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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 1715 by gezelter, Tue May 22 21:55:31 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:
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) {
61	>	struct FrameData {
62	>	int id;                   /**< identification number of the snapshot */
63	>	RealType currentTime;     /**< current time */
64	>	Mat3x3d hmat;             /**< axes of the periodic box in matrix form */
65	>	Mat3x3d invHmat;          /**< the inverse of the Hmat matrix */
66	>	bool orthoRhombic;        /**< is this an orthorhombic periodic box? */
67	>	RealType volume;          /**< total volume of this frame */
68	>	RealType pressure;        /**< pressure of this frame */
69	>	RealType totalEnergy;     /**< total energy of this frame */
70	>	RealType kineticEnergy;   /**< kinetic energy of this frame */
71	>	RealType potentialEnergy; /**< potential energy of this frame */
72	>	RealType temperature;     /**< temperature of this frame */
73	>	RealType chi;             /**< thermostat velocity */
74	>	RealType integralOfChiDt; /**< the actual thermostat */
75	>	RealType electronicTemperature; /**< temperature of the electronic degrees of freedom */
76	>	RealType chiQ;            /**< fluctuating charge thermostat velocity */
77	>	RealType integralOfChiQDt; /**< the actual fluctuating charge thermostat */
78	>	Mat3x3d eta;              /**< barostat matrix */
79	>	Vector3d COM;             /**< location of center of mass */
80	>	Vector3d COMvel;          /**< system center of mass velocity */
81	>	Vector3d COMw;            /**< system center of mass angular velocity */
82	>	Mat3x3d tau;              /**< stress tensor */
83	>	Mat3x3d pressureTensor;   /**< pressure tensor */
84	>	Vector3d systemDipole;    /**< total system dipole moment */
85	>	};
86
74	–	}
87
88	+	/**
89	+	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
90	+	* @brief Snapshot class is a repository class for storing dynamic data during
91	+	*  Simulation
92	+	* Every snapshot class will contain one DataStorage for atoms and one DataStorage
93	+	*  for rigid bodies.
94	+	*/
95	+	class Snapshot {
96	+	public:
97
98	<	/** Returns the id of this Snapshot */
99	<	int getID() {
100	<	return id_;
101	<	}
98	>	Snapshot(int nAtoms, int nRigidbodies,
99	>	int nCutoffGroups) : atomData(nAtoms),
100	>	rigidbodyData(nRigidbodies),
101	>	cgData(nCutoffGroups, DataStorage::dslPosition),
102	>	orthoTolerance_(1e-6), hasCOM_(false), hasVolume_(false){
103	>
104	>	frameData.id = -1;
105	>	frameData.currentTime = 0;
106	>	frameData.hmat = Mat3x3d(0.0);
107	>	frameData.invHmat = Mat3x3d(0.0);
108	>	frameData.orthoRhombic = false;
109	>	frameData.volume = 0.0;
110	>	frameData.pressure = 0.0;
111	>	frameData.totalEnergy = 0.0;
112	>	frameData.kineticEnergy = 0.0;
113	>	frameData.potentialEnergy = 0.0;
114	>	frameData.temperature = 0.0;
115	>	frameData.chi = 0.0;
116	>	frameData.integralOfChiDt = 0.0;
117	>	frameData.electronicTemperature = 0.0;
118	>	frameData.chiQ = 0.0;
119	>	frameData.integralOfChiQDt = 0.0;
120	>	frameData.eta = Mat3x3d(0.0);
121	>	frameData.COM = V3Zero;
122	>	frameData.COMvel = V3Zero;
123	>	frameData.COMw = V3Zero;
124	>	frameData.tau = Mat3x3d(0.0);
125	>	frameData.pressureTensor = Mat3x3d(0.0);
126	>	frameData.systemDipole = V3Zero;
127	>	}
128
129	<	/** Sets the id of this Snapshot */
