ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 1 | Line 1
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) : atomData(nAtoms),
73	+	rigidbodyData(nRigidbodies),
74	+	currentTime_(0),
75	+	orthoTolerance_(1e-6),
76	+	orthoRhombic_(0),
77	+	chi_(0.0),
78	+	integralOfChiDt_(0.0),
79	+	eta_(0.0), id_(-1),
80	+	hasCOM_(false), hasVolume_(false), volume_(0.0) {
81
82	<	//forward declaration
48	<	class Snapshot;
49	<	class SnapshotManager;
50	<	class StuntDouble;
51	<
52	<	/**
53	<	* @class DataStorage
54	<	* @warning do not try to insert element into (or ease element from) private member data
55	<	* of DataStorage directly.
56	<	*/
57	<	class DataStorage {
58	<	public:
82	>	}
83
84	<	enum{
85	<	slPosition = 1,
86	<	slVelocity = 2,
87	<	slAmat = 4,
88	<	slAngularMomentum = 8,
89	<	slUnitVector = 16,
90	<	slZAngle = 32,
67	<	slForce = 64,
68	<	slTorque = 128
69	<	};
84	>	Snapshot(int nAtoms, int nRigidbodies, int storageLayout)
85	>	: atomData(nAtoms, storageLayout),
86	>	rigidbodyData(nRigidbodies, storageLayout),
87	>	currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0),
88	>	integralOfChiDt_(0.0), eta_(0.0), id_(-1), hasCOM_(false), hasVolume_(false),volume_(0.0)  {
89	>
90	>	}
91
92	<	DataStorage(int size);
92	>	/** Returns the id of this Snapshot */
93	>	int getID() {
94	>	return id_;
95	>	}
96
97	<	/** return the size of this DataStorage */
98	<	int size();
99	<	void resize(int size);
100	<	void reserve(int size);
97	>	/** Sets the id of this Snapshot */
98	>	void setID(int id) {
99	>	id_ = id;
100	>	}
101
102	<	void move(int source, int num, int target);
103	<	int getStorageLayout();
104	<	void setStorageLayout(int layout);
102	>	int getSize() {
103	>	return atomData.getSize() + rigidbodyData.getSize();
104	>	}
105
106	<	double *getArrayPointer(int );
106	>	/** Returns the number of atoms */
107	>	int getNumberOfAtoms() {
108	>	return atomData.getSize();
109	>	}
110
111	<	friend class StuntDouble;
111	>	/** Returns the number of rigid bodies */
112	>	int getNumberOfRigidBodies() {
113	>	return rigidbodyData.getSize();
114	>	}
115
116	<	private:
117	<	int size_;
118	<	int storageLayout_;
119	<	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	<	};
116	>	/** Returns the H-Matrix */
117	>	Mat3x3d getHmat() {
118	>	return hmat_;
119	>	}
120
121	<	/**
122	<	* @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:
121	>	/** Sets the H-Matrix */
122	>	void setHmat(const Mat3x3d& m);
123
124	<	Snapshot(int nAtoms, int nRigidbodies) {
125	<	atomData.resize(nAtoms);
126	<	rigidbodyData.resize(nRigidbodies);
127	<	}
124	>	RealType getVolume() {
125	>	if (hasVolume_){
126	>	return volume_;
127	>	}else{
128	>	return hmat_.determinant();
129	>	}
130	>	}
131
132	<	Snapshot(const Snapshot& s);
132	>	void setVolume(RealType volume){
133	>	hasVolume_=true;
134	>	volume_ = volume;
135	>	}
136
137	<	Snapshot& operator =(const Snapshot& s);
137	>	/** Returns the inverse H-Matrix */
138	>	Mat3x3d getInvHmat() {
139	>	return invHmat_;
140	>	}
141	>
142	>	/** Wrapping the vector according to periodic boundary condition*/
143	>	void wrapVector(Vector3d& v);
144	>	Vector3d getCOM();
145	>	Vector3d getCOMvel();
146	>	Vector3d getCOMw();
147
