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
#	User	Rev	Content
1	gezelter	1930	/*
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	1492	#include "visitors/RigidBodyVisitor.hpp"
43	gezelter	1930
44	tim	1492	#include "primitives/RigidBody.hpp"
45	gezelter	1930
46	tim	1492	#include "math/MatVec3.h"
47	gezelter	1490
48	gezelter	1930
49
50	tim	1625	namespace oopse {
51
52	gezelter	1930
53
54	gezelter	1490	void LipidHeadVisitor::visit(RigidBody* rb){
55	gezelter	1930
56			Vector3d pos;
57
58			Vector3d u(0, 0, 1);
59
60			Vector3d newVec;
61
62	gezelter	1490	GenericData* data;
63	gezelter	1930
64	gezelter	1490	AtomData* atomData;
65	gezelter	1930
66	gezelter	1490	AtomInfo* atomInfo;
67	gezelter	1930
68	gezelter	1490	bool haveAtomData;
69
70	gezelter	1930	RotMat3x3d rotMatrix;
71
72
73
74	gezelter	1490	if(!canVisit(rb->getType()))
75	gezelter	1930
76	gezelter	1490	return;
77
78
79	gezelter	1930
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	gezelter	1490	if(data != NULL){
93
94	gezelter	1930
95
96	gezelter	1490	atomData = dynamic_cast<AtomData*>(data);
97	gezelter	1930
98	gezelter	1490	if(atomData == NULL){
99	gezelter	1930
100			std::cerr << "can not get Atom Data from " << rb->getType() << std::endl;
101
102	gezelter	1490	atomData = new AtomData;
103	gezelter	1930
104	gezelter	1490	haveAtomData = false;
105	gezelter	1930
106	gezelter	1490	}
107	gezelter	1930
108	gezelter	1490	else
109	gezelter	1930
110	gezelter	1490	haveAtomData = true;
111	gezelter	1930
112	gezelter	1490	}
113	gezelter	1930
114	gezelter	1490	else{
115	gezelter	1930
116	gezelter	1490	atomData = new AtomData;
117	gezelter	1930
118	gezelter	1490	haveAtomData = false;
119	gezelter	1930
120	gezelter	1490	}
121
122	gezelter	1930
123
124	gezelter	1490	atomInfo = new AtomInfo;
125	gezelter	1930
126	gezelter	1490	atomInfo->AtomType = "X";
127	gezelter	1930
128	gezelter	1490	atomInfo->pos[0] = pos[0];
129	gezelter	1930
130	gezelter	1490	atomInfo->pos[1] = pos[1];
131	gezelter	1930
132	gezelter	1490	atomInfo->pos[2] = pos[2];
133	gezelter	1930
134	gezelter	1490	atomInfo->dipole[0] = newVec[0];
135	gezelter	1930
136	gezelter	1490	atomInfo->dipole[1] = newVec[1];
137	gezelter	1930
138	gezelter	1490	atomInfo->dipole[2] = newVec[2];
139
140	gezelter	1930
141
142	gezelter	1490	atomData->addAtomInfo(atomInfo);
143
144	gezelter	1930
145
146	gezelter	1490	if(!haveAtomData){
147	gezelter	1930
148	gezelter	1490	atomData->setID("ATOMDATA");
149	gezelter	1930
150	gezelter	1490	rb->addProperty(atomData);
151	gezelter	1930
152	gezelter	1490	}
153	gezelter	1930
154	gezelter	1490
155	gezelter	1930
156	gezelter	1490	}
157
158	gezelter	1930
159
160			void LipidHeadVisitor::addLipidHeadName(const std::string& name){
161
162	gezelter	1490	lipidHeadName.insert(name);
163
164	gezelter	1930
165
166	gezelter	1490	}
167
168	gezelter	1930
169
170			bool LipidHeadVisitor::canVisit(const std::string& name){
171
172	gezelter	1490	return lipidHeadName.find(name) != lipidHeadName.end() ? true : false;
173
174	gezelter	1930
175
176	gezelter	1490	}
177
178	gezelter	1930
179
180			const std::string LipidHeadVisitor::toString(){
181
182	gezelter	1490	char buffer[65535];
183	gezelter	1930
184			std::string result;
185
186			std::set<std::string>::iterator i;
187
188	gezelter	1490
189	gezelter	1930
190	gezelter	1490	sprintf(buffer ,"------------------------------------------------------------------\n");
191	gezelter	1930
