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Comparing trunk/src/visitors/AtomVisitor.cpp (file contents):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1244 by xsun, Wed May 14 21:04:13 2008 UTC

# Line 1 | Line 1
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
# Line 42 | Line 42
42   #include <cstring>
43   #include "visitors/AtomVisitor.hpp"
44   #include "primitives/DirectionalAtom.hpp"
45 – #include "math/MatVec3.h"
45   #include "primitives/RigidBody.hpp"
46  
47   namespace oopse {
48 < void BaseAtomVisitor::visit(RigidBody *rb) {
49 < //vector<Atom*> myAtoms;
50 < //vector<Atom*>::iterator atomIter;
48 >  void BaseAtomVisitor::visit(RigidBody *rb) {
49 >    //vector<Atom*> myAtoms;
50 >    //vector<Atom*>::iterator atomIter;
51  
52 < //myAtoms = rb->getAtoms();
52 >    //myAtoms = rb->getAtoms();
53  
54 < //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
55 < //  (*atomIter)->accept(this);
56 <    }
54 >    //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
55 >    //  (*atomIter)->accept(this);
56 >  }
57  
58 < void BaseAtomVisitor::setVisited(Atom *atom) {
58 >  void BaseAtomVisitor::setVisited(Atom *atom) {
59      GenericData *data;
60      data = atom->getPropertyByName("VISITED");
61  
62      //if visited property is not existed, add it as new property
63      if (data == NULL) {
64 <        data = new GenericData();
65 <        data->setID("VISITED");
66 <        atom->addProperty(data);
64 >      data = new GenericData();
65 >      data->setID("VISITED");
66 >      atom->addProperty(data);
67      }
68 < }
68 >  }
69  
70 < bool BaseAtomVisitor::isVisited(Atom *atom) {
70 >  bool BaseAtomVisitor::isVisited(Atom *atom) {
71      GenericData *data;
72      data = atom->getPropertyByName("VISITED");
73      return data == NULL ? false : true;
74 < }
74 >  }
75  
76 < bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) {
77 <    std::vector<std::string>::iterator strIter;
76 >  bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) {
77 >    std::set<std::string>::iterator strIter;
78 >    strIter = ssdAtomType.find(atomType);
79 >    return strIter != ssdAtomType.end() ? true : false;
80 >  }
81  
82 <    for( strIter = ssdAtomType.begin(); strIter != ssdAtomType.end();
83 <        ++strIter )
82 <  if (*strIter == atomType)
83 <      return true;
82 >  void SSDAtomVisitor::visit(DirectionalAtom *datom) {
83 >    std::vector<AtomInfo*>atoms;
84  
85 <    return false;
86 < }
87 <
88 < void SSDAtomVisitor::visit(DirectionalAtom *datom) {
89 <    std::vector<AtomInfo *>atoms;
90 <
91 <    //we need to convert SSD into 4 differnet atoms
92 <    //one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
93 <    //of the water with a dipole moment
85 >    //we need to convert SSD into 4 different atoms
86 >    //one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of
87 >    //the mass of the water with a dipole moment
88      Vector3d h1(0.0, -0.75695, 0.5206);
89      Vector3d h2(0.0, 0.75695, 0.5206);
90      Vector3d ox(0.0, 0.0, -0.0654);
# Line 107 | Line 101 | void SSDAtomVisitor::visit(DirectionalAtom *datom) {
101  
102      //if atom is not SSD atom, just skip it
103      if (!isSSDAtom(datom->getType()))
104 <        return;
104 >      return;
105  
106      data = datom->getPropertyByName("ATOMDATA");
107  
108      if (data != NULL) {
109 <        atomData = dynamic_cast<AtomData *>(data);
109 >      atomData = dynamic_cast<AtomData *>(data);
110  
111 <        if (atomData == NULL) {
112 <            std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
113 <            atomData = new AtomData;
114 <            haveAtomData = false;
115 <        } else
116 <            haveAtomData = true;
111 >      if (atomData == NULL) {
112 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
113 >        atomData = new AtomData;
114 >        haveAtomData = false;
115 >      } else
116 >        haveAtomData = true;
117      } else {
118 <        atomData = new AtomData;
119 <        haveAtomData = false;
118 >      atomData = new AtomData;
119 >      haveAtomData = false;
120      }
121  
122      pos = datom->getPos();
