src/visitors/RigidBodyVisitor.cpp

 /*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
#include "visitors/RigidBodyVisitor.hpp"

#include "primitives/RigidBody.hpp"

#include "math/MatVec3.h"


namespace oopse {


void LipidHeadVisitor::visit(RigidBody* rb){

  Vector3d pos;

  Vector3d u(0, 0, 1);

  Vector3d newVec;

  GenericData* data;

  AtomData* atomData;

  AtomInfo* atomInfo;

  bool haveAtomData;

  RotMat3x3d rotMatrix;


  if(!canVisit(rb->getType()))

    return;


  pos = rb->getPos();

  rotMatrix = rb->getA();

  //matVecMul3(rotMatrix, u, newVec);

  newVec = rotMatrix * u;

  
  data = rb->getPropertyByName("ATOMDATA");

  if(data != NULL){


    atomData = dynamic_cast<AtomData*>(data);  

    if(atomData == NULL){

      std::cerr << "can not get Atom Data from " << rb->getType() << std::endl;

      atomData = new AtomData; 

      haveAtomData = false;      

    }

    else

      haveAtomData = true;

  }

  else{

    atomData = new AtomData;

    haveAtomData = false;

  }


  atomInfo = new AtomInfo;

  atomInfo->AtomType = "X";

  atomInfo->pos[0] = pos[0];

  atomInfo->pos[1] = pos[1];

  atomInfo->pos[2] = pos[2];

  atomInfo->dipole[0] = newVec[0];

  atomInfo->dipole[1] = newVec[1];

  atomInfo->dipole[2] = newVec[2];


  atomData->addAtomInfo(atomInfo);


  if(!haveAtomData){

    atomData->setID("ATOMDATA");

    rb->addProperty(atomData);

  }

    
}


void LipidHeadVisitor::addLipidHeadName(const std::string& name){

  lipidHeadName.insert(name);


}


bool LipidHeadVisitor::canVisit(const std::string& name){

  return lipidHeadName.find(name) != lipidHeadName.end() ? true : false;


}


const  std::string LipidHeadVisitor::toString(){

  char buffer[65535];

   std::string result;

   std::set<std::string>::iterator i;

  
  sprintf(buffer ,"------------------------------------------------------------------\n");

  result += buffer;

  
  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());

  result += buffer;


  //print the ignore type list

  sprintf(buffer , "lipidHeadName list contains below types:\n");

  result += buffer;


  for(i = lipidHeadName.begin(); i != lipidHeadName.end(); ++i){

    sprintf(buffer ,"%s\t", i->c_str());

    result += buffer;

  }


  sprintf(buffer ,"\n");

  result += buffer;


  sprintf(buffer ,"------------------------------------------------------------------\n");

  result += buffer;


  return result;


}


void RBCOMVisitor::visit(RigidBody* rb){

  AtomData* atomData;

  AtomInfo* atomInfo;

  Vector3d pos;

  
  pos = rb->getPos();

  atomInfo = new AtomInfo;

  atomInfo->AtomType = "X";

  atomInfo->pos[0] = pos[0];

  atomInfo->pos[1] = pos[1];

  atomInfo->pos[2] = pos[2];

  atomInfo->dipole[0] = 0;

  atomInfo->dipole[1] = 0;

  atomInfo->dipole[2] = 0;


  atomData = new AtomData; 

  atomData->setID("ATOMDATA");

  atomData->addAtomInfo(atomInfo);


  rb->addProperty(atomData);

}


const  std::string RBCOMVisitor::toString(){

  char buffer[65535];

   std::string result;

  
  sprintf(buffer ,"------------------------------------------------------------------\n");

  result += buffer;

  
  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());

  result += buffer;


  //print the ignore type list

  sprintf(buffer , "Visitor Description: add a pseudo atom at the center of the mass of the rigidbody\n");

  result += buffer;


  sprintf(buffer ,"------------------------------------------------------------------\n");

  result += buffer;


  return result;


