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Comparing trunk/src/visitors/AtomVisitor.cpp (file contents):
Revision 132 by tim, Thu Oct 21 16:22:01 2004 UTC vs.
Revision 1008 by chrisfen, Wed Jul 19 12:35:31 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 "visitors/AtomVisitor.hpp"
44   #include "primitives/DirectionalAtom.hpp"
4 – #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;
51  
52 < void BaseAtomVisitor::visit(RigidBody* rb){
10 <  //vector<Atom*> myAtoms;
11 <  //vector<Atom*>::iterator atomIter;
52 >    //myAtoms = rb->getAtoms();
53  
54 <  //myAtoms = rb->getAtoms();
55 <  
56 <  //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
16 <  //  (*atomIter)->accept(this);
17 < }
54 >    //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
55 >    //  (*atomIter)->accept(this);
56 >  }
57  
58 < void BaseAtomVisitor::setVisited(Atom* atom){
59 <  GenericData* data;
60 <  data = atom->getProperty("VISITED");
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);  
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 >    }
68    }
29 – }
69  
70 < bool BaseAtomVisitor::isVisited(Atom* atom){
71 <  GenericData* data;
72 <  data = atom->getProperty("VISITED");
73 <  return data == NULL ?  false : true;
74 < }
70 >  bool BaseAtomVisitor::isVisited(Atom *atom) {
71 >    GenericData *data;
72 >    data = atom->getPropertyByName("VISITED");
73 >    return data == NULL ? false : true;
74 >  }
75  
76 < bool SSDAtomVisitor::isSSDAtom(const string& atomType){
77 <  vector<string>::iterator strIter;
78 <  
79 <  for(strIter = ssdAtomType.begin(); strIter != ssdAtomType.end(); ++strIter)
80 <   if(*strIter == atomType)
42 <    return true;
43 <  
44 <  return false;  
45 < }
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 < void SSDAtomVisitor::visit(DirectionalAtom* datom){
82 >  void SSDAtomVisitor::visit(DirectionalAtom *datom) {
83 >    std::vector<AtomInfo*>atoms;
84  
85 <  vector<AtomInfo*> atoms;
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);
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 <  //we need to convert SSD into 4 differnet atoms
103 <  //one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
104 <  //of the water with a dipole moment
54 <  double h1[3] = {0.0, -0.75695, 0.5206};
55 <  double h2[3] = {0.0, 0.75695, 0.5206};
56 <  double ox[3] = {0.0, 0.0, -0.0654};
57 <  double u[3] = {0, 0, 1};
58 <  double rotMatrix[3][3];
59 <  double rotTrans[3][3];
60 <  AtomInfo* atomInfo;
61 <  double pos[3];
62 <  double newVec[3];
63 <  double q[4];
64 <  AtomData* atomData;
65 <  GenericData* data;
66 <  bool haveAtomData;
67 <  
68 <  //if atom is not SSD atom, just skip it
69 <  if(!isSSDAtom(datom->getType()))
70 <    return;
102 >    //if atom is not SSD atom, just skip it
103 >    if (!isSSDAtom(datom->getType()))
104 >      return;
105  
106 <  data = datom->getProperty("ATOMDATA");
73 <  if(data != NULL){
106 >    data = datom->getPropertyByName("ATOMDATA");
107  
108 <    atomData = dynamic_cast<AtomData*>(data);  
109 <    if(atomData == NULL){
110 <      cerr << "can not get Atom Data from " << datom->getType() << endl;
111 <      atomData = new AtomData;
112 <      haveAtomData = false;      
108 >    if (data != NULL) {
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;
117 >    } else {
118 >      atomData = new AtomData;
119 >      haveAtomData = false;
120      }
81 –    else
82 –      haveAtomData = true;
83 –  }
84 –  else{
85 –    atomData = new AtomData;
86 –    haveAtomData = false;
87 –  }
88 –  
89 –  
90 –  datom->getPos(pos);
91 –  datom->getQ(q);
92 –  datom->getA(rotMatrix);
121  
122 <  // We need A^T to convert from body-fixed to space-fixed:
123 <  transposeMat3(rotMatrix, rotTrans);
124 <  
97 <  //center of mass of the water molecule
98 <  matVecMul3(rotTrans, u, newVec);
99 <  atomInfo = new AtomInfo;
100 <  atomInfo->AtomType = "X";
101 <  atomInfo->pos[0] = pos[0];
102 <  atomInfo->pos[1] = pos[1];
103 <  atomInfo->pos[2] = pos[2];
104 <  atomInfo->dipole[0] = newVec[0];
105 <  atomInfo->dipole[1] = newVec[1];
106 <  atomInfo->dipole[2] = newVec[2];
122 >    pos = datom->getPos();
123 >    q = datom->getQ();
124 >    rotMatrix = datom->getA();
125  
126 <  atomData->addAtomInfo(atomInfo);
126 >    // We need A^T to convert from body-fixed to space-fixed:
