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

Comparing trunk/src/visitors/AtomVisitor.cpp (file contents):
Revision 211 by chrisfen, Fri Nov 5 21:45:14 2004 UTC vs.
Revision 1244 by xsun, Wed May 14 21:04:13 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   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);
145 >    //oxygen
146 >    //matVecMul3(rotTrans, ox, newVec);
147 >    newVec = rotTrans * ox;
148  
149 <  //add atom data into atom's property
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 <  if(!haveAtomData){
160 <    atomData->setID("ATOMDATA");
161 <    datom->addProperty(atomData);
162 <  }
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 <  setVisited(datom);
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 < }
185 >    //add atom data into atom's property
186  
187 < const string SSDAtomVisitor::toString(){
188 <  char buffer[65535];
189 <  string result;
190 <  
162 <  sprintf(buffer ,"------------------------------------------------------------------\n");
163 <  result += buffer;
187 >    if (!haveAtomData) {
188 >      atomData->setID("ATOMDATA");
189 >      datom->addProperty(atomData);
190 >    }
191  
192 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
193 <  result += buffer;
192 >    setVisited(datom);
193 >  }
194  
195 <  sprintf(buffer , "Visitor Description: Convert SSD into 4 different atoms\n");
196 <  result += buffer;
195 >  const std::string SSDAtomVisitor::toString() {
196 >    char   buffer[65535];
197 >    std::string result;
198  
199 <  sprintf(buffer ,"------------------------------------------------------------------\n");
200 <  result += buffer;
199 >    sprintf(buffer,
200 >            "------------------------------------------------------------------\n");
201 >    result += buffer;
202  
203 <  return result;
204 < }
203 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
204 >    result += buffer;
205  
206 < bool LinearAtomVisitor::isLinearAtom(const string& atomType){
207 <  vector<string>::iterator strIter;
208 <  
180 <  for(strIter = linearAtomType.begin(); strIter != linearAtomType.end();
181 <      ++strIter)
182 <    if(*strIter == atomType)
183 <      return true;
184 <  
185 <  return false;  
186 < }
187 <
188 < void LinearAtomVisitor::visit(DirectionalAtom* datom){
206 >    sprintf(buffer,
207 >            "Visitor Description: Convert SSD into 4 different atoms\n");
208 >    result += buffer;
209  
210 <  vector<AtomInfo*> atoms;
210 >    sprintf(buffer,
211 >            "------------------------------------------------------------------\n");
212 >    result += buffer;
213  
214 <  //we need to convert linear into 4 different atoms
193 <  double c1[3] = {0.0, 0.0, -1.8};
194 <  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){
213 <
214 <    atomData = dynamic_cast<AtomData*>(data);  
215 <    if(atomData == NULL){
216 <      cerr << "can not get Atom Data from " << datom->getType() << endl;
217 <      atomData = new AtomData;
218 <      haveAtomData = false;      
219 <    }
220 <    else
221 <      haveAtomData = true;
214 >    return result;
215    }
223 –  else{
224 –    atomData = new AtomData;
225 –    haveAtomData = false;
226 –  }
227 –  
228 –  
229 –  datom->getPos(pos);
230 –  datom->getQ(q);
231 –  datom->getA(rotMatrix);
216  
233 –  // We need A^T to convert from body-fixed to space-fixed:
234 –  transposeMat3(rotMatrix, rotTrans);
235 –  
236 –  matVecMul3(rotTrans, c1, newVec);
237 –  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);
217  
218 <  matVecMul3(rotTrans, c2, newVec);
219 <  atomInfo = new AtomInfo;
220 <  atomInfo->AtomType = "C";
221 <  atomInfo->pos[0] = pos[0] + newVec[0];