# Line 138 | Line 132 | void SSDAtomVisitor::visit(DirectionalAtom *datom) {
132      newVec = rotTrans * u;
133  
134      atomInfo = new AtomInfo;
135 <    atomInfo->AtomType = "X";
135 >    atomInfo->atomTypeName = "X";
136      atomInfo->pos[0] = pos[0];
137      atomInfo->pos[1] = pos[1];
138      atomInfo->pos[2] = pos[2];
# Line 153 | Line 147 | void SSDAtomVisitor::visit(DirectionalAtom *datom) {
147      newVec = rotTrans * ox;
148  
149      atomInfo = new AtomInfo;
150 <    atomInfo->AtomType = "O";
150 >    atomInfo->atomTypeName = "O";
151      atomInfo->pos[0] = pos[0] + newVec[0];
152      atomInfo->pos[1] = pos[1] + newVec[1];
153      atomInfo->pos[2] = pos[2] + newVec[2];
# Line 166 | Line 160 | void SSDAtomVisitor::visit(DirectionalAtom *datom) {
160      //matVecMul3(rotTrans, h1, newVec);
161      newVec = rotTrans * h1;
162      atomInfo = new AtomInfo;
163 <    atomInfo->AtomType = "H";
163 >    atomInfo->atomTypeName = "H";
164      atomInfo->pos[0] = pos[0] + newVec[0];
165      atomInfo->pos[1] = pos[1] + newVec[1];
166      atomInfo->pos[2] = pos[2] + newVec[2];
# Line 179 | Line 173 | void SSDAtomVisitor::visit(DirectionalAtom *datom) {
173      //matVecMul3(rotTrans, h2, newVec);
174      newVec = rotTrans * h2;
175      atomInfo = new AtomInfo;
176 <    atomInfo->AtomType = "H";
176 >    atomInfo->atomTypeName = "H";
177      atomInfo->pos[0] = pos[0] + newVec[0];
178      atomInfo->pos[1] = pos[1] + newVec[1];
179      atomInfo->pos[2] = pos[2] + newVec[2];
# Line 191 | Line 185 | void SSDAtomVisitor::visit(DirectionalAtom *datom) {
185      //add atom data into atom's property
186  
187      if (!haveAtomData) {
188 <        atomData->setID("ATOMDATA");
189 <        datom->addProperty(atomData);
188 >      atomData->setID("ATOMDATA");
189 >      datom->addProperty(atomData);
190      }
191  
192      setVisited(datom);
193 < }
193 >  }
194  
195 < const std::string SSDAtomVisitor::toString() {
195 >  const std::string SSDAtomVisitor::toString() {
196      char   buffer[65535];
197      std::string result;
198  
# Line 218 | Line 212 | const std::string SSDAtomVisitor::toString() {
212      result += buffer;
213  
214      return result;
215 < }
215 >  }
216  
223 – bool LinearAtomVisitor::isLinearAtom(const string& atomType){
224 –  vector<string>::iterator strIter;
225 –  
226 –  for(strIter = linearAtomType.begin(); strIter != linearAtomType.end();
227 –      ++strIter)
228 –    if(*strIter == atomType)
229 –      return true;
230 –  
231 –  return false;  
232 – }
217  
218 < void LinearAtomVisitor::visit(DirectionalAtom* datom){
218 >  bool TREDAtomVisitor::isTREDAtom(const std::string&atomType) {
219 >    std::set<std::string>::iterator strIter;
220 >    strIter = tredAtomType.find(atomType);
221 >    return strIter != tredAtomType.end() ? true : false;
222 >  }
223  
224 <  vector<AtomInfo*> atoms;
224 >  void TREDAtomVisitor::visit(DirectionalAtom *datom) {
225 >    std::vector<AtomInfo*>atoms;
226  
227 <  //we need to convert linear into 4 different atoms
228 <  double c1[3] = {0.0, 0.0, -1.8};
229 <  double c2[3] = {0.0, 0.0, -0.6};
230 <  double c3[3] = {0.0, 0.0,  0.6};
231 <  double c4[3] = {0.0, 0.0,  1.8};
232 <  double rotMatrix[3][3];
233 <  double rotTrans[3][3];
234 <  AtomInfo* atomInfo;
235 <  double pos[3];
236 <  double newVec[3];
237 <  double q[4];
238 <  AtomData* atomData;
239 <  GenericData* data;
240 <  bool haveAtomData;
241 <  
242 <  //if atom is not SSD atom, just skip it
254 <  if(!isLinearAtom(datom->getType()))
255 <    return;
256 <  
257 <  data = datom->getProperty("ATOMDATA");
258 <  if(data != NULL){
227 >    // we need to convert a TRED into 4 different atoms:
228 >    // one oxygen atom, two hydrogen atoms, and one atom which is the center of
229 >    // the mass of the water with a dipole moment
230 >    Vector3d h1(0.0, -0.75695, 0.5206);
231 >    Vector3d h2(0.0, 0.75695, 0.5206);
232 >    Vector3d ox(0.0, 0.0, -0.0654);
233 >    Vector3d u(0, 0, 1);
234 >    RotMat3x3d   rotMatrix;
235 >    RotMat3x3d   rotTrans;
236 >    AtomInfo *   atomInfo;
237 >    Vector3d     pos;
238 >    Vector3d     newVec;
239 >    Quat4d       q;