130	<	void setID(int id) {
131	<	id_ = id;
132	<	}
129	>	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
130	>	int storageLayout) : atomData(nAtoms, storageLayout),
131	>	rigidbodyData(nRigidbodies, storageLayout),
132	>	cgData(nCutoffGroups, DataStorage::dslPosition),
133	>	orthoTolerance_(1e-6),
134	>	hasCOM_(false),
135	>	hasVolume_(false) {
136	>	frameData.id = -1;
137	>	frameData.currentTime = 0;
138	>	frameData.hmat = Mat3x3d(0.0);
139	>	frameData.invHmat = Mat3x3d(0.0);
140	>	frameData.orthoRhombic = false;
141	>	frameData.volume = 0.0;
142	>	frameData.pressure = 0.0;
143	>	frameData.totalEnergy = 0.0;
144	>	frameData.kineticEnergy = 0.0;
145	>	frameData.potentialEnergy = 0.0;
146	>	frameData.temperature = 0.0;
147	>	frameData.chi = 0.0;
148	>	frameData.integralOfChiDt = 0.0;
149	>	frameData.electronicTemperature = 0.0;
150	>	frameData.chiQ = 0.0;
151	>	frameData.integralOfChiQDt = 0.0;
152	>	frameData.eta = Mat3x3d(0.0);
153	>	frameData.COM = V3Zero;
154	>	frameData.COMvel = V3Zero;
155	>	frameData.COMw = V3Zero;
156	>	frameData.tau = Mat3x3d(0.0);
157	>	frameData.pressureTensor = Mat3x3d(0.0);
158	>	frameData.systemDipole = V3Zero;
159	>	}
160	>
161	>	/** Returns the id of this Snapshot */
162	>	int getID() {
163	>	return frameData.id;
164	>	}
165
166	<	int getSize() {
167	<	return atomData.getSize() + rigidbodyData.getSize();
168	<	}
166	>	/** Sets the id of this Snapshot */
167	>	void setID(int id) {
168	>	frameData.id = id;
169	>	}
170
171	<	/** Returns the number of atoms */
172	<	int getNumberOfAtoms() {
173	<	return atomData.getSize();
94	<	}
171	>	int getSize() {
172	>	return atomData.getSize() + rigidbodyData.getSize();
173	>	}
174
175	<	/** Returns the number of rigid bodies */
176	<	int getNumberOfRigidBodies() {
177	<	return rigidbodyData.getSize();
178	<	}
175	>	/** Returns the number of atoms */
176	>	int getNumberOfAtoms() {
177	>	return atomData.getSize();
178	>	}
179
180	<	/** Returns the H-Matrix */
181	<	Mat3x3d getHmat() {
182	<	return hmat_;
183	<	}
180	>	/** Returns the number of rigid bodies */
181	>	int getNumberOfRigidBodies() {
182	>	return rigidbodyData.getSize();
183	>	}
184
185	<	/** Sets the H-Matrix */
186	<	void setHmat(const Mat3x3d& m);
185	>	/** Returns the number of rigid bodies */
186	>	int getNumberOfCutoffGroups() {
187	>	return cgData.getSize();
188	>	}
189	>
190	>	/** Returns the H-Matrix */
191	>	Mat3x3d getHmat() {
192	>	return frameData.hmat;
193	>	}
194	>
195	>	/** Sets the H-Matrix */
196	>	void setHmat(const Mat3x3d& m);
197
198	<	double getVolume() {
199	<	return hmat_.determinant();
200	<	}
198	>	RealType getVolume() {
199	>	if (hasVolume_){
200	>	return frameData.volume;
201	>	}else{
202	>	return frameData.hmat.determinant();
203	>	}
204	>	}
205
206	<	/** Returns the inverse H-Matrix */
207	<	Mat3x3d getInvHmat() {
208	<	return invHmat_;
209	<	}
206	>	void setVolume(RealType volume){
207	>	hasVolume_=true;
208	>	frameData.volume = volume;
209	>	}
210
211	<	/** Wrapping the vector according to periodic boundary condition*/
212	<	void wrapVector(Vector3d& v);
211	>	/** Returns the inverse H-Matrix */
212	>	Mat3x3d getInvHmat() {
213	>	return frameData.invHmat;
214	>	}
215
216	+	/** Wrapping the vector according to periodic boundary condition*/
217	+	void wrapVector(Vector3d& v);
218	+	/** Scaling a vector to multiples of the periodic box */
219	+	Vector3d scaleVector(Vector3d &v);