222 <  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);
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 <  matVecMul3(rotTrans, c3, newVec);
225 <  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);
224 >  void TREDAtomVisitor::visit(DirectionalAtom *datom) {
225 >    std::vector<AtomInfo*>atoms;
226  
227 <  matVecMul3(rotTrans, c4, newVec);
228 <  atomInfo = new AtomInfo;
229 <  atomInfo->AtomType = "C";
230 <  atomInfo->pos[0] = pos[0] + newVec[0];
231 <  atomInfo->pos[1] = pos[1] + newVec[1];
232 <  atomInfo->pos[2] = pos[2] + newVec[2];
233 <  atomInfo->dipole[0] = 0.0;
234 <  atomInfo->dipole[1] = 0.0;
235 <  atomInfo->dipole[2] = 0.0;
236 <  atomData->addAtomInfo(atomInfo);
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 <  //add atom data into atom's property
244 >    // if the atom is not a TRED atom, skip it
245 >    if (!isTREDAtom(datom->getType()))
246 >      return;
247  
248 <  if(!haveAtomData){
283 <    atomData->setID("ATOMDATA");
284 <    datom->addProperty(atomData);
285 <  }
248 >    data = datom->getPropertyByName("ATOMDATA");
249  
250 <  setVisited(datom);
250 >    if (data != NULL) {
251 >      atomData = dynamic_cast<AtomData *>(data);
252  
253 < }
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 < const string LinearAtomVisitor::toString(){
265 <  char buffer[65535];
266 <  string result;
294 <  
295 <  sprintf(buffer ,"------------------------------------------------------------------\n");
296 <  result += buffer;
264 >    pos = datom->getPos();
265 >    q = datom->getQ();
266 >    rotMatrix = datom->getA();
267  
268 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
269 <  result += buffer;
268 >    // We need A^T to convert from body-fixed to space-fixed:
269 >    // transposeMat3(rotMatrix, rotTrans);
270 >    rotTrans = rotMatrix.transpose();
271  
272 <  sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
273 <  result += buffer;
272 >    // center of mass of the water molecule
273 >    // matVecMul3(rotTrans, u, newVec);
274 >    newVec = rotTrans * u;
275  
276 <  sprintf(buffer ,"------------------------------------------------------------------\n");
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 <  return result;
308 < }
285 >    atomData->addAtomInfo(atomInfo);
286  
287 < //----------------------------------------------------------------------------//
287 >    // oxygen
288 >    // matVecMul3(rotTrans, ox, newVec);
289 >    newVec = rotTrans * ox;
290  
291 < void DefaultAtomVisitor::visit(Atom* atom){
292 <  AtomData* atomData;
293 <  AtomInfo* atomInfo;
294 <  double pos[3];
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 <  if(isVisited(atom))
302 <    return;
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 < atomInfo =new AtomInfo;
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 <  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;
327 >    // add atom data into atom's property
328  
329 +    if (!haveAtomData) {
330 +      atomData->setID("ATOMDATA");
331 +      datom->addProperty(atomData);
332 +    }
333  
334 <  atomData->addAtomInfo(atomInfo);
335 <  
337 <  atom->addProperty(atomData);
334 >    setVisited(datom);
335 >  }
336  
337 <  setVisited(atom);
338 < }
339 < void DefaultAtomVisitor::visit(DirectionalAtom* datom){
342 <  AtomData* atomData;
343 <  AtomInfo* atomInfo;
344 <  double pos[3];
345 <  double u[3];
337 >  const std::string TREDAtomVisitor::toString() {
338 >    char   buffer[65535];
339 >    std::string result;
340  
341 <  if(isVisited(datom))
342 <    return;
343 <  
350 <  datom->getPos(pos);
351 <  datom->getU(u);
341 >    sprintf(buffer,