127 >    //transposeMat3(rotMatrix, rotTrans);
128 >    rotTrans = rotMatrix.transpose();
129  
130 <  //oxygen
131 <  matVecMul3(rotTrans, ox, newVec);
132 <  atomInfo = new AtomInfo;
113 <  atomInfo->AtomType = "O";
114 <  atomInfo->pos[0] = pos[0] + newVec[0];
115 <  atomInfo->pos[1] = pos[1] + newVec[1];
116 <  atomInfo->pos[2] = pos[2] + newVec[2];
117 <  atomInfo->dipole[0] = 0.0;
118 <  atomInfo->dipole[1] = 0.0;
119 <  atomInfo->dipole[2] = 0.0;
120 <  atomData->addAtomInfo(atomInfo);
130 >    //center of mass of the water molecule
131 >    //matVecMul3(rotTrans, u, newVec);
132 >    newVec = rotTrans * u;
133  
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 <  //hydrogen1
124 <    matVecMul3(rotTrans, h1, newVec);
125 <  atomInfo = new AtomInfo;
126 <  atomInfo->AtomType = "H";
127 <  atomInfo->pos[0] = pos[0] + newVec[0];
128 <  atomInfo->pos[1] = pos[1] + newVec[1];
129 <  atomInfo->pos[2] = pos[2] + newVec[2];
130 <  atomInfo->dipole[0] = 0.0;
131 <  atomInfo->dipole[1] = 0.0;
132 <  atomInfo->dipole[2] = 0.0;
133 <  atomData->addAtomInfo(atomInfo);
143 >    atomData->addAtomInfo(atomInfo);
144  
145 <  //hydrogen2
146 <  matVecMul3(rotTrans, h2, newVec);
147 <  atomInfo = new AtomInfo;
138 <  atomInfo->AtomType = "H";
139 <  atomInfo->pos[0] = pos[0] + newVec[0];
140 <  atomInfo->pos[1] = pos[1] + newVec[1];
141 <  atomInfo->pos[2] = pos[2] + newVec[2];
142 <  atomInfo->dipole[0] = 0.0;
143 <  atomInfo->dipole[1] = 0.0;
144 <  atomInfo->dipole[2] = 0.0;
145 <  atomData->addAtomInfo(atomInfo);
146 <
147 <  //add atom data into atom's property
145 >    //oxygen
146 >    //matVecMul3(rotTrans, ox, newVec);
147 >    newVec = rotTrans * ox;
148  
149 <  if(!haveAtomData){
150 <    atomData->setID("ATOMDATA");
151 <    datom->addProperty(atomData);
152 <  }
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 <  setVisited(datom);
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 < const string SSDAtomVisitor::toString(){
159 <  char buffer[65535];
160 <  string result;
161 <  
162 <  sprintf(buffer ,"------------------------------------------------------------------\n");
163 <  result += buffer;
185 >    //add atom data into atom's property
186  
187 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
188 <  result += buffer;
187 >    if (!haveAtomData) {
188 >      atomData->setID("ATOMDATA");
189 >      datom->addProperty(atomData);
190 >    }
191  
192 <  sprintf(buffer , "Visitor Description: Convert SSD into 4 different atoms\n");
193 <  result += buffer;
192 >    setVisited(datom);
193 >  }
194  
195 <  sprintf(buffer ,"------------------------------------------------------------------\n");
196 <  result += buffer;
195 >  const std::string SSDAtomVisitor::toString() {
196 >    char   buffer[65535];
197 >    std::string result;
198  
199 <  return result;
200 < }
199 >    sprintf(buffer,
200 >            "------------------------------------------------------------------\n");
201 >    result += buffer;
202  
203 < //----------------------------------------------------------------------------//
203 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
204 >    result += buffer;
205  
206 < void DefaultAtomVisitor::visit(Atom* atom){
207 <  AtomData* atomData;
208 <  AtomInfo* atomInfo;
182 <  double pos[3];
206 >    sprintf(buffer,
207 >            "Visitor Description: Convert SSD into 4 different atoms\n");
208 >    result += buffer;
209  
210 <  if(isVisited(atom))
211 <    return;
210 >    sprintf(buffer,
211 >            "------------------------------------------------------------------\n");
212 >    result += buffer;
213  
214 < atomInfo =new AtomInfo;
214 >    return result;
215 >  }
216  
189 –  atomData = new AtomData;
190 –  atomData->setID("ATOMDATA");
191 –
192 –  atom->getPos(pos);
193 –  atomInfo->AtomType = atom->getType();
194 –  atomInfo->pos[0] = pos[0];
195 –  atomInfo->pos[1] = pos[1];
196 –  atomInfo->pos[2] = pos[2];
197 –  atomInfo->dipole[0] = 0.0;
198 –  atomInfo->dipole[1] = 0.0;
199 –  atomInfo->dipole[2] = 0.0;
217  
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 <  atomData->addAtomInfo(atomInfo);
225 <  
204 <  atom->addProperty(atomData);
224 >  void TREDAtomVisitor::visit(DirectionalAtom *datom) {
225 >    std::vector<AtomInfo*>atoms;
226  
227 <  setVisited(atom);
228 < }
