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

Comparing:
trunk/src/brains/Snapshot.hpp (file contents), Revision 146 by tim, Fri Oct 22 23:09:57 2004 UTC vs.
branches/development/src/brains/Snapshot.hpp (file contents), Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC

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1		/*
2	<	* Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
3	<	*
4	<	* Contact: oopse@oopse.org
5	<	*
6	<	* This program is free software; you can redistribute it and/or
7	<	* modify it under the terms of the GNU Lesser General Public License
8	<	* as published by the Free Software Foundation; either version 2.1
9	<	* of the License, or (at your option) any later version.
10	<	* All we ask is that proper credit is given for our work, which includes
11	<	* - but is not limited to - adding the above copyright notice to the beginning
12	<	* of your source code files, and to any copyright notice that you may distribute
13	<	* with programs based on this work.
14	<	*
15	<	* This program is distributed in the hope that it will be useful,
16	<	* but WITHOUT ANY WARRANTY; without even the implied warranty of
17	<	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18	<	* GNU Lesser General Public License for more details.
19	<	*
20	<	* You should have received a copy of the GNU Lesser General Public License
21	<	* along with this program; if not, write to the Free Software
22	<	* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4	+	* The University of Notre Dame grants you ("Licensee") a
5	+	* non-exclusive, royalty free, license to use, modify and
6	+	* redistribute this software in source and binary code form, provided
7	+	* that the following conditions are met:
8	+	*
9	+	* 1. Redistributions of source code must retain the above copyright
10	+	*    notice, this list of conditions and the following disclaimer.
11	+	*
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.
16	+	*
17	+	* This software is provided "AS IS," without a warranty of any
18	+	* kind. All express or implied conditions, representations and
19	+	* warranties, including any implied warranty of merchantability,
20	+	* fitness for a particular purpose or non-infringement, are hereby
21	+	* excluded.  The University of Notre Dame and its licensors shall not
22	+	* be liable for any damages suffered by licensee as a result of
23	+	* using, modifying or distributing the software or its
24	+	* derivatives. In no event will the University of Notre Dame or its
25	+	* licensors be liable for any lost revenue, profit or data, or for
26	+	* direct, indirect, special, consequential, incidental or punitive
27	+	* damages, however caused and regardless of the theory of liability,
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		*/
25	–
26	–	/**
27	–	* @file Snapshot.hpp
28	–	* @author tlin
29	–	* @date 10/20/2004
30	–	* @time 23:56am
31	–	* @version 1.0
32	–	*/
42
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
53
54		#include <vector>
55
56	<	#include "math/Vector3.hpp"
57	<	#include "math/SquareMatrix3.hpp"
56	>	#include "brains/DataStorage.hpp"
57	>	#include "brains/Stats.hpp"
58
59	<	using namespace std;
59	>	namespace OpenMD{
60
61	<	namespace oopse{
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
46	–	//forward declaration
47	–	class Snapshot;
48	–	class SnapshotManager;
87
88	<	/**
89	<	* @struct DataStorage
90	<	* @brief
91	<	*/
92	<	class DataStorage {
93	<	public:
94	<	DataStorage() {};
95	<	DataStorage(size_t size);
96	<	void resize(size_t size);
59	<	void reserve(size_t size);
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	<	//friend Snapshot;
99	<	//friend SnapshotManager;
100	<	//private:
101	<	vector<Vector3d> position;               /** position array */
102	<	vector<Vector3d> velocity;               /** velocity array */
103	<	vector<RotMat3x3d> Amat;            /** rotation matrix array */
104	<	vector<Vector3d> angularMomentum;/** velocity array */
105	<	vector<Vector3d> ul;                /** the lab frame unit vector array*/
106	<	vector<double> zAngle;              /** z -angle array */
107	<	vector<Vector3d> force;               /** force array */
108	<	vector<Vector3d> torque;               /** torque array */
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	<	};
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	<	/**
167	<	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
168	<	* @brief Snapshot class is a repository class for storing dynamic data during
169	<	*  Simulation
170	<	* Every snapshot class will contain one DataStorage  for atoms and one DataStorage
171	<	*  for rigid bodies.
