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Comparing trunk/src/visitors/AtomVisitor.cpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 989 by tim, Sat Jun 17 17:02:33 2006 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 +
42   #include <cstring>
43 < #include "AtomVisitor.hpp"
44 < #include "DirectionalAtom.hpp"
45 < #include "MatVec3.h"
5 < #include "RigidBody.hpp"
43 > #include "visitors/AtomVisitor.hpp"
44 > #include "primitives/DirectionalAtom.hpp"
45 > #include "primitives/RigidBody.hpp"
46  
47 < void BaseAtomVisitor::visit(RigidBody* rb){
48 <  //vector<Atom*> myAtoms;
49 <  //vector<Atom*>::iterator atomIter;
47 > namespace oopse {
48 >  void BaseAtomVisitor::visit(RigidBody *rb) {
49 >    //vector<Atom*> myAtoms;
50 >    //vector<Atom*>::iterator atomIter;
51  
52 <  //myAtoms = rb->getAtoms();
12 <  
13 <  //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
14 <  //  (*atomIter)->accept(this);
15 < }
52 >    //myAtoms = rb->getAtoms();
53  
54 < void BaseAtomVisitor::setVisited(Atom* atom){
55 <  GenericData* data;
19 <  data = atom->getProperty("VISITED");
20 <
21 <  //if visited property is not existed, add it as new property
22 <  if(data == NULL){
23 <    data = new GenericData();
24 <    data->setID("VISITED");
25 <    atom->addProperty(data);  
54 >    //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
55 >    //  (*atomIter)->accept(this);
56    }
27 – }
57  
58 < bool BaseAtomVisitor::isVisited(Atom* atom){
59 <  GenericData* data;
60 <  data = atom->getProperty("VISITED");
32 <  return data == NULL ?  false : true;
33 < }
58 >  void BaseAtomVisitor::setVisited(Atom *atom) {
59 >    GenericData *data;
60 >    data = atom->getPropertyByName("VISITED");
61  
62 < bool SSDAtomVisitor::isSSDAtom(const string& atomType){
63 <  vector<string>::iterator strIter;
64 <  
65 <  for(strIter = ssdAtomType.begin(); strIter != ssdAtomType.end(); ++strIter)
66 <   if(*strIter == atomType)
40 <    return true;
41 <  
42 <  return false;  
43 < }
44 <
45 < void SSDAtomVisitor::visit(DirectionalAtom* datom){
46 <
47 <  vector<AtomInfo*> atoms;
48 <
49 <  //we need to convert SSD into 4 differnet atoms
50 <  //one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
51 <  //of the water with a dipole moment
52 <  double h1[3] = {0.0, -0.75695, 0.5206};
53 <  double h2[3] = {0.0, 0.75695, 0.5206};
54 <  double ox[3] = {0.0, 0.0, -0.0654};
55 <  double u[3] = {0, 0, 1};
56 <  double rotMatrix[3][3];
57 <  double rotTrans[3][3];
58 <  AtomInfo* atomInfo;
59 <  double pos[3];
60 <  double newVec[3];
61 <  double q[4];
62 <  AtomData* atomData;
63 <  GenericData* data;
64 <  bool haveAtomData;
65 <  
66 <  //if atom is not SSD atom, just skip it
67 <  if(!isSSDAtom(datom->getType()))
68 <    return;
69 <
70 <  data = datom->getProperty("ATOMDATA");
71 <  if(data != NULL){
72 <
73 <    atomData = dynamic_cast<AtomData*>(data);  
74 <    if(atomData == NULL){
75 <      cerr << "can not get Atom Data from " << datom->getType() << endl;
76 <      atomData = new AtomData;
77 <      haveAtomData = false;      
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);
67      }
79 –    else
80 –      haveAtomData = true;
68    }
69 <  else{
70 <    atomData = new AtomData;
71 <    haveAtomData = false;
69 >
70 >  bool BaseAtomVisitor::isVisited(Atom *atom) {
71 >    GenericData *data;
72 >    data = atom->getPropertyByName("VISITED");
