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Comparing trunk/OOPSE-4/src/visitors/OtherVisitor.cpp (file contents):
Revision 1625 by tim, Thu Oct 21 16:22:01 2004 UTC vs.
Revision 2097 by tim, Wed Mar 9 17:30:29 2005 UTC

# Line 1 | Line 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
5 + * non-exclusive, royalty free, license to use, modify and
6 + * redistribute this software in source and binary code form, provided
7 + * that the following conditions are met:
8 + *
9 + * 1. Acknowledgement of the program authors must be made in any
10 + *    publication of scientific results based in part on use of the
11 + *    program.  An acceptable form of acknowledgement is citation of
12 + *    the article in which the program was described (Matthew
13 + *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 + *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 + *    Parallel Simulation Engine for Molecular Dynamics,"
16 + *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 + *
18 + * 2. Redistributions of source code must retain the above copyright
19 + *    notice, this list of conditions and the following disclaimer.
20 + *
21 + * 3. Redistributions in binary form must reproduce the above copyright
22 + *    notice, this list of conditions and the following disclaimer in the
23 + *    documentation and/or other materials provided with the
24 + *    distribution.
25 + *
26 + * This software is provided "AS IS," without a warranty of any
27 + * kind. All express or implied conditions, representations and
28 + * warranties, including any implied warranty of merchantability,
29 + * fitness for a particular purpose or non-infringement, are hereby
30 + * excluded.  The University of Notre Dame and its licensors shall not
31 + * be liable for any damages suffered by licensee as a result of
32 + * using, modifying or distributing the software or its
33 + * derivatives. In no event will the University of Notre Dame or its
34 + * licensors be liable for any lost revenue, profit or data, or for
35 + * direct, indirect, special, consequential, incidental or punitive
36 + * damages, however caused and regardless of the theory of liability,
37 + * arising out of the use of or inability to use software, even if the
38 + * University of Notre Dame has been advised of the possibility of
39 + * such damages.
40 + */
41 + #include "selection/SelectionManager.hpp"
42   #include "visitors/OtherVisitor.hpp"
43   #include "primitives/DirectionalAtom.hpp"
44   #include "primitives/RigidBody.hpp"
45   #include "primitives/Molecule.hpp"
46   #include "brains/SimInfo.hpp"
6 –
47   namespace oopse {
48  
49 < //----------------------------------------------------------------------------//
50 < void IgnoreVisitor::visit(Atom* atom){
11 <  if(isIgnoreType(atom->getType()))
12 <    internalVisit(atom);
49 > void WrappingVisitor::visit(Atom *atom) {
50 > internalVisit(atom);
51   }
52  
53 < void IgnoreVisitor::visit(DirectionalAtom* datom){
54 <  if(isIgnoreType(datom->getType()))
17 <    internalVisit(datom);
53 > void WrappingVisitor::visit(DirectionalAtom *datom) {
54 > internalVisit(datom);
55   }
56  
57 < void IgnoreVisitor::visit(RigidBody* rb){
58 <  vector<Atom*> myAtoms;
59 <  vector<Atom*>::iterator atomIter;
23 <  AtomInfo* atomInfo;
24 <  
25 <  if(isIgnoreType(rb->getType())){
26 <    
27 <    internalVisit(rb);
57 > void WrappingVisitor::visit(RigidBody *rb) {
58 > internalVisit(rb);
59 > }
60  
61 <    myAtoms = rb->getAtoms();    
62 <    
63 <    for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
64 <      internalVisit(*atomIter);
61 > void WrappingVisitor::internalVisit(StuntDouble *sd) {
62 >    GenericData *                     data;
63 >    AtomData *                        atomData;
64 >    AtomInfo *                        atomInfo;
65 >    std::vector<AtomInfo *>::iterator i;
66  
67 <  }
35 <  
