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Comparing trunk/OOPSE-2.0/src/visitors/AtomVisitor.cpp (file contents):
Revision 1718 by chrisfen, Fri Nov 5 21:45:14 2004 UTC vs.
Revision 2091 by gezelter, Tue Mar 8 21:07:49 2005 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);  
67 <  }
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 < bool BaseAtomVisitor::isVisited(Atom* atom){
71 <  GenericData* data;
72 <  data = atom->getProperty("VISITED");
73 <  return data == NULL ?  false : true;
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)
41 <   if(*strIter == atomType)
42 <    return true;
43 <  
44 <  return false;  
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
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 +    //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 < const string SSDAtomVisitor::toString(){
196 <  char buffer[65535];
197 <  string result;
161 <  
162 <  sprintf(buffer ,"------------------------------------------------------------------\n");
163 <  result += buffer;
195 > const std::string SSDAtomVisitor::toString() {
196 >    char   buffer[65535];
197 >    std::string result;
198  
199 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
200 <  result += buffer;
199 >    sprintf(buffer,
200 >            "------------------------------------------------------------------\n");
201 >    result += buffer;
202  
203 <  sprintf(buffer , "Visitor Description: Convert SSD into 4 different atoms\n");
204 <  result += buffer;
203 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
204 >    result += buffer;
205  
206 <  sprintf(buffer ,"------------------------------------------------------------------\n");
207 <  result += buffer;
206 >    sprintf(buffer,
207 >            "Visitor Description: Convert SSD into 4 different atoms\n");
208 >    result += buffer;
209  
210 <  return result;
210 >    sprintf(buffer,
211 >            "------------------------------------------------------------------\n");
212 >    result += buffer;
213 >
214 >    return result;
215   }
216  
217 < bool LinearAtomVisitor::isLinearAtom(const string& atomType){
218 <  vector<string>::iterator strIter;
219 <  
220 <  for(strIter = linearAtomType.begin(); strIter != linearAtomType.end();
221 <      ++strIter)
182 <    if(*strIter == atomType)
183 <      return true;
184 <  
185 <  return false;  
217 > bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
218 >    std::set<std::string>::iterator strIter;
219 >    strIter = linearAtomType.find(atomType);
220 >
221 >    return strIter != linearAtomType.end() ? true : false;
222   }
223  
224   void LinearAtomVisitor::visit(DirectionalAtom* datom){
225 <
226 <  vector<AtomInfo*> atoms;
225 >    std::vector<AtomInfo*> atoms;
226 >    //we need to convert linear into 4 different atoms
227 >    Vector3d c1(0.0, 0.0, -1.8);
228 >    Vector3d c2(0.0, 0.0, -0.6);
229 >    Vector3d c3(0.0, 0.0,  0.6);
230 >    Vector3d c4(0.0, 0.0,  1.8);
231 >    RotMat3x3d rotMatrix;
232 >    RotMat3x3d rotTrans;
233 >    AtomInfo* atomInfo;
234 >    Vector3d pos;
235 >    Vector3d newVec;
236 >    Quat4d q;
237 >    AtomData* atomData;
238 >    GenericData* data;
239 >    bool haveAtomData;
240  
241 <  //we need to convert linear into 4 different atoms
242 <  double c1[3] = {0.0, 0.0, -1.8};
243 <  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){
241 >    //if atom is not SSD atom, just skip it
242 >    if(!isLinearAtom(datom->getType()))
243 >        return;
244  
245 <    atomData = dynamic_cast<AtomData*>(data);  
246 <    if(atomData == NULL){
247 <      cerr << "can not get Atom Data from " << datom->getType() << endl;
248 <      atomData = new AtomData;
249 <      haveAtomData = false;      
245 >    data = datom->getPropertyByName("ATOMDATA");
246 >    if(data != NULL){
247 >        atomData = dynamic_cast<AtomData*>(data);  
248 >        if(atomData == NULL){
249 >            std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
