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Comparing trunk/src/visitors/AtomVisitor.cpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 954 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 "AtomVisitor.hpp"
44 < #include "DirectionalAtom.hpp"
45 < #include "MatVec3.h"
5 < #include "RigidBody.hpp"
43 > #include "visitors/AtomVisitor.hpp"
44 > #include "primitives/DirectionalAtom.hpp"
45 > #include "primitives/RigidBody.hpp"
46  
47 < void BaseAtomVisitor::visit(RigidBody* rb){
48 <  //vector<Atom*> myAtoms;
49 <  //vector<Atom*>::iterator atomIter;
47 > namespace oopse {
48 >  void BaseAtomVisitor::visit(RigidBody *rb) {
49 >    //vector<Atom*> myAtoms;
50 >    //vector<Atom*>::iterator atomIter;
51  
52 <  //myAtoms = rb->getAtoms();
12 <  
13 <  //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
14 <  //  (*atomIter)->accept(this);
15 < }
52 >    //myAtoms = rb->getAtoms();
53  
54 < void BaseAtomVisitor::setVisited(Atom* atom){
55 <  GenericData* data;
19 <  data = atom->getProperty("VISITED");
20 <
21 <  //if visited property is not existed, add it as new property
22 <  if(data == NULL){
23 <    data = new GenericData();
24 <    data->setID("VISITED");
25 <    atom->addProperty(data);  
54 >    //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
55 >    //  (*atomIter)->accept(this);
56    }
27 – }
57  
58 < bool BaseAtomVisitor::isVisited(Atom* atom){
59 <  GenericData* data;
60 <  data = atom->getProperty("VISITED");
32 <  return data == NULL ?  false : true;
33 < }
58 >  void BaseAtomVisitor::setVisited(Atom *atom) {
59 >    GenericData *data;
60 >    data = atom->getPropertyByName("VISITED");
61  
62 < bool SSDAtomVisitor::isSSDAtom(const string& atomType){
63 <  vector<string>::iterator strIter;
64 <  
65 <  for(strIter = ssdAtomType.begin(); strIter != ssdAtomType.end(); ++strIter)
66 <   if(*strIter == atomType)
67 <    return true;
68 <  
42 <  return false;  
43 < }
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 >  }
69  
70 < void SSDAtomVisitor::visit(DirectionalAtom* datom){
70 >  bool BaseAtomVisitor::isVisited(Atom *atom) {
71 >    GenericData *data;
72 >    data = atom->getPropertyByName("VISITED");
73 >    return data == NULL ? false : true;
74 >  }
75  
76 <  vector<AtomInfo*> atoms;
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 <  //we need to convert SSD into 4 differnet atoms
83 <  //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;
82 >  void SSDAtomVisitor::visit(DirectionalAtom *datom) {
83 >    std::vector<AtomInfo*>atoms;
84  
85 <  data = datom->getProperty("ATOMDATA");
86 <  if(data != NULL){
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 <    atomData = dynamic_cast<AtomData*>(data);  
103 <    if(atomData == NULL){
104 <      cerr << "can not get Atom Data from " << datom->getType() << endl;
76 <      atomData = new AtomData;
77 <      haveAtomData = false;      
78 <    }
79 <    else
80 <      haveAtomData = true;
81 <  }
82 <  else{
83 <    atomData = new AtomData;
84 <    haveAtomData = false;
85 <  }
86 <  
87 <  
88 <  datom->getPos(pos);
89 <  datom->getQ(q);
90 <  datom->getA(rotMatrix);
102 >    //if atom is not SSD atom, just skip it
103 >    if (!isSSDAtom(datom->getType()))
104 >      return;
105  
106 <  // We need A^T to convert from body-fixed to space-fixed:
93 <  transposeMat3(rotMatrix, rotTrans);
94 <  
95 <  //center of mass of the water molecule
96 <  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];
106 >    data = datom->getPropertyByName("ATOMDATA");
107  
108 <  atomData->addAtomInfo(atomInfo);
108 >    if (data != NULL) {
109 >      atomData = dynamic_cast<AtomData *>(data);
110  
111 <  //oxygen
112 <  matVecMul3(rotTrans, ox, newVec);
113 <  atomInfo = new AtomInfo;
114 <  atomInfo->AtomType = "O";
115 <  atomInfo->pos[0] = pos[0] + newVec[0];
116 <  atomInfo->pos[1] = pos[1] + newVec[1];
117 <  atomInfo->pos[2] = pos[2] + newVec[2];
118 <  atomInfo->dipole[0] = 0.0;
119 <  atomInfo->dipole[1] = 0.0;
120 <  atomInfo->dipole[2] = 0.0;
118 <  atomData->addAtomInfo(atomInfo);