240 >    AtomData *   atomData;
241 >    GenericData *data;
242 >    bool         haveAtomData;
243  
244 <    atomData = dynamic_cast<AtomData*>(data);  
245 <    if(atomData == NULL){
246 <      cerr << "can not get Atom Data from " << datom->getType() << endl;
263 <      atomData = new AtomData;
264 <      haveAtomData = false;      
265 <    }
266 <    else
267 <      haveAtomData = true;
268 <  }
269 <  else{
270 <    atomData = new AtomData;
271 <    haveAtomData = false;
272 <  }
273 <  
274 <  
275 <  datom->getPos(pos);
276 <  datom->getQ(q);
277 <  datom->getA(rotMatrix);
244 >    // if the atom is not a TRED atom, skip it
245 >    if (!isTREDAtom(datom->getType()))
246 >      return;
247  
248 <  // We need A^T to convert from body-fixed to space-fixed:
280 <  transposeMat3(rotMatrix, rotTrans);
281 <  
282 <  matVecMul3(rotTrans, c1, newVec);
283 <  atomInfo = new AtomInfo;
284 <  atomInfo->AtomType = "C";
285 <  atomInfo->pos[0] = pos[0] + newVec[0];
286 <  atomInfo->pos[1] = pos[1] + newVec[1];
287 <  atomInfo->pos[2] = pos[2] + newVec[2];
288 <  atomInfo->dipole[0] = 0.0;
289 <  atomInfo->dipole[1] = 0.0;
290 <  atomInfo->dipole[2] = 0.0;
291 <  atomData->addAtomInfo(atomInfo);
248 >    data = datom->getPropertyByName("ATOMDATA");
249  
250 <  matVecMul3(rotTrans, c2, newVec);
251 <  atomInfo = new AtomInfo;
295 <  atomInfo->AtomType = "C";
296 <  atomInfo->pos[0] = pos[0] + newVec[0];
297 <  atomInfo->pos[1] = pos[1] + newVec[1];
298 <  atomInfo->pos[2] = pos[2] + newVec[2];
299 <  atomInfo->dipole[0] = 0.0;
300 <  atomInfo->dipole[1] = 0.0;
301 <  atomInfo->dipole[2] = 0.0;
302 <  atomData->addAtomInfo(atomInfo);
250 >    if (data != NULL) {
251 >      atomData = dynamic_cast<AtomData *>(data);
252  
253 <  matVecMul3(rotTrans, c3, newVec);
254 <  atomInfo = new AtomInfo;
255 <  atomInfo->AtomType = "C";
256 <  atomInfo->pos[0] = pos[0] + newVec[0];
257 <  atomInfo->pos[1] = pos[1] + newVec[1];
258 <  atomInfo->pos[2] = pos[2] + newVec[2];
259 <  atomInfo->dipole[0] = 0.0;
260 <  atomInfo->dipole[1] = 0.0;
261 <  atomInfo->dipole[2] = 0.0;
262 <  atomData->addAtomInfo(atomInfo);
263 <
264 <  matVecMul3(rotTrans, c4, newVec);
265 <  atomInfo = new AtomInfo;
266 <  atomInfo->AtomType = "C";
267 <  atomInfo->pos[0] = pos[0] + newVec[0];
268 <  atomInfo->pos[1] = pos[1] + newVec[1];
269 <  atomInfo->pos[2] = pos[2] + newVec[2];
270 <  atomInfo->dipole[0] = 0.0;
271 <  atomInfo->dipole[1] = 0.0;
272 <  atomInfo->dipole[2] = 0.0;
273 <  atomData->addAtomInfo(atomInfo);
274 <
275 <  //add atom data into atom's property
276 <
277 <  if(!haveAtomData){
278 <    atomData->setID("ATOMDATA");
279 <    datom->addProperty(atomData);
253 >      if (atomData == NULL) {
254 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
255 >        atomData = new AtomData;
256 >        haveAtomData = false;
257 >      } else
258 >        haveAtomData = true;
259 >    } else {
260 >      atomData = new AtomData;
261 >      haveAtomData = false;
262 >    }
263 >
264 >    pos = datom->getPos();
265 >    q = datom->getQ();
266 >    rotMatrix = datom->getA();
267 >
268 >    // We need A^T to convert from body-fixed to space-fixed:
269 >    // transposeMat3(rotMatrix, rotTrans);
270 >    rotTrans = rotMatrix.transpose();
271 >
272 >    // center of mass of the water molecule
273 >    // matVecMul3(rotTrans, u, newVec);
274 >    newVec = rotTrans * u;
275 >
276 >    atomInfo = new AtomInfo;
277 >    atomInfo->atomTypeName = "TRED";
278 >    atomInfo->pos[0] = pos[0];
279 >    atomInfo->pos[1] = pos[1];
280 >    atomInfo->pos[2] = pos[2];
281 >    atomInfo->dipole[0] = newVec[0];
282 >    atomInfo->dipole[1] = newVec[1];
283 >    atomInfo->dipole[2] = newVec[2];
284 >
285 >    atomData->addAtomInfo(atomInfo);
286 >
287 >    // oxygen
288 >    // matVecMul3(rotTrans, ox, newVec);
289 >    newVec = rotTrans * ox;
290 >
291 >    atomInfo = new AtomInfo;
292 >    atomInfo->atomTypeName = "O";
293 >    atomInfo->pos[0] = pos[0] + newVec[0];
294 >    atomInfo->pos[1] = pos[1] + newVec[1];
295 >    atomInfo->pos[2] = pos[2] + newVec[2];
296 >    atomInfo->dipole[0] = 0.0;
297 >    atomInfo->dipole[1] = 0.0;
298 >    atomInfo->dipole[2] = 0.0;
