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Comparing trunk/OOPSE-4/src/visitors/AtomVisitor.cpp (file contents):
Revision 1718 by chrisfen, Fri Nov 5 21:45:14 2004 UTC vs.
Revision 2749 by tim, Wed May 10 01:44:48 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 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 <  //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
144 <    matVecMul3(rotTrans, h1, newVec);
145 <  atomInfo = new AtomInfo;
146 <  atomInfo->AtomType = "H";
147 <  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 >    //oxygen
146 >    //matVecMul3(rotTrans, ox, newVec);
147 >    newVec = rotTrans * ox;
148  
149 <  //hydrogen2
150 <  matVecMul3(rotTrans, h2, newVec);
151 <  atomInfo = new AtomInfo;
152 <  atomInfo->AtomType = "H";
153 <  atomInfo->pos[0] = pos[0] + newVec[0];
154 <  atomInfo->pos[1] = pos[1] + newVec[1];
155 <  atomInfo->pos[2] = pos[2] + newVec[2];
156 <  atomInfo->dipole[0] = 0.0;
157 <  atomInfo->dipole[1] = 0.0;
144 <  atomInfo->dipole[2] = 0.0;
145 <  atomData->addAtomInfo(atomInfo);
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 <  //add atom data into atom's property
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 <  if(!haveAtomData){
173 <    atomData->setID("ATOMDATA");
174 <    datom->addProperty(atomData);
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 >    //add atom data into atom's property
186 >
187 >    if (!haveAtomData) {
188 >      atomData->setID("ATOMDATA");
189 >      datom->addProperty(atomData);
190 >    }
191 >
192 >    setVisited(datom);
193    }
194  
195 <  setVisited(datom);
195 >  const std::string SSDAtomVisitor::toString() {
196 >    char   buffer[65535];
197 >    std::string result;
198  
199 < }
199 >    sprintf(buffer,
200 >            "------------------------------------------------------------------\n");
201 >    result += buffer;
202  
203 < const string SSDAtomVisitor::toString(){
204 <  char buffer[65535];
160 <  string result;
161 <  
162 <  sprintf(buffer ,"------------------------------------------------------------------\n");
163 <  result += buffer;
203 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
204 >    result += buffer;
205  
206 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
207 <  result += buffer;
206 >    sprintf(buffer,
207 >            "Visitor Description: Convert SSD into 4 different atoms\n");
208 >    result += buffer;
209  
210 <  sprintf(buffer , "Visitor Description: Convert SSD into 4 different atoms\n");
211 <  result += buffer;
210 >    sprintf(buffer,
211 >            "------------------------------------------------------------------\n");
212 >    result += buffer;
213  
214 <  sprintf(buffer ,"------------------------------------------------------------------\n");
215 <  result += buffer;
214 >    return result;
215 >  }
216  
217 <  return result;
218 < }
217 >  bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
218 >    std::set<std::string>::iterator strIter;
219 >    strIter = linearAtomType.find(atomType);
220  
221 < bool LinearAtomVisitor::isLinearAtom(const string& atomType){
222 <  vector<string>::iterator strIter;
179 <  
180 <  for(strIter = linearAtomType.begin(); strIter != linearAtomType.end();
181 <      ++strIter)
182 <    if(*strIter == atomType)
183 <      return true;
184 <  
185 <  return false;  
186 < }
221 >    return strIter != linearAtomType.end() ? true : false;
222 >  }
223  
224 < void LinearAtomVisitor::visit(DirectionalAtom* datom){
224 >  void LinearAtomVisitor::addGayBerneAtomType(const std::string& atomType){
225 >   linearAtomType.insert(atomType);
226 >  }
227  
228 <  vector<AtomInfo*> atoms;
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  
245 <  //we need to convert linear into 4 different atoms
246 <  double c1[3] = {0.0, 0.0, -1.8};
