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Comparing:
trunk/src/brains/Snapshot.hpp (file contents), Revision 122 by tim, Wed Oct 20 05:52:25 2004 UTC vs.
branches/development/src/brains/Snapshot.hpp (file contents), Revision 1550 by gezelter, Wed Apr 27 21:49:59 2011 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41	<
42	<	/**
43	<	* @file Snapshot.hpp
44	<	* @author tlin
45	<	* @date 10/20/2004
46	<	* @time 23:56am
47	<	* @version 1.0
48	<	*/
41	>
42	>	/**
43	>	* @file Snapshot.hpp
44	>	* @author tlin
45	>	* @date 10/20/2004
46	>	* @time 23:56am
47	>	* @version 1.0
48	>	*/
49	>
50		#ifndef BRAINS_SNAPSHOT_HPP
51		#define BRAINS_SNAPSHOT_HPP
35	–	namespace oopse{
52
53	<	/**
54	<	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
55	<	* @brief Snapshot class is a repository class for storing dynamic data during
56	<	*  Simulation
57	<	* @see SimData
58	<	*/
59	<	class Snapshot {
60	<	public:
53	>	#include <vector>
54	>
55	>	#include "brains/DataStorage.hpp"
56	>	#include "brains/Stats.hpp"
57	>
58	>	namespace OpenMD{
59	>
60	>	/**
61	>	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
62	>	* @brief Snapshot class is a repository class for storing dynamic data during
63	>	*  Simulation
64	>	* Every snapshot class will contain one DataStorage for atoms and one DataStorage
65	>	*  for rigid bodies.
66	>	*/
67	>	class Snapshot {
68	>	public:
69
70	<	PropertyMap properties_;
70	>	Snapshot(int nAtoms, int nRigidbodies,
71	>	int nCutoffGroups) : atomData(nAtoms),
72	>	rigidbodyData(nRigidbodies),
73	>	cgData(nCutoffGroups, DataStorage::dslPosition),
74	>	currentTime_(0),
75	>	orthoTolerance_(1e-6),
76	>	orthoRhombic_(0),
77	>	chi_(0.0),
78	>	integralOfChiDt_(0.0),
79	>	eta_(0.0), id_(-1), hasCOM_(false),
80	>	hasVolume_(false), volume_(0.0) {
81	>
82	>	}
83	>
84	>	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
85	>	int storageLayout) : atomData(nAtoms, storageLayout),
86	>	rigidbodyData(nRigidbodies, storageLayout),
87	>	cgData(nCutoffGroups, DataStorage::dslPosition),
88	>	currentTime_(0), orthoTolerance_(1e-6),
89	>	orthoRhombic_(0), chi_(0.0),
90	>	integralOfChiDt_(0.0), eta_(0.0), id_(-1),
91	>	hasCOM_(false), hasVolume_(false),
92	>	volume_(0.0)  {
93	>	}
94	>
95	>	/** Returns the id of this Snapshot */
96	>	int getID() {
97	>	return id_;
98	>	}
99	>
100	>	/** Sets the id of this Snapshot */
101	>	void setID(int id) {
102	>	id_ = id;
103	>	}
104	>
105	>	int getSize() {
106	>	return atomData.getSize() + rigidbodyData.getSize();
107	>	}
108	>
109	>	/** Returns the number of atoms */
110	>	int getNumberOfAtoms() {
111	>	return atomData.getSize();
112	>	}
113	>
114	>	/** Returns the number of rigid bodies */
115	>	int getNumberOfRigidBodies() {
116	>	return rigidbodyData.getSize();
117	>	}
118	>
119	>	/** Returns the number of rigid bodies */
120	>	int getNumberOfCutoffGroups() {
121	>	return cgData.getSize();
122	>	}
123	>
124	>	/** Returns the H-Matrix */
125	>	Mat3x3d getHmat() {
126	>	return hmat_;
127	>	}
128	>
129	>	/** Sets the H-Matrix */
130	>	void setHmat(const Mat3x3d& m);
131
132	<	private:
132	>	RealType getVolume() {
133	>	if (hasVolume_){
134	>	return volume_;
135	>	}else{
136	>	return hmat_.determinant();
137	>	}
138	>	}
139	>
140	>	void setVolume(RealType volume){
141	>	hasVolume_=true;
