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Comparing trunk/OOPSE-2.0/src/visitors/AtomVisitor.cpp (file contents):
Revision 1490 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 1930 by gezelter, Wed Jan 12 22:41:40 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 "AtomVisitor.hpp"
44 < #include "DirectionalAtom.hpp"
45 < #include "MatVec3.h"
46 < #include "RigidBody.hpp"
43 > #include "visitors/AtomVisitor.hpp"
44 > #include "primitives/DirectionalAtom.hpp"
45 > #include "math/MatVec3.h"
46 > #include "primitives/RigidBody.hpp"
47  
48 < void BaseAtomVisitor::visit(RigidBody* rb){
49 <  //vector<Atom*> myAtoms;
50 <  //vector<Atom*>::iterator atomIter;
48 > namespace oopse {
49 > void BaseAtomVisitor::visit(RigidBody *rb) {
50 > //vector<Atom*> myAtoms;
51 > //vector<Atom*>::iterator atomIter;
52  
53 <  //myAtoms = rb->getAtoms();
54 <  
55 <  //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
56 <  //  (*atomIter)->accept(this);
53 > //myAtoms = rb->getAtoms();
54 >
55 > //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
56 > //  (*atomIter)->accept(this);
57 >    }
58 >
59 > void BaseAtomVisitor::setVisited(Atom *atom) {
60 >    GenericData *data;
61 >    data = atom->getPropertyByName("VISITED");
62 >
63 >    //if visited property is not existed, add it as new property
64 >    if (data == NULL) {
65 >        data = new GenericData();
66 >        data->setID("VISITED");
67 >        atom->addProperty(data);
68 >    }
69   }
70  
71 < void BaseAtomVisitor::setVisited(Atom* atom){
72 <  GenericData* data;
73 <  data = atom->getProperty("VISITED");
71 > bool BaseAtomVisitor::isVisited(Atom *atom) {
72 >    GenericData *data;
73 >    data = atom->getPropertyByName("VISITED");
74 >    return data == NULL ? false : true;
75 > }
76  
77 <  //if visited property is not existed, add it as new property
78 <  if(data == NULL){
79 <    data = new GenericData();
80 <    data->setID("VISITED");
81 <    atom->addProperty(data);  
82 <  }
77 > bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) {
78 >    std::vector<std::string>::iterator strIter;
79 >
80 >    for( strIter = ssdAtomType.begin(); strIter != ssdAtomType.end();
81 >        ++strIter )
82 >  if (*strIter == atomType)
83 >      return true;
84 >
85 >    return false;
86   }
87  
88 < bool BaseAtomVisitor::isVisited(Atom* atom){
89 <  GenericData* data;
90 <  data = atom->getProperty("VISITED");
91 <  return data == NULL ?  false : true;
88 > void SSDAtomVisitor::visit(DirectionalAtom *datom) {
89 >    std::vector<AtomInfo *>atoms;
90 >
91 >    //we need to convert SSD into 4 differnet atoms
92 >    //one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
93 >    //of the water with a dipole moment
94 >    Vector3d h1(0.0, -0.75695, 0.5206);
95 >    Vector3d h2(0.0, 0.75695, 0.5206);
96 >    Vector3d ox(0.0, 0.0, -0.0654);
97 >    Vector3d u(0, 0, 1);
98 >    RotMat3x3d   rotMatrix;
99 >    RotMat3x3d   rotTrans;
100 >    AtomInfo *   atomInfo;
101 >    Vector3d     pos;
102 >    Vector3d     newVec;
103 >    Quat4d       q;
104 >    AtomData *   atomData;
105 >    GenericData *data;
106 >    bool         haveAtomData;
107 >
108 >    //if atom is not SSD atom, just skip it
109 >    if (!isSSDAtom(datom->getType()))
110 >        return;
111 >
112 >    data = datom->getPropertyByName("ATOMDATA");
113 >
114 >    if (data != NULL) {
115 >        atomData = dynamic_cast<AtomData *>(data);
116 >
117 >        if (atomData == NULL) {
118 >            std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
119 >            atomData = new AtomData;
120 >            haveAtomData = false;
121 >        } else
122 >            haveAtomData = true;
123 >    } else {
124 >        atomData = new AtomData;
125 >        haveAtomData = false;
126 >    }
127 >
128 >    pos = datom->getPos();
129 >    q = datom->getQ();
130 >    rotMatrix = datom->getA();
