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Comparing branches/new_design/OOPSE-3.0/src/visitors/AtomVisitor.cpp (file contents):
Revision 1683, Thu Oct 28 22:34:02 2004 UTC vs.
Revision 1725 by tim, Wed Nov 10 22:01:06 2004 UTC

# Line 5 | Line 5 | namespace oopse {
5   #include "primitives/RigidBody.hpp"
6  
7   namespace oopse {
8 + void BaseAtomVisitor::visit(RigidBody *rb) {
9 + //vector<Atom*> myAtoms;
10 + //vector<Atom*>::iterator atomIter;
11  
12 < void BaseAtomVisitor::visit(RigidBody* rb){
10 <  //vector<Atom*> myAtoms;
11 <  //vector<Atom*>::iterator atomIter;
12 > //myAtoms = rb->getAtoms();
13  
14 <  //myAtoms = rb->getAtoms();
15 <  
16 <  //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
16 <  //  (*atomIter)->accept(this);
17 < }
14 > //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
15 > //  (*atomIter)->accept(this);
16 >    }
17  
18 < void BaseAtomVisitor::setVisited(Atom* atom){
19 <  GenericData* data;
20 <  data = atom->getProperty("VISITED");
18 > void BaseAtomVisitor::setVisited(Atom *atom) {
19 >    GenericData *data;
20 >    data = atom->getPropertyByName("VISITED");
21  
22 <  //if visited property is not existed, add it as new property
23 <  if(data == NULL){
24 <    data = new GenericData();
25 <    data->setID("VISITED");
26 <    atom->addProperty(data);  
27 <  }
22 >    //if visited property is not existed, add it as new property
23 >    if (data == NULL) {
24 >        data = new GenericData();
25 >        data->setID("VISITED");
26 >        atom->addProperty(data);
27 >    }
28   }
29  
30 < bool BaseAtomVisitor::isVisited(Atom* atom){
31 <  GenericData* data;
32 <  data = atom->getProperty("VISITED");
33 <  return data == NULL ?  false : true;
30 > bool BaseAtomVisitor::isVisited(Atom *atom) {
31 >    GenericData *data;
32 >    data = atom->getPropertyByName("VISITED");
33 >    return data == NULL ? false : true;
34   }
35  
36 < bool SSDAtomVisitor::isSSDAtom(const string& atomType){
37 <  vector<string>::iterator strIter;
38 <  
39 <  for(strIter = ssdAtomType.begin(); strIter != ssdAtomType.end(); ++strIter)
40 <   if(*strIter == atomType)
41 <    return true;
42 <  
43 <  return false;  
36 > bool SSDAtomVisitor::isSSDAtom(const string&atomType) {
37 >    vector<string>::iterator strIter;
38 >
39 >    for( strIter = ssdAtomType.begin(); strIter != ssdAtomType.end();
40 >        ++strIter )
41 >  if (*strIter == atomType)
42 >      return true;
43 >
44 >    return false;
45   }
46  
47 < void SSDAtomVisitor::visit(DirectionalAtom* datom){
47 > void SSDAtomVisitor::visit(DirectionalAtom *datom) {
48 >    vector<AtomInfo *>atoms;
49  
50 <  vector<AtomInfo*> atoms;
50 >    //we need to convert SSD into 4 differnet atoms
51 >    //one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
52 >    //of the water with a dipole moment
53 >    Vector3d h1(0.0, -0.75695, 0.5206);
54 >    Vector3d h2(0.0, 0.75695, 0.5206);
55 >    Vector3d ox(0.0, 0.0, -0.0654);
56 >    Vector3d u(0, 0, 1);
57 >    RotMat3x3d   rotMatrix;
58 >    RotMat3x3d   rotTrans;
59 >    AtomInfo *   atomInfo;
60 >    Vector3d     pos;
61 >    Vector3d     newVec;
62 >    Quat4d       q;
63 >    AtomData *   atomData;
64 >    GenericData *data;
65 >    bool         haveAtomData;
66  
67 <  //we need to convert SSD into 4 differnet atoms
68 <  //one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
69 <  //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;
67 >    //if atom is not SSD atom, just skip it
68 >    if (!isSSDAtom(datom->getType()))
69 >        return;
70  
71 <  data = datom->getProperty("ATOMDATA");
73 <  if(data != NULL){
71 >    data = datom->getPropertyByName("ATOMDATA");
72  
73 <    atomData = dynamic_cast<AtomData*>(data);  
74 <    if(atomData == NULL){
75 <      cerr << "can not get Atom Data from " << datom->getType() << endl;
76 <      atomData = new AtomData;
77 <      haveAtomData = false;      
73 >    if (data != NULL) {
74 >        atomData = dynamic_cast<AtomData *>(data);
75 >
76 >        if (atomData == NULL) {
77 >            cerr << "can not get Atom Data from " << datom->getType() << endl;
78 >            atomData = new AtomData;
79 >            haveAtomData = false;
80 >        } else
81 >            haveAtomData = true;
82 >    } else {