73 >    return data == NULL ? false : true;
74    }
86 –  
87 –  
88 –  datom->getPos(pos);
89 –  datom->getQ(q);
90 –  datom->getA(rotMatrix);
75  
76 <  // We need A^T to convert from body-fixed to space-fixed:
77 <  transposeMat3(rotMatrix, rotTrans);
78 <  
79 <  //center of mass of the water molecule
80 <  matVecMul3(rotTrans, u, newVec);
97 <  atomInfo = new AtomInfo;
98 <  atomInfo->AtomType = "X";
99 <  atomInfo->pos[0] = pos[0];
100 <  atomInfo->pos[1] = pos[1];
101 <  atomInfo->pos[2] = pos[2];
102 <  atomInfo->dipole[0] = newVec[0];
103 <  atomInfo->dipole[1] = newVec[1];
104 <  atomInfo->dipole[2] = newVec[2];
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 <  atomData->addAtomInfo(atomInfo);
82 >  void SSDAtomVisitor::visit(DirectionalAtom *datom) {
83 >    std::vector<AtomInfo*>atoms;
84  
85 <  //oxygen
86 <  matVecMul3(rotTrans, ox, newVec);
87 <  atomInfo = new AtomInfo;
88 <  atomInfo->AtomType = "O";
89 <  atomInfo->pos[0] = pos[0] + newVec[0];
90 <  atomInfo->pos[1] = pos[1] + newVec[1];
91 <  atomInfo->pos[2] = pos[2] + newVec[2];
92 <  atomInfo->dipole[0] = 0.0;
93 <  atomInfo->dipole[1] = 0.0;
94 <  atomInfo->dipole[2] = 0.0;
95 <  atomData->addAtomInfo(atomInfo);
85 >    //we need to convert SSD into 4 differnet atoms
86 >    //one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
87 >    //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);
91 >    Vector3d u(0, 0, 1);
92 >    RotMat3x3d   rotMatrix;
93 >    RotMat3x3d   rotTrans;
94 >    AtomInfo *   atomInfo;
95 >    Vector3d     pos;
96 >    Vector3d     newVec;
97 >    Quat4d       q;
98 >    AtomData *   atomData;
99 >    GenericData *data;
100 >    bool         haveAtomData;
101  
102 +    //if atom is not SSD atom, just skip it
103 +    if (!isSSDAtom(datom->getType()))
104 +      return;
105  
106 <  //hydrogen1
122 <    matVecMul3(rotTrans, h1, newVec);
123 <  atomInfo = new AtomInfo;
124 <  atomInfo->AtomType = "H";
125 <  atomInfo->pos[0] = pos[0] + newVec[0];
126 <  atomInfo->pos[1] = pos[1] + newVec[1];
127 <  atomInfo->pos[2] = pos[2] + newVec[2];
128 <  atomInfo->dipole[0] = 0.0;
129 <  atomInfo->dipole[1] = 0.0;
130 <  atomInfo->dipole[2] = 0.0;
131 <  atomData->addAtomInfo(atomInfo);
106 >    data = datom->getPropertyByName("ATOMDATA");
107  
108 <  //hydrogen2
109 <  matVecMul3(rotTrans, h2, newVec);
135 <  atomInfo = new AtomInfo;
136 <  atomInfo->AtomType = "H";
137 <  atomInfo->pos[0] = pos[0] + newVec[0];
138 <  atomInfo->pos[1] = pos[1] + newVec[1];
139 <  atomInfo->pos[2] = pos[2] + newVec[2];
140 <  atomInfo->dipole[0] = 0.0;
141 <  atomInfo->dipole[1] = 0.0;
142 <  atomInfo->dipole[2] = 0.0;
143 <  atomData->addAtomInfo(atomInfo);
108 >    if (data != NULL) {
109 >      atomData = dynamic_cast<AtomData *>(data);
110  
111 <  //add atom data into atom's property
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;
120 >    }
121  
122 <  if(!haveAtomData){
123 <    atomData->setID("ATOMDATA");
124 <    datom->addProperty(atomData);
150 <  }
122 >    pos = datom->getPos();
123 >    q = datom->getQ();
124 >    rotMatrix = datom->getA();
125  
126 <  setVisited(datom);
126 >    // We need A^T to convert from body-fixed to space-fixed:
127 >    //transposeMat3(rotMatrix, rotTrans);
128 >    rotTrans = rotMatrix.transpose();
129  
130 < }
130 >    //center of mass of the water molecule
131 >    //matVecMul3(rotTrans, u, newVec);
