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

Comparing:
trunk/src/visitors/RigidBodyVisitor.cpp (file contents), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/visitors/RigidBodyVisitor.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 1 | Line 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
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]  Vardeman & Gezelter, in progress (2009).
40	+	*/
41	+
42		#include "visitors/RigidBodyVisitor.hpp"
43		#include "primitives/RigidBody.hpp"
3	–	#include "math/MatVec3.h"
44
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];
45
46	<	if(!canVisit(rb->getType()))
16	<	return;
46	>	namespace OpenMD {
47
48	<	rb->getPos(pos);
49	<	rb->getA(rotMatrix);
50	<	matVecMul3(rotMatrix, u, newVec);
48	>	void LipidHeadVisitor::visit(RigidBody* rb){
49	>	Vector3d pos;
50	>	Vector3d u(0, 0, 1);
51	>	Vector3d newVec;
52	>	GenericData* data;
53	>	AtomData* atomData;
54	>	AtomInfo* atomInfo;
55	>	bool haveAtomData;
56	>	RotMat3x3d rotMatrix;
57
58	<	data = rb->getProperty("ATOMDATA");
59	<	if(data != NULL){
58	>	if(!canVisit(rb->getType()))
59	>	return;
60
61	<	atomData = dynamic_cast<AtomData*>(data);
62	<	if(atomData == NULL){
63	<	cerr << "can not get Atom Data from " << rb->getType() << endl;
64	<	atomData = new AtomData;
65	<	haveAtomData = false;
61	>	pos = rb->getPos();
62	>	rotMatrix = rb->getA();
63	>	//matVecMul3(rotMatrix, u, newVec);
64	>	newVec = rotMatrix * u;
65	>
66	>	data = rb->getPropertyByName("ATOMDATA");
67	>
68	>	if(data != NULL){
69	>	atomData = dynamic_cast<AtomData*>(data);
70	>
71	>	if(atomData == NULL){
72	>	std::cerr << "can not get Atom Data from " << rb->getType() << std::endl;
73	>
74	>	atomData = new AtomData;
75	>	haveAtomData = false;
76	>
77	>	} else
78	>	haveAtomData = true;
79	>
80	>	} else {
81	>	atomData = new AtomData;
82	>	haveAtomData = false;
83	>
84		}
85	<	else
86	<	haveAtomData = true;
85	>
86	>	atomInfo = new AtomInfo;
87	>	atomInfo->atomTypeName = "X";
88	>	atomInfo->pos[0] = pos[0];
89	>	atomInfo->pos[1] = pos[1];
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	>
95	>	atomData->addAtomInfo(atomInfo);
96	>
97	>	if(!haveAtomData){
98	>	atomData->setID("ATOMDATA");
99	>	rb->addProperty(atomData);
100	>	}
101	>
102		}
34	–	else{
35	–	atomData = new AtomData;
36	–	haveAtomData = false;
37	–	}
103
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];
104
105	<	atomData->addAtomInfo(atomInfo);
105	>	void LipidHeadVisitor::addLipidHeadName(const std::string& name){
106	>	lipidHeadName.insert(name);
107
50	–	if(!haveAtomData){
51	–	atomData->setID("ATOMDATA");
52	–	rb->addProperty(atomData);
108		}
54	–
55	–	}
109
110	<	void LipidHeadVisitor::addLipidHeadName(const string& name){
111	<	lipidHeadName.insert(name);
110	>	bool LipidHeadVisitor::canVisit(const std::string& name){
111	>	return lipidHeadName.find(name) != lipidHeadName.end() ? true : false;
112
113	<	}
113	>	}
114
62	–	bool LipidHeadVisitor::canVisit(const string& name){
63	–	return lipidHeadName.find(name) != lipidHeadName.end() ? true : false;
115
116	<	}
116	>	const  std::string LipidHeadVisitor::toString(){
117	>	char buffer[65535];
118	>	std::string result;
119	>	std::set<std::string>::iterator i;
120
121	<	const string LipidHeadVisitor::toString(){
122	<	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;
121	>	sprintf(buffer ,"------------------------------------------------------------------\n");