148	<	/** Returns the id of this Snapshot */
149	<	int getID() {
150	<	return id_;
122	<	}
148	>	RealType getTime() {
149	>	return currentTime_;
150	>	}
151
152	<	/** Sets the id of this Snapshot */
153	<	void setID(int id) {
154	<	id_ = id;
127	<	}
152	>	void increaseTime(RealType dt) {
153	>	setTime(getTime() + dt);
154	>	}
155
156	<	//template<typename T>
157	<	//static typename T::ElemPointerType getArrayPointer(vector<T>& v) {
158	<	//    return v[0]->getArrayPointer();
159	<	//}
156	>	void setTime(RealType time) {
157	>	currentTime_ =time;
158	>	//time at statData is redundant
159	>	statData[Stats::TIME] = currentTime_;
160	>	}
161
162	<	int getSize() {
163	<	return atomData.size() + rigidbodyData.size();
164	<	}
162	>	RealType getChi() {
163	>	return chi_;
164	>	}
165
166	<	/** Returns the number of atoms */
167	<	int getNumberOfAtoms() {
168	<	return atomData.size();
141	<	}
166	>	void setChi(RealType chi) {
167	>	chi_ = chi;
168	>	}
169
170	<	/** Returns the number of rigid bodies */
171	<	int getNumberOfRigidBodies() {
172	<	return rigidbodyData.size();
146	<	}
170	>	RealType getIntegralOfChiDt() {
171	>	return integralOfChiDt_;
172	>	}
173
174	<	/** Returns the H-Matrix */
175	<	Mat3x3d getHmat() {
176	<	return hmat_;
177	<	}
174	>	void setIntegralOfChiDt(RealType integralOfChiDt) {
175	>	integralOfChiDt_ = integralOfChiDt;
176	>	}
177	>
178
179	<	/** Sets the H-Matrix */
180	<	void setHamt(const Mat3x3d& m) {
181	<	hmat_ = m;
156	<	invHmat_ = hmat_.inverse();
157	<	}
179	>	void setOrthoTolerance(RealType orthoTolerance) {
180	>	orthoTolerance_ = orthoTolerance;
181	>	}
182
183	<	/** Returns the inverse H-Matrix */
184	<	Mat3x3d getInvHmat() {
185	<	return invHmat_
162	<	}
183	>	Mat3x3d getEta() {
184	>	return eta_;
185	>	}
186
187	<	double getTimeStamp() {
188	<	return timeStamp_;
189	<	}
187	>	void setEta(const Mat3x3d& eta) {
188	>	eta_ = eta;
189	>	}
190
191	<	void setTimeStamp(double timeStamp) {
192	<	timeStamp_ =timeStamp;
193	<	}
191	>	bool hasCOM() {
192	>	return hasCOM_;
193	>	}
194
195	+	void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
196	+	COM_ = COM;
197	+	COMvel_ = COMvel;
198	+	COMw_ = COMw;
199	+	hasCOM_ = true;
200	+	}
201	+
202	+	DataStorage atomData;
203	+	DataStorage rigidbodyData;
204	+	Stats statData;
205	+
206	+	private:
207	+	RealType currentTime_;
208
209	<	DataStorage atomData;
210	<	DataStorage rigidbodyData;
209	>	Mat3x3d hmat_;
210	>	Mat3x3d invHmat_;
211	>	RealType orthoTolerance_;
212	>	int orthoRhombic_;
213	>	RealType volume_;
214	>
215	>	RealType chi_;
216	>	RealType integralOfChiDt_;
217	>	Mat3x3d eta_;
218	>	Vector3d COM_;
219	>	Vector3d COMvel_;
220	>	Vector3d COMw_;
221	>	int id_; /**< identification number of the snapshot */
222	>	bool hasCOM_;
223	>	bool hasVolume_;
224
225	<	friend class StuntDouble;
177	<
178	<	private:
179	<	double timeStamp_;
180	<	Mat3x3d hmat_;
181	<	Mat3x3d invHmat_;
182	<	int id_; /**< identification number of the snapshot */
183	<	};
225	>	};
226
227	<	typedef DataStorage (Snapshot::*DataStoragePointer);
227	>	typedef DataStorage (Snapshot::*DataStoragePointer);
228		}
229		#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 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines