src/brains/Snapshot.hpp

 /*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
  
 /**
  * @file Snapshot.hpp
  * @author tlin
  * @date 10/20/2004
  * @time 23:56am
  * @version 1.0
  */
  
#ifndef BRAINS_SNAPSHOT_HPP
#define BRAINS_SNAPSHOT_HPP

#include <vector>

#include "brains/DataStorage.hpp"
#include "brains/Stats.hpp"
#include "UseTheForce/DarkSide/simulation_interface.h"

namespace oopse{

    /**
     * @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
     * @brief Snapshot class is a repository class for storing dynamic data during 
     *  Simulation
     * Every snapshot class will contain one DataStorage  for atoms and one DataStorage
     *  for rigid bodies.
     */
    class Snapshot {
        public:
            
            Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies),
                currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0) {

            }

            
            /** Returns the id of this Snapshot */
            int getID() {
                return id_;
            }

            /** Sets the id of this Snapshot */
            void setID(int id) {
                id_ = id;
            }

            int getSize() {
                return atomData.getSize() + rigidbodyData.getSize();
            }

            /** Returns the number of atoms */
            int getNumberOfAtoms() {
                return atomData.getSize();
            }

            /** Returns the number of rigid bodies */
            int getNumberOfRigidBodies() {
                return rigidbodyData.getSize();
            }

            /** Returns the H-Matrix */
            Mat3x3d getHmat() {
                return hmat_;
            }

            /** Sets the H-Matrix */
            void setHmat(const Mat3x3d& m);
            
            double getVolume() {
                return hmat_.determinant();
            }

            /** Returns the inverse H-Matrix */
            Mat3x3d getInvHmat() {
                return invHmat_;
            }

            /** Wrapping the vector according to periodic boundary condition*/
            void wrapVector(Vector3d& v);

            
            double getTime() {
                return currentTime_;
            }

            void increaseTime(double dt) {
                setTime(getTime() + dt);
            }

            void setTime(double time) {
                currentTime_ =time;
                //time at statData is redundant
                statData[Stats::TIME] = currentTime_;
            }

            double getChi() {
                return chi_;
            }

            void setChi(double chi) {
                chi_ = chi;
            }

            double getIntegralOfChiDt() {
                return integralOfChiDt_;
            }

            void setIntegralOfChiDt(double integralOfChiDt) {
                integralOfChiDt_ = integralOfChiDt;
            }
            
            Mat3x3d getEta() {
                return eta_;
            }

            void setEta(const Mat3x3d& eta) {
                eta_ = eta;
            }
            
            DataStorage atomData;
            DataStorage rigidbodyData;
            Stats statData;
            
        private:
            double currentTime_;

            Mat3x3d hmat_;
            Mat3x3d invHmat_;
            int orthoRhombic_;

            double chi_;
            double integralOfChiDt_;
            Mat3x3d eta_;
            
            int id_; /**< identification number of the snapshot */
    };

    typedef DataStorage (Snapshot::*DataStoragePointer); 
}
#endif //BRAINS_SNAPSHOT_HPP
Revision:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 5 months ago) by gezelter
File size:	5655 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	Content
1	/*
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. 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
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*/
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 "brains/DataStorage.hpp"
56	#include "brains/Stats.hpp"
57	#include "UseTheForce/DarkSide/simulation_interface.h"
58
59	namespace oopse{
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) {
73
74	}
75
76
77	/** Returns the id of this Snapshot */
78	int getID() {
79	return id_;
80	}
81
82	/** Sets the id of this Snapshot */
83	void setID(int id) {
84	id_ = id;
85	}
86
87	int getSize() {
88	return atomData.getSize() + rigidbodyData.getSize();
89	}
90
91	/** Returns the number of atoms */
92	int getNumberOfAtoms() {
93	return atomData.getSize();
94	}
95
96	/** Returns the number of rigid bodies */
97	int getNumberOfRigidBodies() {
98	return rigidbodyData.getSize();
99	}
100
101	/** Returns the H-Matrix */
102	Mat3x3d getHmat() {
103	return hmat_;
104	}
105
106	/** Sets the H-Matrix */
107	void setHmat(const Mat3x3d& m);
108
109	double getVolume() {
110	return hmat_.determinant();
111	}
112
113	/** Returns the inverse H-Matrix */
114	Mat3x3d getInvHmat() {
115	return invHmat_;
116	}
117
118	/** Wrapping the vector according to periodic boundary condition*/
119	void wrapVector(Vector3d& v);
120
121
122	double getTime() {
123	return currentTime_;
124	}
125
126	void increaseTime(double dt) {
127	setTime(getTime() + dt);
128	}
129
130	void setTime(double time) {
131	currentTime_ =time;
132	//time at statData is redundant
133	statData[Stats::TIME] = currentTime_;
134	}
135
136	double getChi() {
137	return chi_;
138	}
139
140	void setChi(double chi) {
141	chi_ = chi;
142	}
143
144	double getIntegralOfChiDt() {
145	return integralOfChiDt_;
146	}
147
148	void setIntegralOfChiDt(double integralOfChiDt) {
149	integralOfChiDt_ = integralOfChiDt;
150	}
151
152	Mat3x3d getEta() {
153	return eta_;
154	}
155
156	void setEta(const Mat3x3d& eta) {
157	eta_ = eta;
158	}
159
160	DataStorage atomData;
161	DataStorage rigidbodyData;
162	Stats statData;
163
164	private:
165	double currentTime_;
166
167	Mat3x3d hmat_;
168	Mat3x3d invHmat_;
169	int orthoRhombic_;
170
171	double chi_;
172	double integralOfChiDt_;
173	Mat3x3d eta_;
174
175	int id_; /*< identification number of the snapshot /
176	};
177
178	typedef DataStorage (Snapshot::*DataStoragePointer);
179	}
180	#endif //BRAINS_SNAPSHOT_HPP