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Comparing trunk/src/visitors/AtomVisitor.cpp (file contents):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 1291 by gezelter, Thu Sep 11 19:40:59 2008 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 < 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 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 +    //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  
230 –  atomData->addAtomInfo(atomInfo);
217  
218 <  datom->addProperty(atomData);
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 <  setVisited(datom);
225 < }
224 >  void TREDAtomVisitor::visit(DirectionalAtom *datom) {
225 >    std::vector<AtomInfo*>atoms;
226  
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 < const string DefaultAtomVisitor::toString(){
245 <  char buffer[65535];
246 <  string result;
241 <  
242 <  sprintf(buffer ,"------------------------------------------------------------------\n");
243 <  result += buffer;
244 >    // if the atom is not a TRED atom, skip it
245 >    if (!isTREDAtom(datom->getType()))
246 >      return;
247  
248 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
246 <  result += buffer;
248 >    data = datom->getPropertyByName("ATOMDATA");
249  
250 <  sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n");
251 <  result += buffer;
250 >    if (data != NULL) {
251 >      atomData = dynamic_cast<AtomData *>(data);
252  
253 <  sprintf(buffer ,"------------------------------------------------------------------\n");
254 <  result += buffer;
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 <  return result;
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 >    // 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 >  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 >    //if atom is not linear atom, just skip it
388 >    if(!isLinearAtom(datom->getType()) || !datom->getAtomType()->isGayBerne())
389 >      return;
390 >
391 >    //setup GayBerne type in fortran side
392 >    data = datom->getAtomType()->getPropertyByName("GayBerne");
393 >    if (data != NULL) {
394 >       GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
395 >
396 >       if (gayBerneData != NULL) {
397 >           GayBerneParam gayBerneParam = gayBerneData->getData();
398 >
399 >                          // double halfLen = gayBerneParam.GB_sigma * gayBerneParam.GB_l2b_ratio/2.0;
400 >                          double halfLen = gayBerneParam.GB_l/2.0;
401 >                          c1[2] = -halfLen;
402 >              c2[2] = -halfLen /2;
403 >              c3[2] = halfLen/2;
404 >              c4[2] = halfLen;
405 >                
406 >            }
407 >            
408 >              else {
409 >                    sprintf( painCave.errMsg,
410 >                           "Can not cast GenericData to GayBerneParam\n");
411 >                    painCave.severity = OOPSE_ERROR;
412 >                    painCave.isFatal = 1;
413 >                    simError();          
414 >        }            
415 >    }
416 >
417 >
418 >    data = datom->getPropertyByName("ATOMDATA");
419 >    if(data != NULL){
420 >      atomData = dynamic_cast<AtomData*>(data);  
421 >      if(atomData == NULL){
422 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
423 >        atomData = new AtomData;
424 >        haveAtomData = false;      
425 >      } else {
426 >        haveAtomData = true;
427 >      }
428 >    } else {
429 >      atomData = new AtomData;
430 >      haveAtomData = false;
431 >    }
432 >  
433 >  
434 >    pos = datom->getPos();
435 >    q = datom->getQ();
436 >    rotMatrix = datom->getA();
437 >
438 >    // We need A^T to convert from body-fixed to space-fixed:  
439 >    rotTrans = rotMatrix.transpose();
440 >
441 >    newVec = rotTrans * c1;
442 >    atomInfo = new AtomInfo;
443 >    atomInfo->atomTypeName = "C";