299 >    atomData->addAtomInfo(atomInfo);
300 >
301 >    // hydrogen1
302 >    // matVecMul3(rotTrans, h1, newVec);
303 >    newVec = rotTrans * h1;
304 >    atomInfo = new AtomInfo;
305 >    atomInfo->atomTypeName = "H";
306 >    atomInfo->pos[0] = pos[0] + newVec[0];
307 >    atomInfo->pos[1] = pos[1] + newVec[1];
308 >    atomInfo->pos[2] = pos[2] + newVec[2];
309 >    atomInfo->dipole[0] = 0.0;
310 >    atomInfo->dipole[1] = 0.0;
311 >    atomInfo->dipole[2] = 0.0;
312 >    atomData->addAtomInfo(atomInfo);
313 >
314 >    // hydrogen2
315 >    // matVecMul3(rotTrans, h2, newVec);
316 >    newVec = rotTrans * h2;
317 >    atomInfo = new AtomInfo;
318 >    atomInfo->atomTypeName = "H";
319 >    atomInfo->pos[0] = pos[0] + newVec[0];
320 >    atomInfo->pos[1] = pos[1] + newVec[1];
321 >    atomInfo->pos[2] = pos[2] + newVec[2];
322 >    atomInfo->dipole[0] = 0.0;
323 >    atomInfo->dipole[1] = 0.0;
324 >    atomInfo->dipole[2] = 0.0;
325 >    atomData->addAtomInfo(atomInfo);
326 >
327 >    // add atom data into atom's property
328 >
329 >    if (!haveAtomData) {
330 >      atomData->setID("ATOMDATA");
331 >      datom->addProperty(atomData);
332 >    }
333 >
334 >    setVisited(datom);
335    }
336  
337 <  setVisited(datom);
337 >  const std::string TREDAtomVisitor::toString() {
338 >    char   buffer[65535];
339 >    std::string result;
340  
341 < }
341 >    sprintf(buffer,
342 >            "------------------------------------------------------------------\n");
343 >    result += buffer;
344  
345 < const string LinearAtomVisitor::toString(){
346 <  char buffer[65535];
339 <  string result;
340 <  
341 <  sprintf(buffer ,"------------------------------------------------------------------\n");
342 <  result += buffer;
345 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
346 >    result += buffer;
347  
348 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
349 <  result += buffer;
348 >    sprintf(buffer,
349 >            "Visitor Description: Convert the TRED atom into 4 different atoms\n");
350 >    result += buffer;
351  
352 <  sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
353 <  result += buffer;
352 >    sprintf(buffer,
353 >            "------------------------------------------------------------------\n");
354 >    result += buffer;
355  
356 <  sprintf(buffer ,"------------------------------------------------------------------\n");
357 <  result += buffer;
356 >    return result;
357 >  }
358  
353 –  return result;
354 – }
359  
360 < //----------------------------------------------------------------------------//
360 >  bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
361 >    std::set<std::string>::iterator strIter;
362 >    strIter = linearAtomType.find(atomType);
363  
364 < void DefaultAtomVisitor::visit(Atom *atom) {
364 >    return strIter != linearAtomType.end() ? true : false;
365 >  }
366 >
367 >  void LinearAtomVisitor::addGayBerneAtomType(const std::string& atomType){
368 >   linearAtomType.insert(atomType);
369 >  }
370 >
371 >  void LinearAtomVisitor::visit(DirectionalAtom* datom){
372 >    std::vector<AtomInfo*> atoms;
373 >    //we need to convert linear into 4 different atoms
374 >    Vector3d c1(0.0, 0.0, -1.8);
375 >    Vector3d c2(0.0, 0.0, -0.6);
376 >    Vector3d c3(0.0, 0.0,  0.6);
377 >    Vector3d c4(0.0, 0.0,  1.8);
378 >    RotMat3x3d rotMatrix;
379 >    RotMat3x3d rotTrans;
380 >    AtomInfo* atomInfo;
381 >    Vector3d pos;
382 >    Vector3d newVec;
383 >    Quat4d q;
384 >    AtomData* atomData;
385 >    GenericData* data;
386 >    bool haveAtomData;
387 >    AtomType* atomType;
388 >    //if atom is not linear atom, just skip it
389 >    if(!isLinearAtom(datom->getType()) || !datom->getAtomType()->isGayBerne())
390 >      return;
391 >
392 >    //setup GayBerne type in fortran side
393 >    data = datom->getAtomType()->getPropertyByName("GayBerne");
394 >    if (data != NULL) {
395 >       GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
396 >
397 >       if (gayBerneData != NULL) {
398 >           GayBerneParam gayBerneParam = gayBerneData->getData();
399 >
400 >                          // double halfLen = gayBerneParam.GB_sigma * gayBerneParam.GB_l2b_ratio/2.0;
