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

Comparing:
trunk/src/brains/Snapshot.hpp (file contents), Revision 152 by tim, Tue Oct 26 17:28:53 2004 UTC vs.
branches/development/src/brains/Snapshot.hpp (file contents), Revision 1544 by gezelter, Fri Mar 18 19:31:52 2011 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]  Vardeman & Gezelter, in progress (2009).
40		*/
25	–
26	–	/**
27	–	* @file Snapshot.hpp
28	–	* @author tlin
29	–	* @date 10/20/2004
30	–	* @time 23:56am
31	–	* @version 1.0
32	–	*/
41
42	+	/**
43	+	* @file Snapshot.hpp
44	+	* @author tlin
45	+	* @date 10/20/2004
46	+	* @time 23:56am
47	+	* @version 1.0
48	+	*/
49	+
50		#ifndef BRAINS_SNAPSHOT_HPP
51		#define BRAINS_SNAPSHOT_HPP
52
53		#include <vector>
54
55	<	#include "math/Vector3.hpp"
56	<	#include "math/SquareMatrix3.hpp"
55	>	#include "brains/DataStorage.hpp"
56	>	#include "brains/Stats.hpp"
57	>	#include "UseTheForce/DarkSide/simulation_interface.h"
58
42	–	using namespace std;
59
60	<	namespace oopse{
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
67	+	*  for rigid bodies.
68	+	*/
69	+	class Snapshot {
70	+	public:
71	+
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	<	//forward declaration
85	<	class Snapshot;
86	<	class SnapshotManager;
87	<	class StuntDouble;
84	>	}
85	>
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	<	/**
98	<	* @class DataStorage
99	<	* @warning do not try to insert element into (or ease element from) private member data
100	<	* of DataStorage directly.
56	<	*/
57	<	class DataStorage {
58	<	public:
97	>	/** Returns the id of this Snapshot */
98	>	int getID() {
99	>	return id_;
100	>	}
101
102	<	enum{
103	<	slPosition = 1,
104	<	slVelocity = 2,
105	<	slAmat = 4,
64	<	slAngularMomentum = 8,
65	<	slUnitVector = 16,
66	<	slZAngle = 32,
67	<	slForce = 64,
68	<	slTorque = 128
69	<	};
70	<
71	<	DataStorage(int size);
102	>	/** Sets the id of this Snapshot */
103	>	void setID(int id) {
104	>	id_ = id;
105	>	}
106
107	<	/** return the size of this DataStorage */
108	<	int size();
109	<	void resize(int size);
76	<	void reserve(int size);
107	>	int getSize() {
108	>	return atomData.getSize() + rigidbodyData.getSize();
109	>	}
110
111	<	void move(int source, int num, int target);
112	<	int getStorageLayout();
113	<	void setStorageLayout(int layout);
111	>	/** Returns the number of atoms */
112	>	int getNumberOfAtoms() {
113	>	return atomData.getSize();
114	>	}
115
116	<	double *getArrayPointer(int );
116	>	/** Returns the number of rigid bodies */
117	>	int getNumberOfRigidBodies() {
118	>	return rigidbodyData.getSize();
119	>	}
120
121	<	friend class StuntDouble;
121	>	/** Returns the number of rigid bodies */
122	>	int getNumberOfCutoffGroups() {
123	>	return cgData.getSize();
124	>	}
125
126	<	private:
127	<	int size_;
128	<	int storageLayout_;
129	<	vector<Vector3d> position;               /** position array */
90	<	vector<Vector3d> velocity;               /** velocity array */
91	<	vector<RotMat3x3d> aMat;            /** rotation matrix array */
92	<	vector<Vector3d> angularMomentum;/** velocity array */
93	<	vector<Vector3d> unitVector;                /** the lab frame unit vector array*/
94	<	vector<double> zAngle;              /** z -angle array */
95	<	vector<Vector3d> force;               /** force array */
96	<	vector<Vector3d> torque;               /** torque array */
97	<	};
126	>	/** Returns the H-Matrix */
127	>	Mat3x3d getHmat() {
128	>	return hmat_;
129	>	}
130
131	<	/**
132	<	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
101	<	* @brief Snapshot class is a repository class for storing dynamic data during
102	<	*  Simulation
103	<	* Every snapshot class will contain one DataStorage  for atoms and one DataStorage
104	<	*  for rigid bodies.
105	<	* @see SimData
106	<	*/
107	<	class Snapshot {
108	<	public:
131	>	/** Sets the H-Matrix */
132	>	void setHmat(const Mat3x3d& m);
133
134	<	Snapshot(int nAtoms, int nRigidbodies) {
135	<	atomData.resize(nAtoms);
136	<	rigidbodyData.resize(nRigidbodies);
137	<	}
134	>	RealType getVolume() {
135	>	if (hasVolume_){
136	>	return volume_;
137	>	}else{
138	>	return hmat_.determinant();
139	>	}
140	>	}
141
142	<	Snapshot(const Snapshot& s);
142	>	void setVolume(RealType volume){
143	>	hasVolume_=true;
144	>	volume_ = volume;
145	>	}
146
147	<	Snapshot& operator =(const Snapshot& s);
147	>	/** Returns the inverse H-Matrix */
148	>	Mat3x3d getInvHmat() {
149	>	return invHmat_;
150	>	}
151	>
152	>	/** Wrapping the vector according to periodic boundary condition*/