131 >
132 >    // We need A^T to convert from body-fixed to space-fixed:
133 >    //transposeMat3(rotMatrix, rotTrans);
134 >    rotTrans = rotMatrix.transpose();
135 >
136 >    //center of mass of the water molecule
137 >    //matVecMul3(rotTrans, u, newVec);
138 >    newVec = rotTrans * u;
139 >
140 >    atomInfo = new AtomInfo;
141 >    atomInfo->AtomType = "X";
142 >    atomInfo->pos[0] = pos[0];
143 >    atomInfo->pos[1] = pos[1];
144 >    atomInfo->pos[2] = pos[2];
145 >    atomInfo->dipole[0] = newVec[0];
146 >    atomInfo->dipole[1] = newVec[1];
147 >    atomInfo->dipole[2] = newVec[2];
148 >
149 >    atomData->addAtomInfo(atomInfo);
150 >
151 >    //oxygen
152 >    //matVecMul3(rotTrans, ox, newVec);
153 >    newVec = rotTrans * ox;
154 >
155 >    atomInfo = new AtomInfo;
156 >    atomInfo->AtomType = "O";
157 >    atomInfo->pos[0] = pos[0] + newVec[0];
158 >    atomInfo->pos[1] = pos[1] + newVec[1];
159 >    atomInfo->pos[2] = pos[2] + newVec[2];
160 >    atomInfo->dipole[0] = 0.0;
161 >    atomInfo->dipole[1] = 0.0;
162 >    atomInfo->dipole[2] = 0.0;
163 >    atomData->addAtomInfo(atomInfo);
164 >
165 >    //hydrogen1
166 >    //matVecMul3(rotTrans, h1, newVec);
167 >    newVec = rotTrans * h1;
168 >    atomInfo = new AtomInfo;
169 >    atomInfo->AtomType = "H";
170 >    atomInfo->pos[0] = pos[0] + newVec[0];
171 >    atomInfo->pos[1] = pos[1] + newVec[1];
172 >    atomInfo->pos[2] = pos[2] + newVec[2];
173 >    atomInfo->dipole[0] = 0.0;
174 >    atomInfo->dipole[1] = 0.0;
175 >    atomInfo->dipole[2] = 0.0;
176 >    atomData->addAtomInfo(atomInfo);
177 >
178 >    //hydrogen2
179 >    //matVecMul3(rotTrans, h2, newVec);
180 >    newVec = rotTrans * h2;
181 >    atomInfo = new AtomInfo;
182 >    atomInfo->AtomType = "H";
183 >    atomInfo->pos[0] = pos[0] + newVec[0];
184 >    atomInfo->pos[1] = pos[1] + newVec[1];
185 >    atomInfo->pos[2] = pos[2] + newVec[2];
186 >    atomInfo->dipole[0] = 0.0;
187 >    atomInfo->dipole[1] = 0.0;
188 >    atomInfo->dipole[2] = 0.0;
189 >    atomData->addAtomInfo(atomInfo);
190 >
191 >    //add atom data into atom's property
192 >
193 >    if (!haveAtomData) {
194 >        atomData->setID("ATOMDATA");
195 >        datom->addProperty(atomData);
196 >    }
197 >
198 >    setVisited(datom);
199   }
200  
201 < bool SSDAtomVisitor::isSSDAtom(const string& atomType){
201 > const std::string SSDAtomVisitor::toString() {
202 >    char   buffer[65535];
203 >    std::string result;
204 >
205 >    sprintf(buffer,
206 >            "------------------------------------------------------------------\n");
207 >    result += buffer;
208 >
209 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
210 >    result += buffer;
211 >
212 >    sprintf(buffer,
213 >            "Visitor Description: Convert SSD into 4 different atoms\n");
214 >    result += buffer;
215 >
216 >    sprintf(buffer,
217 >            "------------------------------------------------------------------\n");
218 >    result += buffer;
219 >
220 >    return result;
221 > }
222 >
223 > bool LinearAtomVisitor::isLinearAtom(const string& atomType){
224    vector<string>::iterator strIter;
225    
226 <  for(strIter = ssdAtomType.begin(); strIter != ssdAtomType.end(); ++strIter)
227 <   if(*strIter == atomType)
228 <    return true;
226 >  for(strIter = linearAtomType.begin(); strIter != linearAtomType.end();
227 >      ++strIter)
228 >    if(*strIter == atomType)
229 >      return true;
230    
231    return false;  
232   }
233  
234 < void SSDAtomVisitor::visit(DirectionalAtom* datom){
234 > void LinearAtomVisitor::visit(DirectionalAtom* datom){
235  
236    vector<AtomInfo*> atoms;
237  
238 <  //we need to convert SSD into 4 differnet atoms
239 <  //one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
240 <  //of the water with a dipole moment
241 <  double h1[3] = {0.0, -0.75695, 0.5206};