36 < }
67 >    data = sd->getPropertyByName("ATOMDATA");
68  
69 < bool IgnoreVisitor::isIgnoreType(const string& name){
70 <  return itList.find(name) != itList.end() ? true : false;
40 < }
69 >    if (data != NULL) {
70 >        atomData = dynamic_cast<AtomData *>(data);
71  
72 < void IgnoreVisitor::internalVisit(StuntDouble* sd){
73 <  GenericData* data;
74 <  data = sd->getProperty("IGNORE");
72 >        if (atomData == NULL)
73 >            return;
74 >    } else
75 >        return;
76  
77 <  //if this stuntdoulbe is already marked as ignore just skip it
47 <  if (data == NULL){
48 <    data = new GenericData;
49 <    data->setID("IGNORE");
50 <    sd->addProperty(data);
51 <  }
77 >    Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
78      
79 +    for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
80 +        currSnapshot->wrapVector(atomInfo->pos);
81 +    }
82   }
83  
84 < const string IgnoreVisitor::toString(){
85 <  char buffer[65535];
86 <  string result;
58 <  set<string>::iterator i;
59 <  
60 <  sprintf(buffer ,"------------------------------------------------------------------\n");
61 <  result += buffer;
84 > const std::string WrappingVisitor::toString() {
85 >    char        buffer[65535];
86 >    std::string result;
87  
88 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
89 <  result += buffer;
88 >    sprintf(buffer,
89 >            "------------------------------------------------------------------\n");
90 >    result += buffer;
91  
92 <  sprintf(buffer ,"Visitor Description: ignore  stuntdoubles\n");
93 <  result += buffer;
92 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
93 >    result += buffer;
94  
95 <  //print the ignore type list
96 <  sprintf(buffer , "Ignore type list contains below types:\n");
97 <  result += buffer;
95 >    sprintf(buffer,
96 >            "Visitor Description: wrapping atoms back to periodic box\n");
97 >    result += buffer;
98  
99 <  for(i = itList.begin(); i != itList.end(); ++i){
100 <    sprintf(buffer ,"%s\t", i->c_str());
99 >    sprintf(buffer,
100 >            "------------------------------------------------------------------\n");
101      result += buffer;
102  
103 <  }
78 <  sprintf(buffer ,"\n");
79 <  result += buffer;
80 <
81 <  sprintf(buffer ,"------------------------------------------------------------------\n");
82 <  result += buffer;
83 <
84 <  return result;
103 >    return result;
104   }
105  
106   //----------------------------------------------------------------------------//
107  
108 < void WrappingVisitor::visit(Atom* atom){
109 <  internalVisit(atom);
108 > ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) :
109 >    BaseVisitor() {
110 >    this->info = info;
111 >    visitorName = "ReplicateVisitor";
112 >    this->replicateOpt = opt;
113 >
114 >    //generate the replicate directions
115 >    for( int i = 0; i <= replicateOpt[0]; i++ ) {
116 >        for( int j = 0; j <= replicateOpt[1]; j++ ) {
117 >            for( int k = 0; k <= replicateOpt[2]; k++ ) {
118 >                //skip original frame
119 >                if (i == 0 && j == 0 && k == 0) {
120 >                    continue;
121 >                } else {
122 >                    dir.push_back(Vector3i(i, j, k));
123 >                }
124 >            }
125 >        }
126 >    }
127 >    
128   }
129 < void WrappingVisitor::visit(DirectionalAtom* datom){
130 <  internalVisit(datom);
129 >
130 > void ReplicateVisitor::visit(Atom *atom) {
131 > internalVisit(atom);
132   }
133  
134 < void WrappingVisitor::visit(RigidBody* rb){
135 <  internalVisit(rb);
134 > void ReplicateVisitor::visit(DirectionalAtom *datom) {
135 > internalVisit(datom);
136   }
137  
138 < void WrappingVisitor::internalVisit(StuntDouble* sd){
139 <  GenericData* data;
140 <  AtomData* atomData;
103 <  AtomInfo* atomInfo;
104 <  vector<AtomInfo*>::iterator i;
