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), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) {

    }

    Snapshot(int nAtoms, int nRigidbodies, int storageLayout) 
      : atomData(nAtoms, storageLayout), rigidbodyData(nRigidbodies, storageLayout),
        currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) {

      }
            
    /** 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);
            
    RealType 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);

            
    RealType getTime() {
      return currentTime_;
    }

    void increaseTime(RealType dt) {
      setTime(getTime() + dt);
    }

    void setTime(RealType time) {
      currentTime_ =time;
      //time at statData is redundant
      statData[Stats::TIME] = currentTime_;
    }

    RealType getChi() {
      return chi_;
    }

    void setChi(RealType chi) {
      chi_ = chi;
    }

    RealType getIntegralOfChiDt() {
      return integralOfChiDt_;
    }

    void setIntegralOfChiDt(RealType integralOfChiDt) {
      integralOfChiDt_ = integralOfChiDt;
    }
            

    void setOrthoTolerance(RealType orthoTolerance) {
      orthoTolerance_ = orthoTolerance;
    }

    Mat3x3d getEta() {
      return eta_;
    }

    void setEta(const Mat3x3d& eta) {
      eta_ = eta;
    }
            
    DataStorage atomData;
    DataStorage rigidbodyData;
    Stats statData;
            
  private:
    RealType currentTime_;

    Mat3x3d hmat_;
    Mat3x3d invHmat_;
    RealType orthoTolerance_;
    int orthoRhombic_;

    RealType chi_;
    RealType integralOfChiDt_;
    Mat3x3d eta_;
            
    int id_; /**< identification number of the snapshot */
  };

  typedef DataStorage (Snapshot::*DataStoragePointer); 
}
#endif //BRAINS_SNAPSHOT_HPP
Revision:	1021
Committed:	Wed Aug 2 19:40:39 2006 UTC (18 years, 9 months ago) by gezelter
File size:	5420 byte(s)
Log Message:	starting change of file formats
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* 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	*/
41
42	/**
43	* @file Snapshot.hpp
44	* @author tlin
45	* @date 10/20/2004
46	* @time 23:56am
47	* @version 1.0
48	*/
49
50	#ifndef BRAINS_SNAPSHOT_HPP
51	#define BRAINS_SNAPSHOT_HPP
52
53	#include <vector>
54
55	#include "brains/DataStorage.hpp"
56	#include "brains/Stats.hpp"
57	#include "UseTheForce/DarkSide/simulation_interface.h"
58
59	namespace oopse{
60
61	/**
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
71	Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies),
72	currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) {
73
74	}
75
76	Snapshot(int nAtoms, int nRigidbodies, int storageLayout)
77	: atomData(nAtoms, storageLayout), rigidbodyData(nRigidbodies, storageLayout),
78	currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) {
79
80	}
81
82	/** Returns the id of this Snapshot */
83	int getID() {
84	return id_;
85	}
86
87	/** Sets the id of this Snapshot */
88	void setID(int id) {
89	id_ = id;
90	}
91
92	int getSize() {
93	return atomData.getSize() + rigidbodyData.getSize();
94	}
95
96	/** Returns the number of atoms */
97	int getNumberOfAtoms() {
98	return atomData.getSize();
99	}
100
101	/** Returns the number of rigid bodies */
102	int getNumberOfRigidBodies() {
103	return rigidbodyData.getSize();
104	}
105
106	/** Returns the H-Matrix */
107	Mat3x3d getHmat() {
108	return hmat_;
109	}
110
111	/** Sets the H-Matrix */
112	void setHmat(const Mat3x3d& m);
113
114	RealType getVolume() {
115	return hmat_.determinant();
116	}
117
118	/** Returns the inverse H-Matrix */
119	Mat3x3d getInvHmat() {
120	return invHmat_;
121	}
122
123	/** Wrapping the vector according to periodic boundary condition*/
124	void wrapVector(Vector3d& v);
125
126
127	RealType getTime() {
128	return currentTime_;
129	}
130
131	void increaseTime(RealType dt) {
132	setTime(getTime() + dt);
133	}
134
135	void setTime(RealType time) {
136	currentTime_ =time;
137	//time at statData is redundant
138	statData[Stats::TIME] = currentTime_;
139	}
140
141	RealType getChi() {
142	return chi_;
143	}
144
145	void setChi(RealType chi) {
146	chi_ = chi;
147	}
148
149	RealType getIntegralOfChiDt() {
150	return integralOfChiDt_;
151	}
152
153	void setIntegralOfChiDt(RealType integralOfChiDt) {
154	integralOfChiDt_ = integralOfChiDt;
155	}
156
157
158	void setOrthoTolerance(RealType orthoTolerance) {
159	orthoTolerance_ = orthoTolerance;
160	}
161
162	Mat3x3d getEta() {
163	return eta_;
164	}
165
166	void setEta(const Mat3x3d& eta) {
167	eta_ = eta;
168	}
169
170	DataStorage atomData;
171	DataStorage rigidbodyData;
172	Stats statData;
173
174	private:
175	RealType currentTime_;
176
177	Mat3x3d hmat_;
178	Mat3x3d invHmat_;
179	RealType orthoTolerance_;
180	int orthoRhombic_;
181
182	RealType chi_;
183	RealType integralOfChiDt_;
184	Mat3x3d eta_;
185
186	int id_; /*< identification number of the snapshot /
187	};
188
189	typedef DataStorage (Snapshot::*DataStoragePointer);
190	}
191	#endif //BRAINS_SNAPSHOT_HPP