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

Comparing:
trunk/src/brains/Snapshot.hpp (file contents), Revision 146 by tim, Fri Oct 22 23:09:57 2004 UTC vs.
branches/development/src/brains/Snapshot.hpp (file contents), Revision 1541 by gezelter, Fri Feb 4 20:04:56 2011 UTC

#	Line 1 | Line 1
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		*/
25	–
26	–	/**
27	–	* @file Snapshot.hpp
28	–	* @author tlin
29	–	* @date 10/20/2004
30	–	* @time 23:56am
31	–	* @version 1.0
32	–	*/
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
52
53		#include <vector>
54
55	<	#include "math/Vector3.hpp"
56	<	#include "math/SquareMatrix3.hpp"
55	>	#include "brains/DataStorage.hpp"
56	>	#include "brains/Stats.hpp"
57	>	#include "UseTheForce/DarkSide/simulation_interface.h"
58
42	–	using namespace std;
59
60	<	namespace oopse{
60	>	namespace OpenMD{
61
62	<	//forward declaration
63	<	class Snapshot;
64	<	class SnapshotManager;
65	<
66	<	/**
67	<	* @struct DataStorage
68	<	* @brief
69	<	*/
70	<	class DataStorage {
55	<	public:
56	<	DataStorage() {};
57	<	DataStorage(size_t size);
58	<	void resize(size_t size);
59	<	void reserve(size_t size);
62	>	/**
63	>	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
64	>	* @brief Snapshot class is a repository class for storing dynamic data during
65	>	*  Simulation
66	>	* Every snapshot class will contain one DataStorage for atoms and one DataStorage
67	>	*  for rigid bodies.
68	>	*/
69	>	class Snapshot {
70	>	public:
71
72	<	//friend Snapshot;
73	<	//friend SnapshotManager;
74	<	//private:
75	<	vector<Vector3d> position;               /** position array */
76	<	vector<Vector3d> velocity;               /** velocity array */
77	<	vector<RotMat3x3d> Amat;            /** rotation matrix array */
78	<	vector<Vector3d> angularMomentum;/** velocity array */
79	<	vector<Vector3d> ul;                /** the lab frame unit vector array*/
80	<	vector<double> zAngle;              /** z -angle array */
81	<	vector<Vector3d> force;               /** force array */
82	<	vector<Vector3d> torque;               /** torque array */
72	>	Snapshot(int nAtoms, int nRigidbodies,
73	>	int nCutoffGroups) : atomData(nAtoms),
74	>	rigidbodyData(nRigidbodies),
75	>	cgData(nCutoffGroups, DataStorage::dslPosition),
76	>	currentTime_(0),
77	>	orthoTolerance_(1e-6),
78	>	orthoRhombic_(0),
79	>	chi_(0.0),
80	>	integralOfChiDt_(0.0),
81	>	eta_(0.0), id_(-1), hasCOM_(false),
82	>	hasVolume_(false), volume_(0.0) {
83
84	<	};
84	>	}
85
86	<	/**
87	<	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
88	<	* @brief Snapshot class is a repository class for storing dynamic data during
89	<	*  Simulation
90	<	* Every snapshot class will contain one DataStorage  for atoms and one DataStorage
91	<	*  for rigid bodies.
92	<	* @see SimData
93	<	*/
94	<	class Snapshot {
95	<	public:
86	>	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
87	>	int storageLayout) : atomData(nAtoms, storageLayout),
88	>	rigidbodyData(nRigidbodies, storageLayout),
89	>	cgData(nCutoffGroups, DataStorage::dslPosition),
90	>	currentTime_(0), orthoTolerance_(1e-6),
91	>	orthoRhombic_(0), chi_(0.0),
92	>	integralOfChiDt_(0.0), eta_(0.0), id_(-1),
93	>	hasCOM_(false), hasVolume_(false),
94	>	volume_(0.0)  {
95	>	}
96	>
97	>	/** Returns the id of this Snapshot */
98	>	int getID() {
99	>	return id_;
100	>	}
101	>
102	>	/** Sets the id of this Snapshot */
103	>	void setID(int id) {
104	>	id_ = id;
105	>	}
106	>
107	>	int getSize() {
108	>	return atomData.getSize() + rigidbodyData.getSize();
109	>	}
110	>
111	>	/** Returns the number of atoms */
112	>	int getNumberOfAtoms() {
113	>	return atomData.getSize();
114	>	}
115	>
116	>	/** Returns the number of rigid bodies */
117	>	int getNumberOfRigidBodies() {
118	>	return rigidbodyData.getSize();
119	>	}
120	>
121	>	/** Returns the H-Matrix */
122	>	Mat3x3d getHmat() {
123	>	return hmat_;
124	>	}
125	>
126	>	/** Sets the H-Matrix */
127	>	void setHmat(const Mat3x3d& m);
128
129	<	Snapshot() {}
130	<	Snapshot(int i) {
129	>	RealType getVolume() {
130	>	if (hasVolume_){
131	>	return volume_;
132	>	}else{
133	>	return hmat_.determinant();
134	>	}
135	>	}
136
137	<	}
137	>	void setVolume(RealType volume){
138	>	hasVolume_=true;
139	>	volume_ = volume;
140	>	}
141
142	<	Snapshot(const Snapshot& s);
142	>	/** Returns the inverse H-Matrix */
