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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 1709 by gezelter, Tue May 15 13:04:08 2012 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]  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	<	*/
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
#	Line 54 | Line 55
55
56		#include "brains/DataStorage.hpp"
57		#include "brains/Stats.hpp"
57	–	#include "UseTheForce/DarkSide/simulation_interface.h"
58
59	<	namespace oopse{
59	>	namespace OpenMD{
60
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:
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) : atomData(nAtoms), rigidbodyData(nRigidbodies),
72	<	currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0) {
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	<	}
83	>	}
84
85	<
86	<	/** Returns the id of this Snapshot */
87	<	int getID() {
88	<	return id_;
89	<	}
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	<	/** Sets the id of this Snapshot */
102	<	void setID(int id) {
103	<	id_ = id;
104	<	}
101	>	/** Sets the id of this Snapshot */
102	>	void setID(int id) {
103	>	id_ = id;
104	>	}
105
106	<	int getSize() {
107	<	return atomData.getSize() + rigidbodyData.getSize();
108	<	}
106	>	int getSize() {
107	>	return atomData.getSize() + rigidbodyData.getSize();
108	>	}
109
110	<	/** Returns the number of atoms */
111	<	int getNumberOfAtoms() {
112	<	return atomData.getSize();
113	<	}
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	<	}
115	>	/** Returns the number of rigid bodies */
116	>	int getNumberOfRigidBodies() {
117	>	return rigidbodyData.getSize();
118	>	}
119
120	<	/** Returns the H-Matrix */
121	<	Mat3x3d getHmat() {
122	<	return hmat_;
123	<	}
120	>	/** Returns the number of rigid bodies */
121	>	int getNumberOfCutoffGroups() {
122	>	return cgData.getSize();
123	>	}
124
125	<	/** Sets the H-Matrix */
126	<	void setHmat(const Mat3x3d& m);
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	<	double getVolume() {
134	<	return hmat_.determinant();
135	<	}
133	>	RealType getVolume() {
134	>	if (hasVolume_){
135	>	return volume_;
136	>	}else{
137	>	return hmat_.determinant();
138	>	}
139	>	}
140
141	<	/** Returns the inverse H-Matrix */
142	<	Mat3x3d getInvHmat() {
143	<	return invHmat_;
144	<	}
141	>	void setVolume(RealType volume){
142	>	hasVolume_=true;
143	>	volume_ = volume;
144	>	}
145
146	<	/** Wrapping the vector according to periodic boundary condition*/
147	<	void wrapVector(Vector3d& v);
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	+
156	+
157	+	Vector3d getCOM();
158	+	Vector3d getCOMvel();
159	+	Vector3d getCOMw();
160
161	<	double getTime() {
162	<	return currentTime_;
163	<	}
161	>	RealType getTime() {
162	>	return currentTime_;
163	>	}
164
165	<	void increaseTime(double dt) {
166	<	setTime(getTime() + dt);
167	<	}
165	>	void increaseTime(RealType dt) {
166	>	setTime(getTime() + dt);
167	>	}
168
169	<	void setTime(double time) {
170	<	currentTime_ =time;
171	<	//time at statData is redundant
172	<	statData[Stats::TIME] = currentTime_;
173	<	}
169	>	void setTime(RealType time) {
170	>	currentTime_ =time;
171	>	//time at statData is redundant
172	>	statData[Stats::TIME] = currentTime_;
173	>	}
174
175	<	double getChi() {
176	<	return chi_;
177	<	}
175	>	RealType getChi() {
176	>	return chi_;
177	>	}
178
179	<	void setChi(double chi) {
180	<	chi_ = chi;
181	<	}
179	>	void setChi(RealType chi) {
180	>	chi_ = chi;
181	>	}
182
183	<	double getIntegralOfChiDt() {
184	<	return integralOfChiDt_;
185	<	}
183	>	RealType getIntegralOfChiDt() {
184	>	return integralOfChiDt_;
185	>	}
186
187	<	void setIntegralOfChiDt(double integralOfChiDt) {
188	<	integralOfChiDt_ = integralOfChiDt;
189	<	}
187	>	void setIntegralOfChiDt(RealType integralOfChiDt) {
188	>	integralOfChiDt_ = integralOfChiDt;
189	>	}
190
152	–	Mat3x3d getEta() {
153	–	return eta_;
154	–	}
191
192	<	void setEta(const Mat3x3d& eta) {
193	<	eta_ = eta;
194	<	}
159	<
160	<	DataStorage atomData;
161	<	DataStorage rigidbodyData;
162	<	Stats statData;
163	<
164	<	private:
165	<	double currentTime_;
192	>	void setOrthoTolerance(RealType orthoTolerance) {
193	>	orthoTolerance_ = orthoTolerance;
194	>	}
195
196	<	Mat3x3d hmat_;
197	<	Mat3x3d invHmat_;
198	<	int orthoRhombic_;
196	>	Mat3x3d getEta() {
197	>	return eta_;
198	>	}
199
200	<	double chi_;
201	<	double integralOfChiDt_;
202	<	Mat3x3d eta_;
174	<
175	<	int id_; /**< identification number of the snapshot */
176	<	};
200	>	void setEta(const Mat3x3d& eta) {
201	>	eta_ = eta;
202	>	}
203
204	<	typedef DataStorage (Snapshot::*DataStoragePointer);
204	>	Mat3x3d getTau() {
205	>	return tau_;
206	>	}
207	>
208	>	void setTau(const Mat3x3d& tau) {
209	>	tau_ = tau;
210	>	}
211	>
212	>	bool hasCOM() {
213	>	return hasCOM_;
214	>	}
215	>
216	>	void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
217	>	COM_ = COM;
218	>	COMvel_ = COMvel;
219	>	COMw_ = COMw;
220	>	hasCOM_ = true;
221	>	}
222	>
223	>	DataStorage atomData;
224	>	DataStorage rigidbodyData;
225	>	DataStorage cgData;
226	>	Stats statData;
227	>
228	>	private:
229	>	RealType currentTime_;
230	>
231	>	Mat3x3d hmat_;
232	>	Mat3x3d invHmat_;
233	>	RealType orthoTolerance_;
234	>	int orthoRhombic_;
235	>	RealType volume_;
236	>
237	>	RealType chi_;
238	>	RealType integralOfChiDt_;
239	>	Mat3x3d eta_;
240	>	Vector3d COM_;
241	>	Vector3d COMvel_;
242	>	Vector3d COMw_;
243	>	int id_; /**< identification number of the snapshot */
244	>	bool hasCOM_;
245	>	bool hasVolume_;
246	>	Mat3x3d tau_;
247	>	};
248	>
249	>	typedef DataStorage (Snapshot::*DataStoragePointer);
250		}
251		#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 1709 by gezelter, Tue May 15 13:04:08 2012 UTC

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