83 >        atomData = new AtomData;
84 >        haveAtomData = false;
85      }
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);
86  
87 <  // We need A^T to convert from body-fixed to space-fixed:
88 <  transposeMat3(rotMatrix, rotTrans);
89 <  
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];
87 >    pos = datom->getPos();
88 >    q = datom->getQ();
89 >    rotMatrix = datom->getA();
90  
91 <  atomData->addAtomInfo(atomInfo);
91 >    // We need A^T to convert from body-fixed to space-fixed:
92 >    //transposeMat3(rotMatrix, rotTrans);
93 >    rotTrans = rotMatrix.transpose();
94  
95 <  //oxygen
96 <  matVecMul3(rotTrans, ox, newVec);
97 <  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);
95 >    //center of mass of the water molecule
96 >    //matVecMul3(rotTrans, u, newVec);
97 >    newVec = rotTrans * u;
98  
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];
107  
108 <  //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);
108 >    atomData->addAtomInfo(atomInfo);
109  
110 <  //hydrogen2
111 <  matVecMul3(rotTrans, h2, newVec);
112 <  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);
110 >    //oxygen
111 >    //matVecMul3(rotTrans, ox, newVec);
112 >    newVec = rotTrans * ox;
113  
114 <  //add atom data into atom's property
114 >    atomInfo = new AtomInfo;
115 >    atomInfo->AtomType = "O";
116 >    atomInfo->pos[0] = pos[0] + newVec[0];
117 >    atomInfo->pos[1] = pos[1] + newVec[1];
118 >    atomInfo->pos[2] = pos[2] + newVec[2];
119 >    atomInfo->dipole[0] = 0.0;
120 >    atomInfo->dipole[1] = 0.0;
121 >    atomInfo->dipole[2] = 0.0;
122 >    atomData->addAtomInfo(atomInfo);
123  
124 <  if(!haveAtomData){
125 <    atomData->setID("ATOMDATA");
126 <    datom->addProperty(atomData);
127 <  }
128 <
129 <  setVisited(datom);
124 >    //hydrogen1
125 >    //matVecMul3(rotTrans, h1, newVec);
126 >    newVec = rotTrans * h1;
127 >    atomInfo = new AtomInfo;
128 >    atomInfo->AtomType = "H";
129 >    atomInfo->pos[0] = pos[0] + newVec[0];
130 >    atomInfo->pos[1] = pos[1] + newVec[1];
131 >    atomInfo->pos[2] = pos[2] + newVec[2];
132 >    atomInfo->dipole[0] = 0.0;
133 >    atomInfo->dipole[1] = 0.0;
134 >    atomInfo->dipole[2] = 0.0;
135 >    atomData->addAtomInfo(atomInfo);
136  
137 +    //hydrogen2
138 +    //matVecMul3(rotTrans, h2, newVec);
139 +    newVec = rotTrans * h2;
140 +    atomInfo = new AtomInfo;
141 +    atomInfo->AtomType = "H";
142 +    atomInfo->pos[0] = pos[0] + newVec[0];
143 +    atomInfo->pos[1] = pos[1] + newVec[1];
144 +    atomInfo->pos[2] = pos[2] + newVec[2];
145 +    atomInfo->dipole[0] = 0.0;
146 +    atomInfo->dipole[1] = 0.0;
147 +    atomInfo->dipole[2] = 0.0;
148 +    atomData->addAtomInfo(atomInfo);
149 +
150 +    //add atom data into atom's property
151 +
152 +    if (!haveAtomData) {
153 +        atomData->setID("ATOMDATA");
154 +        datom->addProperty(atomData);
155 +    }
156 +
157 +    setVisited(datom);
158   }
159  
160 < const string SSDAtomVisitor::toString(){
161 <  char buffer[65535];
162 <  string result;
161 <  
162 <  sprintf(buffer ,"------------------------------------------------------------------\n");
163 <  result += buffer;
160 > const string SSDAtomVisitor::toString() {
161 >    char   buffer[65535];
162 >    string result;
163  
164 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
165 <  result += buffer;
164 >    sprintf(buffer,
165 >            "------------------------------------------------------------------\n");
166 >    result += buffer;
167  
168 <  sprintf(buffer , "Visitor Description: Convert SSD into 4 different atoms\n");
169 <  result += buffer;
168 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
169 >    result += buffer;
170  
171 <  sprintf(buffer ,"------------------------------------------------------------------\n");
172 <  result += buffer;
171 >    sprintf(buffer,
172 >            "Visitor Description: Convert SSD into 4 different atoms\n");
173 >    result += buffer;
174  
175 <  return result;
175 >    sprintf(buffer,
176 >            "------------------------------------------------------------------\n");
177 >    result += buffer;
178 >
179 >    return result;
180   }
181  
182   //----------------------------------------------------------------------------//
183  
