfoList;
  IntVec3 dir;
  
  //if there is not atom data, just skip it
  data = sd->getProperty("ATOMDATA");
  if(data != NULL){
    atomData = dynamic_cast<AtomData*>(data);  
    if(atomData == NULL)
      return;
  }
  else
    return;

  
  info->getBoxM(box);

  atomInfoList = atomData->getData();
  
  replicate(atomInfoList, atomData, box);

}

void ReplicateVisitor::replicate(vector<AtomInfo*>& infoList, AtomData* data, double boxM[3][3]){
  AtomInfo * newAtomInfo;
  vector<IntVec3>::iterator dirIter;
  vector<AtomInfo*>::iterator i;
  
  for(dirIter = dir.begin(); dirIter != dir.end(); ++dirIter){
    for(i = infoList.begin(); i != infoList.end(); i++){
      newAtomInfo = new AtomInfo;
      *newAtomInfo = *(*i);    

      for(int j = 0; j < 3; j++)
        newAtomInfo->pos[j] +=   (*dirIter)[0] * boxM[j][0] + (*dirIter)[1]* boxM[j][1] + (*dirIter)[2] * boxM[j][2];

      data->addAtomInfo(newAtomInfo);
    }
  }// end for(dirIter)  
}

const string ReplicateVisitor::toString(){
  char buffer[65535];
  string result;
  set<string>::iterator i;
  
  sprintf(buffer ,"------------------------------------------------------------------\n");
  result += buffer;

  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
  result += buffer;

  sprintf(buffer ,"Visitor Description: replicate the atoms in different direction\n");
  result += buffer;
  
  //print the replicate direction
  sprintf(buffer , "repeatX = %d:\n", replicateOpt[0]);
  result += buffer;

  sprintf(buffer , "repeatY = %d:\n", replicateOpt[1]);
  result += buffer;

  sprintf(buffer , "repeatZ = %d:\n", replicateOpt[2]);
  result += buffer;


  sprintf(buffer,"------------------------------------------------------------------\n");
  result += buffer;

  return result;
}

//----------------------------------------------------------------------------//

XYZVisitor::XYZVisitor(SimInfo* info,  bool printDipole) : BaseVisitor(){
  this->info = info;
  visitorName = "XYZVisitor";
  this->printDipole = printDipole;
}

void XYZVisitor::visit(Atom* atom){
  if(!isIgnore(atom))
    internalVisit(atom);
}

void XYZVisitor::visit(DirectionalAtom* datom){
  if(!isIgnore(datom))
    internalVisit(datom);
}

void XYZVisitor::visit(RigidBody* rb){
  if(!isIgnore(rb))
    internalVisit(rb);

}

void XYZVisitor::internalVisit(StuntDouble* sd){
  GenericData* data;
  AtomData* atomData;
  AtomInfo* atomInfo;
  vector<AtomInfo*>::iterator i;
  char buffer[1024];
  
  //if there is not atom data, just skip it
  data = sd->getProperty("ATOMDATA");
  if(data != NULL){
    atomData = dynamic_cast<AtomData*>(data);  
    if(atomData == NULL)
      return;
  }
  else
    return;

  for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)){

    if(printDipole)
      sprintf(buffer, "%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
                  atomInfo->AtomType.c_str(),
                  atomInfo->pos[0],
                  atomInfo->pos[1],
                  atomInfo->pos[2],
                  atomInfo->dipole[0],
                  atomInfo->dipole[1],
                  atomInfo->dipole[2]);
    else
      sprintf(buffer, "%s%15.8f%15.8f%15.8f",
                  atomInfo->AtomType.c_str(),
                  atomInfo->pos[0],
                  atomInfo->pos[1],
                  atomInfo->pos[2]);   

    frame.push_back(buffer);
              
  }

}

bool XYZVisitor::isIgnore(StuntDouble* sd){
  GenericData* data;
  
  data = sd->getProperty("IGNORE");
  return data ==NULL ? false : true;
}

void XYZVisitor::writeFrame(ostream& outStream){
  vector<string>::iterator i;
  double box[3][3];
  char buffer[1024];

  if(frame.size() == 0)
    cerr << "Current Frame does not contain any atoms" << endl;

