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"
#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), 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) {
                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_);
            }

            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:	1844
Committed:	Fri Dec 3 22:36:06 2004 UTC (19 years, 9 months ago) by tim
File size:	5100 byte(s)
Log Message:	NVE is running
#	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	1793	#include "UseTheForce/DarkSide/simulation_interface.h"
42	tim	1630
43	tim	1615	namespace oopse{
44
45			/**
46			* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
47			* @brief Snapshot class is a repository class for storing dynamic data during
48			* Simulation
49	tim	1639	* Every snapshot class will contain one DataStorage for atoms and one DataStorage
50			* for rigid bodies.
51	tim	1615	*/
52			class Snapshot {
53			public:
54	tim	1639
55	tim	1844	Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies),
56			currentTime_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0) {
57
58	tim	1630	}
59
60	tim	1615
61	tim	1630	/** Returns the id of this Snapshot */
62			int getID() {
63			return id_;
64			}
65
66			/** Sets the id of this Snapshot */
67			void setID(int id) {
68			id_ = id;
69			}
70
71	tim	1642	int getSize() {
72	tim	1648	return atomData.getSize() + rigidbodyData.getSize();
73	tim	1642	}
74	tim	1645
75			/** Returns the number of atoms */
76			int getNumberOfAtoms() {
77	tim	1648	return atomData.getSize();
78	tim	1642	}
79	tim	1645
80			/** Returns the number of rigid bodies */
81			int getNumberOfRigidBodies() {
82	tim	1648	return rigidbodyData.getSize();
83	tim	1642	}
84	tim	1645
85			/** Returns the H-Matrix */
86			Mat3x3d getHmat() {
87			return hmat_;
88			}
89
90			/** Sets the H-Matrix */
91	tim	1727	void setHmat(const Mat3x3d& m) {
92	tim	1645	hmat_ = m;
93			invHmat_ = hmat_.inverse();
94	tim	1727
95			//notify fortran Hmat is changed
96			double fortranHmat[9];
97			double fortranInvHmat[9];
98			hmat_.getArray(fortranHmat);
99			invHmat_.getArray(fortranInvHmat);
100			setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
101	tim	1645	}
102
103	tim	1793	double getVolume() {
104	tim	1727	return hmat_.determinant();
105			}
106
107	tim	1645	/** Returns the inverse H-Matrix */
108			Mat3x3d getInvHmat() {
109	tim	1695	return invHmat_;
110	tim	1645	}
111
112	tim	1727	/** Wrapping the vector according to periodic boundary condition*/
113			void wrapVector(Vector3d& v);
114
115
116	tim	1739	double getTime() {
117			return currentTime_;
118	tim	1645	}
119
120	tim	1820	void increaseTime(double dt) {
121			setTime(getTime() + dt);
122			}
123
124	tim	1739	void setTime(double time) {
125			currentTime_ =time;
126	tim	1727	//time at statData is redundant
127	tim	1739	statData[Stats::TIME] = currentTime_;
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	1739	double currentTime_;
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