342 >            "------------------------------------------------------------------\n");
343 >    result += buffer;
344  
345 <  atomData = new AtomData;
346 <  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];  
345 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
346 >    result += buffer;
347  
348 <  atomData->addAtomInfo(atomInfo);
348 >    sprintf(buffer,
349 >            "Visitor Description: Convert the TRED atom into 4 different atoms\n");
350 >    result += buffer;
351  
352 <  datom->addProperty(atomData);
352 >    sprintf(buffer,
353 >            "------------------------------------------------------------------\n");
354 >    result += buffer;
355 >
356 >    return result;
357 >  }
358  
369 –  setVisited(datom);
370 – }
359  
360 +  bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
361 +    std::set<std::string>::iterator strIter;
362 +    strIter = linearAtomType.find(atomType);
363  
364 < const string DefaultAtomVisitor::toString(){
365 <  char buffer[65535];
366 <  string result;
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 <  sprintf(buffer ,"------------------------------------------------------------------\n");
436 <  result += buffer;
435 >    pos = datom->getPos();
436 >    q = datom->getQ();
437 >    rotMatrix = datom->getA();
438  
439 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
440 <  result += buffer;
439 >    // We need A^T to convert from body-fixed to space-fixed:  
440 >    rotTrans = rotMatrix.transpose();
441  
442 <  sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n");
443 <  result += buffer;
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 <  sprintf(buffer ,"------------------------------------------------------------------\n");
454 <  result += buffer;
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 <  return result;
465 < }    
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 < }//namespace oopse
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 >    Vector3d c1(0.0, 0.0, 0.0);
526 >    Vector3d c2(0.0, 0.0, 1.0);
527 >    RotMat3x3d rotMatrix;
528 >    RotMat3x3d rotTrans;
529 >    AtomInfo* atomInfo;
530 >    Vector3d pos;
531 >    Vector3d newVec;
532 >    Vector3d dVec;
533 >    Quat4d q;
534 >    AtomData* atomData;
535 >    GenericData* data;
536 >    bool haveAtomData;
537 >
538 >    //if atom is not GBlipid atom, just skip it
539 >    if(!isGBLipidAtom(datom->getType()))
540 >      return;
541 >
542 >    data = datom->getPropertyByName("ATOMDATA");
543 >    if(data != NULL){
544 >      atomData = dynamic_cast<AtomData*>(data);  
545 >      if(atomData == NULL){
546 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
547 >        atomData = new AtomData;
548 >        haveAtomData = false;      
549 >      } else {
550 >        haveAtomData = true;
551 >      }
552 >    } else {
553 >      atomData = new AtomData;
554 >      haveAtomData = false;
555 >    }
556 >  
557 >  
558 >    pos = datom->getPos();
559 >    q = datom->getQ();
560 >    rotMatrix = datom->getA();
561 >
562 >    // We need A^T to convert from body-fixed to space-fixed:  
563 >    rotTrans = rotMatrix.transpose();
564 >
565 >    newVec = rotTrans * c1;
566 >    dVec = rotTrans * c2;
567 >    atomInfo = new AtomInfo;
568 >    atomInfo->atomTypeName = "GB";
569 >    atomInfo->pos[0] = pos[0] + newVec[0];
570 >    atomInfo->pos[1] = pos[1] + newVec[1];
571 >    atomInfo->pos[2] = pos[2] + newVec[2];
572 >    atomInfo->dipole[0] = dVec[0];
573 >    atomInfo->dipole[1] = dVec[1];
574 >    atomInfo->dipole[2] = dVec[2];
575 >    atomInfo->hasVector = true;
576 >    atomInfo->charge = 3.0;
577 >    atomInfo->hasCharge = true;