132 >    newVec = rotTrans * u;
133  
134 < const string SSDAtomVisitor::toString(){
135 <  char buffer[65535];
136 <  string result;
137 <  
138 <  sprintf(buffer ,"------------------------------------------------------------------\n");
139 <  result += buffer;
134 >    atomInfo = new AtomInfo;
135 >    atomInfo->atomTypeName = "X";
136 >    atomInfo->pos[0] = pos[0];
137 >    atomInfo->pos[1] = pos[1];
138 >    atomInfo->pos[2] = pos[2];
139 >    atomInfo->dipole[0] = newVec[0];
140 >    atomInfo->dipole[1] = newVec[1];
141 >    atomInfo->dipole[2] = newVec[2];
142  
143 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
164 <  result += buffer;
143 >    atomData->addAtomInfo(atomInfo);
144  
145 <  sprintf(buffer , "Visitor Description: Convert SSD into 4 different atoms\n");
146 <  result += buffer;
145 >    //oxygen
146 >    //matVecMul3(rotTrans, ox, newVec);
147 >    newVec = rotTrans * ox;
148  
149 <  sprintf(buffer ,"------------------------------------------------------------------\n");
150 <  result += buffer;
149 >    atomInfo = new AtomInfo;
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];
154 >    atomInfo->dipole[0] = 0.0;
155 >    atomInfo->dipole[1] = 0.0;
156 >    atomInfo->dipole[2] = 0.0;
157 >    atomData->addAtomInfo(atomInfo);
158  
159 <  return result;
160 < }
159 >    //hydrogen1
160 >    //matVecMul3(rotTrans, h1, newVec);
161 >    newVec = rotTrans * h1;
162 >    atomInfo = new AtomInfo;
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];
167 >    atomInfo->dipole[0] = 0.0;
168 >    atomInfo->dipole[1] = 0.0;
169 >    atomInfo->dipole[2] = 0.0;
170 >    atomData->addAtomInfo(atomInfo);
171  
172 < //----------------------------------------------------------------------------//
172 >    //hydrogen2
173 >    //matVecMul3(rotTrans, h2, newVec);
174 >    newVec = rotTrans * h2;
175 >    atomInfo = new AtomInfo;
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];
180 >    atomInfo->dipole[0] = 0.0;
181 >    atomInfo->dipole[1] = 0.0;
182 >    atomInfo->dipole[2] = 0.0;
183 >    atomData->addAtomInfo(atomInfo);
184  
185 < void DefaultAtomVisitor::visit(Atom* atom){
178 <  AtomData* atomData;
179 <  AtomInfo* atomInfo;
180 <  double pos[3];
185 >    //add atom data into atom's property
186  
187 <  if(isVisited(atom))
188 <    return;
187 >    if (!haveAtomData) {
188 >      atomData->setID("ATOMDATA");
189 >      datom->addProperty(atomData);
190 >    }
191  
192 < atomInfo =new AtomInfo;
192 >    setVisited(datom);
193 >  }
194  
195 <  atomData = new AtomData;
196 <  atomData->setID("ATOMDATA");
197 <
190 <  atom->getPos(pos);
191 <  atomInfo->AtomType = atom->getType();
192 <  atomInfo->pos[0] = pos[0];
193 <  atomInfo->pos[1] = pos[1];
194 <  atomInfo->pos[2] = pos[2];
195 <  atomInfo->dipole[0] = 0.0;
196 <  atomInfo->dipole[1] = 0.0;
197 <  atomInfo->dipole[2] = 0.0;
195 >  const std::string SSDAtomVisitor::toString() {
196 >    char   buffer[65535];
197 >    std::string result;
198  
199 +    sprintf(buffer,
200 +            "------------------------------------------------------------------\n");
201 +    result += buffer;
202  
203 <  atomData->addAtomInfo(atomInfo);
204 <  
202 <  atom->addProperty(atomData);
203 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
204 >    result += buffer;
205  
206 <  setVisited(atom);
207 < }
208 < void DefaultAtomVisitor::visit(DirectionalAtom* datom){
207 <  AtomData* atomData;
