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), 
                                             hasCOM_(false) {

    }

    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), hasCOM_(false)  {

      }
            
    /** 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:	1277
Committed:	Mon Jul 14 12:35:58 2008 UTC (17 years, 3 months ago) by gezelter
File size:	6181 byte(s)
Log Message:	Changes for implementing Amber force field: Added Inversions and worked on BaseAtomTypes so that they'd function with the fortran side.
#	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	chuckv	1112
60	tim	122	namespace oopse{
61
62	gezelter	507	/**
63			* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
64			* @brief Snapshot class is a repository class for storing dynamic data during
65			* Simulation
66			* Every snapshot class will contain one DataStorage for atoms and one DataStorage
67			* for rigid bodies.
68			*/
69			class Snapshot {
70			public:
71	tim	146
72	gezelter	1277	Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms),
73			rigidbodyData(nRigidbodies),
74			currentTime_(0),
75			orthoTolerance_(1e-6),
76			orthoRhombic_(0),
77			chi_(0.0),
78			integralOfChiDt_(0.0),
79			eta_(0.0), id_(-1),
80			hasCOM_(false) {
81	gezelter	246
82	gezelter	507	}
83	tim	137
84	gezelter	507	Snapshot(int nAtoms, int nRigidbodies, int storageLayout)
85	gezelter	1277	: atomData(nAtoms, storageLayout),
86			rigidbodyData(nRigidbodies, storageLayout),
87			currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0),
88			integralOfChiDt_(0.0), eta_(0.0), id_(-1), hasCOM_(false) {
89	tim	316
90	gezelter	507	}
91	tim	122
92	gezelter	507	/** Returns the id of this Snapshot */
93			int getID() {
94			return id_;
95			}
96	tim	137
97	gezelter	507	/** Sets the id of this Snapshot */
98			void setID(int id) {
99			id_ = id;
100			}
101	tim	137
102	gezelter	507	int getSize() {
103			return atomData.getSize() + rigidbodyData.getSize();
104			}
105	tim	152
106	gezelter	507	/** Returns the number of atoms */
107			int getNumberOfAtoms() {
108			return atomData.getSize();
109			}
110	tim	152
111	gezelter	507	/** Returns the number of rigid bodies */
112			int getNumberOfRigidBodies() {
113			return rigidbodyData.getSize();
114			}
115	tim	152
116	gezelter	507	/** Returns the H-Matrix */
117			Mat3x3d getHmat() {
118			return hmat_;
119			}
120	tim	152
121	gezelter	507	/** Sets the H-Matrix */
122			void setHmat(const Mat3x3d& m);
123	gezelter	246
124	tim	963	RealType getVolume() {
125	gezelter	507	return hmat_.determinant();
126			}
127	tim	152
128	gezelter	507	/** Returns the inverse H-Matrix */
129			Mat3x3d getInvHmat() {
130			return invHmat_;
131			}
132	tim	152
133	gezelter	507	/** Wrapping the vector according to periodic boundary condition*/
134			void wrapVector(Vector3d& v);
135	gezelter	1104	Vector3d getCOM();
136			Vector3d getCOMvel();
137			Vector3d getCOMw();
138	gezelter	246
139	tim	963	RealType getTime() {
140	gezelter	507	return currentTime_;
141			}
142	tim	152
143	tim	963	void increaseTime(RealType dt) {
144	gezelter	507	setTime(getTime() + dt);
145			}
146	tim	152
147	tim	963	void setTime(RealType time) {
148	gezelter	507	currentTime_ =time;
149			//time at statData is redundant
150			statData[Stats::TIME] = currentTime_;
151			}
152	tim	152
153	tim	963	RealType getChi() {
154	gezelter	507	return chi_;
155			}
156	gezelter	246
157	tim	963	void setChi(RealType chi) {
158	gezelter	507	chi_ = chi;
159			}
160	gezelter	246
161	tim	963	RealType getIntegralOfChiDt() {
162	gezelter	507	return integralOfChiDt_;
163			}
164	gezelter	246
165	tim	963	void setIntegralOfChiDt(RealType integralOfChiDt) {
166	gezelter	507	integralOfChiDt_ = integralOfChiDt;
167			}
168	gezelter	246
169	gezelter	1021
170			void setOrthoTolerance(RealType orthoTolerance) {
171			orthoTolerance_ = orthoTolerance;
172			}
173
174	gezelter	507	Mat3x3d getEta() {
175			return eta_;
176			}
177	gezelter	246
178	gezelter	507	void setEta(const Mat3x3d& eta) {
179			eta_ = eta;
180			}
181	gezelter	1104
182			bool hasCOM() {
183			return hasCOM_;
184			}
185
186			void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
187			COM_ = COM;
188			COMvel_ = COMvel;
189			COMw_ = COMw;
190			hasCOM_ = true;
191			}
192
193	gezelter	507	DataStorage atomData;
194			DataStorage rigidbodyData;
195			Stats statData;
196	tim	152
197	gezelter	507	private:
198	tim	963	RealType currentTime_;
199	gezelter	246
200	gezelter	507	Mat3x3d hmat_;
201			Mat3x3d invHmat_;
202	gezelter	1021	RealType orthoTolerance_;
203	gezelter	507	int orthoRhombic_;
204	gezelter	246
205	tim	963	RealType chi_;
206			RealType integralOfChiDt_;
207	gezelter	507	Mat3x3d eta_;
208	gezelter	1104	Vector3d COM_;
209			Vector3d COMvel_;
210			Vector3d COMw_;
211			bool hasCOM_;
212	gezelter	246
213	gezelter	507	int id_; /*< identification number of the snapshot /
214			};
215	tim	122
216	gezelter	507	typedef DataStorage (Snapshot::*DataStoragePointer);
217	tim	122	}
218			#endif //BRAINS_SNAPSHOT_HPP