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:	507
Committed:	Fri Apr 15 22:04:00 2005 UTC (20 years, 6 months ago) by gezelter
File size:	5727 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	3	#include "visitors/RigidBodyVisitor.hpp"
43	gezelter	246
44	tim	3	#include "primitives/RigidBody.hpp"
45	gezelter	246
46	gezelter	2
47	tim	132	namespace oopse {
48
49	gezelter	246
50
51	gezelter	507	void LipidHeadVisitor::visit(RigidBody* rb){
52	gezelter	246
53	gezelter	507	Vector3d pos;
54	gezelter	246
55	gezelter	507	Vector3d u(0, 0, 1);
56	gezelter	246
57	gezelter	507	Vector3d newVec;
58	gezelter	246
59	gezelter	507	GenericData* data;
60	gezelter	246
61	gezelter	507	AtomData* atomData;
62	gezelter	246
63	gezelter	507	AtomInfo* atomInfo;
64	gezelter	246
65	gezelter	507	bool haveAtomData;
66	gezelter	2
67	gezelter	507	RotMat3x3d rotMatrix;
68	gezelter	246
69
70
71	gezelter	507	if(!canVisit(rb->getType()))
72	gezelter	246
73	gezelter	507	return;
74	gezelter	2
75
76	gezelter	246
77	gezelter	507	pos = rb->getPos();
78	gezelter	246
79	gezelter	507	rotMatrix = rb->getA();
80	gezelter	246
81	gezelter	507	//matVecMul3(rotMatrix, u, newVec);
82	gezelter	246
83	gezelter	507	newVec = rotMatrix * u;
84	gezelter	246
85
86
87	gezelter	507	data = rb->getPropertyByName("ATOMDATA");
88	gezelter	246
89	gezelter	507	if(data != NULL){
90	gezelter	2
91	gezelter	246
92
93	gezelter	507	atomData = dynamic_cast<AtomData*>(data);
94	gezelter	246
95	gezelter	507	if(atomData == NULL){
96	gezelter	246
97	gezelter	507	std::cerr << "can not get Atom Data from " << rb->getType() << std::endl;
98	gezelter	246
99	gezelter	507	atomData = new AtomData;
100	gezelter	246
101	gezelter	507	haveAtomData = false;
102	gezelter	246
103	gezelter	507	}
104	gezelter	246
105	gezelter	507	else
106	gezelter	246
107	gezelter	507	haveAtomData = true;
108	gezelter	246
109	gezelter	507	}
110	gezelter	246
111	gezelter	507	else{
112	gezelter	246
113	gezelter	507	atomData = new AtomData;
114	gezelter	246
115	gezelter	507	haveAtomData = false;
116	gezelter	246
117	gezelter	507	}
118	gezelter	2
119	gezelter	246
120
121	gezelter	507	atomInfo = new AtomInfo;
122	gezelter	246
123	gezelter	507	atomInfo->atomTypeName = "X";
124	gezelter	246
125	gezelter	507	atomInfo->pos[0] = pos[0];
126	gezelter	246
127	gezelter	507	atomInfo->pos[1] = pos[1];
128	gezelter	246
129	gezelter	507	atomInfo->pos[2] = pos[2];
130	gezelter	246
131	gezelter	507	atomInfo->dipole[0] = newVec[0];
132	gezelter	246
133	gezelter	507	atomInfo->dipole[1] = newVec[1];
134	gezelter	246
135	gezelter	507	atomInfo->dipole[2] = newVec[2];
136	gezelter	2
137	gezelter	246
138
139	gezelter	507	atomData->addAtomInfo(atomInfo);
140	gezelter	2
141	gezelter	246
142
143	gezelter	507	if(!haveAtomData){
144	gezelter	246
145	gezelter	507	atomData->setID("ATOMDATA");
146	gezelter	246
147	gezelter	507	rb->addProperty(atomData);
148	gezelter	246
149	gezelter	507	}
150	gezelter	246
151	gezelter	2
152	gezelter	246
153	gezelter	507	}
154	gezelter	2
155	gezelter	246
156
157	gezelter	507	void LipidHeadVisitor::addLipidHeadName(const std::string& name){
158	gezelter	246
159	gezelter	507	lipidHeadName.insert(name);
160	gezelter	2
161	gezelter	246
162
163	gezelter	507	}
164	gezelter	2
165	gezelter	246
166
167	gezelter	507	bool LipidHeadVisitor::canVisit(const std::string& name){
168	gezelter	246
169	gezelter	507	return lipidHeadName.find(name) != lipidHeadName.end() ? true : false;
170	gezelter	2
171	gezelter	246
172
173	gezelter	507	}
174	gezelter	2
175	gezelter	246
176
177	gezelter	507	const std::string LipidHeadVisitor::toString(){
178	gezelter	246
179	gezelter	507	char buffer[65535];
180	gezelter	246
181	gezelter	507	std::string result;
182	gezelter	246
183	gezelter	507	std::set<std::string>::iterator i;