153	>	void wrapVector(Vector3d& v);
154	>	Vector3d getCOM();
155	>	Vector3d getCOMvel();
156	>	Vector3d getCOMw();
157
158	<	/** Returns the id of this Snapshot */
159	<	int getID() {
160	<	return id_;
122	<	}
158	>	RealType getTime() {
159	>	return currentTime_;
160	>	}
161
162	<	/** Sets the id of this Snapshot */
163	<	void setID(int id) {
164	<	id_ = id;
127	<	}
162	>	void increaseTime(RealType dt) {
163	>	setTime(getTime() + dt);
164	>	}
165
166	<	//template<typename T>
167	<	//static typename T::ElemPointerType getArrayPointer(vector<T>& v) {
168	<	//    return v[0]->getArrayPointer();
169	<	//}
166	>	void setTime(RealType time) {
167	>	currentTime_ =time;
168	>	//time at statData is redundant
169	>	statData[Stats::TIME] = currentTime_;
170	>	}
171
172	<	int getSize() {
173	<	return atomData.size() + rigidbodyData.size();
174	<	}
172	>	RealType getChi() {
173	>	return chi_;
174	>	}
175
176	<	/** Returns the number of atoms */
177	<	int getNumberOfAtoms() {
178	<	return atomData.size();
141	<	}
176	>	void setChi(RealType chi) {
177	>	chi_ = chi;
178	>	}
179
180	<	/** Returns the number of rigid bodies */
181	<	int getNumberOfRigidBodies() {
182	<	return rigidbodyData.size();
146	<	}
180	>	RealType getIntegralOfChiDt() {
181	>	return integralOfChiDt_;
182	>	}
183
184	<	/** Returns the H-Matrix */
185	<	Mat3x3d getHmat() {
186	<	return hmat_;
187	<	}
184	>	void setIntegralOfChiDt(RealType integralOfChiDt) {
185	>	integralOfChiDt_ = integralOfChiDt;
186	>	}
187	>
188
189	<	/** Sets the H-Matrix */
190	<	void setHamt(const Mat3x3d& m) {
191	<	hmat_ = m;
156	<	invHmat_ = hmat_.inverse();
157	<	}
189	>	void setOrthoTolerance(RealType orthoTolerance) {
190	>	orthoTolerance_ = orthoTolerance;
191	>	}
192
193	<	/** Returns the inverse H-Matrix */
194	<	Mat3x3d getInvHmat() {
195	<	return invHmat_
162	<	}
193	>	Mat3x3d getEta() {
194	>	return eta_;
195	>	}
196
197	<	double getTimeStamp() {
198	<	return timeStamp_;
199	<	}
197	>	void setEta(const Mat3x3d& eta) {
198	>	eta_ = eta;
199	>	}
200
201	<	void setTimeStamp(double timeStamp) {
202	<	timeStamp_ =timeStamp;
203	<	}
201	>	bool hasCOM() {
202	>	return hasCOM_;
203	>	}
204
205	+	void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
206	+	COM_ = COM;
207	+	COMvel_ = COMvel;
208	+	COMw_ = COMw;
209	+	hasCOM_ = true;
210	+	}
211
212	<	DataStorage atomData;
213	<	DataStorage rigidbodyData;
212	>	Vector3d getAtomPosByIindex(int iIndex) {
213	>	#ifdef IS_MPI
214	>	return atomIData.position[iIndex];
215	>	#else
216	>	return atomData.position[iIndex];
217	>	#endif
218	>	}
219	>	Vector3d getAtomPosByJindex(int jIndex) {
220	>	#ifdef IS_MPI
221	>	return atomJData.position[jIndex];
222	>	#else
223	>	return atomData.position[jIndex];
224	>	#endif
225	>	}
226	>
227	>	Vector3d getCutoffGroupPosByIindex(int iIndex) {
228	>	#ifdef IS_MPI
229	>	return cgIData.position[iIndex];
230	>	#else
231	>	return cgData.position[iIndex];
232	>	#endif
233	>	}
234	>	Vector3d getCutoffGroupPosByJindex(int jIndex) {
235	>	#ifdef IS_MPI
236	>	return cgJData.position[jIndex];
237	>	#else
238	>	return cgData.position[jIndex];
239	>	#endif
240	>	}
241	>
242	>	DataStorage atomData;
243	>	DataStorage rigidbodyData;
244	>	DataStorage cgData;
245	>	Stats statData;
246	>
247	>	#ifdef IS_MPI
248	>	DataStorage atomIData;
249	>	DataStorage atomJData;
250	>	DataStorage cgIData;
251	>	DataStorage cgJData;
252	>	#endif
253	>
254
255	<	friend class StuntDouble;
255	>	private:
256	>	RealType currentTime_;
257	>
258	>	Mat3x3d hmat_;
259	>	Mat3x3d invHmat_;
260	>	RealType orthoTolerance_;
261	>	int orthoRhombic_;
262	>	RealType volume_;
263	>
264	>	RealType chi_;
265	>	RealType integralOfChiDt_;
266	>	Mat3x3d eta_;
267	>	Vector3d COM_;
268	>	Vector3d COMvel_;
269	>	Vector3d COMw_;
270	>	int id_; /**< identification number of the snapshot */
271	>	bool hasCOM_;
272	>	bool hasVolume_;
273
274	<	private:
179	<	double timeStamp_;
180	<	Mat3x3d hmat_;
181	<	Mat3x3d invHmat_;
182	<	int id_; /**< identification number of the snapshot */
183	<	};
274	>	};
275
276	<	typedef DataStorage (Snapshot::*DataStoragePointer);
276	>	typedef DataStorage (Snapshot::*DataStoragePointer);
277		}
278		#endif //BRAINS_SNAPSHOT_HPP

Comparing:
trunk/src/brains/Snapshot.hpp (property svn:keywords), Revision 152 by tim, Tue Oct 26 17:28:53 2004 UTC vs.
branches/development/src/brains/Snapshot.hpp (property svn:keywords), Revision 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC

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