208 <  AtomInfo* atomInfo;
209 <  double pos[3];
210 <  double u[3];
206 >    sprintf(buffer,
207 >            "Visitor Description: Convert SSD into 4 different atoms\n");
208 >    result += buffer;
209  
210 <  if(isVisited(datom))
211 <    return;
212 <  
215 <  datom->getPos(pos);
216 <  datom->getU(u);
210 >    sprintf(buffer,
211 >            "------------------------------------------------------------------\n");
212 >    result += buffer;
213  
214 <  atomData = new AtomData;
215 <  atomData->setID("ATOMDATA");
220 <  atomInfo =new AtomInfo;
221 <  
222 <  atomInfo->AtomType = datom->getType();
223 <  atomInfo->pos[0] = pos[0];
224 <  atomInfo->pos[1] = pos[1];
225 <  atomInfo->pos[2] = pos[2];
226 <  atomInfo->dipole[0] = u[0];
227 <  atomInfo->dipole[1] = u[1];
228 <  atomInfo->dipole[2] = u[2];  
214 >    return result;
215 >  }
216  
217 <  atomData->addAtomInfo(atomInfo);
218 <
219 <  datom->addProperty(atomData);
233 <
234 <  setVisited(datom);
235 < }
217 >  bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
218 >    std::set<std::string>::iterator strIter;
219 >    strIter = linearAtomType.find(atomType);
220  
221 +    return strIter != linearAtomType.end() ? true : false;
222 +  }
223  
224 < const string DefaultAtomVisitor::toString(){
225 <  char buffer[65535];
226 <  string result;
224 >  void LinearAtomVisitor::addGayBerneAtomType(const std::string& atomType){
225 >   linearAtomType.insert(atomType);
226 >  }
227 >
228 >  void LinearAtomVisitor::visit(DirectionalAtom* datom){
229 >    std::vector<AtomInfo*> atoms;
230 >    //we need to convert linear into 4 different atoms
231 >    Vector3d c1(0.0, 0.0, -1.8);
232 >    Vector3d c2(0.0, 0.0, -0.6);
233 >    Vector3d c3(0.0, 0.0,  0.6);
234 >    Vector3d c4(0.0, 0.0,  1.8);
235 >    RotMat3x3d rotMatrix;
236 >    RotMat3x3d rotTrans;
237 >    AtomInfo* atomInfo;
238 >    Vector3d pos;
239 >    Vector3d newVec;
240 >    Quat4d q;
241 >    AtomData* atomData;
242 >    GenericData* data;
243 >    bool haveAtomData;
244 >    AtomType* atomType;
245 >    //if atom is not SSD atom, just skip it
246 >    if(!isLinearAtom(datom->getType()) || !datom->getAtomType()->isGayBerne())
247 >      return;
248 >
249 >    //setup GayBerne type in fortran side
250 >    data = datom->getAtomType()->getPropertyByName("GayBerne");
251 >    if (data != NULL) {
252 >       GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
253 >
254 >       if (gayBerneData != NULL) {
255 >           GayBerneParam gayBerneParam = gayBerneData->getData();
256 >
257 >                                          double halfLen = gayBerneParam.GB_sigma * gayBerneParam.GB_l2b_ratio/2.0;
258 >                                                        c1[2] = -halfLen;
259 >              c2[2] = -halfLen /2;
260 >              c3[2] = halfLen/2;
261 >              c4[2] = halfLen;
262 >                
263 >            }
264 >            
265 >              else {
266 >                    sprintf( painCave.errMsg,
267 >                           "Can not cast GenericData to GayBerneParam\n");
268 >                    painCave.severity = OOPSE_ERROR;
269 >                    painCave.isFatal = 1;
270 >                    simError();          
271 >        }            
272 >    }
273 >
274 >
275 >    data = datom->getPropertyByName("ATOMDATA");
276 >    if(data != NULL){
277 >      atomData = dynamic_cast<AtomData*>(data);  