220	+
221	+
222	+	Vector3d getCOM();
223	+	Vector3d getCOMvel();
224	+	Vector3d getCOMw();
225
226	<	double getTime() {
227	<	return currentTime_;
228	<	}
226	>	RealType getTime() {
227	>	return frameData.currentTime;
228	>	}
229
230	<	void increaseTime(double dt) {
231	<	setTime(getTime() + dt);
232	<	}
230	>	void increaseTime(RealType dt) {
231	>	setTime(getTime() + dt);
232	>	}
233
234	<	void setTime(double time) {
235	<	currentTime_ =time;
236	<	//time at statData is redundant
237	<	statData[Stats::TIME] = currentTime_;
238	<	}
234	>	void setTime(RealType time) {
235	>	frameData.currentTime =time;
236	>	//time at statData is redundant
237	>	statData[Stats::TIME] = frameData.currentTime;
238	>	}
239
240	<	double getChi() {
241	<	return chi_;
242	<	}
240	>	RealType getChi() {
241	>	return frameData.chi;
242	>	}
243
244	<	void setChi(double chi) {
245	<	chi_ = chi;
246	<	}
244	>	void setChi(RealType chi) {
245	>	frameData.chi = chi;
246	>	}
247
248	<	double getIntegralOfChiDt() {
249	<	return integralOfChiDt_;
250	<	}
248	>	RealType getIntegralOfChiDt() {
249	>	return frameData.integralOfChiDt;
250	>	}
251
252	<	void setIntegralOfChiDt(double integralOfChiDt) {
253	<	integralOfChiDt_ = integralOfChiDt;
254	<	}
252	>	void setIntegralOfChiDt(RealType integralOfChiDt) {
253	>	frameData.integralOfChiDt = integralOfChiDt;
254	>	}
255
256	<	Mat3x3d getEta() {
257	<	return eta_;
258	<	}
256	>	RealType getChiElectronic() {
257	>	return frameData.chiQ;
258	>	}
259
260	<	void setEta(const Mat3x3d& eta) {
261	<	eta_ = eta;
262	<	}
159	<
160	<	DataStorage atomData;
161	<	DataStorage rigidbodyData;
162	<	Stats statData;
163	<
164	<	private:
165	<	double currentTime_;
260	>	void setChiElectronic(RealType chiQ) {
261	>	frameData.chiQ = chiQ;
262	>	}
263
264	<	Mat3x3d hmat_;
265	<	Mat3x3d invHmat_;
266	<	int orthoRhombic_;
264	>	RealType getIntegralOfChiElectronicDt() {
265	>	return frameData.integralOfChiQDt;
266	>	}
267
268	<	double chi_;
269	<	double integralOfChiDt_;
270	<	Mat3x3d eta_;
268	>	void setIntegralOfChiElectronicDt(RealType integralOfChiQDt) {
269	>	frameData.integralOfChiQDt = integralOfChiQDt;
270	>	}
271
175	–	int id_; /**< identification number of the snapshot */
176	–	};
272
273	<	typedef DataStorage (Snapshot::*DataStoragePointer);
273	>	void setOrthoTolerance(RealType orthoTolerance) {
274	>	orthoTolerance_ = orthoTolerance;
275	>	}
276	>
277	>	Mat3x3d getEta() {
278	>	return frameData.eta;
279	>	}
280	>
281	>	void setEta(const Mat3x3d& eta) {
282	>	frameData.eta = eta;
283	>	}
284	>
285	>	Mat3x3d getTau() {
286	>	return frameData.tau;
287	>	}
288	>
289	>	void setTau(const Mat3x3d& tau) {
290	>	frameData.tau = tau;
291	>	}
292	>
293	>	bool hasCOM() {
294	>	return hasCOM_;
295	>	}
296	>
297	>	void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
298	>	frameData.COM = COM;
299	>	frameData.COMvel = COMvel;
300	>	frameData.COMw = COMw;
301	>	hasCOM_ = true;
302	>	}
303	>
304	>	DataStorage atomData;
305	>	DataStorage rigidbodyData;
306	>	DataStorage cgData;
307	>	FrameData frameData;
308	>	Stats statData;
309	>
310	>	private:
311	>	RealType orthoTolerance_;
312	>	bool hasCOM_;
313	>	bool hasVolume_;
314	>	};
315	>
316	>	typedef DataStorage (Snapshot::*DataStoragePointer);
317		}
318		#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 1715 by gezelter, Tue May 22 21:55:31 2012 UTC

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