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) {

            }

            Snapshot(int nAtoms, int nRigidbodies, int storageLayout) 
                : atomData(nAtoms, storageLayout), rigidbodyData(nRigidbodies, storageLayout),
                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:	2000
Committed:	Fri Feb 11 22:41:02 2005 UTC (19 years, 4 months ago) by tim
File size:	5933 byte(s)
Log Message:	adding one more constructor to Snapshot to create customized DataStorage
#	User	Rev	Content
1	gezelter	1930	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	tim	1615	*
4	gezelter	1930	* 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	tim	1615	*/
41	gezelter	1930
42	tim	1615	/**
43			* @file Snapshot.hpp
44			* @author tlin
45			* @date 10/20/2004
46			* @time 23:56am
47			* @version 1.0
48			*/
49	tim	1639
50	tim	1615	#ifndef BRAINS_SNAPSHOT_HPP
51			#define BRAINS_SNAPSHOT_HPP
52	tim	1630
53			#include <vector>
54
55	tim	1648	#include "brains/DataStorage.hpp"
56	gezelter	1930	#include "brains/Stats.hpp"
57			#include "UseTheForce/DarkSide/simulation_interface.h"
58	tim	1630
59	tim	1615	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	tim	1639	* Every snapshot class will contain one DataStorage for atoms and one DataStorage
66			* for rigid bodies.
67	tim	1615	*/
68			class Snapshot {
69			public:
70	tim	1639
71	gezelter	1930	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	tim	1630	}
75
76	tim	2000	Snapshot(int nAtoms, int nRigidbodies, int storageLayout)
77			: atomData(nAtoms, storageLayout), rigidbodyData(nRigidbodies, storageLayout),
78			currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0) {
79
80			}
81	tim	1615
82	tim	1630	/** Returns the id of this Snapshot */
83			int getID() {
84			return id_;
85			}
86
87			/** Sets the id of this Snapshot */
88			void setID(int id) {
89			id_ = id;
90			}
91
92	tim	1642	int getSize() {
93	tim	1648	return atomData.getSize() + rigidbodyData.getSize();
94	tim	1642	}
95	tim	1645
96			/** Returns the number of atoms */
97			int getNumberOfAtoms() {
98	tim	1648	return atomData.getSize();
99	tim	1642	}
100	tim	1645
101			/** Returns the number of rigid bodies */
102			int getNumberOfRigidBodies() {
103	tim	1648	return rigidbodyData.getSize();
104	tim	1642	}
105	tim	1645
106			/** Returns the H-Matrix */
107			Mat3x3d getHmat() {
108			return hmat_;
109			}
110
111			/** Sets the H-Matrix */
112	gezelter	1930	void setHmat(const Mat3x3d& m);
113
114			double getVolume() {
115			return hmat_.determinant();
116	tim	1645	}
117
118			/** Returns the inverse H-Matrix */
119			Mat3x3d getInvHmat() {
120	gezelter	1930	return invHmat_;
121	tim	1645	}
122
123	gezelter	1930	/** Wrapping the vector according to periodic boundary condition*/
124			void wrapVector(Vector3d& v);
125
126
127			double getTime() {
128			return currentTime_;
129	tim	1645	}
130
131	gezelter	1930	void increaseTime(double dt) {
132			setTime(getTime() + dt);
133	tim	1645	}
134
135	gezelter	1930	void setTime(double time) {
136			currentTime_ =time;
137			//time at statData is redundant
138			statData[Stats::TIME] = currentTime_;
139			}
140	tim	1645
141	gezelter	1930	double getChi() {
142			return chi_;
143			}
144
145			void setChi(double chi) {
146			chi_ = chi;
147			}
148
149			double getIntegralOfChiDt() {
150			return integralOfChiDt_;
151			}
152
153			void setIntegralOfChiDt(double integralOfChiDt) {
154			integralOfChiDt_ = integralOfChiDt;
155			}
156
157			Mat3x3d getEta() {
158			return eta_;
159			}
160
161			void setEta(const Mat3x3d& eta) {
162			eta_ = eta;
163			}
164
165	tim	1639	DataStorage atomData;
166			DataStorage rigidbodyData;
167	gezelter	1930	Stats statData;
168	tim	1645
169	tim	1615	private:
170	gezelter	1930	double currentTime_;
171
172	tim	1645	Mat3x3d hmat_;
173			Mat3x3d invHmat_;
174	gezelter	1930	int orthoRhombic_;
175
176			double chi_;
177			double integralOfChiDt_;
178			Mat3x3d eta_;
179
180	tim	1630	int id_; /*< identification number of the snapshot /
181	tim	1615	};
182
183	tim	1642	typedef DataStorage (Snapshot::*DataStoragePointer);
184	tim	1615	}
185			#endif //BRAINS_SNAPSHOT_HPP