247 <  double c2[3] = {0.0, 0.0, -0.6};
195 <  double c3[3] = {0.0, 0.0,  0.6};
196 <  double c4[3] = {0.0, 0.0,  1.8};
197 <  double rotMatrix[3][3];
198 <  double rotTrans[3][3];
199 <  AtomInfo* atomInfo;
200 <  double pos[3];
201 <  double newVec[3];
202 <  double q[4];
203 <  AtomData* atomData;
204 <  GenericData* data;
205 <  bool haveAtomData;
206 <  
207 <  //if atom is not SSD atom, just skip it
208 <  if(!isLinearAtom(datom->getType()))
209 <    return;
210 <  
211 <  data = datom->getProperty("ATOMDATA");
212 <  if(data != NULL){
245 >    //if atom is not SSD atom, just skip it
246 >    if(!isLinearAtom(datom->getType()))
247 >      return;
248  
249 <    atomData = dynamic_cast<AtomData*>(data);  
250 <    if(atomData == NULL){
251 <      cerr << "can not get Atom Data from " << datom->getType() << endl;
252 <      atomData = new AtomData;
253 <      haveAtomData = false;      
249 >    data = datom->getPropertyByName("ATOMDATA");
250 >    if(data != NULL){
251 >      atomData = dynamic_cast<AtomData*>(data);  
252 >      if(atomData == NULL){
253 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
254 >        atomData = new AtomData;
255 >        haveAtomData = false;      
256 >      } else {
257 >        haveAtomData = true;
258 >      }
259 >    } else {
260 >      atomData = new AtomData;
261 >      haveAtomData = false;
262      }
220 –    else
221 –      haveAtomData = true;
222 –  }
223 –  else{
224 –    atomData = new AtomData;
225 –    haveAtomData = false;
226 –  }
263    
264    
265 <  datom->getPos(pos);
266 <  datom->getQ(q);
267 <  datom->getA(rotMatrix);
265 >    pos = datom->getPos();
266 >    q = datom->getQ();
267 >    rotMatrix = datom->getA();
268  
269 <  // We need A^T to convert from body-fixed to space-fixed:
270 <  transposeMat3(rotMatrix, rotTrans);
269 >    // We need A^T to convert from body-fixed to space-fixed:  
270 >    rotTrans = rotMatrix.transpose();
271 >
272 >    newVec = rotTrans * c1;
273 >    atomInfo = new AtomInfo;
274 >    atomInfo->atomTypeName = "C";
275 >    atomInfo->pos[0] = pos[0] + newVec[0];
276 >    atomInfo->pos[1] = pos[1] + newVec[1];
277 >    atomInfo->pos[2] = pos[2] + newVec[2];
278 >    atomInfo->dipole[0] = 0.0;
279 >    atomInfo->dipole[1] = 0.0;
280 >    atomInfo->dipole[2] = 0.0;
281 >    atomData->addAtomInfo(atomInfo);
282 >
283 >    newVec = rotTrans * c2;
284 >    atomInfo = new AtomInfo;
285 >    atomInfo->atomTypeName = "C";
286 >    atomInfo->pos[0] = pos[0] + newVec[0];
287 >    atomInfo->pos[1] = pos[1] + newVec[1];
288 >    atomInfo->pos[2] = pos[2] + newVec[2];
289 >    atomInfo->dipole[0] = 0.0;
290 >    atomInfo->dipole[1] = 0.0;
291 >    atomInfo->dipole[2] = 0.0;
292 >    atomData->addAtomInfo(atomInfo);
293 >
294 >    newVec = rotTrans * c3;
295 >    atomInfo = new AtomInfo;
296 >    atomInfo->atomTypeName = "C";
297 >    atomInfo->pos[0] = pos[0] + newVec[0];
298 >    atomInfo->pos[1] = pos[1] + newVec[1];
299 >    atomInfo->pos[2] = pos[2] + newVec[2];
300 >    atomInfo->dipole[0] = 0.0;
301 >    atomInfo->dipole[1] = 0.0;
302 >    atomInfo->dipole[2] = 0.0;
303 >    atomData->addAtomInfo(atomInfo);
304 >
305 >    newVec = rotTrans * c4;
306 >    atomInfo = new AtomInfo;
307 >    atomInfo->atomTypeName = "C";
308 >    atomInfo->pos[0] = pos[0] + newVec[0];
309 >    atomInfo->pos[1] = pos[1] + newVec[1];
310 >    atomInfo->pos[2] = pos[2] + newVec[2];
311 >    atomInfo->dipole[0] = 0.0;
312 >    atomInfo->dipole[1] = 0.0;
313 >    atomInfo->dipole[2] = 0.0;
314 >    atomData->addAtomInfo(atomInfo);
315 >
316 >    //add atom data into atom's property
317 >
318 >    if(!haveAtomData){
319 >      atomData->setID("ATOMDATA");
320 >      datom->addProperty(atomData);
321 >    }
322 >
323 >    setVisited(datom);
324 >
325 >  }
326 >
327 >  const std::string LinearAtomVisitor::toString(){