578 >    atomData->addAtomInfo(atomInfo);
579 >
580 >    //add atom data into atom's property
581 >
582 >    if(!haveAtomData){
583 >      atomData->setID("ATOMDATA");
584 >      datom->addProperty(atomData);
585 >    }
586 >
587 >    setVisited(datom);
588 >
589 >  }
590 >
591 >  const std::string GBLipidAtomVisitor::toString(){
592 >    char buffer[65535];
593 >    std::string result;
594 >  
595 >    sprintf(buffer ,"------------------------------------------------------------------\n");
596 >    result += buffer;
597 >
598 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
599 >    result += buffer;
600 >
601 >    sprintf(buffer , "Visitor Description: Convert GBlipid into xyz-formatted atom for use with xyz2pov\n");
602 >    result += buffer;
603 >
604 >    sprintf(buffer ,"------------------------------------------------------------------\n");
605 >    result += buffer;
606 >
607 >    return result;
608 >  }
609 >
610 >  bool Ring5gbAtomVisitor::isRing5gbAtom(const std::string& atomType){
611 >    std::set<std::string>::iterator strIter;
612 >    strIter = Ring5gbAtomType.find(atomType);
613 >
614 >    return strIter != Ring5gbAtomType.end() ? true : false;
615 >  }
616 >
617 >  void Ring5gbAtomVisitor::visit(DirectionalAtom* datom){
618 >    std::vector<AtomInfo*> atoms;
619 >    //we need to convert linear into 4 different atoms
620 >    Vector3d c1(0.0, 0.0, -5.5);
621 >    Vector3d c2(0.0, 0.0, -1.8);
622 >    Vector3d c3(0.0, 0.0,  1.8);
623 >    Vector3d c4(0.0, 0.0,  5.5);
624 >    RotMat3x3d rotMatrix;
625 >    RotMat3x3d rotTrans;
626 >    AtomInfo* atomInfo;
627 >    Vector3d pos;
628 >    Vector3d newVec;
629 >    Vector3d dVec;
630 >    Quat4d q;
631 >    AtomData* atomData;
632 >    GenericData* data;
633 >    bool haveAtomData;
634 >
635 >    //if atom is not Ring5GB atom, just skip it
636 >    if(!isRing5gbAtom(datom->getType()))
637 >      return;
638 >
639 >    data = datom->getPropertyByName("ATOMDATA");
640 >    if(data != NULL){
641 >      atomData = dynamic_cast<AtomData*>(data);  
642 >      if(atomData == NULL){
643 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
644 >        atomData = new AtomData;
645 >        haveAtomData = false;      
646 >      } else {
647 >        haveAtomData = true;
648 >      }
649 >    } else {
650 >      atomData = new AtomData;
651 >      haveAtomData = false;
652 >    }
653 >  
654 >  
655 >    pos = datom->getPos();
656 >    q = datom->getQ();
657 >    rotMatrix = datom->getA();
658 >
659 >    // We need A^T to convert from body-fixed to space-fixed:  
660 >    rotTrans = rotMatrix.transpose();
661 >
662 >    newVec = rotTrans * c1;
663 >    atomInfo = new AtomInfo;
664 >    atomInfo->atomTypeName = "K";
665 >    atomInfo->pos[0] = pos[0] + newVec[0];
666 >    atomInfo->pos[1] = pos[1] + newVec[1];
667 >    atomInfo->pos[2] = pos[2] + newVec[2];
668 >    atomInfo->dipole[0] = 0.0;
669 >    atomInfo->dipole[1] = 0.0;
670 >    atomInfo->dipole[2] = 0.0;
671 >    atomData->addAtomInfo(atomInfo);
672 >
673 >    newVec = rotTrans * c2;
674 >    atomInfo = new AtomInfo;
675 >    atomInfo->atomTypeName = "K";
676 >    atomInfo->pos[0] = pos[0] + newVec[0];
677 >    atomInfo->pos[1] = pos[1] + newVec[1];
678 >    atomInfo->pos[2] = pos[2] + newVec[2];
679 >    atomInfo->dipole[0] = 0.0;
680 >    atomInfo->dipole[1] = 0.0;
681 >    atomInfo->dipole[2] = 0.0;
682 >    atomData->addAtomInfo(atomInfo);
683 >
684 >    newVec = rotTrans * c3;
685 >    atomInfo = new AtomInfo;
686 >    atomInfo->atomTypeName = "K";
687 >    atomInfo->pos[0] = pos[0] + newVec[0];
688 >    atomInfo->pos[1] = pos[1] + newVec[1];
689 >    atomInfo->pos[2] = pos[2] + newVec[2];