242 <  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};
238 >  //we need to convert linear into 4 different atoms
239 >  double c1[3] = {0.0, 0.0, -1.8};
240 >  double c2[3] = {0.0, 0.0, -0.6};
241 >  double c3[3] = {0.0, 0.0,  0.6};
242 >  double c4[3] = {0.0, 0.0,  1.8};
243    double rotMatrix[3][3];
244    double rotTrans[3][3];
245    AtomInfo* atomInfo;
# Line 64 | Line 251 | void SSDAtomVisitor::visit(DirectionalAtom* datom){
251    bool haveAtomData;
252    
253    //if atom is not SSD atom, just skip it
254 <  if(!isSSDAtom(datom->getType()))
254 >  if(!isLinearAtom(datom->getType()))
255      return;
256 <
256 >  
257    data = datom->getProperty("ATOMDATA");
258    if(data != NULL){
259  
# Line 92 | Line 279 | void SSDAtomVisitor::visit(DirectionalAtom* datom){
279    // We need A^T to convert from body-fixed to space-fixed:
280    transposeMat3(rotMatrix, rotTrans);
281    
282 <  //center of mass of the water molecule
96 <  matVecMul3(rotTrans, u, newVec);
282 >  matVecMul3(rotTrans, c1, newVec);
283    atomInfo = new AtomInfo;
284 <  atomInfo->AtomType = "X";
285 <  atomInfo->pos[0] = pos[0];
286 <  atomInfo->pos[1] = pos[1];
287 <  atomInfo->pos[2] = pos[2];
288 <  atomInfo->dipole[0] = newVec[0];
289 <  atomInfo->dipole[1] = newVec[1];
290 <  atomInfo->dipole[2] = newVec[2];
105 <
284 >  atomInfo->AtomType = "C";
285 >  atomInfo->pos[0] = pos[0] + newVec[0];
286 >  atomInfo->pos[1] = pos[1] + newVec[1];
287 >  atomInfo->pos[2] = pos[2] + newVec[2];
288 >  atomInfo->dipole[0] = 0.0;
289 >  atomInfo->dipole[1] = 0.0;
290 >  atomInfo->dipole[2] = 0.0;
291    atomData->addAtomInfo(atomInfo);
292  
293 <  //oxygen
109 <  matVecMul3(rotTrans, ox, newVec);
293 >  matVecMul3(rotTrans, c2, newVec);
294    atomInfo = new AtomInfo;
295 <  atomInfo->AtomType = "O";
295 >  atomInfo->AtomType = "C";
296    atomInfo->pos[0] = pos[0] + newVec[0];
297    atomInfo->pos[1] = pos[1] + newVec[1];
298    atomInfo->pos[2] = pos[2] + newVec[2];
# Line 117 | Line 301 | void SSDAtomVisitor::visit(DirectionalAtom* datom){
301    atomInfo->dipole[2] = 0.0;
302    atomData->addAtomInfo(atomInfo);
303  
304 <
121 <  //hydrogen1
122 <    matVecMul3(rotTrans, h1, newVec);
304 >  matVecMul3(rotTrans, c3, newVec);
305    atomInfo = new AtomInfo;
306 <  atomInfo->AtomType = "H";
306 >  atomInfo->AtomType = "C";
307    atomInfo->pos[0] = pos[0] + newVec[0];
308    atomInfo->pos[1] = pos[1] + newVec[1];
309    atomInfo->pos[2] = pos[2] + newVec[2];
# Line 130 | Line 312 | void SSDAtomVisitor::visit(DirectionalAtom* datom){
312    atomInfo->dipole[2] = 0.0;
313    atomData->addAtomInfo(atomInfo);
314  
315 <  //hydrogen2
134 <  matVecMul3(rotTrans, h2, newVec);
315 >  matVecMul3(rotTrans, c4, newVec);
316    atomInfo = new AtomInfo;
317 <  atomInfo->AtomType = "H";
317 >  atomInfo->AtomType = "C";
318    atomInfo->pos[0] = pos[0] + newVec[0];
319    atomInfo->pos[1] = pos[1] + newVec[1];
320    atomInfo->pos[2] = pos[2] + newVec[2];
# Line 153 | Line 334 | const string SSDAtomVisitor::toString(){
334  
335   }
336  
337 < const string SSDAtomVisitor::toString(){
337 > const string LinearAtomVisitor::toString(){
338    char buffer[65535];
339    string result;
340    
# Line 163 | Line 344 | const string SSDAtomVisitor::toString(){
344    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
345    result += buffer;
346  
347 <  sprintf(buffer , "Visitor Description: Convert SSD into 4 different atoms\n");
347 >  sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
348    result += buffer;
349  
350    sprintf(buffer ,"------------------------------------------------------------------\n");
# Line 174 | Line 355 | void DefaultAtomVisitor::visit(Atom* atom){
355  
356   //----------------------------------------------------------------------------//
357  
358 < void DefaultAtomVisitor::visit(Atom* atom){
359 <  AtomData* atomData;
