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);
    Vector3d getCOM();
    Vector3d getCOMvel();
    Vector3d getCOMw();
            
    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;
    }

    bool hasCOM() {
      return hasCOM_;
    }

    void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
      COM_ = COM;
      COMvel_ = COMvel;
      COMw_ = COMw;
      hasCOM_ = true;
    }
                  
    DataStorage atomData;
    DataStorage rigidbodyData;
    Stats statData;
            
  private:
    RealType currentTime_;

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

    RealType chi_;
    RealType integralOfChiDt_;
    Mat3x3d eta_;
    Vector3d COM_;
    Vector3d COMvel_;
    Vector3d COMw_;
    bool hasCOM_;
            
    int id_; /**< identification number of the snapshot */
  };

  typedef DataStorage (Snapshot::*DataStoragePointer); 
}
#endif //BRAINS_SNAPSHOT_HPP
Revision:	1104
Committed:	Fri Dec 29 21:43:18 2006 UTC (18 years, 4 months ago) by gezelter
Original Path:	*trunk/src/brains/Snapshot.hpp*
File size:	5807 byte(s)
Log Message:	Adding the ability to compute Center of Mass properties on reading in a dump file. DumpReader must be told if it needs to do this, however.
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	tim	122	*
4	gezelter	246	* 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	122	*/
41	gezelter	246
42	gezelter	507	/**
43			* @file Snapshot.hpp
44			* @author tlin
45			* @date 10/20/2004
46			* @time 23:56am
47			* @version 1.0
48			*/
49	tim	146
50	tim	122	#ifndef BRAINS_SNAPSHOT_HPP
51			#define BRAINS_SNAPSHOT_HPP
52	tim	137
53			#include <vector>
54
55	tim	155	#include "brains/DataStorage.hpp"
56	gezelter	246	#include "brains/Stats.hpp"
57			#include "UseTheForce/DarkSide/simulation_interface.h"
58	tim	137
59	tim	122	namespace oopse{
60
61	gezelter	507	/**
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	146
71	gezelter	507	Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies),
72	gezelter	1021	currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) {
73	gezelter	246
74	gezelter	507	}
75	tim	137
76	gezelter	507	Snapshot(int nAtoms, int nRigidbodies, int storageLayout)
77			: atomData(nAtoms, storageLayout), rigidbodyData(nRigidbodies, storageLayout),
78	gezelter	1021	currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) {
79	tim	316
80	gezelter	507	}
81	tim	122
82	gezelter	507	/** Returns the id of this Snapshot */
83			int getID() {
84			return id_;
85			}
86	tim	137
87	gezelter	507	/** Sets the id of this Snapshot */
88			void setID(int id) {
89			id_ = id;
90			}
91	tim	137
92	gezelter	507	int getSize() {
93			return atomData.getSize() + rigidbodyData.getSize();
94			}
95	tim	152
96	gezelter	507	/** Returns the number of atoms */
97			int getNumberOfAtoms() {
98			return atomData.getSize();
99			}
100	tim	152
101	gezelter	507	/** Returns the number of rigid bodies */
102			int getNumberOfRigidBodies() {
103			return rigidbodyData.getSize();
104			}
105	tim	152
106	gezelter	507	/** Returns the H-Matrix */
107			Mat3x3d getHmat() {
108			return hmat_;
109			}
110	tim	152
111	gezelter	507	/** Sets the H-Matrix */
112			void setHmat(const Mat3x3d& m);
113	gezelter	246
114	tim	963	RealType getVolume() {
115	gezelter	507	return hmat_.determinant();
116			}
117	tim	152
118	gezelter	507	/** Returns the inverse H-Matrix */
119			Mat3x3d getInvHmat() {
120			return invHmat_;
121			}
122	tim	152
123	gezelter	507	/** Wrapping the vector according to periodic boundary condition*/
124			void wrapVector(Vector3d& v);
125	gezelter	1104	Vector3d getCOM();
126			Vector3d getCOMvel();
127			Vector3d getCOMw();
128	gezelter	246
129	tim	963	RealType getTime() {
130	gezelter	507	return currentTime_;
131			}
132	tim	152
133	tim	963	void increaseTime(RealType dt) {
134	gezelter	507	setTime(getTime() + dt);
135			}
136	tim	152
137	tim	963	void setTime(RealType time) {
138	gezelter	507	currentTime_ =time;
139			//time at statData is redundant
140			statData[Stats::TIME] = currentTime_;
141			}
142	tim	152
143	tim	963	RealType getChi() {
144	gezelter	507	return chi_;
145			}
146	gezelter	246
147	tim	963	void setChi(RealType chi) {
148	gezelter	507	chi_ = chi;
149			}
150	gezelter	246
151	tim	963	RealType getIntegralOfChiDt() {
152	gezelter	507	return integralOfChiDt_;
153			}
154	gezelter	246
155	tim	963	void setIntegralOfChiDt(RealType integralOfChiDt) {
156	gezelter	507	integralOfChiDt_ = integralOfChiDt;
157			}
158	gezelter	246
159	gezelter	1021
160			void setOrthoTolerance(RealType orthoTolerance) {
161			orthoTolerance_ = orthoTolerance;
162			}
163
164	gezelter	507	Mat3x3d getEta() {
165			return eta_;
166			}
167	gezelter	246
168	gezelter	507	void setEta(const Mat3x3d& eta) {
169			eta_ = eta;
170			}
171	gezelter	1104
172			bool hasCOM() {
173			return hasCOM_;
174			}
175
176			void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
177			COM_ = COM;
178			COMvel_ = COMvel;
179			COMw_ = COMw;
180			hasCOM_ = true;
181			}
182
183	gezelter	507	DataStorage atomData;
184			DataStorage rigidbodyData;
185			Stats statData;
186	tim	152
187	gezelter	507	private:
188	tim	963	RealType currentTime_;
189	gezelter	246
190	gezelter	507	Mat3x3d hmat_;
191			Mat3x3d invHmat_;
192	gezelter	1021	RealType orthoTolerance_;
193	gezelter	507	int orthoRhombic_;
194	gezelter	246
195	tim	963	RealType chi_;
196			RealType integralOfChiDt_;
197	gezelter	507	Mat3x3d eta_;
198	gezelter	1104	Vector3d COM_;
199			Vector3d COMvel_;
200			Vector3d COMw_;
201			bool hasCOM_;
202	gezelter	246
203	gezelter	507	int id_; /*< identification number of the snapshot /
204			};
205	tim	122
206	gezelter	507	typedef DataStorage (Snapshot::*DataStoragePointer);
207	tim	122	}
208			#endif //BRAINS_SNAPSHOT_HPP