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 getTime() {
                return currentTime_;
            }

            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:	1739
Committed:	Mon Nov 15 18:02:15 2004 UTC (19 years, 8 months ago) by tim
File size:	5027 byte(s)
Log Message:	finish DumpReader, DumpWriter.Next Step is LJFF and integrators
#	Content
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.
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
34	#ifndef BRAINS_SNAPSHOT_HPP
35	#define BRAINS_SNAPSHOT_HPP
36
37	#include <vector>
38
39	#include "brains/DataStorage.hpp"
40	#include "brains/Stats.hpp"
41
42	using namespace std;
43
44	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	* Every snapshot class will contain one DataStorage for atoms and one DataStorage
51	* for rigid bodies.
52	*/
53	class Snapshot {
54	public:
55
56	Snapshot(int nAtoms, int nRigidbodies) {
57	atomData.resize(nAtoms);
58	rigidbodyData.resize(nRigidbodies);
59	}
60
61	Snapshot(const Snapshot& s);
62
63	Snapshot& operator =(const Snapshot& s);
64
65	/** 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	int getSize() {
76	return atomData.getSize() + rigidbodyData.getSize();
77	}
78
79	/** Returns the number of atoms */
80	int getNumberOfAtoms() {
81	return atomData.getSize();
82	}
83
84	/** Returns the number of rigid bodies */
85	int getNumberOfRigidBodies() {
86	return rigidbodyData.getSize();
87	}
88
89	/** Returns the H-Matrix */
90	Mat3x3d getHmat() {
91	return hmat_;
92	}
93
94	/** Sets the H-Matrix */
95	void setHmat(const Mat3x3d& m) {
96	hmat_ = m;
97	invHmat_ = hmat_.inverse();
98
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	}
106
107	void getVolume() {
108	return hmat_.determinant();
109	}
110
111	/** Returns the inverse H-Matrix */
112	Mat3x3d getInvHmat() {
113	return invHmat_;
114	}
115
116	/** Wrapping the vector according to periodic boundary condition*/
117	void wrapVector(Vector3d& v);
118
119
120	double getTime() {
121	return currentTime_;
122	}
123
124	void setTime(double time) {
125	currentTime_ =time;
126	//time at statData is redundant
127	statData[Stats::TIME] = currentTime_;
128	}
129
130	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	DataStorage atomData;
155	DataStorage rigidbodyData;
156	Stats statData;
157
158	private:
159	double currentTime_;
160
161	Mat3x3d hmat_;
162	Mat3x3d invHmat_;
163	int orthoRhombic_;
164
165	double chi_;
166	double integralOfChiDt_;
167	Mat3x3d eta_;
168
169	int id_; /*< identification number of the snapshot /
170	};
171
172	typedef DataStorage (Snapshot::*DataStoragePointer);
173	}
174	#endif //BRAINS_SNAPSHOT_HPP