138 > void ReplicateVisitor::visit(RigidBody *rb) {
139 > internalVisit(rb);
140 > }
141  
142 <  data = sd->getProperty("ATOMDATA");
143 <  if(data != NULL){
144 <    atomData = dynamic_cast<AtomData*>(data);  
109 <    if(atomData == NULL)
110 <      return;
111 <  }
112 <  else
113 <    return;
142 > void ReplicateVisitor::internalVisit(StuntDouble *sd) {
143 >    GenericData *          data;
144 >    AtomData *             atomData;
145  
146 <  for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i))
147 <    info->wrapVector(atomInfo->pos);
146 >    //if there is not atom data, just skip it
147 >    data = sd->getPropertyByName("ATOMDATA");
148  
149 <  
150 < }
149 >    if (data != NULL) {
150 >        atomData = dynamic_cast<AtomData *>(data);
151  
152 < const string WrappingVisitor::toString(){
153 <  char buffer[65535];
154 <  string result;
155 <  
156 <  sprintf(buffer ,"------------------------------------------------------------------\n");
157 <  result += buffer;
152 >        if (atomData == NULL) {
153 >            return;
154 >        }
155 >    } else {
156 >        return;
157 >    }
158  
159 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
160 <  result += buffer;
159 >    Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
160 >    Mat3x3d box = currSnapshot->getHmat();
161  
162 <  sprintf(buffer ,"Visitor Description: wrapping atoms back to periodic box\n");
132 <  result += buffer;
133 <
134 <  sprintf(buffer,"------------------------------------------------------------------\n");
135 <  result += buffer;
162 >    std::vector<AtomInfo *> atomInfoList = atomData->getData();
163  
164 <  return result;
165 < }
164 >    replicate(atomInfoList, atomData, box);
165 > }
166 >
167 > void ReplicateVisitor::replicate(std::vector<AtomInfo *>&infoList, AtomData *data, const Mat3x3d& box) {
168 >    AtomInfo* newAtomInfo;
169 >    std::vector<Vector3i>::iterator dirIter;
170 >    std::vector<AtomInfo *>::iterator i;
171  
172 < //----------------------------------------------------------------------------//
172 >    for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) {
173 >        for( i = infoList.begin(); i != infoList.end(); i++ ) {
174 >            newAtomInfo = new AtomInfo();
175 >            *newAtomInfo = *(*i);
176  
177 < ReplicateVisitor::ReplicateVisitor(SimInfo* info, IntVec3 opt) : BaseVisitor(){
178 <  this->info = info;
179 <  visitorName = "ReplicateVisitor";
180 <  this->replicateOpt = opt;
181 <  //generate the replicate directions
182 <  for(int i = 0; i <= replicateOpt[0]; i ++)
148 <    for(int j = 0; j <= replicateOpt[1]; j ++)
149 <      for(int k = 0; k <= replicateOpt[2]; k ++)
150 <        //skip original frame
151 <        if(i == 0 && j ==0 && k ==0)
152 <          continue;
153 <        else
154 <          dir.push_back(IntVec3(i, j, k));
155 <  
177 >            for( int j = 0; j < 3; j++ )
178 >                newAtomInfo->pos[j] += (*dirIter)[0]*box(j, 0) + (*dirIter)[1]*box(j, 1) + (*dirIter)[2]*box(j, 2);
179 >
180 >            data->addAtomInfo(newAtomInfo);
181 >        }
182 >    } // end for(dirIter)  
183   }
157 – void ReplicateVisitor::visit(Atom* atom){
158 –  internalVisit(atom);
159 – }
160 – void ReplicateVisitor::visit(DirectionalAtom* datom){
161 –  internalVisit(datom);
162 – }
184  
185 < void ReplicateVisitor::visit(RigidBody* rb){
186 <  internalVisit(rb);
185 > const std::string ReplicateVisitor::toString() {
186 >    char                            buffer[65535];
187 >    std::string                     result;
188 >    std::set<std::string>::iterator i;
189 >
190 >    sprintf(buffer,
191 >            "------------------------------------------------------------------\n");
192 >    result += buffer;
193 >
194 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
195 >    result += buffer;
196 >
197 >    sprintf(buffer,