192	gezelter	1490	result += buffer;
193	gezelter	1930
194	gezelter	1490
195	gezelter	1930
196	gezelter	1490	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
197	gezelter	1930
198	gezelter	1490	result += buffer;
199
200	gezelter	1930
201
202	gezelter	1490	//print the ignore type list
203	gezelter	1930
204	gezelter	1490	sprintf(buffer , "lipidHeadName list contains below types:\n");
205	gezelter	1930
206	gezelter	1490	result += buffer;
207
208	gezelter	1930
209
210	gezelter	1490	for(i = lipidHeadName.begin(); i != lipidHeadName.end(); ++i){
211	gezelter	1930
212	gezelter	1490	sprintf(buffer ,"%s\t", i->c_str());
213	gezelter	1930
214	gezelter	1490	result += buffer;
215	gezelter	1930
216	gezelter	1490	}
217
218	gezelter	1930
219
220	gezelter	1490	sprintf(buffer ,"\n");
221	gezelter	1930
222	gezelter	1490	result += buffer;
223
224	gezelter	1930
225
226	gezelter	1490	sprintf(buffer ,"------------------------------------------------------------------\n");
227	gezelter	1930
228	gezelter	1490	result += buffer;
229
230	gezelter	1930
231
232	gezelter	1490	return result;
233
234	gezelter	1930
235
236	gezelter	1490	}
237
238	gezelter	1930
239
240	gezelter	1490	void RBCOMVisitor::visit(RigidBody* rb){
241	gezelter	1930
242	gezelter	1490	AtomData* atomData;
243	gezelter	1930
244	gezelter	1490	AtomInfo* atomInfo;
245	gezelter	1930
246			Vector3d pos;
247
248	gezelter	1490
249	gezelter	1930
250			pos = rb->getPos();
251
252	gezelter	1490	atomInfo = new AtomInfo;
253	gezelter	1930
254	gezelter	1490	atomInfo->AtomType = "X";
255	gezelter	1930
256	gezelter	1490	atomInfo->pos[0] = pos[0];
257	gezelter	1930
258	gezelter	1490	atomInfo->pos[1] = pos[1];
259	gezelter	1930
260	gezelter	1490	atomInfo->pos[2] = pos[2];
261	gezelter	1930
262	gezelter	1490	atomInfo->dipole[0] = 0;
263	gezelter	1930
264	gezelter	1490	atomInfo->dipole[1] = 0;
265	gezelter	1930
266	gezelter	1490	atomInfo->dipole[2] = 0;
267
268	gezelter	1930
269
270	gezelter	1490	atomData = new AtomData;
271	gezelter	1930
272	gezelter	1490	atomData->setID("ATOMDATA");
273	gezelter	1930
274	gezelter	1490	atomData->addAtomInfo(atomInfo);
275
276	gezelter	1930
277
278	gezelter	1490	rb->addProperty(atomData);
279	gezelter	1930
280	gezelter	1490	}
281
282	gezelter	1930
283
284			const std::string RBCOMVisitor::toString(){
285
286	gezelter	1490	char buffer[65535];
287	gezelter	1930
288			std::string result;
289
290	gezelter	1490
291	gezelter	1930
292	gezelter	1490	sprintf(buffer ,"------------------------------------------------------------------\n");
293	gezelter	1930
294	gezelter	1490	result += buffer;
295	gezelter	1930
296	gezelter	1490
297	gezelter	1930
298	gezelter	1490	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
299	gezelter	1930
300	gezelter	1490	result += buffer;
301
302	gezelter	1930
303
304	gezelter	1490	//print the ignore type list
305	gezelter	1930
306	gezelter	1490	sprintf(buffer , "Visitor Description: add a pseudo atom at the center of the mass of the rigidbody\n");
307	gezelter	1930
308	gezelter	1490	result += buffer;
309
310	gezelter	1930
311
312	gezelter	1490	sprintf(buffer ,"------------------------------------------------------------------\n");
313	gezelter	1930
314	gezelter	1490	result += buffer;
315
316	gezelter	1930
317
318	gezelter	1490	return result;
319
320	gezelter	1930
321
322	gezelter	1490	}
323
324	tim	1625
325	gezelter	1930
326
327
328	tim	1625	}//namespace oopse
329	gezelter	1930