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

Comparing:
trunk/src/brains/Snapshot.hpp (file contents), Revision 316 by tim, Fri Feb 11 22:41:02 2005 UTC vs.
branches/development/src/brains/Snapshot.hpp (file contents), Revision 1562 by gezelter, Thu May 12 17:00:14 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 54 | Line 54
54
55		#include "brains/DataStorage.hpp"
56		#include "brains/Stats.hpp"
57	–	#include "UseTheForce/DarkSide/simulation_interface.h"
57
58	<	namespace oopse{
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:
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	<	Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies),
71	<	currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0) {
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	<	}
82	>	}
83
84	<	Snapshot(int nAtoms, int nRigidbodies, int storageLayout)
85	<	: atomData(nAtoms, storageLayout), rigidbodyData(nRigidbodies, storageLayout),
86	<	currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0) {
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	<	}
101	<
102	<	/** Returns the id of this Snapshot */
103	<	int getID() {
84	<	return id_;
85	<	}
100	>	/** Sets the id of this Snapshot */
101	>	void setID(int id) {
102	>	id_ = id;
103	>	}
104
105	<	/** Sets the id of this Snapshot */
106	<	void setID(int id) {
107	<	id_ = id;
90	<	}
105	>	int getSize() {
106	>	return atomData.getSize() + rigidbodyData.getSize();
107	>	}
108
109	<	int getSize() {
110	<	return atomData.getSize() + rigidbodyData.getSize();
111	<	}
109	>	/** Returns the number of atoms */
110	>	int getNumberOfAtoms() {
111	>	return atomData.getSize();
112	>	}
113
114	<	/** Returns the number of atoms */
115	<	int getNumberOfAtoms() {
116	<	return atomData.getSize();
117	<	}
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 getNumberOfRigidBodies() {
121	<	return rigidbodyData.getSize();
122	<	}
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	<	}
124	>	/** Returns the H-Matrix */
125	>	Mat3x3d getHmat() {
126	>	return hmat_;
127	>	}
128
129	<	/** Sets the H-Matrix */
130	<	void setHmat(const Mat3x3d& m);
129	>	/** Sets the H-Matrix */
130	>	void setHmat(const Mat3x3d& m);
131
132	<	double getVolume() {
133	<	return hmat_.determinant();
134	<	}
132	>	RealType getVolume() {
133	>	if (hasVolume_){
134	>	return volume_;
135	>	}else{
136	>	return hmat_.determinant();
137	>	}
138	>	}
139
140	<	/** Returns the inverse H-Matrix */
141	<	Mat3x3d getInvHmat() {
142	<	return invHmat_;
143	<	}
140	>	void setVolume(RealType volume){
141	>	hasVolume_=true;
142	>	volume_ = volume;
143	>	}
144
145	<	/** Wrapping the vector according to periodic boundary condition*/
146	<	void wrapVector(Vector3d& v);
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	+	/** Scaling a vector to multiples of the periodic box */
153	+	Vector3d scaleVector(Vector3d &v);
154	+
155	+
156	+	Vector3d getCOM();
157	+	Vector3d getCOMvel();
158	+	Vector3d getCOMw();
159
160	<	double getTime() {
161	<	return currentTime_;
162	<	}
160	>	RealType getTime() {
161	>	return currentTime_;
162	>	}
163
164	<	void increaseTime(double dt) {
165	<	setTime(getTime() + dt);
166	<	}
164	>	void increaseTime(RealType dt) {
165	>	setTime(getTime() + dt);
166	>	}
167
168	<	void setTime(double time) {
169	<	currentTime_ =time;
170	<	//time at statData is redundant
171	<	statData[Stats::TIME] = currentTime_;
172	<	}
168	>	void setTime(RealType time) {
169	>	currentTime_ =time;
170	>	//time at statData is redundant
171	>	statData[Stats::TIME] = currentTime_;
172	>	}
173
174	<	double getChi() {
175	<	return chi_;
176	<	}
174	>	RealType getChi() {
175	>	return chi_;
176	>	}
177
178	<	void setChi(double chi) {
179	<	chi_ = chi;
180	<	}
178	>	void setChi(RealType chi) {
179	>	chi_ = chi;
180	>	}
181
182	<	double getIntegralOfChiDt() {
183	<	return integralOfChiDt_;
184	<	}
182	>	RealType getIntegralOfChiDt() {
183	>	return integralOfChiDt_;
184	>	}
185
186	<	void setIntegralOfChiDt(double integralOfChiDt) {
187	<	integralOfChiDt_ = integralOfChiDt;
188	<	}
186	>	void setIntegralOfChiDt(RealType integralOfChiDt) {
187	>	integralOfChiDt_ = integralOfChiDt;
188	>	}
189
157	–	Mat3x3d getEta() {
158	–	return eta_;
159	–	}
190
191	<	void setEta(const Mat3x3d& eta) {
192	<	eta_ = eta;
193	<	}
164	<
165	<	DataStorage atomData;
166	<	DataStorage rigidbodyData;
167	<	Stats statData;
168	<
169	<	private:
170	<	double currentTime_;
191	>	void setOrthoTolerance(RealType orthoTolerance) {
192	>	orthoTolerance_ = orthoTolerance;
193	>	}
194
195	<	Mat3x3d hmat_;
196	<	Mat3x3d invHmat_;
197	<	int orthoRhombic_;
195	>	Mat3x3d getEta() {
196	>	return eta_;
197	>	}
198
199	<	double chi_;
200	<	double integralOfChiDt_;
201	<	Mat3x3d eta_;
199	>	void setEta(const Mat3x3d& eta) {
200	>	eta_ = eta;
201	>	}
202	>
203	>	bool hasCOM() {
204	>	return hasCOM_;
205	>	}
206	>
207	>	void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
208	>	COM_ = COM;
209	>	COMvel_ = COMvel;
210	>	COMw_ = COMw;
211	>	hasCOM_ = true;
212	>	}
213	>
214	>	DataStorage atomData;
215	>	DataStorage rigidbodyData;
216	>	DataStorage cgData;
217	>	Stats statData;
218	>
219	>	private:
220	>	RealType currentTime_;
221	>
222	>	Mat3x3d hmat_;
223	>	Mat3x3d invHmat_;
224	>	RealType orthoTolerance_;
225	>	int orthoRhombic_;
226	>	RealType volume_;
227	>
228	>	RealType chi_;
229	>	RealType integralOfChiDt_;
230	>	Mat3x3d eta_;
231	>	Vector3d COM_;
232	>	Vector3d COMvel_;
233	>	Vector3d COMw_;
234	>	int id_; /**< identification number of the snapshot */
235	>	bool hasCOM_;
236	>	bool hasVolume_;
237
238	<	int id_; /**< identification number of the snapshot */
181	<	};
238	>	};
239
240	<	typedef DataStorage (Snapshot::*DataStoragePointer);
240	>	typedef DataStorage (Snapshot::*DataStoragePointer);
241		}
242		#endif //BRAINS_SNAPSHOT_HPP

Comparing:
trunk/src/brains/Snapshot.hpp (property svn:keywords), Revision 316 by tim, Fri Feb 11 22:41:02 2005 UTC vs.
branches/development/src/brains/Snapshot.hpp (property svn:keywords), Revision 1562 by gezelter, Thu May 12 17:00:14 2011 UTC

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