  //total number of atoms  
  outStream << frame.size() << endl;

  //write comment line
  info->getBoxM(box);
  sprintf(buffer,"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f",
              info->getTime(),
              box[0][0], box[0][1], box[0][2],
              box[1][0], box[1][1], box[1][2],
              box[2][0], box[2][1], box[2][2]);

  outStream << buffer << endl;  

  for(i = frame.begin(); i != frame.end(); ++i)
    outStream << *i << endl;
}

const string XYZVisitor::toString(){
  char buffer[65535];
  string result;
  
  sprintf(buffer ,"------------------------------------------------------------------\n");
  result += buffer;

  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
  result += buffer;

  sprintf(buffer ,"Visitor Description: assemble the atom data and output xyz file\n");
  result += buffer;
 
  sprintf(buffer,"------------------------------------------------------------------\n");
  result += buffer;

  return result;
}

//----------------------------------------------------------------------------//

void PrepareVisitor::internalVisit(Atom * atom){
  GenericData* data;
  AtomData* atomData;

  //if visited property is  existed, remove it
  data = atom->getProperty("VISITED");
  if(data != NULL){
    atom->removeProperty("VISITED");  
  }

  //remove atomdata
  data = atom->getProperty("ATOMDATA");
  if(data != NULL){
    atomData = dynamic_cast<AtomData*>(data);  
    if(atomData != NULL)
      atom->removeProperty("ATOMDATA");
  }
  
}

void PrepareVisitor::internalVisit(RigidBody * rb){
  GenericData* data;
  AtomData* atomData;
  vector<Atom*> myAtoms;
  vector<Atom*>::iterator atomIter;
  
  //if visited property is  existed, remove it
  data = rb->getProperty("VISITED");
  if(data != NULL){
    rb->removeProperty("VISITED");  
  }

  //remove atomdata
  data = rb->getProperty("ATOMDATA");
  if(data != NULL){
    atomData = dynamic_cast<AtomData*>(data);  
    if(atomData != NULL)
      rb->removeProperty("ATOMDATA");
  }

  myAtoms = rb->getAtoms();
    
  for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
   internalVisit (*atomIter);  
}

const string PrepareVisitor::toString(){
  char buffer[65535];
  string result;
  
  sprintf(buffer ,"------------------------------------------------------------------\n");
  result += buffer;

  sprintf(buffer ,"Visitor name: %s", visitorName.c_str());
  result += buffer;

  sprintf(buffer ,"Visitor Description: prepare for operation of other vistors\n");
  result += buffer;

  sprintf(buffer ,"------------------------------------------------------------------\n");
  result += buffer;

  return result;
}

//----------------------------------------------------------------------------//

WaterTypeVisitor:: WaterTypeVisitor(){
  visitorName = "WaterTypeVisitor";
  waterTypeList.insert("TIP3P_RB_0");
  waterTypeList.insert("TIP4P_RB_0");
  waterTypeList.insert("TIP5P_RB_0");
  waterTypeList.insert("SPCE_RB_0");  
}


void WaterTypeVisitor:: visit(RigidBody* rb){
  string rbName;
  vector<Atom*> myAtoms;
  vector<Atom*>::iterator atomIter;
  GenericData* data;
  AtomData* atomData;
  AtomInfo* atomInfo;
  vector<AtomInfo*>::iterator i;
  
  rbName = rb->getType();

  if(waterTypeList.find(rbName) != waterTypeList.end()){

    myAtoms = rb->getAtoms();    
    for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter){

      data = (*atomIter)->getProperty("ATOMDATA");
      if(data != NULL){
        atomData = dynamic_cast<AtomData*>(data);  
        if(atomData == NULL)
          continue;
      }
      else
        continue;
      
      for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)){
        replaceType(atomInfo->AtomType);
      }//end for(atomInfo)

    }//end for(atomIter)
      
  }//end if (waterTypeList.find(rbName) != waterTypeList.end())
  
}

void WaterTypeVisitor:: replaceType(string& atomType){
  atomType = atomType.substr(0, atomType.find('_'));
}

const string WaterTypeVisitor:: toString(){
  char buffer[65535];
  string result;
  
  sprintf(buffer ,"------------------------------------------------------------------\n");
  result += buffer;