198 >            "Visitor Description: replicate the atoms in different direction\n");
199 >    result += buffer;
200 >
201 >    //print the replicate direction
202 >    sprintf(buffer, "repeatX = %d:\n", replicateOpt[0]);
203 >    result += buffer;
204 >
205 >    sprintf(buffer, "repeatY = %d:\n", replicateOpt[1]);
206 >    result += buffer;
207 >
208 >    sprintf(buffer, "repeatZ = %d:\n", replicateOpt[2]);
209 >    result += buffer;
210 >
211 >    sprintf(buffer,
212 >            "------------------------------------------------------------------\n");
213 >    result += buffer;
214 >
215 >    return result;
216   }
217  
218 < void ReplicateVisitor::internalVisit(StuntDouble* sd){
169 <  GenericData* data;
170 <  AtomData* atomData;
171 <  AtomInfo* atomInfo;
172 <  double box[3][3];
173 <  vector<AtomInfo*> atomInfoList;
174 <  IntVec3 dir;
175 <  
176 <  //if there is not atom data, just skip it
177 <  data = sd->getProperty("ATOMDATA");
178 <  if(data != NULL){
179 <    atomData = dynamic_cast<AtomData*>(data);  
180 <    if(atomData == NULL)
181 <      return;
182 <  }
183 <  else
184 <    return;
218 > //----------------------------------------------------------------------------//
219  
220 <  
221 <  info->getBoxM(box);
220 > XYZVisitor::XYZVisitor(SimInfo *info) :
221 >    BaseVisitor(), seleMan(info), evaluator(info){
222 >    this->info = info;
223 >    visitorName = "XYZVisitor";
224  
225 <  atomInfoList = atomData->getData();
190 <  
191 <  replicate(atomInfoList, atomData, box);
225 >    evaluator.loadScriptString("select all");
226  
227 +    if (!evaluator.isDynamic()) {
228 +        seleMan.setSelectionSet(evaluator.evaluate());
229 +    }
230 +
231   }
232  
233 < void ReplicateVisitor::replicate(vector<AtomInfo*>& infoList, AtomData* data, double boxM[3][3]){
234 <  AtomInfo * newAtomInfo;
235 <  vector<IntVec3>::iterator dirIter;
236 <  vector<AtomInfo*>::iterator i;
199 <  
200 <  for(dirIter = dir.begin(); dirIter != dir.end(); ++dirIter){
201 <    for(i = infoList.begin(); i != infoList.end(); i++){
202 <      newAtomInfo = new AtomInfo;
203 <      *newAtomInfo = *(*i);    
233 > XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) :
234 >    BaseVisitor(), seleMan(info), evaluator(info) {
235 >    this->info = info;
236 >    visitorName = "XYZVisitor";
237  
238 <      for(int j = 0; j < 3; j++)
206 <        newAtomInfo->pos[j] +=   (*dirIter)[0] * boxM[j][0] + (*dirIter)[1]* boxM[j][1] + (*dirIter)[2] * boxM[j][2];
238 >    evaluator.loadScriptString(script);
239  
240 <      data->addAtomInfo(newAtomInfo);
240 >    if (!evaluator.isDynamic()) {
241 >        seleMan.setSelectionSet(evaluator.evaluate());
242      }
243 <  }// end for(dirIter)  
243 >          
244   }
245 +    
246 + void XYZVisitor::visit(Atom *atom) {
247 +    if (isSelected(atom))
248 +        internalVisit(atom);
249 + }
250  
251 < const string ReplicateVisitor::toString(){
252 <  char buffer[65535];
253 <  string result;
254 <  set<string>::iterator i;
217 <  
218 <  sprintf(buffer ,"------------------------------------------------------------------\n");
219 <  result += buffer;
251 > void XYZVisitor::visit(DirectionalAtom *datom) {
252 >    if (isSelected(datom))
253 >        internalVisit(datom);
254 > }
255  
256 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
257 <  result += buffer;
256 > void XYZVisitor::visit(RigidBody *rb) {
257 >    if (isSelected(rb))
258 >        internalVisit(rb);
259 > }
260  
261 <  sprintf(buffer ,"Visitor Description: replicate the atoms in different direction\n");
262 <  result += buffer;
263 <  
264 <  //print the replicate direction
265 <  sprintf(buffer , "repeatX = %d:\n", replicateOpt[0]);
266 <  result += buffer;
261 > void XYZVisitor::update() {
262 >    //if dynamic, we need to re-evaluate the selection
263 >    if (evaluator.isDynamic()) {
