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){
  if(isIgnoreType(rb->getType()))
    internalVisit(rb);
}

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", visitorName.c_str());
  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 buffer;
}

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

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;
  double pos[3];
  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 != NULL; atomData->nextAtomInfo(i))
    info->wrapVector(atomInfo->pos);
   
}

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

ReplicateVisitor::ReplicateVisitor(SimInfo* info, IntVec3 replicateOpt) : BaseVisitor(){
  this->info = info;
  visitorName = "ReplicateVisitor";
  this->replicateOpt = replicateOpt;
  //generate the replicate directions
  for(int i = 0; i < replicateOpt[0]; i ++)
    for(int j = 0; i < replicateOpt[1]; j ++)
      for(int k = 0; i < 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", visitorName.c_str());
  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;
}

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

void PrepareVisitor::internalVisit(StuntDouble * sd){
  GenericData* data;
  AtomData* atomData;

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

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

Revision:	1119
Committed:	Mon Apr 19 17:44:48 2004 UTC (21 years, 6 months ago) by tim
File size:	8027 byte(s)
Log Message:	Dump2XYZ is almost working except atoms in rigidbody are double counted
#	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			if(isIgnoreType(rb->getType()))
19			internalVisit(rb);
20			}
21
22			bool IgnoreVisitor::isIgnoreType(const string& name){
23			return itList.find(name) != itList.end() ? true : false;
24			}
25
26			void IgnoreVisitor::internalVisit(StuntDouble* sd){
27			GenericData* data;
28			data = sd->getProperty("IGNORE");
29
30			//if this stuntdoulbe is already marked as ignore just skip it
31			if (data == NULL){
32			data = new GenericData;
33			data->setID("IGNORE");
34			sd->addProperty(data);
35			}
36
37			}
38
39			const string IgnoreVisitor::toString(){
40			char buffer[65535];
41	tim	1119	string result;
42	tim	1118	set<string>::iterator i;
43
44	tim	1119	sprintf(buffer ,"------------------------------------------------------------------\n");
45			result += buffer;
46	tim	1118
47	tim	1119	sprintf(buffer ,"Visitor name: %s", visitorName.c_str());
48			result += buffer;
49
50	tim	1118	//print the ignore type list
51	tim	1119	sprintf(buffer , "Ignore type list contains below types:\n");
52			result += buffer;
53	tim	1118
54	tim	1119	for(i = itList.begin(); i != itList.end(); ++i){
55			sprintf(buffer ,"%s,\t", i->c_str());
56			result += buffer;
57	tim	1118
58	tim	1119	}
59			sprintf(buffer ,"\n");
60			result += buffer;
61
62			sprintf(buffer ,"------------------------------------------------------------------\n");
63			result += buffer;
64
65	tim	1118	return buffer;
66			}
67
68			//----------------------------------------------------------------------------//
69
70			void WrappingVisitor::visit(Atom* atom){
71			internalVisit(atom);
72			}
73			void WrappingVisitor::visit(DirectionalAtom* datom){
74			internalVisit(datom);
75			}
76
77			void WrappingVisitor::visit(RigidBody* rb){
78			internalVisit(rb);
79			}
80
81			void WrappingVisitor::internalVisit(StuntDouble* sd){
82			GenericData* data;
83			AtomData* atomData;
84			AtomInfo* atomInfo;
85			double pos[3];
86			vector<AtomInfo*>::iterator i;
87
88			data = sd->getProperty("ATOMDATA");
89			if(data != NULL)
90			atomData = dynamic_cast<AtomData*>(data);
91			if(atomData == NULL)
92			return;
93			else
94			return;
95
96			for(atomInfo = atomData->beginAtomInfo(i); atomInfo != NULL; atomData->nextAtomInfo(i))
97			info->wrapVector(atomInfo->pos);
98
99			}
100
101			//----------------------------------------------------------------------------//
102
103			ReplicateVisitor::ReplicateVisitor(SimInfo* info, IntVec3 replicateOpt) : BaseVisitor(){
104			this->info = info;
105			visitorName = "ReplicateVisitor";
106			this->replicateOpt = replicateOpt;
107			//generate the replicate directions
108			for(int i = 0; i < replicateOpt[0]; i ++)
109			for(int j = 0; i < replicateOpt[1]; j ++)
110			for(int k = 0; i < replicateOpt[2]; k ++)
111			//skip original frame
112			if(i == 0 && j ==0 && k ==0)
113			continue;
114			else
115			dir.push_back(IntVec3(i, j, k));
116
117			}
118			void ReplicateVisitor::visit(Atom* atom){
119			internalVisit(atom);
120			}
121			void ReplicateVisitor::visit(DirectionalAtom* datom){
122			internalVisit(datom);
123			}
124
125			void ReplicateVisitor::visit(RigidBody* rb){
126			internalVisit(rb);
127			}
128
129			void ReplicateVisitor::internalVisit(StuntDouble* sd){
130			GenericData* data;
131			AtomData* atomData;
132			AtomInfo* atomInfo;
133			double box[3][3];
134			vector<AtomInfo*> atomInfoList;
135			IntVec3 dir;
136
137			//if there is not atom data, just skip it
138			data = sd->getProperty("ATOMDATA");
139			if(data != NULL)