690 >    atomInfo->dipole[0] = 0.0;
691 >    atomInfo->dipole[1] = 0.0;
692 >    atomInfo->dipole[2] = 0.0;
693 >    atomData->addAtomInfo(atomInfo);
694 >
695 >    newVec = rotTrans * c4;
696 >    atomInfo = new AtomInfo;
697 >    atomInfo->atomTypeName = "K";
698 >    atomInfo->pos[0] = pos[0] + newVec[0];
699 >    atomInfo->pos[1] = pos[1] + newVec[1];
700 >    atomInfo->pos[2] = pos[2] + newVec[2];
701 >    atomInfo->dipole[0] = 0.0;
702 >    atomInfo->dipole[1] = 0.0;
703 >    atomInfo->dipole[2] = 0.0;
704 >    atomData->addAtomInfo(atomInfo);
705 >
706 >    //add atom data into atom's property
707 >
708 >    if(!haveAtomData){
709 >      atomData->setID("ATOMDATA");
710 >      datom->addProperty(atomData);
711 >    }
712 >
713 >    setVisited(datom);
714 >
715 >  }
716 >
717 >  const std::string Ring5gbAtomVisitor::toString(){
718 >    char buffer[65535];
719 >    std::string result;
720 >  
721 >    sprintf(buffer ,"------------------------------------------------------------------\n");
722 >    result += buffer;
723 >
724 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
725 >    result += buffer;
726 >
727 >    sprintf(buffer , "Visitor Description: Convert Ring5GB into 4 different K atoms\n");
728 >    result += buffer;
729 >
730 >    sprintf(buffer ,"------------------------------------------------------------------\n");
731 >    result += buffer;
732 >
733 >    return result;
734 >  }
735 >
736 >  bool HeadAtomVisitor::isHeadAtom(const std::string& atomType){
737 >    std::set<std::string>::iterator strIter;
738 >    strIter = HeadAtomType.find(atomType);
739 >
740 >    return strIter != HeadAtomType.end() ? true : false;
741 >  }
742 >
743 >  void HeadAtomVisitor::visit(DirectionalAtom* datom){
744 >    std::vector<AtomInfo*> atoms;
745 >    //we need to convert linear into 2 different atoms
746 >    Vector3d c1(0.0, 0.0, -1.5);
747 >    Vector3d c2(0.0, 0.0, 1.5);
748 >    RotMat3x3d rotMatrix;
749 >    RotMat3x3d rotTrans;
750 >    AtomInfo* atomInfo;
751 >    Vector3d pos;
752 >    Vector3d newVec;
753 >    Vector3d dVec;
754 >    Quat4d q;
755 >    AtomData* atomData;
756 >    GenericData* data;
757 >    bool haveAtomData;
758 >
759 >    //if atom is not Head atom, just skip it
760 >    if(!isHeadAtom(datom->getType()))
761 >      return;
762 >
763 >    data = datom->getPropertyByName("ATOMDATA");
764 >    if(data != NULL){
765 >      atomData = dynamic_cast<AtomData*>(data);  
766 >      if(atomData == NULL){
767 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
768 >        atomData = new AtomData;
769 >        haveAtomData = false;      
770 >      } else {
771 >        haveAtomData = true;
772 >      }
773 >    } else {
774 >      atomData = new AtomData;
775 >      haveAtomData = false;
776 >    }
777 >  
778 >  
779 >    pos = datom->getPos();
780 >    q = datom->getQ();
781 >    rotMatrix = datom->getA();
782 >
783 >    // We need A^T to convert from body-fixed to space-fixed:  
784 >    rotTrans = rotMatrix.transpose();
785 >
786 >    newVec = rotTrans * c1;
787 >    atomInfo = new AtomInfo;
788 >    atomInfo->atomTypeName = "C";
789 >    atomInfo->pos[0] = pos[0] + newVec[0];
790 >    atomInfo->pos[1] = pos[1] + newVec[1];
791 >    atomInfo->pos[2] = pos[2] + newVec[2];
792 >    atomInfo->dipole[0] = 0.0;
793 >    atomInfo->dipole[1] = 0.0;
794 >    atomInfo->dipole[2] = 0.0;
795 >    atomData->addAtomInfo(atomInfo);
796 >
797 >    newVec = rotTrans * c2;
798 >    atomInfo = new AtomInfo;
799 >    atomInfo->atomTypeName = "O";
800 >    atomInfo->pos[0] = pos[0] + newVec[0];
801 >    atomInfo->pos[1] = pos[1] + newVec[1];
802 >    atomInfo->pos[2] = pos[2] + newVec[2];