172	<	* @see SimData
173	<	*/
174	<	class Snapshot {
175	<	public:
166	>	/** Sets the id of this Snapshot */
167	>	void setID(int id) {
168	>	frameData.id = id;
169	>	}
170	>
171	>	int getSize() {
172	>	return atomData.getSize() + rigidbodyData.getSize();
173	>	}
174	>
175	>	/** Returns the number of atoms */
176	>	int getNumberOfAtoms() {
177	>	return atomData.getSize();
178	>	}
179	>
180	>	/** Returns the number of rigid bodies */
181	>	int getNumberOfRigidBodies() {
182	>	return rigidbodyData.getSize();
183	>	}
184	>
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	<	Snapshot() {}
199	<	Snapshot(int i) {
198	>	RealType getVolume() {
199	>	if (hasVolume_){
200	>	return frameData.volume;
201	>	}else{
202	>	return frameData.hmat.determinant();
203	>	}
204	>	}
205
206	<	}
206	>	void setVolume(RealType volume){
207	>	hasVolume_=true;
208	>	frameData.volume = volume;
209	>	}
210
211	<	Snapshot(const Snapshot& s);
211	>	/** Returns the inverse H-Matrix */
212	>	Mat3x3d getInvHmat() {
213	>	return frameData.invHmat;
214	>	}
215
216	<	Snapshot& operator =(const Snapshot& s);
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	<	/** Returns the id of this Snapshot */
227	<	int getID() {
228	<	return id_;
98	<	}
226	>	RealType getTime() {
227	>	return frameData.currentTime;
228	>	}
229
230	<	/** Sets the id of this Snapshot */
231	<	void setID(int id) {
232	<	id_ = id;
103	<	}
230	>	void increaseTime(RealType dt) {
231	>	setTime(getTime() + dt);
232	>	}
233
234	<	//template<typename T>
235	<	//static typename T::ElemPointerType getArrayPointer(vector<T>& v) {
236	<	//    return v[0]->getArrayPointer();
237	<	//}
234	>	void setTime(RealType time) {
235	>	frameData.currentTime =time;
236	>	//time at statData is redundant
237	>	statData[Stats::TIME] = frameData.currentTime;
238	>	}
239
240	<	static double* getArrayPointer(vector<Vector3d>& v) {
241	<	assert(v.size() > 0);
242	<	return v[0].getArrayPointer();
243	<	}
240	>	RealType getChi() {
241	>	return frameData.chi;
242	>	}
243	>
244	>	void setChi(RealType chi) {
245	>	frameData.chi = chi;
246	>	}
247	>
248	>	RealType getIntegralOfChiDt() {
249	>	return frameData.integralOfChiDt;
250	>	}
251	>
252	>	void setIntegralOfChiDt(RealType integralOfChiDt) {
253	>	frameData.integralOfChiDt = integralOfChiDt;
254	>	}
255
256	<	static double* getArrayPointer(vector<RotMat3x3d>& v) {
257	<	assert(v.size() > 0);
258	<	return v[0].getArrayPointer();
259	<	}
256	>	RealType getChiElectronic() {
257	>	return frameData.chiQ;
258	>	}
259	>
260	>	void setChiElectronic(RealType chiQ) {
261	>	frameData.chiQ = chiQ;
262	>	}
263	>
264	>	RealType getIntegralOfChiElectronicDt() {
265	>	return frameData.integralOfChiQDt;
266	>	}
267	>
268	>	void setIntegralOfChiElectronicDt(RealType integralOfChiQDt) {
269	>	frameData.integralOfChiQDt = integralOfChiQDt;
270	>	}
271
120	–	static double* getArrayPointer(vector<double>& v) {
121	–	assert(v.size() > 0);
122	–	return &(v[0]);
123	–	}
124	–
125	–	/** */
126	–	void resize(size_t size);
272
273	+	void setOrthoTolerance(RealType orthoTolerance) {
274	+	orthoTolerance_ = orthoTolerance;
275	+	}
276
277	<	/** */
278	<	void reserve(size_t size);
277	>	Mat3x3d getEta() {
278	>	return frameData.eta;
279	>	}
280
281	<	DataStorage atomData;
282	<	DataStorage rigidbodyData;
281	>	void setEta(const Mat3x3d& eta) {
282	>	frameData.eta = eta;
283	>	}
284
285	<	friend class SnapshotManager;
286	<	private:
285	>	Mat3x3d getTau() {
286	>	return frameData.tau;
287	>	}
288	>
289	>	void setTau(const Mat3x3d& tau) {
290	>	frameData.tau = tau;
291	>	}
292
293	<	int id_; /**< identification number of the snapshot */
294	<	};
293	>	bool hasCOM() {
294	>	return hasCOM_;
295	>	}
296
297	<	typedef DataStorage* (Snapshot::*DataStoragePointer);
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 146 by tim, Fri Oct 22 23:09:57 2004 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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