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root/OpenMD/branches/development/src/visitors/RigidBodyVisitor.cpp

Comparing:
trunk/src/visitors/RigidBodyVisitor.cpp (file contents), Revision 385 by tim, Tue Mar 1 20:10:14 2005 UTC vs.
branches/development/src/visitors/RigidBodyVisitor.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include "visitors/RigidBodyVisitor.hpp"
43	–
44		#include "primitives/RigidBody.hpp"
45
46
47	<	namespace oopse {
47	>	namespace OpenMD {
48
49	+	void LipidHeadVisitor::visit(RigidBody* rb){
50	+	Vector3d pos;
51	+	Vector3d u(0, 0, 1);
52	+	Vector3d newVec;
53	+	GenericData* data;
54	+	AtomData* atomData;
55	+	AtomInfo* atomInfo;
56	+	bool haveAtomData;
57	+	RotMat3x3d rotMatrix;
58
59	+	if(!canVisit(rb->getType()))
60	+	return;
61
62	<	void LipidHeadVisitor::visit(RigidBody* rb){
62	>	pos = rb->getPos();
63	>	rotMatrix = rb->getA();
64	>	//matVecMul3(rotMatrix, u, newVec);
65	>	newVec = rotMatrix * u;
66
67	<	Vector3d pos;
67	>	data = rb->getPropertyByName("ATOMDATA");
68
69	<	Vector3d u(0, 0, 1);
69	>	if(data != NULL){
70	>	atomData = dynamic_cast<AtomData*>(data);
71	>
72	>	if(atomData == NULL){
73	>	std::cerr << "can not get Atom Data from " << rb->getType() << std::endl;
74	>
75	>	atomData = new AtomData;
76	>	haveAtomData = false;
77	>
78	>	} else
79	>	haveAtomData = true;
80	>
81	>	} else {
82	>	atomData = new AtomData;
83	>	haveAtomData = false;
84	>
85	>	}
86
87	<	Vector3d newVec;
87	>	atomInfo = new AtomInfo;
88	>	atomInfo->atomTypeName = "X";
89	>	atomInfo->pos[0] = pos[0];
90	>	atomInfo->pos[1] = pos[1];
91	>	atomInfo->pos[2] = pos[2];
92	>	atomInfo->vec[0] = newVec[0];
93	>	atomInfo->vec[1] = newVec[1];
94	>	atomInfo->vec[2] = newVec[2];
95
96	<	GenericData* data;
96	>	atomData->addAtomInfo(atomInfo);
97
98	<	AtomData* atomData;
99	<
100	<	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	<
98	>	if(!haveAtomData){
99	>	atomData->setID("ATOMDATA");
100	>	rb->addProperty(atomData);
101		}
102
105	–	else
106	–
107	–	haveAtomData = true;
108	–
103		}
104
111	–	else{
105
106	<	atomData = new AtomData;
106	>	void LipidHeadVisitor::addLipidHeadName(const std::string& name){
107	>	lipidHeadName.insert(name);
108
115	–	haveAtomData = false;
116	–
109		}
110
111	+	bool LipidHeadVisitor::canVisit(const std::string& name){
112	+	return lipidHeadName.find(name) != lipidHeadName.end() ? true : false;
113
114	+	}
115
121	–	atomInfo = new AtomInfo;
116
117	<	atomInfo->AtomType = "X";
117	>	const  std::string LipidHeadVisitor::toString(){
118	>	char buffer[65535];
119	>	std::string result;
120	>	std::set<std::string>::iterator i;
121
122	<	atomInfo->pos[0] = pos[0];
122	>	sprintf(buffer ,"------------------------------------------------------------------\n");
123	>	result += buffer;
124
125	<	atomInfo->pos[1] = pos[1];
125	>	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
126	>	result += buffer;
127
128	<	atomInfo->pos[2] = pos[2];
128	>	//print the ignore type list
129	>	sprintf(buffer , "lipidHeadName list contains below types:\n");
130	>	result += buffer;
131
132	<	atomInfo->dipole[0] = newVec[0];
132	>	for(i = lipidHeadName.begin(); i != lipidHeadName.end(); ++i){
133	>	sprintf(buffer ,"%s\t", i->c_str());
134	>	result += buffer;
135	>	}
136
137	<	atomInfo->dipole[1] = newVec[1];
137	>	sprintf(buffer ,"\n");
138	>	result += buffer;
139
140	<	atomInfo->dipole[2] = newVec[2];
140	>	sprintf(buffer ,"------------------------------------------------------------------\n");
141	>	result += buffer;
142
143	+	return result;
144
145	+	}
146
139	–	atomData->addAtomInfo(atomInfo);
147
148	+	void RBCOMVisitor::visit(RigidBody* rb){
149	+	AtomData* atomData;
150	+	AtomInfo* atomInfo;
151	+	Vector3d pos;
152
153	+	pos = rb->getPos();
154	+	atomInfo = new AtomInfo;
155	+	atomInfo->atomTypeName = "X";
156	+	atomInfo->pos[0] = pos[0];
157	+	atomInfo->pos[1] = pos[1];
158	+	atomInfo->pos[2] = pos[2];
159	+	atomInfo->vec[0] = 0;
160	+	atomInfo->vec[1] = 0;
161	+	atomInfo->vec[2] = 0;
162
163	<	if(!haveAtomData){
144	<
163	>	atomData = new AtomData;
164		atomData->setID("ATOMDATA");
165	+	atomData->addAtomInfo(atomInfo);
166
167		rb->addProperty(atomData);
168
169		}
170
151	–
171
172	<	}
172	>	const  std::string RBCOMVisitor::toString(){
173	>	char buffer[65535];
174	>	std::string result;
175
176	+	sprintf(buffer ,"------------------------------------------------------------------\n");
177	+	result += buffer;
178
179	+	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
180	+	result += buffer;
181
182	<	void LipidHeadVisitor::addLipidHeadName(const std::string& name){
182	>	//print the ignore type list
183	>	sprintf(buffer , "Visitor Description: add a pseudo atom at the center of the mass of the rigidbody\n");
184	>	result += buffer;
185
186	<	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	<
186	>	sprintf(buffer ,"------------------------------------------------------------------\n");
187		result += buffer;
188
189	+	return result;
190	+
191		}
192
193	+	}//namespace OpenMD
194
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->AtomType = "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	–

Comparing:
trunk/src/visitors/RigidBodyVisitor.cpp (property svn:keywords), Revision 385 by tim, Tue Mar 1 20:10:14 2005 UTC vs.
branches/development/src/visitors/RigidBodyVisitor.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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