401 >                          double halfLen = gayBerneParam.GB_l/2.0;
402 >                          c1[2] = -halfLen;
403 >              c2[2] = -halfLen /2;
404 >              c3[2] = halfLen/2;
405 >              c4[2] = halfLen;
406 >                
407 >            }
408 >            
409 >              else {
410 >                    sprintf( painCave.errMsg,
411 >                           "Can not cast GenericData to GayBerneParam\n");
412 >                    painCave.severity = OOPSE_ERROR;
413 >                    painCave.isFatal = 1;
414 >                    simError();          
415 >        }            
416 >    }
417 >
418 >
419 >    data = datom->getPropertyByName("ATOMDATA");
420 >    if(data != NULL){
421 >      atomData = dynamic_cast<AtomData*>(data);  
422 >      if(atomData == NULL){
423 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
424 >        atomData = new AtomData;
425 >        haveAtomData = false;      
426 >      } else {
427 >        haveAtomData = true;
428 >      }
429 >    } else {
430 >      atomData = new AtomData;
431 >      haveAtomData = false;
432 >    }
433 >  
434 >  
435 >    pos = datom->getPos();
436 >    q = datom->getQ();
437 >    rotMatrix = datom->getA();
438 >
439 >    // We need A^T to convert from body-fixed to space-fixed:  
440 >    rotTrans = rotMatrix.transpose();
441 >
442 >    newVec = rotTrans * c1;
443 >    atomInfo = new AtomInfo;
444 >    atomInfo->atomTypeName = "C";
445 >    atomInfo->pos[0] = pos[0] + newVec[0];
446 >    atomInfo->pos[1] = pos[1] + newVec[1];
447 >    atomInfo->pos[2] = pos[2] + newVec[2];
448 >    atomInfo->dipole[0] = 0.0;
449 >    atomInfo->dipole[1] = 0.0;
450 >    atomInfo->dipole[2] = 0.0;
451 >    atomData->addAtomInfo(atomInfo);
452 >
453 >    newVec = rotTrans * c2;
454 >    atomInfo = new AtomInfo;
455 >    atomInfo->atomTypeName = "C";
456 >    atomInfo->pos[0] = pos[0] + newVec[0];
457 >    atomInfo->pos[1] = pos[1] + newVec[1];
458 >    atomInfo->pos[2] = pos[2] + newVec[2];
459 >    atomInfo->dipole[0] = 0.0;
460 >    atomInfo->dipole[1] = 0.0;
461 >    atomInfo->dipole[2] = 0.0;
462 >    atomData->addAtomInfo(atomInfo);
463 >
464 >    newVec = rotTrans * c3;
465 >    atomInfo = new AtomInfo;
466 >    atomInfo->atomTypeName = "C";
467 >    atomInfo->pos[0] = pos[0] + newVec[0];
468 >    atomInfo->pos[1] = pos[1] + newVec[1];
469 >    atomInfo->pos[2] = pos[2] + newVec[2];
470 >    atomInfo->dipole[0] = 0.0;
471 >    atomInfo->dipole[1] = 0.0;
472 >    atomInfo->dipole[2] = 0.0;
473 >    atomData->addAtomInfo(atomInfo);
474 >
475 >    newVec = rotTrans * c4;
476 >    atomInfo = new AtomInfo;
477 >    atomInfo->atomTypeName = "C";
478 >    atomInfo->pos[0] = pos[0] + newVec[0];
479 >    atomInfo->pos[1] = pos[1] + newVec[1];
480 >    atomInfo->pos[2] = pos[2] + newVec[2];
481 >    atomInfo->dipole[0] = 0.0;
482 >    atomInfo->dipole[1] = 0.0;
483 >    atomInfo->dipole[2] = 0.0;
484 >    atomData->addAtomInfo(atomInfo);
485 >
486 >    //add atom data into atom's property
487 >
488 >    if(!haveAtomData){
489 >      atomData->setID("ATOMDATA");
490 >      datom->addProperty(atomData);
491 >    }
492 >
493 >    setVisited(datom);
494 >
495 >  }
496 >
497 >  const std::string LinearAtomVisitor::toString(){
498 >    char buffer[65535];
499 >    std::string result;
500 >  
501 >    sprintf(buffer ,"------------------------------------------------------------------\n");
502 >    result += buffer;
503 >
504 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
505 >    result += buffer;
506 >
507 >    sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
508 >    result += buffer;
509 >
510 >    sprintf(buffer ,"------------------------------------------------------------------\n");
511 >    result += buffer;
512 >
513 >    return result;
514 >  }
515 >
516 >  bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){
517 >    std::set<std::string>::iterator strIter;
518 >    strIter = GBLipidAtomType.find(atomType);
519 >
520 >    return strIter != GBLipidAtomType.end() ? true : false;
521 >  }
522 >
523 >  void GBLipidAtomVisitor::visit(DirectionalAtom* datom){
