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root/OpenMD/trunk/src/visitors/RigidBodyVisitor.cpp

Comparing trunk/src/visitors/RigidBodyVisitor.cpp (file contents):
Revision 132 by tim, Thu Oct 21 16:22:01 2004 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 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, 234107 (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"
3	–	#include "math/MatVec3.h"
45
5	–	namespace oopse {
46
47	<	void LipidHeadVisitor::visit(RigidBody* rb){
8	<	double pos[3];
9	<	double u[3] = {0, 0, 1};
10	<	double newVec[3];
11	<	GenericData* data;
12	<	AtomData* atomData;
13	<	AtomInfo* atomInfo;
14	<	bool haveAtomData;
15	<	double rotMatrix[3][3];
47	>	namespace OpenMD {
48
49	<	if(!canVisit(rb->getType()))
50	<	return;
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	<	rb->getPos(pos);
60	<	rb->getA(rotMatrix);
22	<	matVecMul3(rotMatrix, u, newVec);
59	>	if(!canVisit(rb->getType()))
60	>	return;
61
62	<	data = rb->getProperty("ATOMDATA");
63	<	if(data != NULL){
62	>	pos = rb->getPos();
63	>	rotMatrix = rb->getA();
64	>	//matVecMul3(rotMatrix, u, newVec);
65	>	newVec = rotMatrix * u;
66
67	<	atomData = dynamic_cast<AtomData*>(data);
68	<	if(atomData == NULL){
69	<	cerr << "can not get Atom Data from " << rb->getType() << endl;
70	<	atomData = new AtomData;
71	<	haveAtomData = false;
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		}
36	–	else{
37	–	atomData = new AtomData;
38	–	haveAtomData = false;
39	–	}
104
41	–	atomInfo = new AtomInfo;
42	–	atomInfo->AtomType = "X";
43	–	atomInfo->pos[0] = pos[0];
44	–	atomInfo->pos[1] = pos[1];
45	–	atomInfo->pos[2] = pos[2];
46	–	atomInfo->dipole[0] = newVec[0];
47	–	atomInfo->dipole[1] = newVec[1];
48	–	atomInfo->dipole[2] = newVec[2];
105
106	<	atomData->addAtomInfo(atomInfo);
106	>	void LipidHeadVisitor::addLipidHeadName(const std::string& name){
107	>	lipidHeadName.insert(name);
108
52	–	if(!haveAtomData){
53	–	atomData->setID("ATOMDATA");
54	–	rb->addProperty(atomData);
109		}
56	–
57	–	}
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
64	–	bool LipidHeadVisitor::canVisit(const string& name){
65	–	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];
71	<	string result;
72	<	set<string>::iterator i;
73	<
74	<	sprintf(buffer ,"------------------------------------------------------------------\n");
75	<	result += buffer;
76	<
77	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
78	<	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");
82	<	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
89	–	sprintf(buffer ,"\n");
90	–	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){
100	<	AtomData* atomData;
101	<	AtomInfo* atomInfo;
102	<	double pos[3];
103	<
104	<	rb->getPos(pos);
105	<	atomInfo = new AtomInfo;
106	<	atomInfo->AtomType = "X";
107	<	atomInfo->pos[0] = pos[0];
108	<	atomInfo->pos[1] = pos[1];
109	<	atomInfo->pos[2] = pos[2];
110	<	atomInfo->dipole[0] = 0;
111	<	atomInfo->dipole[1] = 0;
112	<	atomInfo->dipole[2] = 0;
167	>	rb->addProperty(atomData);
168
169	<	atomData = new AtomData;
115	<	atomData->setID("ATOMDATA");
116	<	atomData->addAtomInfo(atomInfo);
169	>	}
170
118	–	rb->addProperty(atomData);
119	–	}
171
172	<	const string RBCOMVisitor::toString(){
173	<	char buffer[65535];
174	<	string result;
124	<
125	<	sprintf(buffer ,"------------------------------------------------------------------\n");
126	<	result += buffer;
127	<
128	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
129	<	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");
133	<	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	<	}//namespace oopse
191	>	}
192	>
193	>	}//namespace OpenMD
194	>

Comparing trunk/src/visitors/RigidBodyVisitor.cpp (property svn:keywords):
Revision 132 by tim, Thu Oct 21 16:22:01 2004 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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