444 >    atomInfo->pos[0] = pos[0] + newVec[0];
445 >    atomInfo->pos[1] = pos[1] + newVec[1];
446 >    atomInfo->pos[2] = pos[2] + newVec[2];
447 >    atomInfo->dipole[0] = 0.0;
448 >    atomInfo->dipole[1] = 0.0;
449 >    atomInfo->dipole[2] = 0.0;
450 >    atomData->addAtomInfo(atomInfo);
451 >
452 >    newVec = rotTrans * c2;
453 >    atomInfo = new AtomInfo;
454 >    atomInfo->atomTypeName = "C";
455 >    atomInfo->pos[0] = pos[0] + newVec[0];
456 >    atomInfo->pos[1] = pos[1] + newVec[1];
457 >    atomInfo->pos[2] = pos[2] + newVec[2];
458 >    atomInfo->dipole[0] = 0.0;
459 >    atomInfo->dipole[1] = 0.0;
460 >    atomInfo->dipole[2] = 0.0;
461 >    atomData->addAtomInfo(atomInfo);
462 >
463 >    newVec = rotTrans * c3;
464 >    atomInfo = new AtomInfo;
465 >    atomInfo->atomTypeName = "C";
466 >    atomInfo->pos[0] = pos[0] + newVec[0];
467 >    atomInfo->pos[1] = pos[1] + newVec[1];
468 >    atomInfo->pos[2] = pos[2] + newVec[2];
469 >    atomInfo->dipole[0] = 0.0;
470 >    atomInfo->dipole[1] = 0.0;
471 >    atomInfo->dipole[2] = 0.0;
472 >    atomData->addAtomInfo(atomInfo);
473 >
474 >    newVec = rotTrans * c4;
475 >    atomInfo = new AtomInfo;
476 >    atomInfo->atomTypeName = "C";
477 >    atomInfo->pos[0] = pos[0] + newVec[0];
478 >    atomInfo->pos[1] = pos[1] + newVec[1];
479 >    atomInfo->pos[2] = pos[2] + newVec[2];
480 >    atomInfo->dipole[0] = 0.0;
481 >    atomInfo->dipole[1] = 0.0;
482 >    atomInfo->dipole[2] = 0.0;
483 >    atomData->addAtomInfo(atomInfo);
484 >
485 >    //add atom data into atom's property
486 >
487 >    if(!haveAtomData){
488 >      atomData->setID("ATOMDATA");
489 >      datom->addProperty(atomData);
490 >    }
491 >
492 >    setVisited(datom);
493 >
494 >  }
495 >
496 >  const std::string LinearAtomVisitor::toString(){
497 >    char buffer[65535];
498 >    std::string result;
499 >  
500 >    sprintf(buffer ,"------------------------------------------------------------------\n");
501 >    result += buffer;
502 >
503 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
504 >    result += buffer;
505 >
506 >    sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
507 >    result += buffer;
508 >
509 >    sprintf(buffer ,"------------------------------------------------------------------\n");
510 >    result += buffer;
511 >
512 >    return result;
513 >  }
514 >
515 >  bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){
516 >    std::set<std::string>::iterator strIter;
517 >    strIter = GBLipidAtomType.find(atomType);
518 >
519 >    return strIter != GBLipidAtomType.end() ? true : false;
520 >  }
521 >
522 >  void GBLipidAtomVisitor::visit(DirectionalAtom* datom){
523 >    std::vector<AtomInfo*> atoms;
524 >    Vector3d c1(0.0, 0.0, 0.0);
525 >    Vector3d c2(0.0, 0.0, 1.0);
526 >    RotMat3x3d rotMatrix;
527 >    RotMat3x3d rotTrans;
528 >    AtomInfo* atomInfo;
529 >    Vector3d pos;
530 >    Vector3d newVec;
531 >    Vector3d dVec;
532 >    Quat4d q;
533 >    AtomData* atomData;
534 >    GenericData* data;
535 >    bool haveAtomData;
536 >
537 >    //if atom is not GBlipid atom, just skip it
538 >    if(!isGBLipidAtom(datom->getType()))
539 >      return;
540 >
541 >    data = datom->getPropertyByName("ATOMDATA");
542 >    if(data != NULL){
543 >      atomData = dynamic_cast<AtomData*>(data);  
544 >      if(atomData == NULL){
545 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
546 >        atomData = new AtomData;
547 >        haveAtomData = false;      
548 >      } else {
549 >        haveAtomData = true;
550 >      }
551 >    } else {
552 >      atomData = new AtomData;
553 >      haveAtomData = false;
554 >    }
555 >  
556 >  
557 >    pos = datom->getPos();
558 >    q = datom->getQ();
559 >    rotMatrix = datom->getA();
560 >
561 >    // We need A^T to convert from body-fixed to space-fixed:  