  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
  result += buffer;

  sprintf(buffer ,"Visitor Description: Replace the atom type in water model\n");
  result += buffer;

  sprintf(buffer ,"------------------------------------------------------------------\n");
  result += buffer;

  return result;
}

Revision:	1140
Committed:	Wed Apr 28 22:34:02 2004 UTC (21 years, 6 months ago) by tim
File size:	12494 byte(s)
Log Message:	fix a bug in Molecule.cpp which initialize massRatio before creat the array. fix two bugs in ZconsVisitor
#	User	Rev	Content
1	tim	1118	#include "OtherVisitor.hpp"
2			#include "DirectionalAtom.hpp"
3			#include "RigidBody.hpp"
4			#include "Molecule.hpp"
5			#include "SimInfo.hpp"
6			//----------------------------------------------------------------------------//
7			void IgnoreVisitor::visit(Atom* atom){
8			if(isIgnoreType(atom->getType()))
9			internalVisit(atom);
10			}
11
12			void IgnoreVisitor::visit(DirectionalAtom* datom){
13			if(isIgnoreType(datom->getType()))
14			internalVisit(datom);
15			}
16
17			void IgnoreVisitor::visit(RigidBody* rb){
18	tim	1129	vector<Atom*> myAtoms;
19			vector<Atom*>::iterator atomIter;
20			AtomInfo* atomInfo;
21
22			if(isIgnoreType(rb->getType())){
23
24	tim	1118	internalVisit(rb);
25	tim	1129
26			myAtoms = rb->getAtoms();
27
28			for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
29			internalVisit(*atomIter);
30
31			}
32
33	tim	1118	}
34
35			bool IgnoreVisitor::isIgnoreType(const string& name){
36			return itList.find(name) != itList.end() ? true : false;
37			}
38
39			void IgnoreVisitor::internalVisit(StuntDouble* sd){
40			GenericData* data;
41			data = sd->getProperty("IGNORE");
42
43			//if this stuntdoulbe is already marked as ignore just skip it
44			if (data == NULL){
45			data = new GenericData;
46			data->setID("IGNORE");
47			sd->addProperty(data);
48			}
49
50			}
51
52			const string IgnoreVisitor::toString(){
53			char buffer[65535];
54	tim	1119	string result;
55	tim	1118	set<string>::iterator i;
56
57	tim	1119	sprintf(buffer ,"------------------------------------------------------------------\n");
58			result += buffer;
59	tim	1118
60	tim	1140	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
61	tim	1119	result += buffer;
62
63	tim	1126	sprintf(buffer ,"Visitor Description: ignore stuntdoubles\n");
64			result += buffer;
65
66	tim	1118	//print the ignore type list
67	tim	1119	sprintf(buffer , "Ignore type list contains below types:\n");
68			result += buffer;
69	tim	1118
70	tim	1119	for(i = itList.begin(); i != itList.end(); ++i){
71	tim	1129	sprintf(buffer ,"%s\t", i->c_str());
72	tim	1119	result += buffer;
73	tim	1118
74	tim	1119	}
75			sprintf(buffer ,"\n");
76			result += buffer;
77
78			sprintf(buffer ,"------------------------------------------------------------------\n");
79			result += buffer;
80
81	tim	1129	return result;
82	tim	1118	}
83
84			//----------------------------------------------------------------------------//
85
86			void WrappingVisitor::visit(Atom* atom){
87			internalVisit(atom);
88			}
89			void WrappingVisitor::visit(DirectionalAtom* datom){
90			internalVisit(datom);
91			}
92
93			void WrappingVisitor::visit(RigidBody* rb){
94			internalVisit(rb);
95			}
96
97			void WrappingVisitor::internalVisit(StuntDouble* sd){
98			GenericData* data;
99			AtomData* atomData;
100			AtomInfo* atomInfo;
101			vector<AtomInfo*>::iterator i;
102
103			data = sd->getProperty("ATOMDATA");
104	tim	1126	if(data != NULL){
105	tim	1118	atomData = dynamic_cast<AtomData*>(data);
106			if(atomData == NULL)
107			return;
108	tim	1126	}
109	tim	1118	else
110			return;
111
