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

Comparing:
trunk/src/visitors/RigidBodyVisitor.cpp (file contents), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/visitors/RigidBodyVisitor.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		#include "visitors/RigidBodyVisitor.hpp"
43	–
43		#include "primitives/RigidBody.hpp"
44
45
46	<	namespace oopse {
46	>	namespace OpenMD {
47
49	–
50	–
48		void LipidHeadVisitor::visit(RigidBody* rb){
52	–
49		Vector3d pos;
54	–
50		Vector3d u(0, 0, 1);
56	–
51		Vector3d newVec;
58	–
52		GenericData* data;
60	–
53		AtomData* atomData;
62	–
54		AtomInfo* atomInfo;
64	–
55		bool haveAtomData;
66	–
56		RotMat3x3d rotMatrix;
57
69	–
70	–
58		if(!canVisit(rb->getType()))
72	–
59		return;
60
75	–
76	–
61		pos = rb->getPos();
78	–
62		rotMatrix = rb->getA();
80	–
63		//matVecMul3(rotMatrix, u, newVec);
82	–
64		newVec = rotMatrix * u;
65
85	–
86	–
66		data = rb->getPropertyByName("ATOMDATA");
67
68		if(data != NULL){
90	–
91	–
92	–
69		atomData = dynamic_cast<AtomData*>(data);
70	<
70	>
71		if(atomData == NULL){
96	–
72		std::cerr << "can not get Atom Data from " << rb->getType() << std::endl;
73	<
73	>
74		atomData = new AtomData;
100	–
75		haveAtomData = false;
76	<
77	<	}
104	<
105	<	else
106	<
76	>
77	>	} else
78		haveAtomData = true;
79	<
80	<	}
110	<
111	<	else{
112	<
79	>
80	>	} else {
81		atomData = new AtomData;
114	–
82		haveAtomData = false;
83	<
83	>
84		}
85
119	–
120	–
86		atomInfo = new AtomInfo;
122	–
87		atomInfo->atomTypeName = "X";
124	–
88		atomInfo->pos[0] = pos[0];
126	–
89		atomInfo->pos[1] = pos[1];
128	–
90		atomInfo->pos[2] = pos[2];
91	+	atomInfo->vec[0] = newVec[0];
92	+	atomInfo->vec[1] = newVec[1];
93	+	atomInfo->vec[2] = newVec[2];
94
131	–	atomInfo->dipole[0] = newVec[0];
132	–
133	–	atomInfo->dipole[1] = newVec[1];
134	–
135	–	atomInfo->dipole[2] = newVec[2];
136	–
137	–
138	–
95		atomData->addAtomInfo(atomInfo);
96
141	–
142	–
97		if(!haveAtomData){
144	–
98		atomData->setID("ATOMDATA");
146	–
99		rb->addProperty(atomData);
148	–
100		}
101
151	–
152	–
102		}
103
104
156	–
105		void LipidHeadVisitor::addLipidHeadName(const std::string& name){
158	–
106		lipidHeadName.insert(name);
107
161	–
162	–
108		}
109
165	–
166	–
110		bool LipidHeadVisitor::canVisit(const std::string& name){
168	–
111		return lipidHeadName.find(name) != lipidHeadName.end() ? true : false;
112
171	–
172	–
113		}
114
115
176	–
116		const  std::string LipidHeadVisitor::toString(){
178	–
117		char buffer[65535];
180	–
118		std::string result;
182	–
119		std::set<std::string>::iterator i;
120
185	–
186	–
121		sprintf(buffer ,"------------------------------------------------------------------\n");
188	–
122		result += buffer;
123
191	–
192	–
124		sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
194	–
125		result += buffer;
126
197	–
198	–
127		//print the ignore type list
200	–
128		sprintf(buffer , "lipidHeadName list contains below types:\n");
202	–
129		result += buffer;
130
205	–
206	–
131		for(i = lipidHeadName.begin(); i != lipidHeadName.end(); ++i){
208	–
132		sprintf(buffer ,"%s\t", i->c_str());
210	–
133		result += buffer;
212	–
134		}
135
215	–
216	–
136		sprintf(buffer ,"\n");
218	–
137		result += buffer;
138
221	–
222	–
139		sprintf(buffer ,"------------------------------------------------------------------\n");
224	–
140		result += buffer;
141
227	–
228	–
142		return result;
143
231	–
232	–
144		}
145
146
236	–
147		void RBCOMVisitor::visit(RigidBody* rb){
238	–
148		AtomData* atomData;
240	–
149		AtomInfo* atomInfo;
242	–
150		Vector3d pos;
151
245	–
246	–
152		pos = rb->getPos();
248	–
153		atomInfo = new AtomInfo;
250	–
154		atomInfo->atomTypeName = "X";
252	–
155		atomInfo->pos[0] = pos[0];
254	–
156		atomInfo->pos[1] = pos[1];
256	–
157		atomInfo->pos[2] = pos[2];
158	+	atomInfo->vec[0] = 0;
159	+	atomInfo->vec[1] = 0;
160	+	atomInfo->vec[2] = 0;
161
259	–	atomInfo->dipole[0] = 0;
260	–
261	–	atomInfo->dipole[1] = 0;
262	–
263	–	atomInfo->dipole[2] = 0;
264	–
265	–
266	–
162		atomData = new AtomData;
268	–
163		atomData->setID("ATOMDATA");
270	–
164		atomData->addAtomInfo(atomInfo);
165
273	–
274	–
166		rb->addProperty(atomData);
167
168		}
169
170
280	–
171		const  std::string RBCOMVisitor::toString(){
282	–
172		char buffer[65535];
284	–
173		std::string result;
174
287	–
288	–
175		sprintf(buffer ,"------------------------------------------------------------------\n");
290	–
176		result += buffer;
177
293	–
294	–
178		sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
296	–
179		result += buffer;
180
299	–
300	–
181		//print the ignore type list
302	–
182		sprintf(buffer , "Visitor Description: add a pseudo atom at the center of the mass of the rigidbody\n");
304	–
183		result += buffer;
184
307	–
308	–
185		sprintf(buffer ,"------------------------------------------------------------------\n");
310	–
186		result += buffer;
187
313	–
314	–
188		return result;
189
317	–
318	–
190		}
191
192	+	}//namespace OpenMD
193
322	–
323	–
324	–
325	–	}//namespace oopse
326	–

Comparing:
trunk/src/visitors/RigidBodyVisitor.cpp (property svn:keywords), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/visitors/RigidBodyVisitor.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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