250 >            atomData = new AtomData;
251 >            haveAtomData = false;      
252 >        } else {
253 >            haveAtomData = true;
254 >        }
255 >    } else {
256 >        atomData = new AtomData;
257 >        haveAtomData = false;
258      }
220 –    else
221 –      haveAtomData = true;
222 –  }
223 –  else{
224 –    atomData = new AtomData;
225 –    haveAtomData = false;
226 –  }
259    
260    
261 <  datom->getPos(pos);
262 <  datom->getQ(q);
263 <  datom->getA(rotMatrix);
261 >    pos = datom->getPos();
262 >    q = datom->getQ();
263 >    rotMatrix = datom->getA();
264  
265 <  // We need A^T to convert from body-fixed to space-fixed:
266 <  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);
265 >    // We need A^T to convert from body-fixed to space-fixed:  
266 >    rotTrans = rotMatrix.transpose();
267  
268 <  matVecMul3(rotTrans, c2, newVec);
269 <  atomInfo = new AtomInfo;
270 <  atomInfo->AtomType = "C";
271 <  atomInfo->pos[0] = pos[0] + newVec[0];
272 <  atomInfo->pos[1] = pos[1] + newVec[1];
273 <  atomInfo->pos[2] = pos[2] + newVec[2];
274 <  atomInfo->dipole[0] = 0.0;
275 <  atomInfo->dipole[1] = 0.0;
276 <  atomInfo->dipole[2] = 0.0;
277 <  atomData->addAtomInfo(atomInfo);
268 >    newVec = rotTrans * c1;
269 >    atomInfo = new AtomInfo;
270 >    atomInfo->atomTypeName = "C";
271 >    atomInfo->pos[0] = pos[0] + newVec[0];
272 >    atomInfo->pos[1] = pos[1] + newVec[1];
273 >    atomInfo->pos[2] = pos[2] + newVec[2];
274 >    atomInfo->dipole[0] = 0.0;
275 >    atomInfo->dipole[1] = 0.0;
276 >    atomInfo->dipole[2] = 0.0;
277 >    atomData->addAtomInfo(atomInfo);
278  
279 <  matVecMul3(rotTrans, c3, newVec);
280 <  atomInfo = new AtomInfo;
281 <  atomInfo->AtomType = "C";
282 <  atomInfo->pos[0] = pos[0] + newVec[0];
283 <  atomInfo->pos[1] = pos[1] + newVec[1];
284 <  atomInfo->pos[2] = pos[2] + newVec[2];
285 <  atomInfo->dipole[0] = 0.0;
286 <  atomInfo->dipole[1] = 0.0;
287 <  atomInfo->dipole[2] = 0.0;
288 <  atomData->addAtomInfo(atomInfo);
279 >    newVec = rotTrans * c2;
280 >    atomInfo = new AtomInfo;
281 >    atomInfo->atomTypeName = "C";
282 >    atomInfo->pos[0] = pos[0] + newVec[0];
283 >    atomInfo->pos[1] = pos[1] + newVec[1];
284 >    atomInfo->pos[2] = pos[2] + newVec[2];
285 >    atomInfo->dipole[0] = 0.0;
286 >    atomInfo->dipole[1] = 0.0;
287 >    atomInfo->dipole[2] = 0.0;
288 >    atomData->addAtomInfo(atomInfo);
289  
290 <  matVecMul3(rotTrans, c4, newVec);
291 <  atomInfo = new AtomInfo;
292 <  atomInfo->AtomType = "C";
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);
290 >    newVec = rotTrans * c3;
291 >    atomInfo = new AtomInfo;
292 >    atomInfo->atomTypeName = "C";
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 <  //add atom data into atom's property
301 >    newVec = rotTrans * c4;
302 >    atomInfo = new AtomInfo;
303 >    atomInfo->atomTypeName = "C";
304 >    atomInfo->pos[0] = pos[0] + newVec[0];
305 >    atomInfo->pos[1] = pos[1] + newVec[1];
306 >    atomInfo->pos[2] = pos[2] + newVec[2];
307 >    atomInfo->dipole[0] = 0.0;
308 >    atomInfo->dipole[1] = 0.0;
309 >    atomInfo->dipole[2] = 0.0;
310 >    atomData->addAtomInfo(atomInfo);
311  
312 <  if(!haveAtomData){
283 <    atomData->setID("ATOMDATA");
284 <    datom->addProperty(atomData);
285 <  }
312 >    //add atom data into atom's property
313  
314 <  setVisited(datom);
314 >    if(!haveAtomData){
315 >        atomData->setID("ATOMDATA");
316 >        datom->addProperty(atomData);
317 >    }
318  
319 +    setVisited(datom);
320 +
321   }
322  
323 < const string LinearAtomVisitor::toString(){
323 > const std::string LinearAtomVisitor::toString(){
324    char buffer[65535];
325 <  string result;
325 >  std::string result;
326    
327    sprintf(buffer ,"------------------------------------------------------------------\n");
328    result += buffer;
# Line 309 | Line 341 | void DefaultAtomVisitor::visit(Atom* atom){
341  