112	tim	1126	for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i))
113	tim	1118	info->wrapVector(atomInfo->pos);
114	tim	1126
115	tim	1118
116			}
117
118	tim	1126	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	tim	1118	//----------------------------------------------------------------------------//
138
139	tim	1126	ReplicateVisitor::ReplicateVisitor(SimInfo* info, IntVec3 opt) : BaseVisitor(){
140	tim	1118	this->info = info;
141			visitorName = "ReplicateVisitor";
142	tim	1126	this->replicateOpt = opt;
143	tim	1118	//generate the replicate directions
144	tim	1126	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	tim	1118	//skip original frame
148			if(i == 0 && j ==0 && k ==0)
149			continue;
150			else
151			dir.push_back(IntVec3(i, j, k));
152
153			}
154			void ReplicateVisitor::visit(Atom* atom){
155			internalVisit(atom);
156			}
157			void ReplicateVisitor::visit(DirectionalAtom* datom){
158			internalVisit(datom);
159			}
160
161			void ReplicateVisitor::visit(RigidBody* rb){
162			internalVisit(rb);
163			}
164
165			void ReplicateVisitor::internalVisit(StuntDouble* sd){
166			GenericData* data;
167			AtomData* atomData;
168			AtomInfo* atomInfo;
169			double box[3][3];
170			vector<AtomInfo*> atomInfoList;
171			IntVec3 dir;
172
173			//if there is not atom data, just skip it
174			data = sd->getProperty("ATOMDATA");
175	tim	1126	if(data != NULL){
176	tim	1118	atomData = dynamic_cast<AtomData*>(data);
177			if(atomData == NULL)
178			return;
179	tim	1126	}
180	tim	1118	else
181			return;
182
183
184			info->getBoxM(box);
185
186			atomInfoList = atomData->getData();
187
188			replicate(atomInfoList, atomData, box);
189
190			}
191
192			void ReplicateVisitor::replicate(vector<AtomInfo>& infoList, AtomData data, double boxM[3][3]){
193			AtomInfo * newAtomInfo;
194			vector<IntVec3>::iterator dirIter;
195			vector<AtomInfo*>::iterator i;
196
197			for(dirIter = dir.begin(); dirIter != dir.end(); ++dirIter){
198			for(i = infoList.begin(); i != infoList.end(); i++){
199			newAtomInfo = new AtomInfo;
200			newAtomInfo = (*i);
201
202			for(int j = 0; j < 3; j++)
203			newAtomInfo->pos[j] += (dirIter)[0] boxM[j][0] + (dirIter)[1] boxM[j][1] + (dirIter)[2] boxM[j][2];
204
205			data->addAtomInfo(newAtomInfo);
206			}
207			}// end for(dirIter)
208			}
209
210			const string ReplicateVisitor::toString(){
211			char buffer[65535];
212	tim	1119	string result;
213	tim	1118	set<string>::iterator i;
214
215	tim	1119	sprintf(buffer ,"------------------------------------------------------------------\n");
216			result += buffer;
217	tim	1118
218	tim	1126	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
219	tim	1119	result += buffer;
220
221	tim	1126	sprintf(buffer ,"Visitor Description: replicate the atoms in different direction\n");
222			result += buffer;
223
224	tim	1118	//print the replicate direction
225	tim	1119	sprintf(buffer , "repeatX = %d:\n", replicateOpt[0]);
226			result += buffer;
227	tim	1118
228	tim	1119	sprintf(buffer , "repeatY = %d:\n", replicateOpt[1]);
229			result += buffer;
230	tim	1118
231	tim	1119	sprintf(buffer , "repeatZ = %d:\n", replicateOpt[2]);
232			result += buffer;
233
234
235	tim	1118	sprintf(buffer,"------------------------------------------------------------------\n");
236	tim	1119	result += buffer;
237	tim	1118
238	tim	1119	return result;
239	tim	1118	}
240
241			//----------------------------------------------------------------------------//
242
243			XYZVisitor::XYZVisitor(SimInfo* info, bool printDipole) : BaseVisitor(){
244			this->info = info;
245			visitorName = "XYZVisitor";
246			this->printDipole = printDipole;