264 >       seleMan.setSelectionSet(evaluator.evaluate());
265 >    }
266 > }
267  
268 <  sprintf(buffer , "repeatY = %d:\n", replicateOpt[1]);
269 <  result += buffer;
268 > void XYZVisitor::internalVisit(StuntDouble *sd) {
269 >    GenericData *                     data;
270 >    AtomData *                        atomData;
271 >    AtomInfo *                        atomInfo;
272 >    std::vector<AtomInfo *>::iterator i;
273 >    char                              buffer[1024];
274  
275 <  sprintf(buffer , "repeatZ = %d:\n", replicateOpt[2]);
276 <  result += buffer;
275 >    //if there is not atom data, just skip it
276 >    data = sd->getPropertyByName("ATOMDATA");
277  
278 +    if (data != NULL) {
279 +        atomData = dynamic_cast<AtomData *>(data);
280  
281 <  sprintf(buffer,"------------------------------------------------------------------\n");
282 <  result += buffer;
281 >        if (atomData == NULL)
282 >            return;
283 >    } else
284 >        return;
285 >
286 >    for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
287 >        atomInfo = atomData->nextAtomInfo(i) ) {
288 >        sprintf(buffer,
289 >                "%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
290 >                atomInfo->atomTypeName.c_str(),
291 >                atomInfo->pos[0],
292 >                atomInfo->pos[1],
293 >                atomInfo->pos[2],
294 >                atomInfo->dipole[0],
295 >                atomInfo->dipole[1],
296 >                atomInfo->dipole[2]);
297 >        frame.push_back(buffer);
298 >    }
299 > }
300 >
301 > bool XYZVisitor::isSelected(StuntDouble *sd) {
302 >    return seleMan.isSelected(sd);
303 > }
304 >
305 > void XYZVisitor::writeFrame(std::ostream &outStream) {
306 >    std::vector<std::string>::iterator i;
307 >    char buffer[1024];
308 >
309 >    if (frame.size() == 0)
310 >        std::cerr << "Current Frame does not contain any atoms" << std::endl;
311  
312 <  return result;
313 < }
312 >    //total number of atoms  
313 >    outStream << frame.size() << std::endl;
314  
315 < //----------------------------------------------------------------------------//
315 >    //write comment line
316 >    Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
317 >    Mat3x3d box = currSnapshot->getHmat();
318 >    
319 >    sprintf(buffer,
320 >            "%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f",
321 >            currSnapshot->getTime(),
322 >            box(0, 0), box(0, 1), box(0, 2),
323 >            box(1, 0), box(1, 1), box(1, 2),
324 >            box(2, 0), box(2, 1), box(2, 2));
325  
326 < XYZVisitor::XYZVisitor(SimInfo* info,  bool printDipole) : BaseVisitor(){
247 <  this->info = info;
248 <  visitorName = "XYZVisitor";
249 <  this->printDipole = printDipole;
250 < }
326 >    outStream << buffer << std::endl;
327  
328 < void XYZVisitor::visit(Atom* atom){
329 <  if(!isIgnore(atom))
254 <    internalVisit(atom);
328 >    for( i = frame.begin(); i != frame.end(); ++i )
329 >        outStream << *i << std::endl;
330   }
331  
332 < void XYZVisitor::visit(DirectionalAtom* datom){
333 <  if(!isIgnore(datom))
334 <    internalVisit(datom);
260 < }
332 > const std::string XYZVisitor::toString() {
333 >    char        buffer[65535];
334 >    std::string result;
335  
336 < void XYZVisitor::visit(RigidBody* rb){
337 <  if(!isIgnore(rb))
338 <    internalVisit(rb);
336 >    sprintf(buffer,
337 >            "------------------------------------------------------------------\n");
338 >    result += buffer;
339  
340 < }
340 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
341 >    result += buffer;
342  
343 < void XYZVisitor::internalVisit(StuntDouble* sd){
344 <  GenericData* data;
345 <  AtomData* atomData;
271 <  AtomInfo* atomInfo;
272 <  vector<AtomInfo*>::iterator i;
273 <  char buffer[1024];
274 <  
275 <  //if there is not atom data, just skip it
