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"


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->atomTypeName = "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->atomTypeName = "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:	2091
Committed:	Tue Mar 8 21:07:49 2005 UTC (19 years, 4 months ago) by gezelter
File size:	5553 byte(s)
Log Message:	fixing a strange icc8 bug (we think).
#	Content
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"
45
46
47	namespace oopse {
48
49
50
51	void LipidHeadVisitor::visit(RigidBody* rb){
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;
66
67	RotMat3x3d rotMatrix;
68
69
70
71	if(!canVisit(rb->getType()))
72
73	return;
74
75
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
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->atomTypeName = "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
156
157	void LipidHeadVisitor::addLipidHeadName(const std::string& name){
158
159	lipidHeadName.insert(name);
160
161
162
163	}
164
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
176
177	const std::string LipidHeadVisitor::toString(){
178
179	char buffer[65535];
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
243	Vector3d pos;
244
245
246
247	pos = rb->getPos();
248
249	atomInfo = new AtomInfo;
250
251	atomInfo->atomTypeName = "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
280
281	const std::string RBCOMVisitor::toString(){
282
283	char buffer[65535];
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