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:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 5 months ago) by gezelter
File size:	5573 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	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	#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	std::cerr << "can not get Atom Data from " << rb->getType() << std::endl;
101
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	void LipidHeadVisitor::addLipidHeadName(const std::string& name){
161
162	lipidHeadName.insert(name);
163
164
165
166	}
167
168
169
170	bool LipidHeadVisitor::canVisit(const std::string& name){
171
172	return lipidHeadName.find(name) != lipidHeadName.end() ? true : false;
173
174
175
176	}
177
178
179
180	const std::string LipidHeadVisitor::toString(){
181
182	char buffer[65535];
183
184	std::string result;
185
186	std::set<std::string>::iterator i;
187
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	const std::string RBCOMVisitor::toString(){
285
286	char buffer[65535];
287
288	std::string result;
289
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