276 <  data = sd->getProperty("ATOMDATA");
277 <  if(data != NULL){
278 <    atomData = dynamic_cast<AtomData*>(data);  
279 <    if(atomData == NULL)
280 <      return;
281 <  }
282 <  else
283 <    return;
343 >    sprintf(buffer,
344 >            "Visitor Description: assemble the atom data and output xyz file\n");
345 >    result += buffer;
346  
347 <  for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)){
347 >    sprintf(buffer,
348 >            "------------------------------------------------------------------\n");
349 >    result += buffer;
350  
351 <    if(printDipole)
288 <      sprintf(buffer, "%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
289 <                  atomInfo->AtomType.c_str(),
290 <                  atomInfo->pos[0],
291 <                  atomInfo->pos[1],
292 <                  atomInfo->pos[2],
293 <                  atomInfo->dipole[0],
294 <                  atomInfo->dipole[1],
295 <                  atomInfo->dipole[2]);
296 <    else
297 <      sprintf(buffer, "%s%15.8f%15.8f%15.8f",
298 <                  atomInfo->AtomType.c_str(),
299 <                  atomInfo->pos[0],
300 <                  atomInfo->pos[1],
301 <                  atomInfo->pos[2]);  
302 <
303 <    frame.push_back(buffer);
304 <              
305 <  }
306 <
351 >    return result;
352   }
353  
354 < bool XYZVisitor::isIgnore(StuntDouble* sd){
310 <  GenericData* data;
311 <  
312 <  data = sd->getProperty("IGNORE");
313 <  return data ==NULL ? false : true;
314 < }
354 > //----------------------------------------------------------------------------//
355  
356 < void XYZVisitor::writeFrame(ostream& outStream){
357 <  vector<string>::iterator i;
358 <  double box[3][3];
319 <  char buffer[1024];
356 > void PrepareVisitor::internalVisit(Atom *atom) {
357 >    GenericData *data;
358 >    AtomData *   atomData;
359  
360 <  if(frame.size() == 0)
361 <    cerr << "Current Frame does not contain any atoms" << endl;
360 >    //if visited property is  existed, remove it
361 >    data = atom->getPropertyByName("VISITED");
362  
363 <  //total number of atoms  
364 <  outStream << frame.size() << endl;
363 >    if (data != NULL) {
364 >    atom->removeProperty("VISITED");
365 >    }
366  
367 <  //write comment line
368 <  info->getBoxM(box);
329 <  sprintf(buffer,"%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f;%15.8f%15.8f%15.8f",
330 <              info->getTime(),
331 <              box[0][0], box[0][1], box[0][2],
332 <              box[1][0], box[1][1], box[1][2],
333 <              box[2][0], box[2][1], box[2][2]);
367 >    //remove atomdata
368 >    data = atom->getPropertyByName("ATOMDATA");
369  
370 <  outStream << buffer << endl;  
370 >    if (data != NULL) {
371 >        atomData = dynamic_cast<AtomData *>(data);
372  
373 <  for(i = frame.begin(); i != frame.end(); ++i)
374 <    outStream << *i << endl;
373 >        if (atomData != NULL)
374 >            atom->removeProperty("ATOMDATA");
375 >    }
376   }
377  
378 < const string XYZVisitor::toString(){
379 <  char buffer[65535];
380 <  string result;
381 <  
382 <  sprintf(buffer ,"------------------------------------------------------------------\n");
346 <  result += buffer;
378 > void PrepareVisitor::internalVisit(RigidBody *rb) {
379 >    GenericData* data;
380 >    AtomData* atomData;
381 >    std::vector<Atom *> myAtoms;
382 >    std::vector<Atom *>::iterator atomIter;
383  
384 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
385 <  result += buffer;
384 >    //if visited property is  existed, remove it
385 >    data = rb->getPropertyByName("VISITED");
386  
387 <  sprintf(buffer ,"Visitor Description: assemble the atom data and output xyz file\n");
388 <  result += buffer;
389 <
354 <  sprintf(buffer,"------------------------------------------------------------------\n");
355 <  result += buffer;
387 >    if (data != NULL) {