278 >      if(atomData == NULL){
279 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
280 >        atomData = new AtomData;
281 >        haveAtomData = false;      
282 >      } else {
283 >        haveAtomData = true;
284 >      }
285 >    } else {
286 >      atomData = new AtomData;
287 >      haveAtomData = false;
288 >    }
289 >  
290    
291 <  sprintf(buffer ,"------------------------------------------------------------------\n");
292 <  result += buffer;
291 >    pos = datom->getPos();
292 >    q = datom->getQ();
293 >    rotMatrix = datom->getA();
294  
295 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
296 <  result += buffer;
295 >    // We need A^T to convert from body-fixed to space-fixed:  
296 >    rotTrans = rotMatrix.transpose();
297  
298 <  sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n");
299 <  result += buffer;
298 >    newVec = rotTrans * c1;
299 >    atomInfo = new AtomInfo;
300 >    atomInfo->atomTypeName = "C";
301 >    atomInfo->pos[0] = pos[0] + newVec[0];
302 >    atomInfo->pos[1] = pos[1] + newVec[1];
303 >    atomInfo->pos[2] = pos[2] + newVec[2];
304 >    atomInfo->dipole[0] = 0.0;
305 >    atomInfo->dipole[1] = 0.0;
306 >    atomInfo->dipole[2] = 0.0;
307 >    atomData->addAtomInfo(atomInfo);
308  
309 <  sprintf(buffer ,"------------------------------------------------------------------\n");
310 <  result += buffer;
309 >    newVec = rotTrans * c2;
310 >    atomInfo = new AtomInfo;
311 >    atomInfo->atomTypeName = "C";
312 >    atomInfo->pos[0] = pos[0] + newVec[0];
313 >    atomInfo->pos[1] = pos[1] + newVec[1];
314 >    atomInfo->pos[2] = pos[2] + newVec[2];
315 >    atomInfo->dipole[0] = 0.0;
316 >    atomInfo->dipole[1] = 0.0;
317 >    atomInfo->dipole[2] = 0.0;
318 >    atomData->addAtomInfo(atomInfo);
319  
320 <  return result;
321 < }    
320 >    newVec = rotTrans * c3;
321 >    atomInfo = new AtomInfo;
322 >    atomInfo->atomTypeName = "C";
323 >    atomInfo->pos[0] = pos[0] + newVec[0];
324 >    atomInfo->pos[1] = pos[1] + newVec[1];
325 >    atomInfo->pos[2] = pos[2] + newVec[2];
326 >    atomInfo->dipole[0] = 0.0;
327 >    atomInfo->dipole[1] = 0.0;
328 >    atomInfo->dipole[2] = 0.0;
329 >    atomData->addAtomInfo(atomInfo);
330 >
331 >    newVec = rotTrans * c4;
332 >    atomInfo = new AtomInfo;
333 >    atomInfo->atomTypeName = "C";
334 >    atomInfo->pos[0] = pos[0] + newVec[0];
335 >    atomInfo->pos[1] = pos[1] + newVec[1];
336 >    atomInfo->pos[2] = pos[2] + newVec[2];
337 >    atomInfo->dipole[0] = 0.0;
338 >    atomInfo->dipole[1] = 0.0;
339 >    atomInfo->dipole[2] = 0.0;
340 >    atomData->addAtomInfo(atomInfo);
341 >
342 >    //add atom data into atom's property
343 >
344 >    if(!haveAtomData){
345 >      atomData->setID("ATOMDATA");
346 >      datom->addProperty(atomData);
347 >    }
348 >
349 >    setVisited(datom);
350 >
351 >  }
352 >
353 >  const std::string LinearAtomVisitor::toString(){
354 >    char buffer[65535];
355 >    std::string result;
356 >  
357 >    sprintf(buffer ,"------------------------------------------------------------------\n");
358 >    result += buffer;
359 >
360 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
361 >    result += buffer;
362 >
363 >    sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
364 >    result += buffer;
365 >
366 >    sprintf(buffer ,"------------------------------------------------------------------\n");
