src/brains/Snapshot.hpp

/*
 * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
 * 
 * Contact: oopse@oopse.org
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */
 
 /**
  * @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"

using namespace std;

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.resize(nAtoms);
                rigidbodyData.resize(nRigidbodies);
            }

            Snapshot(const Snapshot& s);

            Snapshot& operator =(const Snapshot& s);
            
            /** 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) {
                hmat_ = m;
                invHmat_ = hmat_.inverse();
                
                //notify fortran Hmat is changed
                double fortranHmat[9];
                double fortranInvHmat[9];
                hmat_.getArray(fortranHmat);
                invHmat_.getArray(fortranInvHmat);
                setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
            }

            void 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 getTimeStamp() {
                return timeStamp_;
            }

            void setTimeStamp(double timeStamp) {
                timeStamp_ =timeStamp;
                //time at statData is redundant
                statData[Stats::TIME] = timeStamp_;
            }

            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 timeStamp_;

            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:	1727
Committed:	Thu Nov 11 16:41:58 2004 UTC (19 years, 7 months ago) by tim
File size:	5039 byte(s)
Log Message:	add Snapshot.cpp, remove useless mpiSimulation
#	User	Rev	Content
1	tim	1615	/*
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.
23			*
24			*/
25
26			/**
27			* @file Snapshot.hpp
28			* @author tlin
29			* @date 10/20/2004
30			* @time 23:56am
31			* @version 1.0
32			*/
33	tim	1639
34	tim	1615	#ifndef BRAINS_SNAPSHOT_HPP
35			#define BRAINS_SNAPSHOT_HPP
36	tim	1630
37			#include <vector>
38
39	tim	1648	#include "brains/DataStorage.hpp"
40	tim	1710	#include "brains/Stats.hpp"
41	tim	1630
42			using namespace std;
43
44	tim	1615	namespace oopse{
45
46			/**
47			* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
48			* @brief Snapshot class is a repository class for storing dynamic data during
49			* Simulation
50	tim	1639	* Every snapshot class will contain one DataStorage for atoms and one DataStorage
51			* for rigid bodies.
52	tim	1615	*/
53			class Snapshot {
54			public:
55	tim	1639
56	tim	1642	Snapshot(int nAtoms, int nRigidbodies) {
57			atomData.resize(nAtoms);
58			rigidbodyData.resize(nRigidbodies);
59	tim	1630	}
60
61			Snapshot(const Snapshot& s);
62
63			Snapshot& operator =(const Snapshot& s);
64	tim	1615
65	tim	1630	/** Returns the id of this Snapshot */
66			int getID() {
67			return id_;
68			}
69
70			/** Sets the id of this Snapshot */
71			void setID(int id) {
72			id_ = id;
73			}
74
75	tim	1642	int getSize() {
76	tim	1648	return atomData.getSize() + rigidbodyData.getSize();
77	tim	1642	}
78	tim	1645
79			/** Returns the number of atoms */
80			int getNumberOfAtoms() {
81	tim	1648	return atomData.getSize();
82	tim	1642	}
83	tim	1645
84			/** Returns the number of rigid bodies */
85			int getNumberOfRigidBodies() {
86	tim	1648	return rigidbodyData.getSize();
87	tim	1642	}
88	tim	1645
89			/** Returns the H-Matrix */
90			Mat3x3d getHmat() {
91			return hmat_;
92			}
93
94			/** Sets the H-Matrix */
95	tim	1727	void setHmat(const Mat3x3d& m) {
96	tim	1645	hmat_ = m;
97			invHmat_ = hmat_.inverse();
98	tim	1727
99			//notify fortran Hmat is changed
100			double fortranHmat[9];
101			double fortranInvHmat[9];
102			hmat_.getArray(fortranHmat);
103			invHmat_.getArray(fortranInvHmat);
104			setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
105	tim	1645	}
106
107	tim	1727	void getVolume() {
108			return hmat_.determinant();
109			}
110
111	tim	1645	/** Returns the inverse H-Matrix */
112			Mat3x3d getInvHmat() {
113	tim	1695	return invHmat_;
114	tim	1645	}
115
116	tim	1727	/** Wrapping the vector according to periodic boundary condition*/
117			void wrapVector(Vector3d& v);
118
119
120	tim	1645	double getTimeStamp() {
121			return timeStamp_;
122			}
123
124			void setTimeStamp(double timeStamp) {
125			timeStamp_ =timeStamp;
126	tim	1727	//time at statData is redundant
127			statData[Stats::TIME] = timeStamp_;
128	tim	1645	}
129
130	tim	1727	double getChi() {
131			return chi_;
132			}
133
134			void setChi(double chi) {
135			chi_ = chi;
136			}
137
138			double getIntegralOfChiDt() {
139			return integralOfChiDt_;
140			}
141
142			void setIntegralOfChiDt(double integralOfChiDt) {
143			integralOfChiDt_ = integralOfChiDt;
144			}
145
146			Mat3x3d getEta() {
147			return eta_;
148			}
149
150			void setEta(const Mat3x3d& eta) {
151			eta_ = eta;
152			}
153
154	tim	1639	DataStorage atomData;
155			DataStorage rigidbodyData;
156	tim	1710	Stats statData;
157	tim	1645
158	tim	1615	private:
159	tim	1645	double timeStamp_;
160	tim	1727
161	tim	1645	Mat3x3d hmat_;
162			Mat3x3d invHmat_;
163	tim	1727	int orthoRhombic_;
164
165			double chi_;
166			double integralOfChiDt_;
167			Mat3x3d eta_;
168
169	tim	1630	int id_; /*< identification number of the snapshot /
170	tim	1615	};
171
172	tim	1642	typedef DataStorage (Snapshot::*DataStoragePointer);
173	tim	1615	}
174			#endif //BRAINS_SNAPSHOT_HPP