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root/OpenMD/branches/development/src/brains/Snapshot.hpp

Comparing:
trunk/src/brains/Snapshot.hpp (file contents), Revision 137 by tim, Thu Oct 21 21:31:39 2004 UTC vs.
branches/development/src/brains/Snapshot.hpp (file contents), Revision 1708 by gezelter, Tue May 15 13:02:10 2012 UTC

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1		/*
2	<	* Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
3	<	*
4	<	* Contact: oopse@oopse.org
5	<	*
6	<	* This program is free software; you can redistribute it and/or
7	<	* modify it under the terms of the GNU Lesser General Public License
8	<	* as published by the Free Software Foundation; either version 2.1
9	<	* of the License, or (at your option) any later version.
10	<	* All we ask is that proper credit is given for our work, which includes
11	<	* - but is not limited to - adding the above copyright notice to the beginning
12	<	* of your source code files, and to any copyright notice that you may distribute
13	<	* with programs based on this work.
14	<	*
15	<	* This program is distributed in the hope that it will be useful,
16	<	* but WITHOUT ANY WARRANTY; without even the implied warranty of
17	<	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18	<	* GNU Lesser General Public License for more details.
19	<	*
20	<	* You should have received a copy of the GNU Lesser General Public License
21	<	* along with this program; if not, write to the Free Software
22	<	* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
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	<	/**
44	<	* @file Snapshot.hpp
45	<	* @author tlin
46	<	* @date 10/20/2004
47	<	* @time 23:56am
48	<	* @version 1.0
49	<	*/
42	>
43	>	/**
44	>	* @file Snapshot.hpp
45	>	* @author tlin
46	>	* @date 10/20/2004
47	>	* @time 23:56am
48	>	* @version 1.0
49	>	*/
50	>
51		#ifndef BRAINS_SNAPSHOT_HPP
52		#define BRAINS_SNAPSHOT_HPP
53
54		#include <vector>
55
56	<	#include "math/Vector3.hpp"
57	<	#include "math/SquareMatrix3.hpp"
56	>	#include "brains/DataStorage.hpp"
57	>	#include "brains/Stats.hpp"
58
59	<	using namespace std;
59	>	namespace OpenMD{
60
61	<	namespace oopse{
61	>	/**
62	>	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
63	>	* @brief Snapshot class is a repository class for storing dynamic data during
64	>	*  Simulation
65	>	* Every snapshot class will contain one DataStorage for atoms and one DataStorage
66	>	*  for rigid bodies.
67	>	*/
68	>	class Snapshot {
69	>	public:
70	>
71	>	Snapshot(int nAtoms, int nRigidbodies,
72	>	int nCutoffGroups) : atomData(nAtoms),
73	>	rigidbodyData(nRigidbodies),
74	>	cgData(nCutoffGroups, DataStorage::dslPosition),
75	>	currentTime_(0),
76	>	orthoTolerance_(1e-6),
77	>	orthoRhombic_(0),
78	>	chi_(0.0),
79	>	integralOfChiDt_(0.0),
80	>	eta_(0.0), id_(-1), hasCOM_(false),
81	>	volume_(0.0), hasVolume_(false) {
82
83	<	/**
46	<	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
47	<	* @brief Snapshot class is a repository class for storing dynamic data during
48	<	*  Simulation
49	<	* @see SimData
50	<	*/
51	<	class Snapshot {
52	<	public:
83	>	}
84
85	<	Snapshot(int i) {
85	>	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
86	>	int storageLayout) : atomData(nAtoms, storageLayout),
87	>	rigidbodyData(nRigidbodies, storageLayout),
88	>	cgData(nCutoffGroups, DataStorage::dslPosition),
89	>	currentTime_(0), orthoTolerance_(1e-6),
90	>	orthoRhombic_(0), chi_(0.0),
91	>	integralOfChiDt_(0.0), eta_(0.0), id_(-1),
92	>	hasCOM_(false), volume_(0.0),
93	>	hasVolume_(false) {
94	>	}
95	>
96	>	/** Returns the id of this Snapshot */
97	>	int getID() {
98	>	return id_;
99	>	}
100
101	<	}
101	>	/** Sets the id of this Snapshot */
102	>	void setID(int id) {
103	>	id_ = id;
104	>	}
105
106	<	Snapshot(const Snapshot& s);
106	>	int getSize() {
107	>	return atomData.getSize() + rigidbodyData.getSize();
108	>	}
109
110	<	Snapshot& operator =(const Snapshot& s);
110	>	/** Returns the number of atoms */
111	>	int getNumberOfAtoms() {
112	>	return atomData.getSize();
113	>	}
114	>
115	>	/** Returns the number of rigid bodies */
116	>	int getNumberOfRigidBodies() {