184 < void DefaultAtomVisitor::visit(Atom* atom){
185 <  AtomData* atomData;
186 <  AtomInfo* atomInfo;
187 <  double pos[3];
184 > void DefaultAtomVisitor::visit(Atom *atom) {
185 >    AtomData *atomData;
186 >    AtomInfo *atomInfo;
187 >    Vector3d  pos;
188  
189 <  if(isVisited(atom))
190 <    return;
189 >    if (isVisited(atom))
190 >        return;
191  
192 < atomInfo =new AtomInfo;
192 >    atomInfo = new AtomInfo;
193  
194 <  atomData = new AtomData;
195 <  atomData->setID("ATOMDATA");
191 <
192 <  atom->getPos(pos);
193 <  atomInfo->AtomType = atom->getType();
194 <  atomInfo->pos[0] = pos[0];
195 <  atomInfo->pos[1] = pos[1];
196 <  atomInfo->pos[2] = pos[2];
197 <  atomInfo->dipole[0] = 0.0;
198 <  atomInfo->dipole[1] = 0.0;
199 <  atomInfo->dipole[2] = 0.0;
194 >    atomData = new AtomData;
195 >    atomData->setID("ATOMDATA");
196  
197 +    pos = atom->getPos();
198 +    atomInfo->AtomType = atom->getType();
199 +    atomInfo->pos[0] = pos[0];
200 +    atomInfo->pos[1] = pos[1];
201 +    atomInfo->pos[2] = pos[2];
202 +    atomInfo->dipole[0] = 0.0;
203 +    atomInfo->dipole[1] = 0.0;
204 +    atomInfo->dipole[2] = 0.0;
205  
206 <  atomData->addAtomInfo(atomInfo);
203 <  
204 <  atom->addProperty(atomData);
206 >    atomData->addAtomInfo(atomInfo);
207  
208 <  setVisited(atom);
208 >    atom->addProperty(atomData);
209 >
210 >    setVisited(atom);
211   }
208 – void DefaultAtomVisitor::visit(DirectionalAtom* datom){
209 –  AtomData* atomData;
210 –  AtomInfo* atomInfo;
211 –  double pos[3];
212 –  double u[3];
212  
213 <  if(isVisited(datom))
214 <    return;
215 <  
216 <  datom->getPos(pos);
217 <  datom->getU(u);
213 > void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
214 >    AtomData *atomData;
215 >    AtomInfo *atomInfo;
216 >    Vector3d  pos;
217 >    Vector3d  u;
218  
219 <  atomData = new AtomData;
220 <  atomData->setID("ATOMDATA");
222 <  atomInfo =new AtomInfo;
223 <  
224 <  atomInfo->AtomType = datom->getType();
225 <  atomInfo->pos[0] = pos[0];
226 <  atomInfo->pos[1] = pos[1];
227 <  atomInfo->pos[2] = pos[2];
228 <  atomInfo->dipole[0] = u[0];
229 <  atomInfo->dipole[1] = u[1];
230 <  atomInfo->dipole[2] = u[2];  
219 >    if (isVisited(datom))
220 >        return;
221  
222 <  atomData->addAtomInfo(atomInfo);
222 >    pos = datom->getPos();
223 >    u = datom->getUnitVector();
224  
225 <  datom->addProperty(atomData);
225 >    atomData = new AtomData;
226 >    atomData->setID("ATOMDATA");
227 >    atomInfo = new AtomInfo;
228  
229 <  setVisited(datom);
230 < }
229 >    atomInfo->AtomType = datom->getType();
230 >    atomInfo->pos[0] = pos[0];
231 >    atomInfo->pos[1] = pos[1];
232 >    atomInfo->pos[2] = pos[2];
233 >    atomInfo->dipole[0] = u[0];
234 >    atomInfo->dipole[1] = u[1];
235 >    atomInfo->dipole[2] = u[2];
236  
237 +    atomData->addAtomInfo(atomInfo);
238  
239 < const string DefaultAtomVisitor::toString(){
241 <  char buffer[65535];
242 <  string result;
243 <  
244 <  sprintf(buffer ,"------------------------------------------------------------------\n");
245 <  result += buffer;
239 >    datom->addProperty(atomData);
240  
241 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
242 <  result += buffer;
241 >    setVisited(datom);
242 > }
243  
244 <  sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n");
245 <  result += buffer;
244 > const string DefaultAtomVisitor::toString() {
245 >    char   buffer[65535];
246 >    string result;
247  
248 <  sprintf(buffer ,"------------------------------------------------------------------\n");
249 <  result += buffer;
248 >    sprintf(buffer,
249 >            "------------------------------------------------------------------\n");
250 >    result += buffer;
251  
252 <  return result;
253 < }    
252 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
253 >    result += buffer;
254  
255 < }//namespace oopse
255 >    sprintf(buffer,
256 >            "Visitor Description: copy atom infomation into atom data\n");
257 >    result += buffer;
258 >
259 >    sprintf(buffer,
260 >            "------------------------------------------------------------------\n");
261 >    result += buffer;
262 >
263 >    return result;
264 > }
265 > } //namespace oopse

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