367 >    result += buffer;
368 >
369 >    return result;
370 >  }
371 >
372 >  bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){
373 >    std::set<std::string>::iterator strIter;
374 >    strIter = GBLipidAtomType.find(atomType);
375 >
376 >    return strIter != GBLipidAtomType.end() ? true : false;
377 >  }
378 >
379 >  void GBLipidAtomVisitor::visit(DirectionalAtom* datom){
380 >    std::vector<AtomInfo*> atoms;
381 >    //we need to convert linear into 4 different atoms
382 >    Vector3d c1(0.0, 0.0, -6.25);
383 >    Vector3d c2(0.0, 0.0, -2.1);
384 >    Vector3d c3(0.0, 0.0,  2.1);
385 >    Vector3d c4(0.0, 0.0,  6.25);
386 >    RotMat3x3d rotMatrix;
387 >    RotMat3x3d rotTrans;
388 >    AtomInfo* atomInfo;
389 >    Vector3d pos;
390 >    Vector3d newVec;
391 >    Quat4d q;
392 >    AtomData* atomData;
393 >    GenericData* data;
394 >    bool haveAtomData;
395 >
396 >    //if atom is not GBlipid atom, just skip it
397 >    if(!isGBLipidAtom(datom->getType()))
398 >      return;
399 >
400 >    data = datom->getPropertyByName("ATOMDATA");
401 >    if(data != NULL){
402 >      atomData = dynamic_cast<AtomData*>(data);  
403 >      if(atomData == NULL){
404 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
405 >        atomData = new AtomData;
406 >        haveAtomData = false;      
407 >      } else {
408 >        haveAtomData = true;
409 >      }
410 >    } else {
411 >      atomData = new AtomData;
412 >      haveAtomData = false;
413 >    }
414 >  
415 >  
416 >    pos = datom->getPos();
417 >    q = datom->getQ();
418 >    rotMatrix = datom->getA();
419 >
420 >    // We need A^T to convert from body-fixed to space-fixed:  
421 >    rotTrans = rotMatrix.transpose();
422 >
423 >    newVec = rotTrans * c1;
424 >    atomInfo = new AtomInfo;
425 >    atomInfo->atomTypeName = "K";
426 >    atomInfo->pos[0] = pos[0] + newVec[0];
427 >    atomInfo->pos[1] = pos[1] + newVec[1];
428 >    atomInfo->pos[2] = pos[2] + newVec[2];
429 >    atomInfo->dipole[0] = 0.0;
430 >    atomInfo->dipole[1] = 0.0;
431 >    atomInfo->dipole[2] = 0.0;
432 >    atomData->addAtomInfo(atomInfo);
433 >
434 >    newVec = rotTrans * c2;
435 >    atomInfo = new AtomInfo;
436 >    atomInfo->atomTypeName = "K";
437 >    atomInfo->pos[0] = pos[0] + newVec[0];
438 >    atomInfo->pos[1] = pos[1] + newVec[1];
439 >    atomInfo->pos[2] = pos[2] + newVec[2];
440 >    atomInfo->dipole[0] = 0.0;
441 >    atomInfo->dipole[1] = 0.0;
442 >    atomInfo->dipole[2] = 0.0;
443 >    atomData->addAtomInfo(atomInfo);
444 >
445 >    newVec = rotTrans * c3;
446 >    atomInfo = new AtomInfo;
447 >    atomInfo->atomTypeName = "K";
448 >    atomInfo->pos[0] = pos[0] + newVec[0];
449 >    atomInfo->pos[1] = pos[1] + newVec[1];
450 >    atomInfo->pos[2] = pos[2] + newVec[2];
451 >    atomInfo->dipole[0] = 0.0;
452 >    atomInfo->dipole[1] = 0.0;
453 >    atomInfo->dipole[2] = 0.0;
454 >    atomData->addAtomInfo(atomInfo);
455 >
456 >    newVec = rotTrans * c4;
457 >    atomInfo = new AtomInfo;
458 >    atomInfo->atomTypeName = "K";
459 >    atomInfo->pos[0] = pos[0] + newVec[0];
460 >    atomInfo->pos[1] = pos[1] + newVec[1];
461 >    atomInfo->pos[2] = pos[2] + newVec[2];
462 >    atomInfo->dipole[0] = 0.0;
463 >    atomInfo->dipole[1] = 0.0;
464 >    atomInfo->dipole[2] = 0.0;
465 >    atomData->addAtomInfo(atomInfo);
466 >
467 >    //add atom data into atom's property
468 >