524 >    std::vector<AtomInfo*> atoms;
525 >    Vector3d c1(0.0, 0.0, 0.0);
526 >    Vector3d c2(0.0, 0.0, 1.0);
527 >    RotMat3x3d rotMatrix;
528 >    RotMat3x3d rotTrans;
529 >    AtomInfo* atomInfo;
530 >    Vector3d pos;
531 >    Vector3d newVec;
532 >    Vector3d dVec;
533 >    Quat4d q;
534 >    AtomData* atomData;
535 >    GenericData* data;
536 >    bool haveAtomData;
537 >
538 >    //if atom is not GBlipid atom, just skip it
539 >    if(!isGBLipidAtom(datom->getType()))
540 >      return;
541 >
542 >    data = datom->getPropertyByName("ATOMDATA");
543 >    if(data != NULL){
544 >      atomData = dynamic_cast<AtomData*>(data);  
545 >      if(atomData == NULL){
546 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
547 >        atomData = new AtomData;
548 >        haveAtomData = false;      
549 >      } else {
550 >        haveAtomData = true;
551 >      }
552 >    } else {
553 >      atomData = new AtomData;
554 >      haveAtomData = false;
555 >    }
556 >  
557 >  
558 >    pos = datom->getPos();
559 >    q = datom->getQ();
560 >    rotMatrix = datom->getA();
561 >
562 >    // We need A^T to convert from body-fixed to space-fixed:  
563 >    rotTrans = rotMatrix.transpose();
564 >
565 >    newVec = rotTrans * c1;
566 >    dVec = rotTrans * c2;
567 >    atomInfo = new AtomInfo;
568 >    atomInfo->atomTypeName = "GB";
569 >    atomInfo->pos[0] = pos[0] + newVec[0];
570 >    atomInfo->pos[1] = pos[1] + newVec[1];
571 >    atomInfo->pos[2] = pos[2] + newVec[2];
572 >    atomInfo->dipole[0] = dVec[0];
573 >    atomInfo->dipole[1] = dVec[1];
574 >    atomInfo->dipole[2] = dVec[2];
575 >    atomInfo->hasVector = true;
576 >    atomInfo->charge = 3.0;
577 >    atomInfo->hasCharge = true;
578 >    atomData->addAtomInfo(atomInfo);
579 >
580 >    //add atom data into atom's property
581 >
582 >    if(!haveAtomData){
583 >      atomData->setID("ATOMDATA");
584 >      datom->addProperty(atomData);
585 >    }
586 >
587 >    setVisited(datom);
588 >
589 >  }
590 >
591 >  const std::string GBLipidAtomVisitor::toString(){
592 >    char buffer[65535];
593 >    std::string result;
594 >  
595 >    sprintf(buffer ,"------------------------------------------------------------------\n");
596 >    result += buffer;
597 >
598 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
599 >    result += buffer;
600 >
601 >    sprintf(buffer , "Visitor Description: Convert GBlipid into xyz-formatted atom for use with xyz2pov\n");
602 >    result += buffer;
603 >
604 >    sprintf(buffer ,"------------------------------------------------------------------\n");
605 >    result += buffer;
606 >
607 >    return result;
608 >  }
609 >
610 >  bool Ring5gbAtomVisitor::isRing5gbAtom(const std::string& atomType){
611 >    std::set<std::string>::iterator strIter;
612 >    strIter = Ring5gbAtomType.find(atomType);
613 >
614 >    return strIter != Ring5gbAtomType.end() ? true : false;
615 >  }
616 >
617 >  void Ring5gbAtomVisitor::visit(DirectionalAtom* datom){
618 >    std::vector<AtomInfo*> atoms;
619 >    //we need to convert linear into 4 different atoms
620 >    Vector3d c1(0.0, 0.0, -5.5);
621 >    Vector3d c2(0.0, 0.0, -1.8);
622 >    Vector3d c3(0.0, 0.0,  1.8);
623 >    Vector3d c4(0.0, 0.0,  5.5);
624 >    RotMat3x3d rotMatrix;
625 >    RotMat3x3d rotTrans;
626 >    AtomInfo* atomInfo;
627 >    Vector3d pos;
628 >    Vector3d newVec;
629 >    Vector3d dVec;
630 >    Quat4d q;
631 >    AtomData* atomData;
632 >    GenericData* data;
633 >    bool haveAtomData;
634 >
635 >    //if atom is not Ring5GB atom, just skip it
636 >    if(!isRing5gbAtom(datom->getType()))
637 >      return;
638 >
639 >    data = datom->getPropertyByName("ATOMDATA");
640 >    if(data != NULL){
641 >      atomData = dynamic_cast<AtomData*>(data);  
642 >      if(atomData == NULL){
643 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
644 >        atomData = new AtomData;
645 >        haveAtomData = false;      
646 >      } else {
647 >        haveAtomData = true;
648 >      }
649 >    } else {
650 >      atomData = new AtomData;
651 >      haveAtomData = false;
652 >    }
653 >  
654 >  
655 >    pos = datom->getPos();