562 >    rotTrans = rotMatrix.transpose();
563 >
564 >    newVec = rotTrans * c1;
565 >    dVec = rotTrans * c2;
566 >    atomInfo = new AtomInfo;
567 >    atomInfo->atomTypeName = "GB";
568 >    atomInfo->pos[0] = pos[0] + newVec[0];
569 >    atomInfo->pos[1] = pos[1] + newVec[1];
570 >    atomInfo->pos[2] = pos[2] + newVec[2];
571 >    atomInfo->dipole[0] = dVec[0];
572 >    atomInfo->dipole[1] = dVec[1];
573 >    atomInfo->dipole[2] = dVec[2];
574 >    atomInfo->hasVector = true;
575 >    atomInfo->charge = 3.0;
576 >    atomInfo->hasCharge = true;
577 >    atomData->addAtomInfo(atomInfo);
578 >
579 >    //add atom data into atom's property
580 >
581 >    if(!haveAtomData){
582 >      atomData->setID("ATOMDATA");
583 >      datom->addProperty(atomData);
584 >    }
585 >
586 >    setVisited(datom);
587 >
588 >  }
589 >
590 >  const std::string GBLipidAtomVisitor::toString(){
591 >    char buffer[65535];
592 >    std::string result;
593 >  
594 >    sprintf(buffer ,"------------------------------------------------------------------\n");
595 >    result += buffer;
596 >
597 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
598 >    result += buffer;
599 >
600 >    sprintf(buffer , "Visitor Description: Convert GBlipid into xyz-formatted atom for use with xyz2pov\n");
601 >    result += buffer;
602 >
603 >    sprintf(buffer ,"------------------------------------------------------------------\n");
604 >    result += buffer;
605 >
606 >    return result;
607 >  }
608 >
609 >  bool Ring5gbAtomVisitor::isRing5gbAtom(const std::string& atomType){
610 >    std::set<std::string>::iterator strIter;
611 >    strIter = Ring5gbAtomType.find(atomType);
612 >
613 >    return strIter != Ring5gbAtomType.end() ? true : false;
614 >  }
615 >
616 >  void Ring5gbAtomVisitor::visit(DirectionalAtom* datom){
617 >    std::vector<AtomInfo*> atoms;
618 >    //we need to convert linear into 4 different atoms
619 >    Vector3d c1(0.0, 0.0, -5.5);
620 >    Vector3d c2(0.0, 0.0, -1.8);
621 >    Vector3d c3(0.0, 0.0,  1.8);
622 >    Vector3d c4(0.0, 0.0,  5.5);
623 >    RotMat3x3d rotMatrix;
624 >    RotMat3x3d rotTrans;
625 >    AtomInfo* atomInfo;
626 >    Vector3d pos;
627 >    Vector3d newVec;
628 >    Vector3d dVec;
629 >    Quat4d q;
630 >    AtomData* atomData;
631 >    GenericData* data;
632 >    bool haveAtomData;
633 >
634 >    //if atom is not Ring5GB atom, just skip it
635 >    if(!isRing5gbAtom(datom->getType()))
636 >      return;
637 >
638 >    data = datom->getPropertyByName("ATOMDATA");
639 >    if(data != NULL){
640 >      atomData = dynamic_cast<AtomData*>(data);  
641 >      if(atomData == NULL){
642 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
643 >        atomData = new AtomData;
644 >        haveAtomData = false;      
645 >      } else {
646 >        haveAtomData = true;
647 >      }
648 >    } else {
649 >      atomData = new AtomData;
650 >      haveAtomData = false;
651 >    }
652 >  
653 >  
654 >    pos = datom->getPos();
655 >    q = datom->getQ();
656 >    rotMatrix = datom->getA();
657 >
658 >    // We need A^T to convert from body-fixed to space-fixed:  
659 >    rotTrans = rotMatrix.transpose();
660 >
661 >    newVec = rotTrans * c1;
662 >    atomInfo = new AtomInfo;
663 >    atomInfo->atomTypeName = "K";
664 >    atomInfo->pos[0] = pos[0] + newVec[0];
665 >    atomInfo->pos[1] = pos[1] + newVec[1];
666 >    atomInfo->pos[2] = pos[2] + newVec[2];
667 >    atomInfo->dipole[0] = 0.0;
668 >    atomInfo->dipole[1] = 0.0;
669 >    atomInfo->dipole[2] = 0.0;
670 >    atomData->addAtomInfo(atomInfo);
671 >
672 >    newVec = rotTrans * c2;
673 >    atomInfo = new AtomInfo;
674 >    atomInfo->atomTypeName = "K";
675 >    atomInfo->pos[0] = pos[0] + newVec[0];
676 >    atomInfo->pos[1] = pos[1] + newVec[1];
677 >    atomInfo->pos[2] = pos[2] + newVec[2];
678 >    atomInfo->dipole[0] = 0.0;