469 >    if(!haveAtomData){
470 >      atomData->setID("ATOMDATA");
471 >      datom->addProperty(atomData);
472 >    }
473 >
474 >    setVisited(datom);
475 >
476 >  }
477 >
478 >  const std::string GBLipidAtomVisitor::toString(){
479 >    char buffer[65535];
480 >    std::string result;
481 >  
482 >    sprintf(buffer ,"------------------------------------------------------------------\n");
483 >    result += buffer;
484 >
485 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
486 >    result += buffer;
487 >
488 >    sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n");
489 >    result += buffer;
490 >
491 >    sprintf(buffer ,"------------------------------------------------------------------\n");
492 >    result += buffer;
493 >
494 >    return result;
495 >  }
496 >
497 >  //----------------------------------------------------------------------------//
498 >
499 >  void DefaultAtomVisitor::visit(Atom *atom) {
500 >    AtomData *atomData;
501 >    AtomInfo *atomInfo;
502 >    Vector3d  pos;
503 >
504 >    if (isVisited(atom))
505 >      return;
506 >
507 >    atomInfo = new AtomInfo;
508 >
509 >    atomData = new AtomData;
510 >    atomData->setID("ATOMDATA");
511 >
512 >    pos = atom->getPos();
513 >    atomInfo->atomTypeName = atom->getType();
514 >    atomInfo->pos[0] = pos[0];
515 >    atomInfo->pos[1] = pos[1];
516 >    atomInfo->pos[2] = pos[2];
517 >    atomInfo->dipole[0] = 0.0;
518 >    atomInfo->dipole[1] = 0.0;
519 >    atomInfo->dipole[2] = 0.0;
520 >
521 >    atomData->addAtomInfo(atomInfo);
522 >
523 >    atom->addProperty(atomData);
524 >
525 >    setVisited(atom);
526 >  }
527 >
528 >  void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
529 >    AtomData *atomData;
530 >    AtomInfo *atomInfo;
531 >    Vector3d  pos;
532 >    Vector3d  u;
533 >
534 >    if (isVisited(datom))
535 >      return;
536 >
537 >    pos = datom->getPos();
538 >    if (datom->getAtomType()->isGayBerne()) {
539 >        u = datom->getA().transpose()*V3Z;        
540 >    } else if (datom->getAtomType()->isMultipole()) {
541 >        u = datom->getElectroFrame().getColumn(2);
542 >    }
543 >    atomData = new AtomData;
544 >    atomData->setID("ATOMDATA");
545 >    atomInfo = new AtomInfo;
546 >
547 >    atomInfo->atomTypeName = datom->getType();
548 >    atomInfo->pos[0] = pos[0];
549 >    atomInfo->pos[1] = pos[1];
550 >    atomInfo->pos[2] = pos[2];
551 >    atomInfo->dipole[0] = u[0];
552 >    atomInfo->dipole[1] = u[1];
553 >    atomInfo->dipole[2] = u[2];
554 >
555 >    atomData->addAtomInfo(atomInfo);
556 >
557 >    datom->addProperty(atomData);
558 >
559 >    setVisited(datom);
560 >  }
561 >
562 >  const std::string DefaultAtomVisitor::toString() {
563 >    char   buffer[65535];
564 >    std::string result;
565 >
566 >    sprintf(buffer,
567 >            "------------------------------------------------------------------\n");
568 >    result += buffer;
569 >
570 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
571 >    result += buffer;
572 >
573 >    sprintf(buffer,
574 >            "Visitor Description: copy atom infomation into atom data\n");
575 >    result += buffer;
576 >
577 >    sprintf(buffer,
578 >            "------------------------------------------------------------------\n");
579 >    result += buffer;
580 >
581 >    return result;
582 >  }
583 > } //namespace oopse

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