656 >    q = datom->getQ();
657 >    rotMatrix = datom->getA();
658 >
659 >    // We need A^T to convert from body-fixed to space-fixed:  
660 >    rotTrans = rotMatrix.transpose();
661 >
662 >    newVec = rotTrans * c1;
663 >    atomInfo = new AtomInfo;
664 >    atomInfo->atomTypeName = "K";
665 >    atomInfo->pos[0] = pos[0] + newVec[0];
666 >    atomInfo->pos[1] = pos[1] + newVec[1];
667 >    atomInfo->pos[2] = pos[2] + newVec[2];
668 >    atomInfo->dipole[0] = 0.0;
669 >    atomInfo->dipole[1] = 0.0;
670 >    atomInfo->dipole[2] = 0.0;
671 >    atomData->addAtomInfo(atomInfo);
672 >
673 >    newVec = rotTrans * c2;
674 >    atomInfo = new AtomInfo;
675 >    atomInfo->atomTypeName = "K";
676 >    atomInfo->pos[0] = pos[0] + newVec[0];
677 >    atomInfo->pos[1] = pos[1] + newVec[1];
678 >    atomInfo->pos[2] = pos[2] + newVec[2];
679 >    atomInfo->dipole[0] = 0.0;
680 >    atomInfo->dipole[1] = 0.0;
681 >    atomInfo->dipole[2] = 0.0;
682 >    atomData->addAtomInfo(atomInfo);
683 >
684 >    newVec = rotTrans * c3;
685 >    atomInfo = new AtomInfo;
686 >    atomInfo->atomTypeName = "K";
687 >    atomInfo->pos[0] = pos[0] + newVec[0];
688 >    atomInfo->pos[1] = pos[1] + newVec[1];
689 >    atomInfo->pos[2] = pos[2] + newVec[2];
690 >    atomInfo->dipole[0] = 0.0;
691 >    atomInfo->dipole[1] = 0.0;
692 >    atomInfo->dipole[2] = 0.0;
693 >    atomData->addAtomInfo(atomInfo);
694 >
695 >    newVec = rotTrans * c4;
696 >    atomInfo = new AtomInfo;
697 >    atomInfo->atomTypeName = "K";
698 >    atomInfo->pos[0] = pos[0] + newVec[0];
699 >    atomInfo->pos[1] = pos[1] + newVec[1];
700 >    atomInfo->pos[2] = pos[2] + newVec[2];
701 >    atomInfo->dipole[0] = 0.0;
702 >    atomInfo->dipole[1] = 0.0;
703 >    atomInfo->dipole[2] = 0.0;
704 >    atomData->addAtomInfo(atomInfo);
705 >
706 >    //add atom data into atom's property
707 >
708 >    if(!haveAtomData){
709 >      atomData->setID("ATOMDATA");
710 >      datom->addProperty(atomData);
711 >    }
712 >
713 >    setVisited(datom);
714 >
715 >  }
716 >
717 >  const std::string Ring5gbAtomVisitor::toString(){
718 >    char buffer[65535];
719 >    std::string result;
720 >  
721 >    sprintf(buffer ,"------------------------------------------------------------------\n");
722 >    result += buffer;
723 >
724 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
725 >    result += buffer;
726 >
727 >    sprintf(buffer , "Visitor Description: Convert Ring5GB into 4 different K atoms\n");
728 >    result += buffer;
729 >
730 >    sprintf(buffer ,"------------------------------------------------------------------\n");
731 >    result += buffer;
732 >
733 >    return result;
734 >  }
735 >
736 >  bool HeadAtomVisitor::isHeadAtom(const std::string& atomType){
737 >    std::set<std::string>::iterator strIter;
738 >    strIter = HeadAtomType.find(atomType);
739 >
740 >    return strIter != HeadAtomType.end() ? true : false;
741 >  }
742 >
743 >  void HeadAtomVisitor::visit(DirectionalAtom* datom){
744 >    std::vector<AtomInfo*> atoms;
745 >    //we need to convert linear into 2 different atoms
746 >    Vector3d c1(0.0, 0.0, -1.5);
747 >    Vector3d c2(0.0, 0.0, 1.5);
748 >    RotMat3x3d rotMatrix;
749 >    RotMat3x3d rotTrans;
750 >    AtomInfo* atomInfo;
751 >    Vector3d pos;
752 >    Vector3d newVec;
753 >    Vector3d dVec;
754 >    Quat4d q;
755 >    AtomData* atomData;
756 >    GenericData* data;
757 >    bool haveAtomData;
758 >
759 >    //if atom is not Head atom, just skip it
760 >    if(!isHeadAtom(datom->getType()))
761 >      return;
762 >
763 >    data = datom->getPropertyByName("ATOMDATA");
764 >    if(data != NULL){
765 >      atomData = dynamic_cast<AtomData*>(data);  
766 >      if(atomData == NULL){
767 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
768 >        atomData = new AtomData;
769 >        haveAtomData = false;      
770 >      } else {
771 >        haveAtomData = true;
772 >      }
773 >    } else {
774 >      atomData = new AtomData;
775 >      haveAtomData = false;
776 >    }
777 >  
778 >  
779 >    pos = datom->getPos();
780 >    q = datom->getQ();
781 >    rotMatrix = datom->getA();
782 >