679 >    atomInfo->dipole[1] = 0.0;
680 >    atomInfo->dipole[2] = 0.0;
681 >    atomData->addAtomInfo(atomInfo);
682 >
683 >    newVec = rotTrans * c3;
684 >    atomInfo = new AtomInfo;
685 >    atomInfo->atomTypeName = "K";
686 >    atomInfo->pos[0] = pos[0] + newVec[0];
687 >    atomInfo->pos[1] = pos[1] + newVec[1];
688 >    atomInfo->pos[2] = pos[2] + newVec[2];
689 >    atomInfo->dipole[0] = 0.0;
690 >    atomInfo->dipole[1] = 0.0;
691 >    atomInfo->dipole[2] = 0.0;
692 >    atomData->addAtomInfo(atomInfo);
693 >
694 >    newVec = rotTrans * c4;
695 >    atomInfo = new AtomInfo;
696 >    atomInfo->atomTypeName = "K";
697 >    atomInfo->pos[0] = pos[0] + newVec[0];
698 >    atomInfo->pos[1] = pos[1] + newVec[1];
699 >    atomInfo->pos[2] = pos[2] + newVec[2];
700 >    atomInfo->dipole[0] = 0.0;
701 >    atomInfo->dipole[1] = 0.0;
702 >    atomInfo->dipole[2] = 0.0;
703 >    atomData->addAtomInfo(atomInfo);
704 >
705 >    //add atom data into atom's property
706 >
707 >    if(!haveAtomData){
708 >      atomData->setID("ATOMDATA");
709 >      datom->addProperty(atomData);
710 >    }
711 >
712 >    setVisited(datom);
713 >
714 >  }
715 >
716 >  const std::string Ring5gbAtomVisitor::toString(){
717 >    char buffer[65535];
718 >    std::string result;
719 >  
720 >    sprintf(buffer ,"------------------------------------------------------------------\n");
721 >    result += buffer;
722 >
723 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
724 >    result += buffer;
725 >
726 >    sprintf(buffer , "Visitor Description: Convert Ring5GB into 4 different K atoms\n");
727 >    result += buffer;
728 >
729 >    sprintf(buffer ,"------------------------------------------------------------------\n");
730 >    result += buffer;
731 >
732 >    return result;
733 >  }
734 >
735 >  bool HeadAtomVisitor::isHeadAtom(const std::string& atomType){
736 >    std::set<std::string>::iterator strIter;
737 >    strIter = HeadAtomType.find(atomType);
738 >
739 >    return strIter != HeadAtomType.end() ? true : false;
740 >  }
741 >
742 >  void HeadAtomVisitor::visit(DirectionalAtom* datom){
743 >    std::vector<AtomInfo*> atoms;
744 >    //we need to convert linear into 2 different atoms
745 >    Vector3d c1(0.0, 0.0, -1.5);
746 >    Vector3d c2(0.0, 0.0, 1.5);
747 >    RotMat3x3d rotMatrix;
748 >    RotMat3x3d rotTrans;
749 >    AtomInfo* atomInfo;
750 >    Vector3d pos;
751 >    Vector3d newVec;
752 >    Vector3d dVec;
753 >    Quat4d q;
754 >    AtomData* atomData;
755 >    GenericData* data;
756 >    bool haveAtomData;
757 >
758 >    //if atom is not Head atom, just skip it
759 >    if(!isHeadAtom(datom->getType()))
760 >      return;
761 >
762 >    data = datom->getPropertyByName("ATOMDATA");
763 >    if(data != NULL){
764 >      atomData = dynamic_cast<AtomData*>(data);  
765 >      if(atomData == NULL){
766 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
767 >        atomData = new AtomData;
768 >        haveAtomData = false;      
769 >      } else {
770 >        haveAtomData = true;
771 >      }
772 >    } else {
773 >      atomData = new AtomData;
774 >      haveAtomData = false;
775 >    }
776 >  
777 >  
778 >    pos = datom->getPos();
779 >    q = datom->getQ();
780 >    rotMatrix = datom->getA();
781 >
782 >    // We need A^T to convert from body-fixed to space-fixed:  
783 >    rotTrans = rotMatrix.transpose();
784 >
785 >    newVec = rotTrans * c1;
786 >    atomInfo = new AtomInfo;
787 >    atomInfo->atomTypeName = "C";
788 >    atomInfo->pos[0] = pos[0] + newVec[0];
789 >    atomInfo->pos[1] = pos[1] + newVec[1];
790 >    atomInfo->pos[2] = pos[2] + newVec[2];
791 >    atomInfo->dipole[0] = 0.0;
792 >    atomInfo->dipole[1] = 0.0;
793 >    atomInfo->dipole[2] = 0.0;
794 >    atomData->addAtomInfo(atomInfo);
795 >
796 >    newVec = rotTrans * c2;
