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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 1540 by gezelter, Mon Jan 17 21:34:36 2011 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 56 | Line 56
56		#include "brains/Stats.hpp"
57		#include "UseTheForce/DarkSide/simulation_interface.h"
58
59	–	namespace oopse{
59
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
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), id_(-1) {
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		}
85
86	<	Snapshot(int nAtoms, int nRigidbodies, int storageLayout)
87	<	: atomData(nAtoms, storageLayout), rigidbodyData(nRigidbodies, storageLayout),
88	<	currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) {
89	<
90	<	}
91	<
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_;
#	Line 111 | Line 126 | namespace oopse{
126		/** Sets the H-Matrix */
127		void setHmat(const Mat3x3d& m);
128
129	<	double getVolume() {
130	<	return hmat_.determinant();
129	>	RealType getVolume() {
130	>	if (hasVolume_){
131	>	return volume_;
132	>	}else{
133	>	return hmat_.determinant();
134	>	}
135		}
136
137	+	void setVolume(RealType volume){
138	+	hasVolume_=true;
139	+	volume_ = volume;
140	+	}
141	+
142		/** Returns the inverse H-Matrix */
143		Mat3x3d getInvHmat() {
144		return invHmat_;
#	Line 122 | Line 146 | namespace oopse{
146
147		/** Wrapping the vector according to periodic boundary condition*/
148		void wrapVector(Vector3d& v);
149	<
149	>	Vector3d getCOM();
150	>	Vector3d getCOMvel();
151	>	Vector3d getCOMw();
152
153	<	double getTime() {
153	>	RealType getTime() {
154		return currentTime_;
155		}
156
157	<	void increaseTime(double dt) {
157	>	void increaseTime(RealType dt) {
158		setTime(getTime() + dt);
159		}
160
161	<	void setTime(double time) {
161	>	void setTime(RealType time) {
162		currentTime_ =time;
163		//time at statData is redundant
164		statData[Stats::TIME] = currentTime_;
165		}
166
167	<	double getChi() {
167	>	RealType getChi() {
168		return chi_;
169		}
170
171	<	void setChi(double chi) {
171	>	void setChi(RealType chi) {
172		chi_ = chi;
173		}
174
175	<	double getIntegralOfChiDt() {
175	>	RealType getIntegralOfChiDt() {
176		return integralOfChiDt_;
177		}
178
179	<	void setIntegralOfChiDt(double integralOfChiDt) {
179	>	void setIntegralOfChiDt(RealType integralOfChiDt) {
180		integralOfChiDt_ = integralOfChiDt;
181		}
182
183	+
184	+	void setOrthoTolerance(RealType orthoTolerance) {
185	+	orthoTolerance_ = orthoTolerance;
186	+	}
187	+
188		Mat3x3d getEta() {
189		return eta_;
190		}
#	Line 161 | Line 192 | namespace oopse{
192		void setEta(const Mat3x3d& eta) {
193		eta_ = eta;
194		}
195	<
195	>
196	>	bool hasCOM() {
197	>	return hasCOM_;
198	>	}
199	>
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	>	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	+
241	+	#ifdef IS_MPI
242	+	DataStorage atomIData;
243	+	DataStorage atomJData;
244	+	DataStorage cgIData;
245	+	DataStorage cgJData;
246	+	#endif
247	+
248		Stats statData;
249
250		private:
251	<	double currentTime_;
251	>	RealType currentTime_;
252
253		Mat3x3d hmat_;
254		Mat3x3d invHmat_;
255	+	RealType orthoTolerance_;
256		int orthoRhombic_;
257	+	RealType volume_;
258
259	<	double chi_;
260	<	double integralOfChiDt_;
259	>	RealType chi_;
260	>	RealType integralOfChiDt_;
261		Mat3x3d eta_;
262	<
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);

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 1540 by gezelter, Mon Jan 17 21:34:36 2011 UTC

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