328 >    char buffer[65535];
329 >    std::string result;
330    
331 <  matVecMul3(rotTrans, c1, newVec);
332 <  atomInfo = new AtomInfo;
238 <  atomInfo->AtomType = "C";
239 <  atomInfo->pos[0] = pos[0] + newVec[0];
240 <  atomInfo->pos[1] = pos[1] + newVec[1];
241 <  atomInfo->pos[2] = pos[2] + newVec[2];
242 <  atomInfo->dipole[0] = 0.0;
243 <  atomInfo->dipole[1] = 0.0;
244 <  atomInfo->dipole[2] = 0.0;
245 <  atomData->addAtomInfo(atomInfo);
331 >    sprintf(buffer ,"------------------------------------------------------------------\n");
332 >    result += buffer;
333  
334 <  matVecMul3(rotTrans, c2, newVec);
335 <  atomInfo = new AtomInfo;
249 <  atomInfo->AtomType = "C";
250 <  atomInfo->pos[0] = pos[0] + newVec[0];
251 <  atomInfo->pos[1] = pos[1] + newVec[1];
252 <  atomInfo->pos[2] = pos[2] + newVec[2];
253 <  atomInfo->dipole[0] = 0.0;
254 <  atomInfo->dipole[1] = 0.0;
255 <  atomInfo->dipole[2] = 0.0;
256 <  atomData->addAtomInfo(atomInfo);
334 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
335 >    result += buffer;
336  
337 <  matVecMul3(rotTrans, c3, newVec);
338 <  atomInfo = new AtomInfo;
260 <  atomInfo->AtomType = "C";
261 <  atomInfo->pos[0] = pos[0] + newVec[0];
262 <  atomInfo->pos[1] = pos[1] + newVec[1];
263 <  atomInfo->pos[2] = pos[2] + newVec[2];
264 <  atomInfo->dipole[0] = 0.0;
265 <  atomInfo->dipole[1] = 0.0;
266 <  atomInfo->dipole[2] = 0.0;
267 <  atomData->addAtomInfo(atomInfo);
337 >    sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
338 >    result += buffer;
339  
340 <  matVecMul3(rotTrans, c4, newVec);
341 <  atomInfo = new AtomInfo;
271 <  atomInfo->AtomType = "C";
272 <  atomInfo->pos[0] = pos[0] + newVec[0];
273 <  atomInfo->pos[1] = pos[1] + newVec[1];
274 <  atomInfo->pos[2] = pos[2] + newVec[2];
275 <  atomInfo->dipole[0] = 0.0;
276 <  atomInfo->dipole[1] = 0.0;
277 <  atomInfo->dipole[2] = 0.0;
278 <  atomData->addAtomInfo(atomInfo);
340 >    sprintf(buffer ,"------------------------------------------------------------------\n");
341 >    result += buffer;
342  
343 <  //add atom data into atom's property
343 >    return result;
344 >  }
345  
346 <  if(!haveAtomData){
347 <    atomData->setID("ATOMDATA");
348 <    datom->addProperty(atomData);
346 >  bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){
347 >    std::set<std::string>::iterator strIter;
348 >    strIter = GBLipidAtomType.find(atomType);
349 >
350 >    return strIter != GBLipidAtomType.end() ? true : false;
351    }
352  
353 <  setVisited(datom);
353 >  void GBLipidAtomVisitor::visit(DirectionalAtom* datom){
354 >    std::vector<AtomInfo*> atoms;
355 >    //we need to convert linear into 4 different atoms
356 >    Vector3d c1(0.0, 0.0, -6.25);
357 >    Vector3d c2(0.0, 0.0, -2.1);
358 >    Vector3d c3(0.0, 0.0,  2.1);
359 >    Vector3d c4(0.0, 0.0,  6.25);
360 >    RotMat3x3d rotMatrix;
361 >    RotMat3x3d rotTrans;
362 >    AtomInfo* atomInfo;
363 >    Vector3d pos;
364 >    Vector3d newVec;
365 >    Quat4d q;
366 >    AtomData* atomData;
367 >    GenericData* data;
368 >    bool haveAtomData;
369  
370 < }
370 >    //if atom is not GBlipid atom, just skip it
371 >    if(!isGBLipidAtom(datom->getType()))
372 >      return;
373  
374 < const string LinearAtomVisitor::toString(){
375 <  char buffer[65535];
376 <  string result;
374 >    data = datom->getPropertyByName("ATOMDATA");
375 >    if(data != NULL){
376 >      atomData = dynamic_cast<AtomData*>(data);  
377 >      if(atomData == NULL){
378 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
379 >        atomData = new AtomData;
380 >        haveAtomData = false;      
381 >      } else {
382 >        haveAtomData = true;
383 >      }
384 >    } else {
385 >      atomData = new AtomData;
386 >      haveAtomData = false;
387 >    }
388 >  
389    