}


}//namespace oopse

Revision:	1927
Committed:	Wed Jan 12 17:14:35 2005 UTC (21 years, 1 month ago) by tim
File size:	5573 byte(s)
Log Message:	change license
#	User	Rev	Content
1	tim	1927	/*
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	tim	1825	#include "visitors/RigidBodyVisitor.hpp"
43
44			#include "primitives/RigidBody.hpp"
45
46			#include "math/MatVec3.h"
47
48
49
50			namespace oopse {
51
52
53
54			void LipidHeadVisitor::visit(RigidBody* rb){
55
56			Vector3d pos;
57
58			Vector3d u(0, 0, 1);
59
60			Vector3d newVec;
61
62			GenericData* data;
63
64			AtomData* atomData;
65
66			AtomInfo* atomInfo;
67
68			bool haveAtomData;
69
70			RotMat3x3d rotMatrix;
71
72
73
74			if(!canVisit(rb->getType()))
75
76			return;
77
78
79
80			pos = rb->getPos();
81
82			rotMatrix = rb->getA();
83
84			//matVecMul3(rotMatrix, u, newVec);
85
86			newVec = rotMatrix * u;
87
88
89
90			data = rb->getPropertyByName("ATOMDATA");
91
92			if(data != NULL){
93
94
95
96			atomData = dynamic_cast<AtomData*>(data);
97
98			if(atomData == NULL){
99
100	tim	1830	std::cerr << "can not get Atom Data from " << rb->getType() << std::endl;
101	tim	1825
102			atomData = new AtomData;
103
104			haveAtomData = false;
105
106			}
107
108			else
109
110			haveAtomData = true;
111
112			}
113
114			else{
115
116			atomData = new AtomData;
117
118			haveAtomData = false;
119
120			}
121
122
123
124			atomInfo = new AtomInfo;
125
126			atomInfo->AtomType = "X";
127
128			atomInfo->pos[0] = pos[0];
129
130			atomInfo->pos[1] = pos[1];
131
132			atomInfo->pos[2] = pos[2];
133
134			atomInfo->dipole[0] = newVec[0];
135
136			atomInfo->dipole[1] = newVec[1];
137
138			atomInfo->dipole[2] = newVec[2];
139
140
141
142			atomData->addAtomInfo(atomInfo);
143
144
145
146			if(!haveAtomData){
147
148			atomData->setID("ATOMDATA");
149
150			rb->addProperty(atomData);
151
152			}
153
154
155
156			}
157
158
159
160	tim	1832	void LipidHeadVisitor::addLipidHeadName(const std::string& name){
161	tim	1825
162			lipidHeadName.insert(name);
163
164
165
166			}
167
168
169
170	tim	1832	bool LipidHeadVisitor::canVisit(const std::string& name){
171	tim	1825
172			return lipidHeadName.find(name) != lipidHeadName.end() ? true : false;
173
174
175
176			}
177
178
179
180	tim	1829	const std::string LipidHeadVisitor::toString(){
181	tim	1825
182			char buffer[65535];
183
184	tim	1829	std::string result;
185	tim	1825
186	tim	1832	std::set<std::string>::iterator i;
187	tim	1825
188
189
190			sprintf(buffer ,"------------------------------------------------------------------\n");
191
192			result += buffer;
193
194
195
196			sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
197
198			result += buffer;
199
200
201
202			//print the ignore type list
203
204			sprintf(buffer , "lipidHeadName list contains below types:\n");
205
206			result += buffer;
207
208
209
210			for(i = lipidHeadName.begin(); i != lipidHeadName.end(); ++i){
211
212			sprintf(buffer ,"%s\t", i->c_str());
213
214			result += buffer;
215
216			}
217
218
219
220			sprintf(buffer ,"\n");
221
222			result += buffer;
223
224
225
226			sprintf(buffer ,"------------------------------------------------------------------\n");
227
228			result += buffer;
229
230
231
232			return result;
233
234
235
236			}
237
238
239
240			void RBCOMVisitor::visit(RigidBody* rb){
241
242			AtomData* atomData;
243
244			AtomInfo* atomInfo;
245
246			Vector3d pos;
247
248
249
250			pos = rb->getPos();
251
252			atomInfo = new AtomInfo;
253
254			atomInfo->AtomType = "X";
255
256			atomInfo->pos[0] = pos[0];
257
258			atomInfo->pos[1] = pos[1];
259
260			atomInfo->pos[2] = pos[2];
261
262			atomInfo->dipole[0] = 0;
263
264			atomInfo->dipole[1] = 0;
265
266			atomInfo->dipole[2] = 0;
267
268
269
270			atomData = new AtomData;
271
272			atomData->setID("ATOMDATA");
273
274			atomData->addAtomInfo(atomInfo);
275
276
277
278			rb->addProperty(atomData);
279
280			}
281
282
283
284	tim	1829	const std::string RBCOMVisitor::toString(){
285	tim	1825
286			char buffer[65535];
287
288	tim	1829	std::string result;
289	tim	1825
290
291
292			sprintf(buffer ,"------------------------------------------------------------------\n");
293
294			result += buffer;
295
296
297
298			sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
299
300			result += buffer;
301
302
303
304			//print the ignore type list
305
306			sprintf(buffer , "Visitor Description: add a pseudo atom at the center of the mass of the rigidbody\n");
307
308			result += buffer;
309
310
311
312			sprintf(buffer ,"------------------------------------------------------------------\n");
313
314			result += buffer;
315
316
317
318			return result;
319
320
321
322			}
323
324
325
326
327
328			}//namespace oopse
329