ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/visitors/AtomVisitor.cpp
(Generate patch)

Comparing trunk/src/visitors/AtomVisitor.cpp (file contents):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1008 by chrisfen, Wed Jul 19 12:35:31 2006 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;
247 <      atomData = new AtomData;
248 <      haveAtomData = false;      
244 >    // if the atom is not a TRED atom, skip it
245 >    if (!isTREDAtom(datom->getType()))
246 >      return;
247 >
248 >    data = datom->getPropertyByName("ATOMDATA");
249 >
250 >    if (data != NULL) {
251 >      atomData = dynamic_cast<AtomData *>(data);
252 >
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 <    else
264 <      haveAtomData = true;
265 <  }
266 <  else{
270 <    atomData = new AtomData;
271 <    haveAtomData = false;
272 <  }
273 <  
274 <  
275 <  datom->getPos(pos);
276 <  datom->getQ(q);
277 <  datom->getA(rotMatrix);
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 <  
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);
268 >    // We need A^T to convert from body-fixed to space-fixed:
269 >    // transposeMat3(rotMatrix, rotTrans);
270 >    rotTrans = rotMatrix.transpose();
271  
272 <  matVecMul3(rotTrans, c2, newVec);
273 <  atomInfo = new AtomInfo;
274 <  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);
272 >    // center of mass of the water molecule
273 >    // matVecMul3(rotTrans, u, newVec);
274 >    newVec = rotTrans * u;
275  
276 <  matVecMul3(rotTrans, c3, newVec);
277 <  atomInfo = new AtomInfo;
278 <  atomInfo->AtomType = "C";
279 <  atomInfo->pos[0] = pos[0] + newVec[0];
280 <  atomInfo->pos[1] = pos[1] + newVec[1];
281 <  atomInfo->pos[2] = pos[2] + newVec[2];
282 <  atomInfo->dipole[0] = 0.0;
283 <  atomInfo->dipole[1] = 0.0;
312 <  atomInfo->dipole[2] = 0.0;
313 <  atomData->addAtomInfo(atomInfo);
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 <  matVecMul3(rotTrans, c4, newVec);
316 <  atomInfo = new AtomInfo;
317 <  atomInfo->AtomType = "C";
318 <  atomInfo->pos[0] = pos[0] + newVec[0];
319 <  atomInfo->pos[1] = pos[1] + newVec[1];
320 <  atomInfo->pos[2] = pos[2] + newVec[2];
321 <  atomInfo->dipole[0] = 0.0;
322 <  atomInfo->dipole[1] = 0.0;
323 <  atomInfo->dipole[2] = 0.0;
324 <  atomData->addAtomInfo(atomInfo);
285 >    atomData->addAtomInfo(atomInfo);
286  
287 <  //add atom data into atom's property
287 >    // oxygen
288 >    // matVecMul3(rotTrans, ox, newVec);
289 >    newVec = rotTrans * ox;
290  
291 <  if(!haveAtomData){
292 <    atomData->setID("ATOMDATA");
293 <    datom->addProperty(atomData);
294 <  }
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 <  setVisited(datom);
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 < }
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 < const string LinearAtomVisitor::toString(){
338 <  char buffer[65535];
339 <  string result;
340 <  
341 <  sprintf(buffer ,"------------------------------------------------------------------\n");
342 <  result += buffer;
327 >    // add atom data into atom's property
328  
329 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
330 <  result += buffer;
329 >    if (!haveAtomData) {
330 >      atomData->setID("ATOMDATA");
331 >      datom->addProperty(atomData);
332 >    }
333  
334 <  sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
335 <  result += buffer;
334 >    setVisited(datom);
335 >  }
336  
337 <  sprintf(buffer ,"------------------------------------------------------------------\n");
338 <  result += buffer;
337 >  const std::string TREDAtomVisitor::toString() {