390 <  sprintf(buffer ,"------------------------------------------------------------------\n");
391 <  result += buffer;
390 >    pos = datom->getPos();
391 >    q = datom->getQ();
392 >    rotMatrix = datom->getA();
393  
394 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
395 <  result += buffer;
394 >    // We need A^T to convert from body-fixed to space-fixed:  
395 >    rotTrans = rotMatrix.transpose();
396  
397 <  sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
398 <  result += buffer;
397 >    newVec = rotTrans * c1;
398 >    atomInfo = new AtomInfo;
399 >    atomInfo->atomTypeName = "K";
400 >    atomInfo->pos[0] = pos[0] + newVec[0];
401 >    atomInfo->pos[1] = pos[1] + newVec[1];
402 >    atomInfo->pos[2] = pos[2] + newVec[2];
403 >    atomInfo->dipole[0] = 0.0;
404 >    atomInfo->dipole[1] = 0.0;
405 >    atomInfo->dipole[2] = 0.0;
406 >    atomData->addAtomInfo(atomInfo);
407  
408 <  sprintf(buffer ,"------------------------------------------------------------------\n");
409 <  result += buffer;
408 >    newVec = rotTrans * c2;
409 >    atomInfo = new AtomInfo;
410 >    atomInfo->atomTypeName = "K";
411 >    atomInfo->pos[0] = pos[0] + newVec[0];
412 >    atomInfo->pos[1] = pos[1] + newVec[1];
413 >    atomInfo->pos[2] = pos[2] + newVec[2];
414 >    atomInfo->dipole[0] = 0.0;
415 >    atomInfo->dipole[1] = 0.0;
416 >    atomInfo->dipole[2] = 0.0;
417 >    atomData->addAtomInfo(atomInfo);
418  
419 <  return result;
420 < }
419 >    newVec = rotTrans * c3;
420 >    atomInfo = new AtomInfo;
421 >    atomInfo->atomTypeName = "K";
422 >    atomInfo->pos[0] = pos[0] + newVec[0];
423 >    atomInfo->pos[1] = pos[1] + newVec[1];
424 >    atomInfo->pos[2] = pos[2] + newVec[2];
425 >    atomInfo->dipole[0] = 0.0;
426 >    atomInfo->dipole[1] = 0.0;
427 >    atomInfo->dipole[2] = 0.0;
428 >    atomData->addAtomInfo(atomInfo);
429  
430 < //----------------------------------------------------------------------------//
430 >    newVec = rotTrans * c4;
431 >    atomInfo = new AtomInfo;
432 >    atomInfo->atomTypeName = "K";
433 >    atomInfo->pos[0] = pos[0] + newVec[0];
434 >    atomInfo->pos[1] = pos[1] + newVec[1];
435 >    atomInfo->pos[2] = pos[2] + newVec[2];
436 >    atomInfo->dipole[0] = 0.0;
437 >    atomInfo->dipole[1] = 0.0;
438 >    atomInfo->dipole[2] = 0.0;
439 >    atomData->addAtomInfo(atomInfo);
440  
441 < void DefaultAtomVisitor::visit(Atom* atom){
313 <  AtomData* atomData;
314 <  AtomInfo* atomInfo;
315 <  double pos[3];
441 >    //add atom data into atom's property
442  
443 <  if(isVisited(atom))
444 <    return;
443 >    if(!haveAtomData){
444 >      atomData->setID("ATOMDATA");
445 >      datom->addProperty(atomData);
446 >    }
447  
448 < atomInfo =new AtomInfo;
448 >    setVisited(datom);
449  
450 <  atomData = new AtomData;
323 <  atomData->setID("ATOMDATA");
324 <
325 <  atom->getPos(pos);
326 <  atomInfo->AtomType = atom->getType();
327 <  atomInfo->pos[0] = pos[0];
328 <  atomInfo->pos[1] = pos[1];
329 <  atomInfo->pos[2] = pos[2];
330 <  atomInfo->dipole[0] = 0.0;
331 <  atomInfo->dipole[1] = 0.0;
332 <  atomInfo->dipole[2] = 0.0;
450 >  }
451  
452 <
453 <  atomData->addAtomInfo(atomInfo);
452 >  const std::string GBLipidAtomVisitor::toString(){
453 >    char buffer[65535];
454 >    std::string result;
455    
456 <  atom->addProperty(atomData);
456 >    sprintf(buffer ,"------------------------------------------------------------------\n");
457 >    result += buffer;
458  
459 <  setVisited(atom);
460 < }
341 < void DefaultAtomVisitor::visit(DirectionalAtom* datom){
342 <  AtomData* atomData;
343 <  AtomInfo* atomInfo;
344 <  double pos[3];
345 <  double u[3];
459 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
460 >    result += buffer;
461  
462 <  if(isVisited(datom))
463 <    return;
349 <  