143	>	Mat3x3d getInvHmat() {
144	>	return invHmat_;
145	>	}
146
147	<	Snapshot& operator =(const Snapshot& s);
147	>	/** Wrapping the vector according to periodic boundary condition*/
148	>	void wrapVector(Vector3d& v);
149	>	Vector3d getCOM();
150	>	Vector3d getCOMvel();
151	>	Vector3d getCOMw();
152
153	<	/** Returns the id of this Snapshot */
154	<	int getID() {
155	<	return id_;
98	<	}
153	>	RealType getTime() {
154	>	return currentTime_;
155	>	}
156
157	<	/** Sets the id of this Snapshot */
158	<	void setID(int id) {
159	<	id_ = id;
103	<	}
157	>	void increaseTime(RealType dt) {
158	>	setTime(getTime() + dt);
159	>	}
160
161	<	//template<typename T>
162	<	//static typename T::ElemPointerType getArrayPointer(vector<T>& v) {
163	<	//    return v[0]->getArrayPointer();
164	<	//}
161	>	void setTime(RealType time) {
162	>	currentTime_ =time;
163	>	//time at statData is redundant
164	>	statData[Stats::TIME] = currentTime_;
165	>	}
166
167	<	static double* getArrayPointer(vector<Vector3d>& v) {
168	<	assert(v.size() > 0);
169	<	return v[0].getArrayPointer();
170	<	}
167	>	RealType getChi() {
168	>	return chi_;
169	>	}
170	>
171	>	void setChi(RealType chi) {
172	>	chi_ = chi;
173	>	}
174	>
175	>	RealType getIntegralOfChiDt() {
176	>	return integralOfChiDt_;
177	>	}
178	>
179	>	void setIntegralOfChiDt(RealType integralOfChiDt) {
180	>	integralOfChiDt_ = integralOfChiDt;
181	>	}
182
115	–	static double* getArrayPointer(vector<RotMat3x3d>& v) {
116	–	assert(v.size() > 0);
117	–	return v[0].getArrayPointer();
118	–	}
119	–
120	–	static double* getArrayPointer(vector<double>& v) {
121	–	assert(v.size() > 0);
122	–	return &(v[0]);
123	–	}
124	–
125	–	/** */
126	–	void resize(size_t size);
183
184	+	void setOrthoTolerance(RealType orthoTolerance) {
185	+	orthoTolerance_ = orthoTolerance;
186	+	}
187
188	<	/** */
189	<	void reserve(size_t size);
188	>	Mat3x3d getEta() {
189	>	return eta_;
190	>	}
191
192	<	DataStorage atomData;
193	<	DataStorage rigidbodyData;
192	>	void setEta(const Mat3x3d& eta) {
193	>	eta_ = eta;
194	>	}
195
196	<	friend class SnapshotManager;
197	<	private:
196	>	bool hasCOM() {
197	>	return hasCOM_;
198	>	}
199
200	<	int id_; /**< identification number of the snapshot */
201	<	};
200	>	void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
201	>	COM_ = COM;
202	>	COMvel_ = COMvel;
203	>	COMw_ = COMw;
204	>	hasCOM_ = true;
205	>	}
206
207	<	typedef DataStorage* (Snapshot::*DataStoragePointer);
207	>	Vector3d getAtomPosByIindex(int iIndex) {
208	>	#ifdef IS_MPI
209	>	return atomIData.position[iIndex];
210	>	#else
211	>	return atomData.position[iIndex];
212	>	#endif
213	>	}
214	>	Vector3d getAtomPosByJindex(int jIndex) {
215	>	#ifdef IS_MPI
216	>	return atomJData.position[jIndex];
217	>	#else
218	>	return atomData.position[jIndex];
219	>	#endif
220	>	}
221	>
222	>	Vector3d getCutoffGroupPosByIindex(int iIndex) {
223	>	#ifdef IS_MPI
224	>	return cgIData.position[iIndex];
225	>	#else
226	>	return cgData.position[iIndex];
227	>	#endif
228	>	}
229	>	Vector3d getCutoffGroupPosByJindex(int jIndex) {
230	>	#ifdef IS_MPI
231	>	return cgJData.position[jIndex];
232	>	#else
233	>	return cgData.position[jIndex];
234	>	#endif
235	>	}
236	>
237	>	DataStorage atomData;
238	>	DataStorage rigidbodyData;
239	>	DataStorage cgData;
240	>	Stats statData;
241	>
242	>	#ifdef IS_MPI
243	>	DataStorage atomIData;
244	>	DataStorage atomJData;
245	>	DataStorage cgIData;
246	>	DataStorage cgJData;
247	>	#endif
248	>
249	>
250	>	private:
251	>	RealType currentTime_;
252	>
253	>	Mat3x3d hmat_;
254	>	Mat3x3d invHmat_;
255	>	RealType orthoTolerance_;
256	>	int orthoRhombic_;
257	>	RealType volume_;
258	>
259	>	RealType chi_;
260	>	RealType integralOfChiDt_;
261	>	Mat3x3d eta_;
262	>	Vector3d COM_;
263	>	Vector3d COMvel_;
264	>	Vector3d COMw_;
265	>	int id_; /**< identification number of the snapshot */
266	>	bool hasCOM_;
267	>	bool hasVolume_;
268	>
269	>	};
270	>
271	>	typedef DataStorage (Snapshot::*DataStoragePointer);
272		}
273		#endif //BRAINS_SNAPSHOT_HPP

Comparing:
trunk/src/brains/Snapshot.hpp (property svn:keywords), Revision 146 by tim, Fri Oct 22 23:09:57 2004 UTC vs.
branches/development/src/brains/Snapshot.hpp (property svn:keywords), Revision 1541 by gezelter, Fri Feb 4 20:04:56 2011 UTC

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