140			atomData = dynamic_cast<AtomData*>(data);
141			if(atomData == NULL)
142			return;
143			else
144			return;
145
146
147			info->getBoxM(box);
148
149			atomInfoList = atomData->getData();
150
151			replicate(atomInfoList, atomData, box);
152
153			}
154
155			void ReplicateVisitor::replicate(vector<AtomInfo>& infoList, AtomData data, double boxM[3][3]){
156			AtomInfo * newAtomInfo;
157			vector<IntVec3>::iterator dirIter;
158			vector<AtomInfo*>::iterator i;
159
160			for(dirIter = dir.begin(); dirIter != dir.end(); ++dirIter){
161			for(i = infoList.begin(); i != infoList.end(); i++){
162			newAtomInfo = new AtomInfo;
163			newAtomInfo = (*i);
164
165			for(int j = 0; j < 3; j++)
166			newAtomInfo->pos[j] += (dirIter)[0] boxM[j][0] + (dirIter)[1] boxM[j][1] + (dirIter)[2] boxM[j][2];
167
168			data->addAtomInfo(newAtomInfo);
169			}
170			}// end for(dirIter)
171			}
172
173			const string ReplicateVisitor::toString(){
174			char buffer[65535];
175	tim	1119	string result;
176	tim	1118	set<string>::iterator i;
177
178	tim	1119	sprintf(buffer ,"------------------------------------------------------------------\n");
179			result += buffer;
180	tim	1118
181	tim	1119	sprintf(buffer ,"Visitor name: %s", visitorName.c_str());
182			result += buffer;
183
184	tim	1118	//print the replicate direction
185	tim	1119	sprintf(buffer , "repeatX = %d:\n", replicateOpt[0]);
186			result += buffer;
187	tim	1118
188	tim	1119	sprintf(buffer , "repeatY = %d:\n", replicateOpt[1]);
189			result += buffer;
190	tim	1118
191	tim	1119	sprintf(buffer , "repeatZ = %d:\n", replicateOpt[2]);
192			result += buffer;
193
194
195	tim	1118	sprintf(buffer,"------------------------------------------------------------------\n");
196	tim	1119	result += buffer;
197	tim	1118
198	tim	1119	return result;
199	tim	1118	}
200
201			//----------------------------------------------------------------------------//
202
203			XYZVisitor::XYZVisitor(SimInfo* info, bool printDipole) : BaseVisitor(){
204			this->info = info;
205			visitorName = "XYZVisitor";
206			this->printDipole = printDipole;
207			}
208
209			void XYZVisitor::visit(Atom* atom){
210			if(!isIgnore(atom))
211			internalVisit(atom);
212			}
213
214			void XYZVisitor::visit(DirectionalAtom* datom){
215			if(!isIgnore(datom))
216			internalVisit(datom);
217			}
218
219			void XYZVisitor::visit(RigidBody* rb){
220			if(!isIgnore(rb))
221			internalVisit(rb);
222
223			}
224
225			void XYZVisitor::internalVisit(StuntDouble* sd){
226			GenericData* data;
227			AtomData* atomData;
228			AtomInfo* atomInfo;
229			vector<AtomInfo*>::iterator i;
230			char buffer[1024];
231
232			//if there is not atom data, just skip it
233			data = sd->getProperty("ATOMDATA");
234	tim	1119	if(data != NULL){
235	tim	1118	atomData = dynamic_cast<AtomData*>(data);
236			if(atomData == NULL)
237			return;
238	tim	1119	}
239	tim	1118	else
240			return;
241
242			for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)){
243
244			if(printDipole)
245			sprintf(buffer, "%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
246	tim	1119	atomInfo->AtomType.c_str(),
247	tim	1118	atomInfo->pos[0],
248			atomInfo->pos[1],
249			atomInfo->pos[2],
250			atomInfo->dipole[0],
251			atomInfo->dipole[1],
252			atomInfo->dipole[2]);
253			else
254			sprintf(buffer, "%s%15.8f%15.8f%15.8f",
255	tim	1119	atomInfo->AtomType.c_str(),
256	tim	1118	atomInfo->pos[0],
257			atomInfo->pos[1],
258			atomInfo->pos[2]);
259			}
260
261			frame.push_back(buffer);
262
263			}
264
265			bool XYZVisitor::isIgnore(StuntDouble* sd){
266			GenericData* data;
267
268			data = sd->getProperty("IGNORE");
269			return data ==NULL ? false : true;
270			}
271
272			void XYZVisitor::writeFrame(ostream& outStream){
273			vector<string>::iterator i;
274			double box[3][3];
275			char buffer[1024];
276
277			if(frame.size() == 0)
278			cerr << "Current Frame does not contain any atoms" << endl;
279
280			//total number of atoms
281			outStream << frame.size() << endl;
282
283			//write comment line
284			info->getBoxM(box);
285			sprintf(buffer,"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f",
286			info->getTime(),
287			box[0][0], box[0][1], box[0][2],
288			box[1][0], box[1][1], box[1][2],
289			box[2][0], box[2][1], box[2][2]);
290
291			outStream << buffer << endl;
292
293			for(i = frame.begin(); i != frame.end(); ++i)
294			outStream << *i << endl;
295			}
296
297			//----------------------------------------------------------------------------//
298
299			void PrepareVisitor::internalVisit(StuntDouble * sd){
300			GenericData* data;
301			AtomData* atomData;
302
303			//if visited property is existed, remove it
304			data = sd->getProperty("VISITED");
305			if(data != NULL){
306			sd->removeProperty("VISITED");
307			}
308
309			//remove atomdata
310			data = sd->getProperty("ATOMDATA");
311	tim	1119	if(data != NULL){
312	tim	1118	atomData = dynamic_cast<AtomData*>(data);
313			if(atomData != NULL)
314			sd->removeProperty("ATOMDATA");
315	tim	1119	}
316
317	tim	1118	}
318