783 >    // We need A^T to convert from body-fixed to space-fixed:  
784 >    rotTrans = rotMatrix.transpose();
785 >
786 >    newVec = rotTrans * c1;
787 >    atomInfo = new AtomInfo;
788 >    atomInfo->atomTypeName = "C";
789 >    atomInfo->pos[0] = pos[0] + newVec[0];
790 >    atomInfo->pos[1] = pos[1] + newVec[1];
791 >    atomInfo->pos[2] = pos[2] + newVec[2];
792 >    atomInfo->dipole[0] = 0.0;
793 >    atomInfo->dipole[1] = 0.0;
794 >    atomInfo->dipole[2] = 0.0;
795 >    atomData->addAtomInfo(atomInfo);
796 >
797 >    newVec = rotTrans * c2;
798 >    atomInfo = new AtomInfo;
799 >    atomInfo->atomTypeName = "O";
800 >    atomInfo->pos[0] = pos[0] + newVec[0];
801 >    atomInfo->pos[1] = pos[1] + newVec[1];
802 >    atomInfo->pos[2] = pos[2] + newVec[2];
803 >    atomInfo->dipole[0] = 0.0;
804 >    atomInfo->dipole[1] = 0.0;
805 >    atomInfo->dipole[2] = 0.0;
806 >    atomData->addAtomInfo(atomInfo);
807 >
808 >    //add atom data into atom's property
809 >
810 >    if(!haveAtomData){
811 >      atomData->setID("ATOMDATA");
812 >      datom->addProperty(atomData);
813 >    }
814 >
815 >    setVisited(datom);
816 >
817 >  }
818 >
819 >  const std::string HeadAtomVisitor::toString(){
820 >    char buffer[65535];
821 >    std::string result;
822 >  
823 >    sprintf(buffer ,"------------------------------------------------------------------\n");
824 >    result += buffer;
825 >
826 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
827 >    result += buffer;
828 >
829 >    sprintf(buffer , "Visitor Description: Convert HEAD into C atom and O atom\n");
830 >    result += buffer;
831 >
832 >    sprintf(buffer ,"------------------------------------------------------------------\n");
833 >    result += buffer;
834 >
835 >    return result;
836 >  }
837 >
838 >
839 >  //----------------------------------------------------------------------------//
840 >
841 >  void DefaultAtomVisitor::visit(Atom *atom) {
842      AtomData *atomData;
843      AtomInfo *atomInfo;
844      Vector3d  pos;
845  
846      if (isVisited(atom))
847 <        return;
847 >      return;
848  
849      atomInfo = new AtomInfo;
850  
# Line 369 | Line 852 | void DefaultAtomVisitor::visit(Atom *atom) {
852      atomData->setID("ATOMDATA");
853  
854      pos = atom->getPos();
855 <    atomInfo->AtomType = atom->getType();
855 >    atomInfo->atomTypeName = atom->getType();
856      atomInfo->pos[0] = pos[0];
857      atomInfo->pos[1] = pos[1];
858      atomInfo->pos[2] = pos[2];
# Line 382 | Line 865 | void DefaultAtomVisitor::visit(Atom *atom) {
865      atom->addProperty(atomData);
866  
867      setVisited(atom);
868 < }
868 >  }
869  
870 < void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
870 >  void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
871      AtomData *atomData;
872      AtomInfo *atomInfo;
873      Vector3d  pos;
874      Vector3d  u;
875  
876      if (isVisited(datom))
877 <        return;
877 >      return;
878  
879      pos = datom->getPos();
880 <    u = datom->getElectroFrame().getColumn(3);
881 <
880 >    if (datom->getAtomType()->isGayBerne()) {
881 >        u = datom->getA().transpose()*V3Z;        
882 >    } else if (datom->getAtomType()->isMultipole()) {
883 >        u = datom->getElectroFrame().getColumn(2);
884 >    }
885      atomData = new AtomData;
886      atomData->setID("ATOMDATA");
887      atomInfo = new AtomInfo;
888  
889 <    atomInfo->AtomType = datom->getType();
889 >    atomInfo->atomTypeName = datom->getType();
890      atomInfo->pos[0] = pos[0];
891      atomInfo->pos[1] = pos[1];
892      atomInfo->pos[2] = pos[2];
# Line 413 | Line 899 | void DefaultAtomVisitor::visit(DirectionalAtom *datom)
899      datom->addProperty(atomData);
900  
901      setVisited(datom);
902 < }
902 >  }
903  
904 < const std::string DefaultAtomVisitor::toString() {
904 >  const std::string DefaultAtomVisitor::toString() {
905      char   buffer[65535];
906      std::string result;
907  
# Line 435 | Line 921 | const std::string DefaultAtomVisitor::toString() {
921      result += buffer;
922  
923      return result;
924 < }
924 >  }
925   } //namespace oopse

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