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).
#	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	gezelter	1490
47	tim	1625	namespace oopse {
48
49	gezelter	1930
50
51	gezelter	1490	void LipidHeadVisitor::visit(RigidBody* rb){
52	gezelter	1930
53			Vector3d pos;
54
55			Vector3d u(0, 0, 1);
56
57			Vector3d newVec;
58
59	gezelter	1490	GenericData* data;
60	gezelter	1930
61	gezelter	1490	AtomData* atomData;
62	gezelter	1930
63	gezelter	1490	AtomInfo* atomInfo;
64	gezelter	1930
65	gezelter	1490	bool haveAtomData;
66
67	gezelter	1930	RotMat3x3d rotMatrix;
68
69
70
71	gezelter	1490	if(!canVisit(rb->getType()))
72	gezelter	1930
73	gezelter	1490	return;
74
75
76	gezelter	1930
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	gezelter	1490	if(data != NULL){
90
91	gezelter	1930
92
93	gezelter	1490	atomData = dynamic_cast<AtomData*>(data);
94	gezelter	1930
95	gezelter	1490	if(atomData == NULL){
96	gezelter	1930
97			std::cerr << "can not get Atom Data from " << rb->getType() << std::endl;
98
99	gezelter	1490	atomData = new AtomData;
100	gezelter	1930
101	gezelter	1490	haveAtomData = false;
102	gezelter	1930
103	gezelter	1490	}
104	gezelter	1930
105	gezelter	1490	else
106	gezelter	1930
107	gezelter	1490	haveAtomData = true;
108	gezelter	1930
109	gezelter	1490	}
110	gezelter	1930
111	gezelter	1490	else{
112	gezelter	1930
113	gezelter	1490	atomData = new AtomData;
114	gezelter	1930
115	gezelter	1490	haveAtomData = false;
116	gezelter	1930
117	gezelter	1490	}
118
119	gezelter	1930
120
121	gezelter	1490	atomInfo = new AtomInfo;
122	gezelter	1930
123	gezelter	2091	atomInfo->atomTypeName = "X";
124	gezelter	1930
125	gezelter	1490	atomInfo->pos[0] = pos[0];
126	gezelter	1930
127	gezelter	1490	atomInfo->pos[1] = pos[1];
128	gezelter	1930
129	gezelter	1490	atomInfo->pos[2] = pos[2];
130	gezelter	1930
131	gezelter	1490	atomInfo->dipole[0] = newVec[0];
132	gezelter	1930
133	gezelter	1490	atomInfo->dipole[1] = newVec[1];
134	gezelter	1930
135	gezelter	1490	atomInfo->dipole[2] = newVec[2];
136
137	gezelter	1930
138
139	gezelter	1490	atomData->addAtomInfo(atomInfo);
140
141	gezelter	1930
142
143	gezelter	1490	if(!haveAtomData){
144	gezelter	1930
145	gezelter	1490	atomData->setID("ATOMDATA");
146	gezelter	1930
147	gezelter	1490	rb->addProperty(atomData);
148	gezelter	1930
149	gezelter	1490	}
150	gezelter	1930
151	gezelter	1490
152	gezelter	1930
153	gezelter	1490	}
154
155	gezelter	1930
156
157			void LipidHeadVisitor::addLipidHeadName(const std::string& name){
158
159	gezelter	1490	lipidHeadName.insert(name);
160
161	gezelter	1930
162
163	gezelter	1490	}
164
165	gezelter	1930
166
167			bool LipidHeadVisitor::canVisit(const std::string& name){
168
169	gezelter	1490	return lipidHeadName.find(name) != lipidHeadName.end() ? true : false;
170
171	gezelter	1930
172
173	gezelter	1490	}
174
175	gezelter	1930
176
177			const std::string LipidHeadVisitor::toString(){
178
179	gezelter	1490	char buffer[65535];
180	gezelter	1930
181			std::string result;
182
183			std::set<std::string>::iterator i;
184
185	gezelter	1490
186	gezelter	1930
187	gezelter	1490	sprintf(buffer ,"------------------------------------------------------------------\n");
188	gezelter	1930
189	gezelter	1490	result += buffer;
190	gezelter	1930
191	gezelter	1490
192	gezelter	1930
