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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 1708 by gezelter, Tue May 15 13:02:10 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	>	/**
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,
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	<	//forward declaration
47	<	class Snapshot;
48	<	class SnapshotManager;
83	>	}
84
85	<	/**
86	<	* @struct DataStorage
87	<	* @brief
88	<	*/
89	<	class DataStorage {
90	<	public:
91	<	DataStorage() {};
92	<	DataStorage(size_t size);
93	<	void resize(size_t size);
94	<	void reserve(size_t size);
95	<
96	<	//friend Snapshot;
97	<	//friend SnapshotManager;
98	<	//private:
99	<	vector<Vector3d> position;               /** position array */
65	<	vector<Vector3d> velocity;               /** velocity array */
66	<	vector<RotMat3x3d> Amat;            /** rotation matrix array */
67	<	vector<Vector3d> angularMomentum;/** velocity array */
68	<	vector<Vector3d> ul;                /** the lab frame unit vector array*/
69	<	vector<double> zAngle;              /** z -angle array */
70	<	vector<Vector3d> force;               /** force array */
71	<	vector<Vector3d> torque;               /** torque array */
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_;
99	>	}
100
101	<	};
101	>	/** Sets the id of this Snapshot */
102	>	void setID(int id) {
103	>	id_ = id;
104	>	}
105
106	<	/**
107	<	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
108	<	* @brief Snapshot class is a repository class for storing dynamic data during
109	<	*  Simulation
110	<	* Every snapshot class will contain one DataStorage  for atoms and one DataStorage
111	<	*  for rigid bodies.
112	<	* @see SimData
113	<	*/
114	<	class Snapshot {
115	<	public:
106	>	int getSize() {
107	>	return atomData.getSize() + rigidbodyData.getSize();
108	>	}
109	>
110	>	/** Returns the number of atoms */
111	>	int getNumberOfAtoms() {
112	>	return atomData.getSize();
113	>	}
114	>
115	>	/** Returns the number of rigid bodies */
116	>	int getNumberOfRigidBodies() {
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_;
128	>	}
129	>
130	>	/** Sets the H-Matrix */
131	>	void setHmat(const Mat3x3d& m);
132
133	<	Snapshot() {}
134	<	Snapshot(int i) {
133	>	RealType getVolume() {
134	>	if (hasVolume_){
135	>	return volume_;
136	>	}else{
137	>	return hmat_.determinant();
138	>	}
139	>	}
140
141	<	}
141	>	void setVolume(RealType volume){
142	>	hasVolume_=true;
143	>	volume_ = volume;
144	>	}
145
146	<	Snapshot(const Snapshot& s);
146	>	/** Returns the inverse H-Matrix */
147	>	Mat3x3d getInvHmat() {
148	>	return invHmat_;
149	>	}
150
151	<	Snapshot& operator =(const Snapshot& s);
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	<	/** Returns the id of this Snapshot */
162	<	int getID() {
163	<	return id_;
98	<	}
161	>	RealType getTime() {
162	>	return currentTime_;
163	>	}
164
165	<	/** Sets the id of this Snapshot */
166	<	void setID(int id) {
167	<	id_ = id;
103	<	}
165	>	void increaseTime(RealType dt) {
166	>	setTime(getTime() + dt);
167	>	}
168
169	<	//template<typename T>
170	<	//static typename T::ElemPointerType getArrayPointer(vector<T>& v) {
171	<	//    return v[0]->getArrayPointer();
172	<	//}
169	>	void setTime(RealType time) {
170	>	currentTime_ =time;
171	>	//time at statData is redundant
172	>	statData[Stats::TIME] = currentTime_;
173	>	}
174
175	<	static double* getArrayPointer(vector<Vector3d>& v) {
176	<	assert(v.size() > 0);
177	<	return v[0].getArrayPointer();
178	<	}
175	>	RealType getChi() {
176	>	return chi_;
177	>	}
178	>
179	>	void setChi(RealType chi) {
180	>	chi_ = chi;
181	>	}
182	>
183	>	RealType getIntegralOfChiDt() {
184	>	return integralOfChiDt_;
185	>	}
186	>
187	>	void setIntegralOfChiDt(RealType integralOfChiDt) {
188	>	integralOfChiDt_ = integralOfChiDt;
189	>	}
190
115	–	static double* getArrayPointer(vector<RotMat3x3d>& v) {
116	–	assert(v.size() > 0);
117	–	return v[0].getArrayPointer();
118	–	}
119	–
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);
191
192	+	void setOrthoTolerance(RealType orthoTolerance) {
193	+	orthoTolerance_ = orthoTolerance;
194	+	}
195
196	<	/** */
197	<	void reserve(size_t size);
196	>	Mat3x3d getEta() {
197	>	return eta_;
198	>	}
199
200	<	DataStorage atomData;
201	<	DataStorage rigidbodyData;
200	>	void setEta(const Mat3x3d& eta) {
201	>	eta_ = eta;
202	>	}
203
204	<	friend class SnapshotManager;
205	<	private:
204	>	bool hasCOM() {
205	>	return hasCOM_;
206	>	}
207
208	<	int id_; /**< identification number of the snapshot */
209	<	};
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	<	typedef DataStorage* (Snapshot::*DataStoragePointer);
215	>	DataStorage atomData;
216	>	DataStorage rigidbodyData;
217	>	DataStorage cgData;
218	>	Stats statData;
219	>
220	>	private:
221	>	RealType currentTime_;
222	>
223	>	Mat3x3d hmat_;
224	>	Mat3x3d invHmat_;
225	>	RealType orthoTolerance_;
226	>	int orthoRhombic_;
227	>	RealType volume_;
228	>
229	>	RealType chi_;
230	>	RealType integralOfChiDt_;
231	>	Mat3x3d eta_;
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);
242		}
243		#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 1708 by gezelter, Tue May 15 13:02:10 2012 UTC

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