360 <  AtomInfo* atomInfo;
361 <  double pos[3];
358 > void DefaultAtomVisitor::visit(Atom *atom) {
359 >    AtomData *atomData;
360 >    AtomInfo *atomInfo;
361 >    Vector3d  pos;
362  
363 <  if(isVisited(atom))
364 <    return;
363 >    if (isVisited(atom))
364 >        return;
365  
366 < atomInfo =new AtomInfo;
366 >    atomInfo = new AtomInfo;
367  
368 <  atomData = new AtomData;
369 <  atomData->setID("ATOMDATA");
189 <
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;
368 >    atomData = new AtomData;
369 >    atomData->setID("ATOMDATA");
370  
371 +    pos = atom->getPos();
372 +    atomInfo->AtomType = atom->getType();
373 +    atomInfo->pos[0] = pos[0];
374 +    atomInfo->pos[1] = pos[1];
375 +    atomInfo->pos[2] = pos[2];
376 +    atomInfo->dipole[0] = 0.0;
377 +    atomInfo->dipole[1] = 0.0;
378 +    atomInfo->dipole[2] = 0.0;
379  
380 <  atomData->addAtomInfo(atomInfo);
201 <  
202 <  atom->addProperty(atomData);
380 >    atomData->addAtomInfo(atomInfo);
381  
382 <  setVisited(atom);
382 >    atom->addProperty(atomData);
383 >
384 >    setVisited(atom);
385   }
206 – void DefaultAtomVisitor::visit(DirectionalAtom* datom){
207 –  AtomData* atomData;
208 –  AtomInfo* atomInfo;
209 –  double pos[3];
210 –  double u[3];
386  
387 <  if(isVisited(datom))
388 <    return;
389 <  
390 <  datom->getPos(pos);
391 <  datom->getU(u);
387 > void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
388 >    AtomData *atomData;
389 >    AtomInfo *atomInfo;
390 >    Vector3d  pos;
391 >    Vector3d  u;
392  
393 <  atomData = new AtomData;
394 <  atomData->setID("ATOMDATA");
220 <  atomInfo =new AtomInfo;
221 <  
222 <  atomInfo->AtomType = datom->getType();
223 <  atomInfo->pos[0] = pos[0];
224 <  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];  
393 >    if (isVisited(datom))
394 >        return;
395  
396 <  atomData->addAtomInfo(atomInfo);
396 >    pos = datom->getPos();
397 >    u = datom->getElectroFrame().getColumn(3);
398  
399 <  datom->addProperty(atomData);
399 >    atomData = new AtomData;
400 >    atomData->setID("ATOMDATA");
401 >    atomInfo = new AtomInfo;
402  
403 <  setVisited(datom);
403 >    atomInfo->AtomType = datom->getType();
404 >    atomInfo->pos[0] = pos[0];
405 >    atomInfo->pos[1] = pos[1];
406 >    atomInfo->pos[2] = pos[2];
407 >    atomInfo->dipole[0] = u[0];
408 >    atomInfo->dipole[1] = u[1];
409 >    atomInfo->dipole[2] = u[2];
410 >
411 >    atomData->addAtomInfo(atomInfo);
412 >
413 >    datom->addProperty(atomData);
414 >
415 >    setVisited(datom);
416   }
417  
418 + const std::string DefaultAtomVisitor::toString() {
419 +    char   buffer[65535];
420 +    std::string result;
421  
422 < const string DefaultAtomVisitor::toString(){
423 <  char buffer[65535];
424 <  string result;
241 <  
242 <  sprintf(buffer ,"------------------------------------------------------------------\n");
243 <  result += buffer;
422 >    sprintf(buffer,
423 >            "------------------------------------------------------------------\n");
424 >    result += buffer;
425  
426 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
427 <  result += buffer;
426 >    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
427 >    result += buffer;
428  
429 <  sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n");
430 <  result += buffer;
429 >    sprintf(buffer,
430 >            "Visitor Description: copy atom infomation into atom data\n");
431 >    result += buffer;
432  
433 <  sprintf(buffer ,"------------------------------------------------------------------\n");
434 <  result += buffer;
433 >    sprintf(buffer,
434 >            "------------------------------------------------------------------\n");
435 >    result += buffer;
436  
437 <  return result;
438 < }    
437 >    return result;
438 > }
439 > } //namespace oopse

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