797 >    atomInfo = new AtomInfo;
798 >    atomInfo->atomTypeName = "O";
799 >    atomInfo->pos[0] = pos[0] + newVec[0];
800 >    atomInfo->pos[1] = pos[1] + newVec[1];
801 >    atomInfo->pos[2] = pos[2] + newVec[2];
802 >    atomInfo->dipole[0] = 0.0;
803 >    atomInfo->dipole[1] = 0.0;
804 >    atomInfo->dipole[2] = 0.0;
805 >    atomData->addAtomInfo(atomInfo);
806 >
807 >    //add atom data into atom's property
808 >
809 >    if(!haveAtomData){
810 >      atomData->setID("ATOMDATA");
811 >      datom->addProperty(atomData);
812 >    }
813 >
814 >    setVisited(datom);
815 >
816 >  }
817 >
818 >  const std::string HeadAtomVisitor::toString(){
819 >    char buffer[65535];
820 >    std::string result;
821 >  
822 >    sprintf(buffer ,"------------------------------------------------------------------\n");
823 >    result += buffer;
824 >
825 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
826 >    result += buffer;
827 >
828 >    sprintf(buffer , "Visitor Description: Convert HEAD into C atom and O atom\n");
829 >    result += buffer;
830 >
831 >    sprintf(buffer ,"------------------------------------------------------------------\n");
832 >    result += buffer;
833 >
834 >    return result;
835 >  }
836 >
837 >
838 >  //----------------------------------------------------------------------------//
839 >
840 >  void DefaultAtomVisitor::visit(Atom *atom) {
841 >    AtomData *atomData;
842 >    AtomInfo *atomInfo;
843 >    Vector3d  pos;
844 >
845 >    if (isVisited(atom))
846 >      return;
847 >
848 >    atomInfo = new AtomInfo;
849 >
850 >    atomData = new AtomData;
851 >    atomData->setID("ATOMDATA");
852 >
853 >    pos = atom->getPos();
854 >    atomInfo->atomTypeName = atom->getType();
855 >    atomInfo->pos[0] = pos[0];
856 >    atomInfo->pos[1] = pos[1];
857 >    atomInfo->pos[2] = pos[2];
858 >    atomInfo->dipole[0] = 0.0;
859 >    atomInfo->dipole[1] = 0.0;
860 >    atomInfo->dipole[2] = 0.0;
861 >
862 >    atomData->addAtomInfo(atomInfo);
863 >
864 >    atom->addProperty(atomData);
865 >
866 >    setVisited(atom);
867 >  }
868 >
869 >  void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
870 >    AtomData *atomData;
871 >    AtomInfo *atomInfo;
872 >    Vector3d  pos;
873 >    Vector3d  u;
874 >
875 >    if (isVisited(datom))
876 >      return;
877 >
878 >    pos = datom->getPos();
879 >    if (datom->getAtomType()->isGayBerne()) {
880 >        u = datom->getA().transpose()*V3Z;        
881 >    } else if (datom->getAtomType()->isMultipole()) {
882 >        u = datom->getElectroFrame().getColumn(2);
883 >    }
884 >    atomData = new AtomData;
885 >    atomData->setID("ATOMDATA");
886 >    atomInfo = new AtomInfo;
887 >
888 >    atomInfo->atomTypeName = datom->getType();
889 >    atomInfo->pos[0] = pos[0];
890 >    atomInfo->pos[1] = pos[1];
891 >    atomInfo->pos[2] = pos[2];
892 >    atomInfo->dipole[0] = u[0];
893 >    atomInfo->dipole[1] = u[1];
894 >    atomInfo->dipole[2] = u[2];
895 >
896 >    atomData->addAtomInfo(atomInfo);
897 >
898 >    datom->addProperty(atomData);
899 >
900 >    setVisited(datom);
901 >  }
902 >
903 >  const std::string DefaultAtomVisitor::toString() {
904 >    char   buffer[65535];
905 >    std::string result;
906 >
907 >    sprintf(buffer,
908 >            "------------------------------------------------------------------\n");
909 >    result += buffer;
910 >
911 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
912 >    result += buffer;
913 >
914 >    sprintf(buffer,
915 >            "Visitor Description: copy atom infomation into atom data\n");
916 >    result += buffer;
917 >
918 >    sprintf(buffer,
919 >            "------------------------------------------------------------------\n");
920 >    result += buffer;
921 >
922 >    return result;
923 >  }
924 > } //namespace oopse

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