229 < void DefaultAtomVisitor::visit(DirectionalAtom* datom){
230 <  AtomData* atomData;
231 <  AtomInfo* atomInfo;
232 <  double pos[3];
233 <  double u[3];
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 <  if(isVisited(datom))
245 <    return;
246 <  
217 <  datom->getPos(pos);
218 <  datom->getU(u);
244 >    // if the atom is not a TRED atom, skip it
245 >    if (!isTREDAtom(datom->getType()))
246 >      return;
247  
248 <  atomData = new AtomData;
221 <  atomData->setID("ATOMDATA");
222 <  atomInfo =new AtomInfo;
223 <  
224 <  atomInfo->AtomType = datom->getType();
225 <  atomInfo->pos[0] = pos[0];
226 <  atomInfo->pos[1] = pos[1];
227 <  atomInfo->pos[2] = pos[2];
228 <  atomInfo->dipole[0] = u[0];
229 <  atomInfo->dipole[1] = u[1];
230 <  atomInfo->dipole[2] = u[2];  
248 >    data = datom->getPropertyByName("ATOMDATA");
249  
250 <  atomData->addAtomInfo(atomInfo);
250 >    if (data != NULL) {
251 >      atomData = dynamic_cast<AtomData *>(data);
252  
253 <  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 <  setVisited(datom);
265 < }
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 < const string DefaultAtomVisitor::toString(){
273 <  char buffer[65535];
274 <  string result;
243 <  
244 <  sprintf(buffer ,"------------------------------------------------------------------\n");
245 <  result += buffer;
272 >    // center of mass of the water molecule
273 >    // matVecMul3(rotTrans, u, newVec);
274 >    newVec = rotTrans * u;
275  
276 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
277 <  result += buffer;
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 <  sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n");
251 <  result += buffer;
285 >    atomData->addAtomInfo(atomInfo);
286  
287 <  sprintf(buffer ,"------------------------------------------------------------------\n");
288 <  result += buffer;
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 <  return result;
302 < }    
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 < }//namespace oopse
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 >  const std::string TREDAtomVisitor::toString() {
338 >    char   buffer[65535];
339 >    std::string result;
340 >
341 >    sprintf(buffer,
342 >            "------------------------------------------------------------------\n");
343 >    result += buffer;
344 >
345 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
346 >    result += buffer;
347 >
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;
650 >
651 >    atomInfo = new AtomInfo;
652 >
653 >    atomData = new AtomData;
654 >    atomData->setID("ATOMDATA");
655 >
656 >    pos = atom->getPos();
657 >    atomInfo->atomTypeName = atom->getType();
658 >    atomInfo->pos[0] = pos[0];
659 >    atomInfo->pos[1] = pos[1];
660 >    atomInfo->pos[2] = pos[2];
661 >    atomInfo->dipole[0] = 0.0;
662 >    atomInfo->dipole[1] = 0.0;
663 >    atomInfo->dipole[2] = 0.0;
664 >
665 >    atomData->addAtomInfo(atomInfo);
666 >
667 >    atom->addProperty(atomData);
668 >
669 >    setVisited(atom);
670 >  }
671 >
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;
680 >
681 >    pos = datom->getPos();
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->atomTypeName = datom->getType();
692 >    atomInfo->pos[0] = pos[0];
693 >    atomInfo->pos[1] = pos[1];
694 >    atomInfo->pos[2] = pos[2];
695 >    atomInfo->dipole[0] = u[0];
696 >    atomInfo->dipole[1] = u[1];
697 >    atomInfo->dipole[2] = u[2];
698 >
699 >    atomData->addAtomInfo(atomInfo);
700 >
701 >    datom->addProperty(atomData);
702 >
703 >    setVisited(datom);
704 >  }
705 >
706 >  const std::string DefaultAtomVisitor::toString() {
707 >    char   buffer[65535];
708 >    std::string result;
709 >
710 >    sprintf(buffer,
711 >            "------------------------------------------------------------------\n");
712 >    result += buffer;
713 >
714 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
715 >    result += buffer;
716 >
717 >    sprintf(buffer,
718 >            "Visitor Description: copy atom infomation into atom data\n");
719 >    result += buffer;
720 >
721 >    sprintf(buffer,
722 >            "------------------------------------------------------------------\n");
723 >    result += buffer;
724 >
725 >    return result;
726 >  }
727 > } //namespace oopse

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