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 +    pos = datom->getPos();
123 +    q = datom->getQ();
124 +    rotMatrix = datom->getA();
125  
126 <  //hydrogen1
127 <    matVecMul3(rotTrans, h1, newVec);
128 <  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);
126 >    // We need A^T to convert from body-fixed to space-fixed:
127 >    //transposeMat3(rotMatrix, rotTrans);
128 >    rotTrans = rotMatrix.transpose();
129  
130 <  //hydrogen2
131 <  matVecMul3(rotTrans, h2, newVec);
132 <  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);
130 >    //center of mass of the water molecule
131 >    //matVecMul3(rotTrans, u, newVec);
132 >    newVec = rotTrans * u;
133  
134 <  //add atom data into atom's property
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 <  if(!haveAtomData){
148 <    atomData->setID("ATOMDATA");
149 <    datom->addProperty(atomData);
150 <  }
143 >    atomData->addAtomInfo(atomInfo);
144  
145 <  setVisited(datom);
145 >    //oxygen
146 >    //matVecMul3(rotTrans, ox, newVec);
147 >    newVec = rotTrans * ox;
148  
149 < }
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 < const string SSDAtomVisitor::toString(){
160 <  char buffer[65535];
161 <  string result;
162 <  
163 <  sprintf(buffer ,"------------------------------------------------------------------\n");
164 <  result += buffer;
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 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
173 <  result += buffer;
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 <  sprintf(buffer , "Visitor Description: Convert SSD into 4 different atoms\n");
167 <  result += buffer;
185 >    //add atom data into atom's property
186  
187 <  sprintf(buffer ,"------------------------------------------------------------------\n");
188 <  result += buffer;
187 >    if (!haveAtomData) {
188 >      atomData->setID("ATOMDATA");
189 >      datom->addProperty(atomData);
190 >    }
191  
192 <  return result;
193 < }
192 >    setVisited(datom);
193 >  }
194  
195 < //----------------------------------------------------------------------------//
195 >  const std::string SSDAtomVisitor::toString() {
196 >    char   buffer[65535];
197 >    std::string result;
198  
199 < void DefaultAtomVisitor::visit(Atom* atom){
200 <  AtomData* atomData;
201 <  AtomInfo* atomInfo;
180 <  double pos[3];
199 >    sprintf(buffer,
200 >            "------------------------------------------------------------------\n");
201 >    result += buffer;
202  
203 <  if(isVisited(atom))
204 <    return;
203 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
204 >    result += buffer;
205  
206 < atomInfo =new AtomInfo;
206 >    sprintf(buffer,
207 >            "Visitor Description: Convert SSD into 4 different atoms\n");
208 >    result += buffer;
209  
210 <  atomData = new AtomData;
211 <  atomData->setID("ATOMDATA");
212 <
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;
210 >    sprintf(buffer,
211 >            "------------------------------------------------------------------\n");
212 >    result += buffer;
213  
214 +    return result;
215 +  }
216  
217 <  atomData->addAtomInfo(atomInfo);
218 <  
219 <  atom->addProperty(atomData);
217 >  bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
218 >    std::set<std::string>::iterator strIter;
219 >    strIter = linearAtomType.find(atomType);
220  
221 <  setVisited(atom);
222 < }
206 < void DefaultAtomVisitor::visit(DirectionalAtom* datom){
207 <  AtomData* atomData;
208 <  AtomInfo* atomInfo;
209 <  double pos[3];
210 <  double u[3];
221 >    return strIter != linearAtomType.end() ? true : false;
222 >  }
223  
224 <  if(isVisited(datom))
225 <    return;
226 <  
215 <  datom->getPos(pos);
216 <  datom->getU(u);
224 >  void LinearAtomVisitor::addGayBerneAtomType(const std::string& atomType){
225 >   linearAtomType.insert(atomType);
226 >  }
227  
228 <  atomData = new AtomData;
229 <  atomData->setID("ATOMDATA");
230 <  atomInfo =new AtomInfo;
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 >    //if atom is not SSD atom, just skip it
