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

Comparing:
trunk/src/brains/Snapshot.hpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/Snapshot.hpp (file contents), Revision 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC

#	Line 1 | Line 1
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
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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	<	*/
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
#	Line 56 | Line 56
56		#include "brains/Stats.hpp"
57		#include "UseTheForce/DarkSide/simulation_interface.h"
58
59	–	namespace oopse{
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:
60	>	namespace OpenMD{
61	>
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	<	Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies),
73	<	currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0) {
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	<	/** Returns the id of this Snapshot */
88	<	int getID() {
89	<	return id_;
90	<	}
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	<	}
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	<	}
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	<	}
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	<	}
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	<	}
121	>	/** Returns the number of rigid bodies */
122	>	int getNumberOfCutoffGroups() {
123	>	return cgData.getSize();
124	>	}
125
126	<	/** Sets the H-Matrix */
127	<	void setHmat(const Mat3x3d& m);
126	>	/** Returns the H-Matrix */
127	>	Mat3x3d getHmat() {
128	>	return hmat_;
129	>	}
130	>
131	>	/** Sets the H-Matrix */
132	>	void setHmat(const Mat3x3d& m);
133
134	<	double getVolume() {
135	<	return hmat_.determinant();
136	<	}
134	>	RealType getVolume() {
135	>	if (hasVolume_){
136	>	return volume_;
137	>	}else{
138	>	return hmat_.determinant();
139	>	}
140	>	}
141
142	<	/** Returns the inverse H-Matrix */
143	<	Mat3x3d getInvHmat() {
144	<	return invHmat_;
145	<	}
142	>	void setVolume(RealType volume){
143	>	hasVolume_=true;
144	>	volume_ = volume;
145	>	}
146
147	<	/** Wrapping the vector according to periodic boundary condition*/
148	<	void wrapVector(Vector3d& v);
147	>	/** Returns the inverse H-Matrix */
148	>	Mat3x3d getInvHmat() {
149	>	return invHmat_;
150	>	}
151
152	+	/** Wrapping the vector according to periodic boundary condition*/
153	+	void wrapVector(Vector3d& v);
154	+	Vector3d getCOM();
155	+	Vector3d getCOMvel();
156	+	Vector3d getCOMw();
157
158	<	double getTime() {
159	<	return currentTime_;
160	<	}
158	>	RealType getTime() {
159	>	return currentTime_;
160	>	}
161
162	<	void increaseTime(double dt) {
163	<	setTime(getTime() + dt);
164	<	}
162	>	void increaseTime(RealType dt) {
163	>	setTime(getTime() + dt);
164	>	}
165
166	<	void setTime(double time) {
167	<	currentTime_ =time;
168	<	//time at statData is redundant
169	<	statData[Stats::TIME] = currentTime_;
170	<	}
166	>	void setTime(RealType time) {
167	>	currentTime_ =time;
168	>	//time at statData is redundant
169	>	statData[Stats::TIME] = currentTime_;
170	>	}
171
172	<	double getChi() {
173	<	return chi_;
174	<	}
172	>	RealType getChi() {
173	>	return chi_;
174	>	}
175
176	<	void setChi(double chi) {
177	<	chi_ = chi;
178	<	}
176	>	void setChi(RealType chi) {
177	>	chi_ = chi;
178	>	}
179
180	<	double getIntegralOfChiDt() {
181	<	return integralOfChiDt_;
182	<	}
180	>	RealType getIntegralOfChiDt() {
181	>	return integralOfChiDt_;
182	>	}
183
184	<	void setIntegralOfChiDt(double integralOfChiDt) {
185	<	integralOfChiDt_ = integralOfChiDt;
186	<	}
184	>	void setIntegralOfChiDt(RealType integralOfChiDt) {
185	>	integralOfChiDt_ = integralOfChiDt;
186	>	}
187
152	–	Mat3x3d getEta() {
153	–	return eta_;
154	–	}
188
189	<	void setEta(const Mat3x3d& eta) {
190	<	eta_ = eta;
191	<	}
189	>	void setOrthoTolerance(RealType orthoTolerance) {
190	>	orthoTolerance_ = orthoTolerance;
191	>	}
192	>
193	>	Mat3x3d getEta() {
194	>	return eta_;
195	>	}
196	>
197	>	void setEta(const Mat3x3d& eta) {
198	>	eta_ = eta;
199	>	}
200	>
201	>	bool hasCOM() {
202	>	return hasCOM_;
203	>	}
204	>
205	>	void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
206	>	COM_ = COM;
207	>	COMvel_ = COMvel;
208	>	COMw_ = COMw;
209	>	hasCOM_ = true;
210	>	}
211	>
212	>	Vector3d getAtomPosByIindex(int iIndex) {
213	>	#ifdef IS_MPI
214	>	return atomIData.position[iIndex];
215	>	#else
216	>	return atomData.position[iIndex];
217	>	#endif
218	>	}
219	>	Vector3d getAtomPosByJindex(int jIndex) {
220	>	#ifdef IS_MPI
221	>	return atomJData.position[jIndex];
222	>	#else
223	>	return atomData.position[jIndex];
224	>	#endif
225	>	}
226	>
227	>	Vector3d getCutoffGroupPosByIindex(int iIndex) {
228	>	#ifdef IS_MPI
229	>	return cgIData.position[iIndex];
230	>	#else
231	>	return cgData.position[iIndex];
232	>	#endif
233	>	}
234	>	Vector3d getCutoffGroupPosByJindex(int jIndex) {
235	>	#ifdef IS_MPI
236	>	return cgJData.position[jIndex];
237	>	#else
238	>	return cgData.position[jIndex];
239	>	#endif
240	>	}
241	>
242	>	DataStorage atomData;
243	>	DataStorage rigidbodyData;
244	>	DataStorage cgData;
245	>	Stats statData;
246	>
247	>	#ifdef IS_MPI
248	>	DataStorage atomIData;
249	>	DataStorage atomJData;
250	>	DataStorage cgIData;
251	>	DataStorage cgJData;
252	>	#endif
253	>
254
255	<	DataStorage atomData;
256	<	DataStorage rigidbodyData;
162	<	Stats statData;
163	<
164	<	private:
165	<	double currentTime_;
255	>	private:
256	>	RealType currentTime_;
257
258	<	Mat3x3d hmat_;
259	<	Mat3x3d invHmat_;
260	<	int orthoRhombic_;
258	>	Mat3x3d hmat_;
259	>	Mat3x3d invHmat_;
260	>	RealType orthoTolerance_;
261	>	int orthoRhombic_;
262	>	RealType volume_;
263
264	<	double chi_;
265	<	double integralOfChiDt_;
266	<	Mat3x3d eta_;
264	>	RealType chi_;
265	>	RealType integralOfChiDt_;
266	>	Mat3x3d eta_;
267	>	Vector3d COM_;
268	>	Vector3d COMvel_;
269	>	Vector3d COMw_;
270	>	int id_; /**< identification number of the snapshot */
271	>	bool hasCOM_;
272	>	bool hasVolume_;
273
274	<	int id_; /**< identification number of the snapshot */
176	<	};
274	>	};
275
276	<	typedef DataStorage (Snapshot::*DataStoragePointer);
276	>	typedef DataStorage (Snapshot::*DataStoragePointer);
277		}
278		#endif //BRAINS_SNAPSHOT_HPP

Comparing:
trunk/src/brains/Snapshot.hpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/Snapshot.hpp (property svn:keywords), Revision 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC

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