142	>	volume_ = volume;
143	>	}
144	>
145	>	/** Returns the inverse H-Matrix */
146	>	Mat3x3d getInvHmat() {
147	>	return invHmat_;
148	>	}
149	>
150	>	/** Wrapping the vector according to periodic boundary condition*/
151	>	void wrapVector(Vector3d& v);
152	>	Vector3d getCOM();
153	>	Vector3d getCOMvel();
154	>	Vector3d getCOMw();
155
156	<	};
156	>	RealType getTime() {
157	>	return currentTime_;
158	>	}
159
160	+	void increaseTime(RealType dt) {
161	+	setTime(getTime() + dt);
162	+	}
163	+
164	+	void setTime(RealType time) {
165	+	currentTime_ =time;
166	+	//time at statData is redundant
167	+	statData[Stats::TIME] = currentTime_;
168	+	}
169	+
170	+	RealType getChi() {
171	+	return chi_;
172	+	}
173	+
174	+	void setChi(RealType chi) {
175	+	chi_ = chi;
176	+	}
177	+
178	+	RealType getIntegralOfChiDt() {
179	+	return integralOfChiDt_;
180	+	}
181	+
182	+	void setIntegralOfChiDt(RealType integralOfChiDt) {
183	+	integralOfChiDt_ = integralOfChiDt;
184	+	}
185	+
186	+
187	+	void setOrthoTolerance(RealType orthoTolerance) {
188	+	orthoTolerance_ = orthoTolerance;
189	+	}
190	+
191	+	Mat3x3d getEta() {
192	+	return eta_;
193	+	}
194	+
195	+	void setEta(const Mat3x3d& eta) {
196	+	eta_ = eta;
197	+	}
198	+
199	+	bool hasCOM() {
200	+	return hasCOM_;
201	+	}
202	+
203	+	void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
204	+	COM_ = COM;
205	+	COMvel_ = COMvel;
206	+	COMw_ = COMw;
207	+	hasCOM_ = true;
208	+	}
209	+
210	+	Vector3d getAtomPosByIindex(int iIndex) {
211	+	#ifdef IS_MPI
212	+	return atomIData.position[iIndex];
213	+	#else
214	+	return atomData.position[iIndex];
215	+	#endif
216	+	}
217	+	Vector3d getAtomPosByJindex(int jIndex) {
218	+	#ifdef IS_MPI
219	+	return atomJData.position[jIndex];
220	+	#else
221	+	return atomData.position[jIndex];
222	+	#endif
223	+	}
224	+
225	+	Vector3d getCutoffGroupPosByIindex(int iIndex) {
226	+	#ifdef IS_MPI
227	+	return cgIData.position[iIndex];
228	+	#else
229	+	return cgData.position[iIndex];
230	+	#endif
231	+	}
232	+	Vector3d getCutoffGroupPosByJindex(int jIndex) {
233	+	#ifdef IS_MPI
234	+	return cgJData.position[jIndex];
235	+	#else
236	+	return cgData.position[jIndex];
237	+	#endif
238	+	}
239	+
240	+	DataStorage atomData;
241	+	DataStorage rigidbodyData;
242	+	DataStorage cgData;
243	+	Stats statData;
244	+
245	+	#ifdef IS_MPI
246	+	DataStorage atomIData;
247	+	DataStorage atomJData;
248	+	DataStorage cgIData;
249	+	DataStorage cgJData;
250	+	#endif
251	+
252	+
253	+	private:
254	+	RealType currentTime_;
255	+
256	+	Mat3x3d hmat_;
257	+	Mat3x3d invHmat_;
258	+	RealType orthoTolerance_;
259	+	int orthoRhombic_;
260	+	RealType volume_;
261	+
262	+	RealType chi_;
263	+	RealType integralOfChiDt_;
264	+	Mat3x3d eta_;
265	+	Vector3d COM_;
266	+	Vector3d COMvel_;
267	+	Vector3d COMw_;
268	+	int id_; /**< identification number of the snapshot */
269	+	bool hasCOM_;
270	+	bool hasVolume_;
271	+
272	+	};
273	+
274	+	typedef DataStorage (Snapshot::*DataStoragePointer);
275		}
276		#endif //BRAINS_SNAPSHOT_HPP

Comparing:
trunk/src/brains/Snapshot.hpp (property svn:keywords), Revision 122 by tim, Wed Oct 20 05:52:25 2004 UTC vs.
branches/development/src/brains/Snapshot.hpp (property svn:keywords), Revision 1550 by gezelter, Wed Apr 27 21:49:59 2011 UTC

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