246 >    if(!isLinearAtom(datom->getType()))
247 >      return;
248 >
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 >    }
263 >  
264    
265 <  atomInfo->AtomType = datom->getType();
266 <  atomInfo->pos[0] = pos[0];
267 <  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];  
265 >    pos = datom->getPos();
266 >    q = datom->getQ();
267 >    rotMatrix = datom->getA();
268  
269 <  atomData->addAtomInfo(atomInfo);
269 >    // We need A^T to convert from body-fixed to space-fixed:  
270 >    rotTrans = rotMatrix.transpose();
271  
272 <  datom->addProperty(atomData);
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 <  setVisited(datom);
284 < }
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 < const string DefaultAtomVisitor::toString(){
306 <  char buffer[65535];
307 <  string result;
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 <  sprintf(buffer ,"------------------------------------------------------------------\n");
332 <  result += buffer;
331 >    sprintf(buffer ,"------------------------------------------------------------------\n");
332 >    result += buffer;
333  
334 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
335 <  result += buffer;
334 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
335 >    result += buffer;
336  
337 <  sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n");
338 <  result += buffer;
337 >    sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
338 >    result += buffer;
339  
340 <  sprintf(buffer ,"------------------------------------------------------------------\n");
341 <  result += buffer;
340 >    sprintf(buffer ,"------------------------------------------------------------------\n");
341 >    result += buffer;
342  
343 <  return result;
344 < }    
343 >    return result;
344 >  }
345 >
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 >  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 >    //if atom is not GBlipid atom, just skip it
371 >    if(!isGBLipidAtom(datom->getType()))
372 >      return;
373 >
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 >    pos = datom->getPos();
391 >    q = datom->getQ();
392 >    rotMatrix = datom->getA();
393 >
394 >    // We need A^T to convert from body-fixed to space-fixed:  
395 >    rotTrans = rotMatrix.transpose();
396 >
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 >    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 >    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 >    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 >    //add atom data into atom's property
442 >
443 >    if(!haveAtomData){
444 >      atomData->setID("ATOMDATA");
445 >      datom->addProperty(atomData);
446 >    }
447 >
448 >    setVisited(datom);
449 >
450 >  }
451 >
452 >  const std::string GBLipidAtomVisitor::toString(){
453 >    char buffer[65535];
454 >    std::string result;
455 >  
456 >    sprintf(buffer ,"------------------------------------------------------------------\n");
457 >    result += buffer;
458 >
459 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
460 >    result += buffer;
461 >
462 >    sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n");
463 >    result += buffer;
464 >
465 >    sprintf(buffer ,"------------------------------------------------------------------\n");
466 >    result += buffer;
467 >
468 >    return result;
469 >  }
470 >
471 >  //----------------------------------------------------------------------------//
472 >
473 >  void DefaultAtomVisitor::visit(Atom *atom) {
474 >    AtomData *atomData;
475 >    AtomInfo *atomInfo;
476 >    Vector3d  pos;
477 >
478 >    if (isVisited(atom))
479 >      return;
480 >
481 >    atomInfo = new AtomInfo;
482 >
483 >    atomData = new AtomData;
484 >    atomData->setID("ATOMDATA");
485 >
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 >    atomData->addAtomInfo(atomInfo);
496 >
497 >    atom->addProperty(atomData);
498 >
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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