350 <  datom->getPos(pos);
351 <  datom->getU(u);
462 >    sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n");
463 >    result += buffer;
464  
465 <  atomData = new AtomData;
466 <  atomData->setID("ATOMDATA");
355 <  atomInfo =new AtomInfo;
356 <  
357 <  atomInfo->AtomType = datom->getType();
358 <  atomInfo->pos[0] = pos[0];
359 <  atomInfo->pos[1] = pos[1];
360 <  atomInfo->pos[2] = pos[2];
361 <  atomInfo->dipole[0] = u[0];
362 <  atomInfo->dipole[1] = u[1];
363 <  atomInfo->dipole[2] = u[2];  
465 >    sprintf(buffer ,"------------------------------------------------------------------\n");
466 >    result += buffer;
467  
468 <  atomData->addAtomInfo(atomInfo);
468 >    return result;
469 >  }
470  
471 <  datom->addProperty(atomData);
471 >  //----------------------------------------------------------------------------//
472  
473 <  setVisited(datom);
474 < }
473 >  void DefaultAtomVisitor::visit(Atom *atom) {
474 >    AtomData *atomData;
475 >    AtomInfo *atomInfo;
476 >    Vector3d  pos;
477  
478 +    if (isVisited(atom))
479 +      return;
480  
481 < const string DefaultAtomVisitor::toString(){
374 <  char buffer[65535];
375 <  string result;
376 <  
377 <  sprintf(buffer ,"------------------------------------------------------------------\n");
378 <  result += buffer;
481 >    atomInfo = new AtomInfo;
482  
483 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
484 <  result += buffer;
483 >    atomData = new AtomData;
484 >    atomData->setID("ATOMDATA");
485  
486 <  sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n");
487 <  result += buffer;
486 >    pos = atom->getPos();
487 >    atomInfo->atomTypeName = atom->getType();
488 >    atomInfo->pos[0] = pos[0];
489 >    atomInfo->pos[1] = pos[1];
490 >    atomInfo->pos[2] = pos[2];
491 >    atomInfo->dipole[0] = 0.0;
492 >    atomInfo->dipole[1] = 0.0;
493 >    atomInfo->dipole[2] = 0.0;
494  
495 <  sprintf(buffer ,"------------------------------------------------------------------\n");
387 <  result += buffer;
495 >    atomData->addAtomInfo(atomInfo);
496  
497 <  return result;
390 < }    
497 >    atom->addProperty(atomData);
498  
499 < }//namespace oopse
499 >    setVisited(atom);
500 >  }
501 >
502 >  void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
503 >    AtomData *atomData;
504 >    AtomInfo *atomInfo;
505 >    Vector3d  pos;
506 >    Vector3d  u;
507 >
508 >    if (isVisited(datom))
509 >      return;
510 >
511 >    pos = datom->getPos();
512 >    u = datom->getElectroFrame().getColumn(2);
513 >
514 >    atomData = new AtomData;
515 >    atomData->setID("ATOMDATA");
516 >    atomInfo = new AtomInfo;
517 >
518 >    atomInfo->atomTypeName = datom->getType();
519 >    atomInfo->pos[0] = pos[0];
520 >    atomInfo->pos[1] = pos[1];
521 >    atomInfo->pos[2] = pos[2];
522 >    atomInfo->dipole[0] = u[0];
523 >    atomInfo->dipole[1] = u[1];
524 >    atomInfo->dipole[2] = u[2];
525 >
526 >    atomData->addAtomInfo(atomInfo);
527 >
528 >    datom->addProperty(atomData);
529 >
530 >    setVisited(datom);
531 >  }
532 >
533 >  const std::string DefaultAtomVisitor::toString() {
534 >    char   buffer[65535];
535 >    std::string result;
536 >
537 >    sprintf(buffer,
538 >            "------------------------------------------------------------------\n");
539 >    result += buffer;
540 >
541 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
542 >    result += buffer;
543 >
544 >    sprintf(buffer,
545 >            "Visitor Description: copy atom infomation into atom data\n");
546 >    result += buffer;
547 >
548 >    sprintf(buffer,
549 >            "------------------------------------------------------------------\n");
550 >    result += buffer;
551 >
552 >    return result;
553 >  }
554 > } //namespace oopse

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