122	>	result += buffer;
123
124	<	//print the ignore type list
125	<	sprintf(buffer , "lipidHeadName list contains below types:\n");
80	<	result += buffer;
124	>	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
125	>	result += buffer;
126
127	<	for(i = lipidHeadName.begin(); i != lipidHeadName.end(); ++i){
128	<	sprintf(buffer ,"%s\t", i->c_str());
127	>	//print the ignore type list
128	>	sprintf(buffer , "lipidHeadName list contains below types:\n");
129		result += buffer;
130	+
131	+	for(i = lipidHeadName.begin(); i != lipidHeadName.end(); ++i){
132	+	sprintf(buffer ,"%s\t", i->c_str());
133	+	result += buffer;
134	+	}
135	+
136	+	sprintf(buffer ,"\n");
137	+	result += buffer;
138	+
139	+	sprintf(buffer ,"------------------------------------------------------------------\n");
140	+	result += buffer;
141	+
142	+	return result;
143	+
144		}
145
87	–	sprintf(buffer ,"\n");
88	–	result += buffer;
146
147	<	sprintf(buffer ,"------------------------------------------------------------------\n");
148	<	result += buffer;
147	>	void RBCOMVisitor::visit(RigidBody* rb){
148	>	AtomData* atomData;
149	>	AtomInfo* atomInfo;
150	>	Vector3d pos;
151
152	<	return result;
152	>	pos = rb->getPos();
153	>	atomInfo = new AtomInfo;
154	>	atomInfo->atomTypeName = "X";
155	>	atomInfo->pos[0] = pos[0];
156	>	atomInfo->pos[1] = pos[1];
157	>	atomInfo->pos[2] = pos[2];
158	>	atomInfo->vec[0] = 0;
159	>	atomInfo->vec[1] = 0;
160	>	atomInfo->vec[2] = 0;
161
162	<	}
162	>	atomData = new AtomData;
163	>	atomData->setID("ATOMDATA");
164	>	atomData->addAtomInfo(atomInfo);
165
166	<	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;
166	>	rb->addProperty(atomData);
167
168	<	atomData = new AtomData;
113	<	atomData->setID("ATOMDATA");
114	<	atomData->addAtomInfo(atomInfo);
168	>	}
169
116	–	rb->addProperty(atomData);
117	–	}
170
171	<	const string RBCOMVisitor::toString(){
172	<	char buffer[65535];
173	<	string result;
122	<
123	<	sprintf(buffer ,"------------------------------------------------------------------\n");
124	<	result += buffer;
125	<
126	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
127	<	result += buffer;
171	>	const  std::string RBCOMVisitor::toString(){
172	>	char buffer[65535];
173	>	std::string result;
174
175	<	//print the ignore type list
176	<	sprintf(buffer , "Visitor Description: add a pseudo atom at the center of the mass of the rigidbody\n");
131	<	result += buffer;
175	>	sprintf(buffer ,"------------------------------------------------------------------\n");
176	>	result += buffer;
177
178	<	sprintf(buffer ,"------------------------------------------------------------------\n");
179	<	result += buffer;
178	>	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
179	>	result += buffer;
180
181	<	return result;
181	>	//print the ignore type list
182	>	sprintf(buffer , "Visitor Description: add a pseudo atom at the center of the mass of the rigidbody\n");
183	>	result += buffer;
184
185	<	}
185	>	sprintf(buffer ,"------------------------------------------------------------------\n");
186	>	result += buffer;
187
188	+	return result;
189	+
190	+	}
191	+
192	+	}//namespace OpenMD
193	+

Comparing:
trunk/src/visitors/RigidBodyVisitor.cpp (property svn:keywords), Revision 3 by tim, Fri Sep 24 16:27:58 2004 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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