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Comparing:
trunk/src/visitors/RigidBodyVisitor.cpp (file contents), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 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	<	#include "RigidBodyVisitor.hpp"
2	<	#include "RigidBody.hpp"
3	<	#include "MatVec3.h"
1	>	/*
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. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
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.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
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"
44	>	#include "primitives/RigidBody.hpp"
45
5	–	void LipidHeadVisitor::visit(RigidBody* rb){
6	–	double pos[3];
7	–	double u[3] = {0, 0, 1};
8	–	double newVec[3];
9	–	GenericData* data;
10	–	AtomData* atomData;
11	–	AtomInfo* atomInfo;
12	–	bool haveAtomData;
13	–	double rotMatrix[3][3];
46
47	<	if(!canVisit(rb->getType()))
16	<	return;
47	>	namespace OpenMD {
48
49	<	rb->getPos(pos);
50	<	rb->getA(rotMatrix);
51	<	matVecMul3(rotMatrix, u, newVec);
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	<	data = rb->getProperty("ATOMDATA");
60	<	if(data != NULL){
59	>	if(!canVisit(rb->getType()))
60	>	return;
61
62	<	atomData = dynamic_cast<AtomData*>(data);
63	<	if(atomData == NULL){
64	<	cerr << "can not get Atom Data from " << rb->getType() << endl;
65	<	atomData = new AtomData;
66	<	haveAtomData = false;
62	>	pos = rb->getPos();
63	>	rotMatrix = rb->getA();
64	>	//matVecMul3(rotMatrix, u, newVec);
65	>	newVec = rotMatrix * u;
66	>
67	>	data = rb->getPropertyByName("ATOMDATA");
68	>
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	<	else
87	<	haveAtomData = true;
86	>
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	>	atomData->addAtomInfo(atomInfo);
97	>
98	>	if(!haveAtomData){
99	>	atomData->setID("ATOMDATA");
100	>	rb->addProperty(atomData);
101	>	}
102	>
103		}
34	–	else{
35	–	atomData = new AtomData;
36	–	haveAtomData = false;
37	–	}
104
39	–	atomInfo = new AtomInfo;
40	–	atomInfo->AtomType = "X";
41	–	atomInfo->pos[0] = pos[0];
42	–	atomInfo->pos[1] = pos[1];
43	–	atomInfo->pos[2] = pos[2];
44	–	atomInfo->dipole[0] = newVec[0];
45	–	atomInfo->dipole[1] = newVec[1];
46	–	atomInfo->dipole[2] = newVec[2];
105
106	<	atomData->addAtomInfo(atomInfo);
106	>	void LipidHeadVisitor::addLipidHeadName(const std::string& name){
107	>	lipidHeadName.insert(name);
108
50	–	if(!haveAtomData){
51	–	atomData->setID("ATOMDATA");
52	–	rb->addProperty(atomData);
109		}
54	–
55	–	}
110
111	<	void LipidHeadVisitor::addLipidHeadName(const string& name){
112	<	lipidHeadName.insert(name);
111	>	bool LipidHeadVisitor::canVisit(const std::string& name){
112	>	return lipidHeadName.find(name) != lipidHeadName.end() ? true : false;
113
114	<	}
114	>	}
115
62	–	bool LipidHeadVisitor::canVisit(const string& name){
63	–	return lipidHeadName.find(name) != lipidHeadName.end() ? true : false;
116
117	<	}
117	>	const  std::string LipidHeadVisitor::toString(){
118	>	char buffer[65535];
119	>	std::string result;
120	>	std::set<std::string>::iterator i;
121
122	<	const string LipidHeadVisitor::toString(){
123	<	char buffer[65535];
69	<	string result;
70	<	set<string>::iterator i;
71	<
72	<	sprintf(buffer ,"------------------------------------------------------------------\n");
73	<	result += buffer;
74	<
75	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
76	<	result += buffer;
122	>	sprintf(buffer ,"------------------------------------------------------------------\n");
123	>	result += buffer;
124
125	<	//print the ignore type list
126	<	sprintf(buffer , "lipidHeadName list contains below types:\n");
80	<	result += buffer;
125	>	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
126	>	result += buffer;
127
128	<	for(i = lipidHeadName.begin(); i != lipidHeadName.end(); ++i){
129	<	sprintf(buffer ,"%s\t", i->c_str());
128	>	//print the ignore type list
129	>	sprintf(buffer , "lipidHeadName list contains below types:\n");
130		result += buffer;
131	+
132	+	for(i = lipidHeadName.begin(); i != lipidHeadName.end(); ++i){
133	+	sprintf(buffer ,"%s\t", i->c_str());
134	+	result += buffer;
135	+	}
136	+
137	+	sprintf(buffer ,"\n");
138	+	result += buffer;
139	+
140	+	sprintf(buffer ,"------------------------------------------------------------------\n");
141	+	result += buffer;
142	+
143	+	return result;
144	+
145		}
146
87	–	sprintf(buffer ,"\n");
88	–	result += buffer;
147
148	<	sprintf(buffer ,"------------------------------------------------------------------\n");
149	<	result += buffer;
148	>	void RBCOMVisitor::visit(RigidBody* rb){
149	>	AtomData* atomData;
150	>	AtomInfo* atomInfo;
151	>	Vector3d pos;
152
153	<	return result;
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	<	}
163	>	atomData = new AtomData;
164	>	atomData->setID("ATOMDATA");
165	>	atomData->addAtomInfo(atomInfo);
166
167	<	void RBCOMVisitor::visit(RigidBody* rb){
98	<	AtomData* atomData;
99	<	AtomInfo* atomInfo;
100	<	double pos[3];
101	<
102	<	rb->getPos(pos);
103	<	atomInfo = new AtomInfo;
104	<	atomInfo->AtomType = "X";
105	<	atomInfo->pos[0] = pos[0];
106	<	atomInfo->pos[1] = pos[1];
107	<	atomInfo->pos[2] = pos[2];
108	<	atomInfo->dipole[0] = 0;
109	<	atomInfo->dipole[1] = 0;
110	<	atomInfo->dipole[2] = 0;
167	>	rb->addProperty(atomData);
168
169	<	atomData = new AtomData;
113	<	atomData->setID("ATOMDATA");
114	<	atomData->addAtomInfo(atomInfo);
169	>	}
170
116	–	rb->addProperty(atomData);
117	–	}
171
172	<	const string RBCOMVisitor::toString(){
173	<	char buffer[65535];
174	<	string result;
122	<
123	<	sprintf(buffer ,"------------------------------------------------------------------\n");
124	<	result += buffer;
125	<
126	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
127	<	result += buffer;
172	>	const  std::string RBCOMVisitor::toString(){
173	>	char buffer[65535];
174	>	std::string result;
175
176	<	//print the ignore type list
177	<	sprintf(buffer , "Visitor Description: add a pseudo atom at the center of the mass of the rigidbody\n");
131	<	result += buffer;
176	>	sprintf(buffer ,"------------------------------------------------------------------\n");
177	>	result += buffer;
178
179	<	sprintf(buffer ,"------------------------------------------------------------------\n");
180	<	result += buffer;
179	>	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
180	>	result += buffer;
181
182	<	return result;
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	<	}
186	>	sprintf(buffer ,"------------------------------------------------------------------\n");
187	>	result += buffer;
188
189	+	return result;
190	+
191	+	}
192	+
193	+	}//namespace OpenMD
194	+

Comparing:
trunk/src/visitors/RigidBodyVisitor.cpp (property svn:keywords), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 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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