342   //----------------------------------------------------------------------------//
343  
344 < void DefaultAtomVisitor::visit(Atom* atom){
345 <  AtomData* atomData;
346 <  AtomInfo* atomInfo;
347 <  double pos[3];
344 > void DefaultAtomVisitor::visit(Atom *atom) {
345 >    AtomData *atomData;
346 >    AtomInfo *atomInfo;
347 >    Vector3d  pos;
348  
349 <  if(isVisited(atom))
350 <    return;
349 >    if (isVisited(atom))
350 >        return;
351  
352 < atomInfo =new AtomInfo;
352 >    atomInfo = new AtomInfo;
353  
354 <  atomData = new AtomData;
355 <  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;
354 >    atomData = new AtomData;
355 >    atomData->setID("ATOMDATA");
356  
357 +    pos = atom->getPos();
358 +    atomInfo->atomTypeName = atom->getType();
359 +    printf("setting a type to %s\n", atom->getType().c_str());
360 +    atomInfo->pos[0] = pos[0];
361 +    atomInfo->pos[1] = pos[1];
362 +    atomInfo->pos[2] = pos[2];
363 +    atomInfo->dipole[0] = 0.0;
364 +    atomInfo->dipole[1] = 0.0;
365 +    atomInfo->dipole[2] = 0.0;
366  
367 <  atomData->addAtomInfo(atomInfo);
336 <  
337 <  atom->addProperty(atomData);
367 >    atomData->addAtomInfo(atomInfo);
368  
369 <  setVisited(atom);
369 >    atom->addProperty(atomData);
370 >
371 >    setVisited(atom);
372   }
341 – void DefaultAtomVisitor::visit(DirectionalAtom* datom){
342 –  AtomData* atomData;
343 –  AtomInfo* atomInfo;
344 –  double pos[3];
345 –  double u[3];
373  
374 <  if(isVisited(datom))
375 <    return;
376 <  
377 <  datom->getPos(pos);
378 <  datom->getU(u);
374 > void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
375 >    AtomData *atomData;
376 >    AtomInfo *atomInfo;
377 >    Vector3d  pos;
378 >    Vector3d  u;
379  
380 <  atomData = new AtomData;
381 <  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];  
380 >    if (isVisited(datom))
381 >        return;
382  
383 <  atomData->addAtomInfo(atomInfo);
383 >    pos = datom->getPos();
384 >    u = datom->getElectroFrame().getColumn(2);
385  
386 <  datom->addProperty(atomData);
386 >    atomData = new AtomData;
387 >    atomData->setID("ATOMDATA");
388 >    atomInfo = new AtomInfo;
389  
390 <  setVisited(datom);
391 < }
390 >    atomInfo->atomTypeName = datom->getType();
391 >    atomInfo->pos[0] = pos[0];
392 >    atomInfo->pos[1] = pos[1];
393 >    atomInfo->pos[2] = pos[2];
394 >    atomInfo->dipole[0] = u[0];
395 >    atomInfo->dipole[1] = u[1];
396 >    atomInfo->dipole[2] = u[2];
397  
398 +    atomData->addAtomInfo(atomInfo);
399  
400 < const string DefaultAtomVisitor::toString(){
374 <  char buffer[65535];
375 <  string result;
376 <  
377 <  sprintf(buffer ,"------------------------------------------------------------------\n");
378 <  result += buffer;
400 >    datom->addProperty(atomData);
401  
402 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
403 <  result += buffer;
402 >    setVisited(datom);
403 > }
404  
405 <  sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n");
406 <  result += buffer;
405 > const std::string DefaultAtomVisitor::toString() {
406 >    char   buffer[65535];
407 >    std::string result;
408  
409 <  sprintf(buffer ,"------------------------------------------------------------------\n");
410 <  result += buffer;
409 >    sprintf(buffer,
410 >            "------------------------------------------------------------------\n");
411 >    result += buffer;
412  
413 <  return result;
414 < }    
413 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
414 >    result += buffer;
415  
416 < }//namespace oopse
416 >    sprintf(buffer,
417 >            "Visitor Description: copy atom infomation into atom data\n");
418 >    result += buffer;
419 >
420 >    sprintf(buffer,
421 >            "------------------------------------------------------------------\n");
422 >    result += buffer;
423 >
424 >    return result;
425 > }
426 > } //namespace oopse

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