388 >    rb->removeProperty("VISITED");
389 >    }
390  
391 <  return result;
392 < }
391 >    //remove atomdata
392 >    data = rb->getPropertyByName("ATOMDATA");
393  
394 < //----------------------------------------------------------------------------//
394 >    if (data != NULL) {
395 >        atomData = dynamic_cast<AtomData *>(data);
396  
397 < void PrepareVisitor::internalVisit(Atom * atom){
398 <  GenericData* data;
399 <  AtomData* atomData;
397 >        if (atomData != NULL)
398 >            rb->removeProperty("ATOMDATA");
399 >    }
400  
401 <  //if visited property is  existed, remove it
367 <  data = atom->getProperty("VISITED");
368 <  if(data != NULL){
369 <    atom->removeProperty("VISITED");  
370 <  }
401 >    myAtoms = rb->getAtoms();
402  
403 <  //remove atomdata
404 <  data = atom->getProperty("ATOMDATA");
374 <  if(data != NULL){
375 <    atomData = dynamic_cast<AtomData*>(data);  
376 <    if(atomData != NULL)
377 <      atom->removeProperty("ATOMDATA");
378 <  }
379 <  
403 >    for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter )
404 >        internalVisit(*atomIter);
405   }
406  
407 < void PrepareVisitor::internalVisit(RigidBody * rb){
408 <  GenericData* data;
409 <  AtomData* atomData;
410 <  vector<Atom*> myAtoms;
411 <  vector<Atom*>::iterator atomIter;
412 <  
413 <  //if visited property is  existed, remove it
414 <  data = rb->getProperty("VISITED");
415 <  if(data != NULL){
416 <    rb->removeProperty("VISITED");  
417 <  }
418 <
419 <  //remove atomdata
420 <  data = rb->getProperty("ATOMDATA");
421 <  if(data != NULL){
422 <    atomData = dynamic_cast<AtomData*>(data);  
423 <    if(atomData != NULL)
424 <      rb->removeProperty("ATOMDATA");
425 <  }
426 <
402 <  myAtoms = rb->getAtoms();
403 <    
404 <  for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
405 <   internalVisit (*atomIter);  
407 > const std::string PrepareVisitor::toString() {
408 >     char buffer[65535];
409 >     std::string result;
410 >
411 >     sprintf(buffer,
412 >             "------------------------------------------------------------------\n");
413 >     result += buffer;
414 >
415 >     sprintf(buffer, "Visitor name: %s", visitorName.c_str());
416 >     result += buffer;
417 >
418 >     sprintf(buffer,
419 >             "Visitor Description: prepare for operation of other vistors\n");
420 >     result += buffer;
421 >
422 >     sprintf(buffer,
423 >             "------------------------------------------------------------------\n");
424 >     result += buffer;
425 >
426 >     return result;
427   }
428  
408 – const string PrepareVisitor::toString(){
409 –  char buffer[65535];
410 –  string result;
411 –  
412 –  sprintf(buffer ,"------------------------------------------------------------------\n");
413 –  result += buffer;
414 –
415 –  sprintf(buffer ,"Visitor name: %s", visitorName.c_str());
416 –  result += buffer;
417 –
418 –  sprintf(buffer ,"Visitor Description: prepare for operation of other vistors\n");
419 –  result += buffer;
420 –
421 –  sprintf(buffer ,"------------------------------------------------------------------\n");
422 –  result += buffer;
423 –
424 –  return result;
425 – }
426 –
429   //----------------------------------------------------------------------------//
430  
431 < WaterTypeVisitor:: WaterTypeVisitor(){
432 <  visitorName = "WaterTypeVisitor";
433 <  waterTypeList.insert("TIP3P_RB_0");
434 <  waterTypeList.insert("TIP4P_RB_0");
435 <  waterTypeList.insert("TIP5P_RB_0");
436 <  waterTypeList.insert("SPCE_RB_0");  
431 > WaterTypeVisitor::WaterTypeVisitor() {
432 >    visitorName = "WaterTypeVisitor";
433 >    waterTypeList.insert("TIP3P_RB_0");
434 >    waterTypeList.insert("TIP4P_RB_0");
435 >    waterTypeList.insert("TIP5P_RB_0");
436 >    waterTypeList.insert("SPCE_RB_0");
437   }
438  
439 + void WaterTypeVisitor::visit(RigidBody *rb) {