803 >    atomInfo->dipole[0] = 0.0;
804 >    atomInfo->dipole[1] = 0.0;
805 >    atomInfo->dipole[2] = 0.0;
806 >    atomData->addAtomInfo(atomInfo);
807 >
808 >    //add atom data into atom's property
809 >
810 >    if(!haveAtomData){
811 >      atomData->setID("ATOMDATA");
812 >      datom->addProperty(atomData);
813 >    }
814 >
815 >    setVisited(datom);
816 >
817 >  }
818 >
819 >  const std::string HeadAtomVisitor::toString(){
820 >    char buffer[65535];
821 >    std::string result;
822 >  
823 >    sprintf(buffer ,"------------------------------------------------------------------\n");
824 >    result += buffer;
825 >
826 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
827 >    result += buffer;
828 >
829 >    sprintf(buffer , "Visitor Description: Convert HEAD into C atom and O atom\n");
830 >    result += buffer;
831 >
832 >    sprintf(buffer ,"------------------------------------------------------------------\n");
833 >    result += buffer;
834 >
835 >    return result;
836 >  }
837 >
838 >
839 >  //----------------------------------------------------------------------------//
840 >
841 >  void DefaultAtomVisitor::visit(Atom *atom) {
842 >    AtomData *atomData;
843 >    AtomInfo *atomInfo;
844 >    Vector3d  pos;
845 >
846 >    if (isVisited(atom))
847 >      return;
848 >
849 >    atomInfo = new AtomInfo;
850 >
851 >    atomData = new AtomData;
852 >    atomData->setID("ATOMDATA");
853 >
854 >    pos = atom->getPos();
855 >    atomInfo->atomTypeName = atom->getType();
856 >    atomInfo->pos[0] = pos[0];
857 >    atomInfo->pos[1] = pos[1];
858 >    atomInfo->pos[2] = pos[2];
859 >    atomInfo->dipole[0] = 0.0;
860 >    atomInfo->dipole[1] = 0.0;
861 >    atomInfo->dipole[2] = 0.0;
862 >
863 >    atomData->addAtomInfo(atomInfo);
864 >
865 >    atom->addProperty(atomData);
866 >
867 >    setVisited(atom);
868 >  }
869 >
870 >  void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
871 >    AtomData *atomData;
872 >    AtomInfo *atomInfo;
873 >    Vector3d  pos;
874 >    Vector3d  u;
875 >
876 >    if (isVisited(datom))
877 >      return;
878 >
879 >    pos = datom->getPos();
880 >    if (datom->getAtomType()->isGayBerne()) {
881 >        u = datom->getA().transpose()*V3Z;        
882 >    } else if (datom->getAtomType()->isMultipole()) {
883 >        u = datom->getElectroFrame().getColumn(2);
884 >    }
885 >    atomData = new AtomData;
886 >    atomData->setID("ATOMDATA");
887 >    atomInfo = new AtomInfo;
888 >
889 >    atomInfo->atomTypeName = datom->getType();
890 >    atomInfo->pos[0] = pos[0];
891 >    atomInfo->pos[1] = pos[1];
892 >    atomInfo->pos[2] = pos[2];
893 >    atomInfo->dipole[0] = u[0];
894 >    atomInfo->dipole[1] = u[1];
895 >    atomInfo->dipole[2] = u[2];
896 >
897 >    atomData->addAtomInfo(atomInfo);
898 >
899 >    datom->addProperty(atomData);
900 >
901 >    setVisited(datom);
902 >  }
903 >
904 >  const std::string DefaultAtomVisitor::toString() {
905 >    char   buffer[65535];
906 >    std::string result;
907 >
908 >    sprintf(buffer,
909 >            "------------------------------------------------------------------\n");
910 >    result += buffer;
911 >
912 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
913 >    result += buffer;
914 >
915 >    sprintf(buffer,
916 >            "Visitor Description: copy atom infomation into atom data\n");
917 >    result += buffer;
918 >
919 >    sprintf(buffer,
920 >            "------------------------------------------------------------------\n");
921 >    result += buffer;
922 >
923 >    return result;
924 >  }
925 > } //namespace oopse

Diff Legend

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