247			}
248
249			void XYZVisitor::visit(Atom* atom){
250			if(!isIgnore(atom))
251			internalVisit(atom);
252			}
253
254			void XYZVisitor::visit(DirectionalAtom* datom){
255			if(!isIgnore(datom))
256			internalVisit(datom);
257			}
258
259			void XYZVisitor::visit(RigidBody* rb){
260			if(!isIgnore(rb))
261			internalVisit(rb);
262
263			}
264
265			void XYZVisitor::internalVisit(StuntDouble* sd){
266			GenericData* data;
267			AtomData* atomData;
268			AtomInfo* atomInfo;
269			vector<AtomInfo*>::iterator i;
270			char buffer[1024];
271
272			//if there is not atom data, just skip it
273			data = sd->getProperty("ATOMDATA");
274	tim	1119	if(data != NULL){
275	tim	1118	atomData = dynamic_cast<AtomData*>(data);
276			if(atomData == NULL)
277			return;
278	tim	1119	}
279	tim	1118	else
280			return;
281
282			for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)){
283
284			if(printDipole)
285			sprintf(buffer, "%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
286	tim	1119	atomInfo->AtomType.c_str(),
287	tim	1118	atomInfo->pos[0],
288			atomInfo->pos[1],
289			atomInfo->pos[2],
290			atomInfo->dipole[0],
291			atomInfo->dipole[1],
292			atomInfo->dipole[2]);
293			else
294			sprintf(buffer, "%s%15.8f%15.8f%15.8f",
295	tim	1119	atomInfo->AtomType.c_str(),
296	tim	1118	atomInfo->pos[0],
297			atomInfo->pos[1],
298	tim	1126	atomInfo->pos[2]);
299
300			frame.push_back(buffer);
301
302	tim	1118	}
303
304			}
305
306			bool XYZVisitor::isIgnore(StuntDouble* sd){
307			GenericData* data;
308
309			data = sd->getProperty("IGNORE");
310			return data ==NULL ? false : true;
311			}
312
313			void XYZVisitor::writeFrame(ostream& outStream){
314			vector<string>::iterator i;
315			double box[3][3];
316			char buffer[1024];
317
318			if(frame.size() == 0)
319			cerr << "Current Frame does not contain any atoms" << endl;
320
321			//total number of atoms
322			outStream << frame.size() << endl;
323
324			//write comment line
325			info->getBoxM(box);
326			sprintf(buffer,"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f",
327			info->getTime(),
328			box[0][0], box[0][1], box[0][2],
329			box[1][0], box[1][1], box[1][2],
330			box[2][0], box[2][1], box[2][2]);
331
332			outStream << buffer << endl;
333
334			for(i = frame.begin(); i != frame.end(); ++i)
335			outStream << *i << endl;
336			}
337
338	tim	1126	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	tim	1129	sprintf(buffer ,"Visitor Description: assemble the atom data and output xyz file\n");
349	tim	1126	result += buffer;
350
351			sprintf(buffer,"------------------------------------------------------------------\n");
352			result += buffer;
353
354			return result;
355			}
356
357	tim	1118	//----------------------------------------------------------------------------//
358
359	tim	1120	void PrepareVisitor::internalVisit(Atom * atom){
360	tim	1118	GenericData* data;
361			AtomData* atomData;
362
363			//if visited property is existed, remove it
364	tim	1120	data = atom->getProperty("VISITED");
365	tim	1118	if(data != NULL){
366	tim	1120	atom->removeProperty("VISITED");
367	tim	1118	}
368
369			//remove atomdata
370	tim	1120	data = atom->getProperty("ATOMDATA");
371	tim	1119	if(data != NULL){
372	tim	1118	atomData = dynamic_cast<AtomData*>(data);
373			if(atomData != NULL)
374	tim	1120	atom->removeProperty("ATOMDATA");
375	tim	1119	}
376
377	tim	1118	}
378
379	tim	1120	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	tim	1126	}
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	tim	1127	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
482	tim	1126	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