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:	2204
Committed:	Fri Apr 15 22:04:00 2005 UTC (19 years, 2 months ago) by gezelter
File size:	5202 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	gezelter	2204	/**
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	gezelter	2204	/**
62			* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
63			* @brief Snapshot class is a repository class for storing dynamic data during
64			* Simulation
65			* Every snapshot class will contain one DataStorage for atoms and one DataStorage
66			* for rigid bodies.
67			*/
68			class Snapshot {
69			public:
70	tim	1639
71	gezelter	2204	Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies),
72			currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0) {
73	gezelter	1930
74	gezelter	2204	}
75	tim	1630
76	gezelter	2204	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	tim	2000
80	gezelter	2204	}
81	tim	1615
82	gezelter	2204	/** Returns the id of this Snapshot */
83			int getID() {
84			return id_;
85			}
86	tim	1630
87	gezelter	2204	/** Sets the id of this Snapshot */
88			void setID(int id) {
89			id_ = id;
90			}
91	tim	1630
92	gezelter	2204	int getSize() {
93			return atomData.getSize() + rigidbodyData.getSize();
94			}
95	tim	1645
96	gezelter	2204	/** Returns the number of atoms */
97			int getNumberOfAtoms() {
98			return atomData.getSize();
99			}
100	tim	1645
101	gezelter	2204	/** Returns the number of rigid bodies */
102			int getNumberOfRigidBodies() {
103			return rigidbodyData.getSize();
104			}
105	tim	1645
106	gezelter	2204	/** Returns the H-Matrix */
107			Mat3x3d getHmat() {
108			return hmat_;
109			}
110	tim	1645
111	gezelter	2204	/** Sets the H-Matrix */
112			void setHmat(const Mat3x3d& m);
113	gezelter	1930
114	gezelter	2204	double getVolume() {
115			return hmat_.determinant();
116			}
117	tim	1645
118	gezelter	2204	/** Returns the inverse H-Matrix */
119			Mat3x3d getInvHmat() {
120			return invHmat_;
121			}
122	tim	1645
123	gezelter	2204	/** Wrapping the vector according to periodic boundary condition*/
124			void wrapVector(Vector3d& v);
125	gezelter	1930
126
127	gezelter	2204	double getTime() {
128			return currentTime_;
129			}
130	tim	1645
131	gezelter	2204	void increaseTime(double dt) {
132			setTime(getTime() + dt);
133			}
134	tim	1645
135	gezelter	2204	void setTime(double time) {
136			currentTime_ =time;
137			//time at statData is redundant
138			statData[Stats::TIME] = currentTime_;
139			}
140	tim	1645
141	gezelter	2204	double getChi() {
142			return chi_;
143			}
144	gezelter	1930
145	gezelter	2204	void setChi(double chi) {
146			chi_ = chi;
147			}
148	gezelter	1930
149	gezelter	2204	double getIntegralOfChiDt() {
150			return integralOfChiDt_;
151			}
152	gezelter	1930
153	gezelter	2204	void setIntegralOfChiDt(double integralOfChiDt) {
154			integralOfChiDt_ = integralOfChiDt;
155			}
156	gezelter	1930
157	gezelter	2204	Mat3x3d getEta() {
158			return eta_;
159			}
160	gezelter	1930
161	gezelter	2204	void setEta(const Mat3x3d& eta) {
162			eta_ = eta;
163			}
164	gezelter	1930
165	gezelter	2204	DataStorage atomData;
166			DataStorage rigidbodyData;
167			Stats statData;
168	tim	1645
169	gezelter	2204	private:
170			double currentTime_;
171	gezelter	1930
172	gezelter	2204	Mat3x3d hmat_;
173			Mat3x3d invHmat_;
174			int orthoRhombic_;
175	gezelter	1930
176	gezelter	2204	double chi_;
177			double integralOfChiDt_;
178			Mat3x3d eta_;
179	gezelter	1930
180	gezelter	2204	int id_; /*< identification number of the snapshot /
181			};
182	tim	1615
183	gezelter	2204	typedef DataStorage (Snapshot::*DataStoragePointer);
184	tim	1615	}
185			#endif //BRAINS_SNAPSHOT_HPP