193	gezelter	1490	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
194	gezelter	1930
195	gezelter	1490	result += buffer;
196
197	gezelter	1930
198
199	gezelter	1490	//print the ignore type list
200	gezelter	1930
201	gezelter	1490	sprintf(buffer , "lipidHeadName list contains below types:\n");
202	gezelter	1930
203	gezelter	1490	result += buffer;
204
205	gezelter	1930
206
207	gezelter	1490	for(i = lipidHeadName.begin(); i != lipidHeadName.end(); ++i){
208	gezelter	1930
209	gezelter	1490	sprintf(buffer ,"%s\t", i->c_str());
210	gezelter	1930
211	gezelter	1490	result += buffer;
212	gezelter	1930
213	gezelter	1490	}
214
215	gezelter	1930
216
217	gezelter	1490	sprintf(buffer ,"\n");
218	gezelter	1930
219	gezelter	1490	result += buffer;
220
221	gezelter	1930
222
223	gezelter	1490	sprintf(buffer ,"------------------------------------------------------------------\n");
224	gezelter	1930
225	gezelter	1490	result += buffer;
226
227	gezelter	1930
228
229	gezelter	1490	return result;
230
231	gezelter	1930
232
233	gezelter	1490	}
234
235	gezelter	1930
236
237	gezelter	1490	void RBCOMVisitor::visit(RigidBody* rb){
238	gezelter	1930
239	gezelter	1490	AtomData* atomData;
240	gezelter	1930
241	gezelter	1490	AtomInfo* atomInfo;
242	gezelter	1930
243			Vector3d pos;
244
245	gezelter	1490
246	gezelter	1930
247			pos = rb->getPos();
248
249	gezelter	1490	atomInfo = new AtomInfo;
250	gezelter	1930
251	gezelter	2091	atomInfo->atomTypeName = "X";
252	gezelter	1930
253	gezelter	1490	atomInfo->pos[0] = pos[0];
254	gezelter	1930
255	gezelter	1490	atomInfo->pos[1] = pos[1];
256	gezelter	1930
257	gezelter	1490	atomInfo->pos[2] = pos[2];
258	gezelter	1930
259	gezelter	1490	atomInfo->dipole[0] = 0;
260	gezelter	1930
261	gezelter	1490	atomInfo->dipole[1] = 0;
262	gezelter	1930
263	gezelter	1490	atomInfo->dipole[2] = 0;
264
265	gezelter	1930
266
267	gezelter	1490	atomData = new AtomData;
268	gezelter	1930
269	gezelter	1490	atomData->setID("ATOMDATA");
270	gezelter	1930
271	gezelter	1490	atomData->addAtomInfo(atomInfo);
272
273	gezelter	1930
274
275	gezelter	1490	rb->addProperty(atomData);
276	gezelter	1930
277	gezelter	1490	}
278
279	gezelter	1930
280
281			const std::string RBCOMVisitor::toString(){
282
283	gezelter	1490	char buffer[65535];
284	gezelter	1930
285			std::string result;
286
287	gezelter	1490
288	gezelter	1930
289	gezelter	1490	sprintf(buffer ,"------------------------------------------------------------------\n");
290	gezelter	1930
291	gezelter	1490	result += buffer;
292	gezelter	1930
293	gezelter	1490
294	gezelter	1930
295	gezelter	1490	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
296	gezelter	1930
297	gezelter	1490	result += buffer;
298
299	gezelter	1930
300
301	gezelter	1490	//print the ignore type list
302	gezelter	1930
303	gezelter	1490	sprintf(buffer , "Visitor Description: add a pseudo atom at the center of the mass of the rigidbody\n");
304	gezelter	1930
305	gezelter	1490	result += buffer;
306
307	gezelter	1930
308
309	gezelter	1490	sprintf(buffer ,"------------------------------------------------------------------\n");
310	gezelter	1930
311	gezelter	1490	result += buffer;
312
313	gezelter	1930
314
315	gezelter	1490	return result;
316
317	gezelter	1930
318
319	gezelter	1490	}
320
321	tim	1625
322	gezelter	1930
323
324
325	tim	1625	}//namespace oopse
326	gezelter	1930