338 >    char   buffer[65535];
339 >    std::string result;
340  
341 <  return result;
342 < }
341 >    sprintf(buffer,
342 >            "------------------------------------------------------------------\n");
343 >    result += buffer;
344  
345 < //----------------------------------------------------------------------------//
345 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
346 >    result += buffer;
347  
348 < void DefaultAtomVisitor::visit(Atom *atom) {
348 >    sprintf(buffer,
349 >            "Visitor Description: Convert the TRED atom into 4 different atoms\n");
350 >    result += buffer;
351 >
352 >    sprintf(buffer,
353 >            "------------------------------------------------------------------\n");
354 >    result += buffer;
355 >
356 >    return result;
357 >  }
358 >
359 >
360 >  bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
361 >    std::set<std::string>::iterator strIter;
362 >    strIter = linearAtomType.find(atomType);
363 >
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 >    //we need to convert linear into 4 different atoms
526 >    Vector3d c1(0.0, 0.0, -6.25);
527 >    Vector3d c2(0.0, 0.0, -2.1);
528 >    Vector3d c3(0.0, 0.0,  2.1);
529 >    Vector3d c4(0.0, 0.0,  6.25);
530 >    RotMat3x3d rotMatrix;
531 >    RotMat3x3d rotTrans;
532 >    AtomInfo* atomInfo;
533 >    Vector3d pos;
534 >    Vector3d newVec;
535 >    Quat4d q;
536 >    AtomData* atomData;
537 >    GenericData* data;
538 >    bool haveAtomData;
539 >
540 >    //if atom is not GBlipid atom, just skip it
541 >    if(!isGBLipidAtom(datom->getType()))
542 >      return;
543 >
544 >    data = datom->getPropertyByName("ATOMDATA");
545 >    if(data != NULL){
546 >      atomData = dynamic_cast<AtomData*>(data);  
547 >      if(atomData == NULL){
548 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
549 >        atomData = new AtomData;
550 >        haveAtomData = false;      
551 >      } else {
552 >        haveAtomData = true;
553 >      }
554 >    } else {
555 >      atomData = new AtomData;
556 >      haveAtomData = false;
557 >    }
558 >  
559 >  
560 >    pos = datom->getPos();
561 >    q = datom->getQ();
562 >    rotMatrix = datom->getA();
563 >
564 >    // We need A^T to convert from body-fixed to space-fixed:  
565 >    rotTrans = rotMatrix.transpose();
566 >
567 >    newVec = rotTrans * c1;
568 >    atomInfo = new AtomInfo;
569 >    atomInfo->atomTypeName = "K";
570 >    atomInfo->pos[0] = pos[0] + newVec[0];
571 >    atomInfo->pos[1] = pos[1] + newVec[1];
572 >    atomInfo->pos[2] = pos[2] + newVec[2];
573 >    atomInfo->dipole[0] = 0.0;
574 >    atomInfo->dipole[1] = 0.0;
575 >    atomInfo->dipole[2] = 0.0;
576 >    atomData->addAtomInfo(atomInfo);
577 >
578 >    newVec = rotTrans * c2;
579 >    atomInfo = new AtomInfo;
580 >    atomInfo->atomTypeName = "K";
581 >    atomInfo->pos[0] = pos[0] + newVec[0];
582 >    atomInfo->pos[1] = pos[1] + newVec[1];
583 >    atomInfo->pos[2] = pos[2] + newVec[2];
584 >    atomInfo->dipole[0] = 0.0;
585 >    atomInfo->dipole[1] = 0.0;
586 >    atomInfo->dipole[2] = 0.0;
587 >    atomData->addAtomInfo(atomInfo);
588 >
589 >    newVec = rotTrans * c3;
590 >    atomInfo = new AtomInfo;
591 >    atomInfo->atomTypeName = "K";
592 >    atomInfo->pos[0] = pos[0] + newVec[0];
593 >    atomInfo->pos[1] = pos[1] + newVec[1];
594 >    atomInfo->pos[2] = pos[2] + newVec[2];
595 >    atomInfo->dipole[0] = 0.0;
596 >    atomInfo->dipole[1] = 0.0;
597 >    atomInfo->dipole[2] = 0.0;
598 >    atomData->addAtomInfo(atomInfo);
599 >
600 >    newVec = rotTrans * c4;
601 >    atomInfo = new AtomInfo;