184	gezelter	246
185	gezelter	2
186	gezelter	246
187	gezelter	507	sprintf(buffer ,"------------------------------------------------------------------\n");
188	gezelter	246
189	gezelter	507	result += buffer;
190	gezelter	246
191	gezelter	2
192	gezelter	246
193	gezelter	507	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
194	gezelter	246
195	gezelter	507	result += buffer;
196	gezelter	2
197	gezelter	246
198
199	gezelter	507	//print the ignore type list
200	gezelter	246
201	gezelter	507	sprintf(buffer , "lipidHeadName list contains below types:\n");
202	gezelter	246
203	gezelter	507	result += buffer;
204	gezelter	2
205	gezelter	246
206
207	gezelter	507	for(i = lipidHeadName.begin(); i != lipidHeadName.end(); ++i){
208	gezelter	246
209	gezelter	507	sprintf(buffer ,"%s\t", i->c_str());
210	gezelter	246
211	gezelter	507	result += buffer;
212	gezelter	246
213	gezelter	507	}
214	gezelter	2
215	gezelter	246
216
217	gezelter	507	sprintf(buffer ,"\n");
218	gezelter	246
219	gezelter	507	result += buffer;
220	gezelter	2
221	gezelter	246
222
223	gezelter	507	sprintf(buffer ,"------------------------------------------------------------------\n");
224	gezelter	246
225	gezelter	507	result += buffer;
226	gezelter	2
227	gezelter	246
228
229	gezelter	507	return result;
230	gezelter	2
231	gezelter	246
232
233	gezelter	507	}
234	gezelter	2
235	gezelter	246
236
237	gezelter	507	void RBCOMVisitor::visit(RigidBody* rb){
238	gezelter	246
239	gezelter	507	AtomData* atomData;
240	gezelter	246
241	gezelter	507	AtomInfo* atomInfo;
242	gezelter	246
243	gezelter	507	Vector3d pos;
244	gezelter	246
245	gezelter	2
246	gezelter	246
247	gezelter	507	pos = rb->getPos();
248	gezelter	246
249	gezelter	507	atomInfo = new AtomInfo;
250	gezelter	246
251	gezelter	507	atomInfo->atomTypeName = "X";
252	gezelter	246
253	gezelter	507	atomInfo->pos[0] = pos[0];
254	gezelter	246
255	gezelter	507	atomInfo->pos[1] = pos[1];
256	gezelter	246
257	gezelter	507	atomInfo->pos[2] = pos[2];
258	gezelter	246
259	gezelter	507	atomInfo->dipole[0] = 0;
260	gezelter	246
261	gezelter	507	atomInfo->dipole[1] = 0;
262	gezelter	246
263	gezelter	507	atomInfo->dipole[2] = 0;
264	gezelter	2
265	gezelter	246
266
267	gezelter	507	atomData = new AtomData;
268	gezelter	246
269	gezelter	507	atomData->setID("ATOMDATA");
270	gezelter	246
271	gezelter	507	atomData->addAtomInfo(atomInfo);
272	gezelter	2
273	gezelter	246
274
275	gezelter	507	rb->addProperty(atomData);
276	gezelter	246
277	gezelter	507	}
278	gezelter	2
279	gezelter	246
280
281	gezelter	507	const std::string RBCOMVisitor::toString(){
282	gezelter	246
283	gezelter	507	char buffer[65535];
284	gezelter	246
285	gezelter	507	std::string result;
286	gezelter	246
287	gezelter	2
288	gezelter	246
289	gezelter	507	sprintf(buffer ,"------------------------------------------------------------------\n");
290	gezelter	246
291	gezelter	507	result += buffer;
292	gezelter	246
293	gezelter	2
294	gezelter	246
295	gezelter	507	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
296	gezelter	246
297	gezelter	507	result += buffer;
298	gezelter	2
299	gezelter	246
300
301	gezelter	507	//print the ignore type list
302	gezelter	246
303	gezelter	507	sprintf(buffer , "Visitor Description: add a pseudo atom at the center of the mass of the rigidbody\n");
304	gezelter	246
305	gezelter	507	result += buffer;
306	gezelter	2
307	gezelter	246
308
309	gezelter	507	sprintf(buffer ,"------------------------------------------------------------------\n");
310	gezelter	246
311	gezelter	507	result += buffer;
312	gezelter	2
313	gezelter	246
314
315	gezelter	507	return result;
316	gezelter	2
317	gezelter	246
318
319	gezelter	507	}
320	gezelter	2
321	tim	132
322	gezelter	246
323
324
325	tim	132	}//namespace oopse
326	gezelter	246