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

Comparing:
trunk/src/brains/Snapshot.hpp (file contents), Revision 665 by tim, Thu Oct 13 22:26:47 2005 UTC vs.
branches/development/src/brains/Snapshot.hpp (file contents), Revision 1708 by gezelter, Tue May 15 13:02:10 2012 UTC

#	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		/**
#	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
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), id_(-1) {
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		}
84
85	<	Snapshot(int nAtoms, int nRigidbodies, int storageLayout)
86	<	: atomData(nAtoms, storageLayout), rigidbodyData(nRigidbodies, storageLayout),
87	<	currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) {
88	<
89	<	}
90	<
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_;
#	Line 103 | Line 117 | namespace oopse{
117		return rigidbodyData.getSize();
118		}
119
120	+	/** Returns the number of rigid bodies */
121	+	int getNumberOfCutoffGroups() {
122	+	return cgData.getSize();
123	+	}
124	+
125		/** Returns the H-Matrix */
126		Mat3x3d getHmat() {
127		return hmat_;
#	Line 111 | Line 130 | namespace oopse{
130		/** Sets the H-Matrix */
131		void setHmat(const Mat3x3d& m);
132
133	<	double getVolume() {
134	<	return hmat_.determinant();
133	>	RealType getVolume() {
134	>	if (hasVolume_){
135	>	return volume_;
136	>	}else{
137	>	return hmat_.determinant();
138	>	}
139		}
140
141	+	void setVolume(RealType volume){
142	+	hasVolume_=true;
143	+	volume_ = volume;
144	+	}
145	+
146		/** Returns the inverse H-Matrix */
147		Mat3x3d getInvHmat() {
148		return invHmat_;
#	Line 122 | Line 150 | namespace oopse{
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() {
161	>	RealType getTime() {
162		return currentTime_;
163		}
164
165	<	void increaseTime(double dt) {
165	>	void increaseTime(RealType dt) {
166		setTime(getTime() + dt);
167		}
168
169	<	void setTime(double time) {
169	>	void setTime(RealType time) {
170		currentTime_ =time;
171		//time at statData is redundant
172		statData[Stats::TIME] = currentTime_;
173		}
174
175	<	double getChi() {
175	>	RealType getChi() {
176		return chi_;
177		}
178
179	<	void setChi(double chi) {
179	>	void setChi(RealType chi) {
180		chi_ = chi;
181		}
182
183	<	double getIntegralOfChiDt() {
183	>	RealType getIntegralOfChiDt() {
184		return integralOfChiDt_;
185		}
186
187	<	void setIntegralOfChiDt(double integralOfChiDt) {
187	>	void setIntegralOfChiDt(RealType integralOfChiDt) {
188		integralOfChiDt_ = integralOfChiDt;
189		}
190
191	+
192	+	void setOrthoTolerance(RealType orthoTolerance) {
193	+	orthoTolerance_ = orthoTolerance;
194	+	}
195	+
196		Mat3x3d getEta() {
197		return eta_;
198		}
#	Line 161 | Line 200 | namespace oopse{
200		void setEta(const Mat3x3d& eta) {
201		eta_ = eta;
202		}
203	<
203	>
204	>	bool hasCOM() {
205	>	return hasCOM_;
206	>	}
207	>
208	>	void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
209	>	COM_ = COM;
210	>	COMvel_ = COMvel;
211	>	COMw_ = COMw;
212	>	hasCOM_ = true;
213	>	}
214	>
215		DataStorage atomData;
216		DataStorage rigidbodyData;
217	+	DataStorage cgData;
218		Stats statData;
219	<
219	>
220		private:
221	<	double currentTime_;
221	>	RealType currentTime_;
222
223		Mat3x3d hmat_;
224		Mat3x3d invHmat_;
225	+	RealType orthoTolerance_;
226		int orthoRhombic_;
227	+	RealType volume_;
228
229	<	double chi_;
230	<	double integralOfChiDt_;
229	>	RealType chi_;
230	>	RealType integralOfChiDt_;
231		Mat3x3d eta_;
232	<
232	>	Vector3d COM_;
233	>	Vector3d COMvel_;
234	>	Vector3d COMw_;
235		int id_; /**< identification number of the snapshot */
236	+	bool hasCOM_;
237	+	bool hasVolume_;
238	+
239		};
240
241		typedef DataStorage (Snapshot::*DataStoragePointer);

Comparing:
trunk/src/brains/Snapshot.hpp (property svn:keywords), Revision 665 by tim, Thu Oct 13 22:26:47 2005 UTC vs.
branches/development/src/brains/Snapshot.hpp (property svn:keywords), Revision 1708 by gezelter, Tue May 15 13:02:10 2012 UTC

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