602 >    atomInfo->atomTypeName = "K";
603 >    atomInfo->pos[0] = pos[0] + newVec[0];
604 >    atomInfo->pos[1] = pos[1] + newVec[1];
605 >    atomInfo->pos[2] = pos[2] + newVec[2];
606 >    atomInfo->dipole[0] = 0.0;
607 >    atomInfo->dipole[1] = 0.0;
608 >    atomInfo->dipole[2] = 0.0;
609 >    atomData->addAtomInfo(atomInfo);
610 >
611 >    //add atom data into atom's property
612 >
613 >    if(!haveAtomData){
614 >      atomData->setID("ATOMDATA");
615 >      datom->addProperty(atomData);
616 >    }
617 >
618 >    setVisited(datom);
619 >
620 >  }
621 >
622 >  const std::string GBLipidAtomVisitor::toString(){
623 >    char buffer[65535];
624 >    std::string result;
625 >  
626 >    sprintf(buffer ,"------------------------------------------------------------------\n");
627 >    result += buffer;
628 >
629 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
630 >    result += buffer;
631 >
632 >    sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n");
633 >    result += buffer;
634 >
635 >    sprintf(buffer ,"------------------------------------------------------------------\n");
636 >    result += buffer;
637 >
638 >    return result;
639 >  }
640 >
641 >  //----------------------------------------------------------------------------//
642 >
643 >  void DefaultAtomVisitor::visit(Atom *atom) {
644      AtomData *atomData;
645      AtomInfo *atomInfo;
646      Vector3d  pos;
647  
648      if (isVisited(atom))
649 <        return;
649 >      return;
650  
651      atomInfo = new AtomInfo;
652  
# Line 369 | Line 654 | void DefaultAtomVisitor::visit(Atom *atom) {
654      atomData->setID("ATOMDATA");
655  
656      pos = atom->getPos();
657 <    atomInfo->AtomType = atom->getType();
657 >    atomInfo->atomTypeName = atom->getType();
658      atomInfo->pos[0] = pos[0];
659      atomInfo->pos[1] = pos[1];
660      atomInfo->pos[2] = pos[2];
# Line 382 | Line 667 | void DefaultAtomVisitor::visit(Atom *atom) {
667      atom->addProperty(atomData);
668  
669      setVisited(atom);
670 < }
670 >  }
671  
672 < void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
672 >  void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
673      AtomData *atomData;
674      AtomInfo *atomInfo;
675      Vector3d  pos;
676      Vector3d  u;
677  
678      if (isVisited(datom))
679 <        return;
679 >      return;
680  
681      pos = datom->getPos();
682 <    u = datom->getElectroFrame().getColumn(3);
683 <
682 >    if (datom->getAtomType()->isGayBerne()) {
683 >        u = datom->getA().transpose()*V3Z;        
684 >    } else if (datom->getAtomType()->isMultipole()) {
685 >        u = datom->getElectroFrame().getColumn(2);
686 >    }
687      atomData = new AtomData;
688      atomData->setID("ATOMDATA");
689      atomInfo = new AtomInfo;
690  
691 <    atomInfo->AtomType = datom->getType();
691 >    atomInfo->atomTypeName = datom->getType();
692      atomInfo->pos[0] = pos[0];
693      atomInfo->pos[1] = pos[1];
694      atomInfo->pos[2] = pos[2];
# Line 413 | Line 701 | void DefaultAtomVisitor::visit(DirectionalAtom *datom)
701      datom->addProperty(atomData);
702  
703      setVisited(datom);
704 < }
704 >  }
705  
706 < const std::string DefaultAtomVisitor::toString() {
706 >  const std::string DefaultAtomVisitor::toString() {
707      char   buffer[65535];
708      std::string result;
709  
# Line 435 | Line 723 | const std::string DefaultAtomVisitor::toString() {
723      result += buffer;
724  
725      return result;
726 < }
726 >  }
727   } //namespace oopse

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines