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) : currentTime_(0), chi_(0), integralOfChiDt_(0), eta_(0) {
                atomData.resize(nAtoms);
                rigidbodyData.resize(nRigidbodies);
            }

            
            /** 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:	1765
Committed:	Mon Nov 22 20:55:52 2004 UTC (19 years, 7 months ago) by tim
File size:	4989 byte(s)
Log Message:	adding section parsers
#	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	1765	Snapshot(int nAtoms, int nRigidbodies) : currentTime_(0), chi_(0), integralOfChiDt_(0), eta_(0) {
57	tim	1642	atomData.resize(nAtoms);
58			rigidbodyData.resize(nRigidbodies);
59	tim	1630	}
60
61	tim	1615
62	tim	1630	/** Returns the id of this Snapshot */
63			int getID() {
64			return id_;
65			}
66
67			/** Sets the id of this Snapshot */
68			void setID(int id) {
69			id_ = id;
70			}
71
72	tim	1642	int getSize() {
73	tim	1648	return atomData.getSize() + rigidbodyData.getSize();
74	tim	1642	}
75	tim	1645
76			/** Returns the number of atoms */
77			int getNumberOfAtoms() {
78	tim	1648	return atomData.getSize();
79	tim	1642	}
80	tim	1645
81			/** Returns the number of rigid bodies */
82			int getNumberOfRigidBodies() {
83	tim	1648	return rigidbodyData.getSize();
84	tim	1642	}
85	tim	1645
86			/** Returns the H-Matrix */
87			Mat3x3d getHmat() {
88			return hmat_;
89			}
90
91			/** Sets the H-Matrix */
92	tim	1727	void setHmat(const Mat3x3d& m) {
93	tim	1645	hmat_ = m;
94			invHmat_ = hmat_.inverse();
95	tim	1727
96			//notify fortran Hmat is changed
97			double fortranHmat[9];
98			double fortranInvHmat[9];
99			hmat_.getArray(fortranHmat);
100			invHmat_.getArray(fortranInvHmat);
101			setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
102	tim	1645	}
103
104	tim	1727	void getVolume() {
105			return hmat_.determinant();
106			}
107
108	tim	1645	/** Returns the inverse H-Matrix */
109			Mat3x3d getInvHmat() {
110	tim	1695	return invHmat_;
111	tim	1645	}
112
113	tim	1727	/** Wrapping the vector according to periodic boundary condition*/
114			void wrapVector(Vector3d& v);
115
116
117	tim	1739	double getTime() {
118			return currentTime_;
119	tim	1645	}
120
121	tim	1739	void setTime(double time) {
122			currentTime_ =time;
123	tim	1727	//time at statData is redundant
124	tim	1739	statData[Stats::TIME] = currentTime_;
125	tim	1645	}
126
127	tim	1727	double getChi() {
128			return chi_;
129			}
130
131			void setChi(double chi) {
132			chi_ = chi;
133			}
134
135			double getIntegralOfChiDt() {
136			return integralOfChiDt_;
137			}
138
139			void setIntegralOfChiDt(double integralOfChiDt) {
140			integralOfChiDt_ = integralOfChiDt;
141			}
142
143			Mat3x3d getEta() {
144			return eta_;
145			}
146
147			void setEta(const Mat3x3d& eta) {
148			eta_ = eta;
149			}
150
151	tim	1639	DataStorage atomData;
152			DataStorage rigidbodyData;
153	tim	1710	Stats statData;
154	tim	1645
155	tim	1615	private:
156	tim	1739	double currentTime_;
157	tim	1727
158	tim	1645	Mat3x3d hmat_;
159			Mat3x3d invHmat_;
160	tim	1727	int orthoRhombic_;
161
162			double chi_;
163			double integralOfChiDt_;
164			Mat3x3d eta_;
165
166	tim	1630	int id_; /*< identification number of the snapshot /
167	tim	1615	};
168
169	tim	1642	typedef DataStorage (Snapshot::*DataStoragePointer);
170	tim	1615	}
171			#endif //BRAINS_SNAPSHOT_HPP