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Comparing trunk/OOPSE-2.0/src/visitors/RigidBodyVisitor.cpp (file contents):
Revision 1492 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 2069 by tim, Tue Mar 1 20:10:14 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 "visitors/RigidBodyVisitor.hpp"
43 +
44   #include "primitives/RigidBody.hpp"
3 – #include "math/MatVec3.h"
45  
46 +
47 + namespace oopse {
48 +
49 +
50 +
51   void LipidHeadVisitor::visit(RigidBody* rb){
52 <  double pos[3];
53 <  double u[3] = {0, 0, 1};
54 <  double newVec[3];
52 >
53 >  Vector3d pos;
54 >
55 >  Vector3d u(0, 0, 1);
56 >
57 >  Vector3d newVec;
58 >
59    GenericData* data;
60 +
61    AtomData* atomData;
62 +
63    AtomInfo* atomInfo;
64 +
65    bool haveAtomData;
13 –  double rotMatrix[3][3];
66  
67 +  RotMat3x3d rotMatrix;
68 +
69 +
70 +
71    if(!canVisit(rb->getType()))
72 +
73      return;
74  
18 –  rb->getPos(pos);
19 –  rb->getA(rotMatrix);
20 –  matVecMul3(rotMatrix, u, newVec);
75  
76 <  data = rb->getProperty("ATOMDATA");
76 >
77 >  pos = rb->getPos();
78 >
79 >  rotMatrix = rb->getA();
80 >
81 >  //matVecMul3(rotMatrix, u, newVec);
82 >
83 >  newVec = rotMatrix * u;
84 >
85 >  
86 >
87 >  data = rb->getPropertyByName("ATOMDATA");
88 >
89    if(data != NULL){
90  
91 +
92 +
93      atomData = dynamic_cast<AtomData*>(data);  
94 +
95      if(atomData == NULL){
96 <      cerr << "can not get Atom Data from " << rb->getType() << endl;
96 >
97 >      std::cerr << "can not get Atom Data from " << rb->getType() << std::endl;
98 >
99        atomData = new AtomData;
100 +
101        haveAtomData = false;      
102 +
103      }
104 +
105      else
106 +
107        haveAtomData = true;
108 +
109    }
110 +
111    else{
112 +
113      atomData = new AtomData;
114 +
115      haveAtomData = false;
116 +
117    }
118  
119 +
120 +
121    atomInfo = new AtomInfo;
122 +
123    atomInfo->AtomType = "X";
124 +
125    atomInfo->pos[0] = pos[0];
126 +
127    atomInfo->pos[1] = pos[1];
128 +
129    atomInfo->pos[2] = pos[2];
130 +
131    atomInfo->dipole[0] = newVec[0];
132 +
133    atomInfo->dipole[1] = newVec[1];
134 +
135    atomInfo->dipole[2] = newVec[2];
136  
137 +
138 +
139    atomData->addAtomInfo(atomInfo);
140  
141 +
142 +
143    if(!haveAtomData){
144 +
145      atomData->setID("ATOMDATA");
146 +
147      rb->addProperty(atomData);
148 +
149    }
150 +
151      
152 +
153   }
154  
155 < void LipidHeadVisitor::addLipidHeadName(const string& name){
155 >
156 >
157 > void LipidHeadVisitor::addLipidHeadName(const std::string& name){
158 >
159    lipidHeadName.insert(name);
160  
161 +
162 +
163   }
164  
165 < bool LipidHeadVisitor::canVisit(const string& name){
165 >
166 >
167 > bool LipidHeadVisitor::canVisit(const std::string& name){
168 >
169    return lipidHeadName.find(name) != lipidHeadName.end() ? true : false;
170  
171 +
172 +
173   }
174  
175 < const string LipidHeadVisitor::toString(){
175 >
176 >
177 > const  std::string LipidHeadVisitor::toString(){
178 >
179    char buffer[65535];
180 <  string result;
181 <  set<string>::iterator i;
180 >
181 >   std::string result;
182 >
183 >   std::set<std::string>::iterator i;
184 >
185    
186 +
187    sprintf(buffer ,"------------------------------------------------------------------\n");
188 +
189    result += buffer;
190 +
191    
192 +
193    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
194 +
195    result += buffer;
196  
197 +
198 +
199    //print the ignore type list
200 +
201    sprintf(buffer , "lipidHeadName list contains below types:\n");
202 +
203    result += buffer;
204  
205 +
206 +
207    for(i = lipidHeadName.begin(); i != lipidHeadName.end(); ++i){
208 +
209      sprintf(buffer ,"%s\t", i->c_str());
210 +
211      result += buffer;
212 +
213    }
214  
215 +
216 +
217    sprintf(buffer ,"\n");
218 +
219    result += buffer;
220  
221 +
222 +
223    sprintf(buffer ,"------------------------------------------------------------------\n");
224 +
225    result += buffer;
226  
227 +
228 +
229    return result;
230  
231 +
232 +
233   }
234  
235 +
236 +
237   void RBCOMVisitor::visit(RigidBody* rb){
238 +
239    AtomData* atomData;
240 +
241    AtomInfo* atomInfo;
242 <  double pos[3];
242 >
243 >  Vector3d pos;
244 >
245    
246 <  rb->getPos(pos);
246 >
247 >  pos = rb->getPos();
248 >
249    atomInfo = new AtomInfo;
250 +
251    atomInfo->AtomType = "X";
252 +
253    atomInfo->pos[0] = pos[0];
254 +
255    atomInfo->pos[1] = pos[1];
256 +
257    atomInfo->pos[2] = pos[2];
258 +
259    atomInfo->dipole[0] = 0;
260 +
261    atomInfo->dipole[1] = 0;
262 +
263    atomInfo->dipole[2] = 0;
264  
265 +
266 +
267    atomData = new AtomData;
268 +
269    atomData->setID("ATOMDATA");
270 +
271    atomData->addAtomInfo(atomInfo);
272  
273 +
274 +
275    rb->addProperty(atomData);
276 +
277   }
278  
279 < const string RBCOMVisitor::toString(){
279 >
280 >
281 > const  std::string RBCOMVisitor::toString(){
282 >
283    char buffer[65535];
284 <  string result;
284 >
285 >   std::string result;
286 >
287    
288 +
289    sprintf(buffer ,"------------------------------------------------------------------\n");
290 +
291    result += buffer;
292 +
293    
294 +
295    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
296 +
297    result += buffer;
298  
299 +
300 +
301    //print the ignore type list
302 +
303    sprintf(buffer , "Visitor Description: add a pseudo atom at the center of the mass of the rigidbody\n");
304 +
305    result += buffer;
306  
307 +
308 +
309    sprintf(buffer ,"------------------------------------------------------------------\n");
310 +
311    result += buffer;
312  
313 +
314 +
315    return result;
316  
317 +
318 +
319   }
320  
321 +
322 +
323 +
324 +
325 + }//namespace oopse
326 +

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