117	>	return rigidbodyData.getSize();
118	>	}
119	>
120	>	/** Returns the number of rigid bodies */
121	>	int getNumberOfCutoffGroups() {
122	>	return cgData.getSize();
123	>	}
124	>
125	>	/** Returns the H-Matrix */
126	>	Mat3x3d getHmat() {
127	>	return hmat_;
128	>	}
129	>
130	>	/** Sets the H-Matrix */
131	>	void setHmat(const Mat3x3d& m);
132
133	<	/** Returns the id of this Snapshot */
134	<	int getID() {
135	<	return id_;
136	<	}
133	>	RealType getVolume() {
134	>	if (hasVolume_){
135	>	return volume_;
136	>	}else{
137	>	return hmat_.determinant();
138	>	}
139	>	}
140
141	<	/** Sets the id of this Snapshot */
142	<	void setID(int id) {
143	<	id_ = id;
144	<	}
141	>	void setVolume(RealType volume){
142	>	hasVolume_=true;
143	>	volume_ = volume;
144	>	}
145
146	<	/** */
147	<	Snapshot* clone() {
148	<	return new Snapshot(*this);
149	<	}
146	>	/** Returns the inverse H-Matrix */
147	>	Mat3x3d getInvHmat() {
148	>	return invHmat_;
149	>	}
150
151	+	/** Wrapping the vector according to periodic boundary condition*/
152	+	void wrapVector(Vector3d& v);
153	+	/** Scaling a vector to multiples of the periodic box */
154	+	Vector3d scaleVector(Vector3d &v);
155
78	–	//template<typename T>
79	–	//static typename T::ElemPointerType getArrayPointer(vector<T>& v) {
80	–	//    return v[0]->getArrayPointer();
81	–	//}
156
157	<	static double* getArrayPointer(vector<Vector3d>& v) {
158	<	return v[0].getArrayPointer();
159	<	}
157	>	Vector3d getCOM();
158	>	Vector3d getCOMvel();
159	>	Vector3d getCOMw();
160
161	<	static double* getArrayPointer(vector<RotMat3x3d>& v) {
162	<	return v[0].getArrayPointer();
163	<	}
161	>	RealType getTime() {
162	>	return currentTime_;
163	>	}
164	>
165	>	void increaseTime(RealType dt) {
166	>	setTime(getTime() + dt);
167	>	}
168	>
169	>	void setTime(RealType time) {
170	>	currentTime_ =time;
171	>	//time at statData is redundant
172	>	statData[Stats::TIME] = currentTime_;
173	>	}
174	>
175	>	RealType getChi() {
176	>	return chi_;
177	>	}
178	>
179	>	void setChi(RealType chi) {
180	>	chi_ = chi;
181	>	}
182	>
183	>	RealType getIntegralOfChiDt() {
184	>	return integralOfChiDt_;
185	>	}
186	>
187	>	void setIntegralOfChiDt(RealType integralOfChiDt) {
188	>	integralOfChiDt_ = integralOfChiDt;
189	>	}
190
91	–	static double* getArrayPointer(vector<double>& v) {
92	–	assert(v.size() > 0);
93	–	return &(v[0]);
94	–	}
95	–
96	–	vector<Vector3d> pos;
97	–	vector<Vector3d> vel;
98	–	vector<Vector3d> frc;
99	–	vector<Vector3d> trq;
100	–	vector<RotMat3x3d> Amat;
101	–	vector<Vector3d> mu;
102	–	vector<Vector3d> ul;
103	–	vector<double> zAngle;
104	–
105	–	private:
191
192	<	int id_; /**< identification number of the snapshot */
193	<	};
192	>	void setOrthoTolerance(RealType orthoTolerance) {
193	>	orthoTolerance_ = orthoTolerance;
194	>	}
195
196	+	Mat3x3d getEta() {
197	+	return eta_;
198	+	}
199	+
200	+	void setEta(const Mat3x3d& eta) {
201	+	eta_ = eta;
202	+	}
203	+
204	+	bool hasCOM() {
205	+	return hasCOM_;
206	+	}
207	+
208	+	void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
209	+	COM_ = COM;
210	+	COMvel_ = COMvel;
211	+	COMw_ = COMw;
212	+	hasCOM_ = true;
213	+	}
214	+
215	+	DataStorage atomData;
216	+	DataStorage rigidbodyData;
217	+	DataStorage cgData;
218	+	Stats statData;
219	+
220	+	private:
221	+	RealType currentTime_;
222	+
223	+	Mat3x3d hmat_;
224	+	Mat3x3d invHmat_;
225	+	RealType orthoTolerance_;
226	+	int orthoRhombic_;
227	+	RealType volume_;
228	+
229	+	RealType chi_;
230	+	RealType integralOfChiDt_;
231	+	Mat3x3d eta_;
232	+	Vector3d COM_;
233	+	Vector3d COMvel_;
234	+	Vector3d COMw_;
235	+	int id_; /**< identification number of the snapshot */
236	+	bool hasCOM_;
237	+	bool hasVolume_;
238	+
239	+	};
240	+
241	+	typedef DataStorage (Snapshot::*DataStoragePointer);
242		}
243		#endif //BRAINS_SNAPSHOT_HPP

Comparing:
trunk/src/brains/Snapshot.hpp (property svn:keywords), Revision 137 by tim, Thu Oct 21 21:31:39 2004 UTC vs.
branches/development/src/brains/Snapshot.hpp (property svn:keywords), Revision 1708 by gezelter, Tue May 15 13:02:10 2012 UTC

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