440 +    std::string rbName;
441 +    std::vector<Atom *> myAtoms;
442 +    std::vector<Atom *>::iterator atomIter;
443 +    GenericData* data;
444 +    AtomData* atomData;
445 +    AtomInfo* atomInfo;
446 +    std::vector<AtomInfo *>::iterator i;
447  
448 < void WaterTypeVisitor:: visit(RigidBody* rb){
439 <  string rbName;
440 <  vector<Atom*> myAtoms;
441 <  vector<Atom*>::iterator atomIter;
442 <  GenericData* data;
443 <  AtomData* atomData;
444 <  AtomInfo* atomInfo;
445 <  vector<AtomInfo*>::iterator i;
446 <  
447 <  rbName = rb->getType();
448 >    rbName = rb->getType();
449  
450 <  if(waterTypeList.find(rbName) != waterTypeList.end()){
450 >    if (waterTypeList.find(rbName) != waterTypeList.end()) {
451 >        myAtoms = rb->getAtoms();
452  
453 <    myAtoms = rb->getAtoms();    
454 <    for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter){
453 >        for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
454 >            ++atomIter ) {
455 >            data = (*atomIter)->getPropertyByName("ATOMDATA");
456  
457 <      data = (*atomIter)->getProperty("ATOMDATA");
458 <      if(data != NULL){
456 <        atomData = dynamic_cast<AtomData*>(data);  
457 <        if(atomData == NULL)
458 <          continue;
459 <      }
460 <      else
461 <        continue;
462 <      
463 <      for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)){
464 <        replaceType(atomInfo->AtomType);
465 <      }//end for(atomInfo)
457 >            if (data != NULL) {
458 >                atomData = dynamic_cast<AtomData *>(data);
459  
460 <    }//end for(atomIter)
461 <      
462 <  }//end if (waterTypeList.find(rbName) != waterTypeList.end())
463 <  
471 < }
460 >                if (atomData == NULL)
461 >                    continue;
462 >            } else
463 >                continue;
464  
465 < void WaterTypeVisitor:: replaceType(string& atomType){
466 <  atomType = atomType.substr(0, atomType.find('_'));
465 >            for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
466 >                 atomInfo = atomData->nextAtomInfo(i) ) {
467 >              atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName);
468 >            } //end for(atomInfo)
469 >        }     //end for(atomIter)
470 >    }         //end if (waterTypeList.find(rbName) != waterTypeList.end())
471   }
472  
473 < const string WaterTypeVisitor:: toString(){
474 <  char buffer[65535];
475 <  string result;
480 <  
481 <  sprintf(buffer ,"------------------------------------------------------------------\n");
482 <  result += buffer;
473 >  std::string WaterTypeVisitor::trimmedName(const std::string&atomTypeName) {
474 >    return atomTypeName.substr(0, atomTypeName.find('_'));
475 >  }
476  
477 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
478 <  result += buffer;
477 > const std::string WaterTypeVisitor::toString() {
478 >    char buffer[65535];
479 >    std::string result;
480  
481 <  sprintf(buffer ,"Visitor Description: Replace the atom type in water model\n");
482 <  result += buffer;
481 >    sprintf(buffer,
482 >            "------------------------------------------------------------------\n");
483 >    result += buffer;
484  
485 <  sprintf(buffer ,"------------------------------------------------------------------\n");
486 <  result += buffer;
485 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
486 >    result += buffer;
487  
488 <  return result;
489 < }
488 >    sprintf(buffer,
489 >            "Visitor Description: Replace the atom type in water model\n");
490 >    result += buffer;
491  
492 +    sprintf(buffer,
493 +            "------------------------------------------------------------------\n");
494 +    result += buffer;
495  
496 < }//namespace oopse
496 >    return result;
497 > }
498 >
499 > } //namespace oopse

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