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:	3432
Committed:	Mon Jul 14 12:35:58 2008 UTC (16 years, 9 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.
#	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
60	namespace oopse{
61
62	/**
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
72	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
82	}
83
84	Snapshot(int nAtoms, int nRigidbodies, int storageLayout)
85	: 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
90	}
91
92	/** Returns the id of this Snapshot */
93	int getID() {
94	return id_;
95	}
96
97	/** Sets the id of this Snapshot */
98	void setID(int id) {
99	id_ = id;
100	}
101
102	int getSize() {
103	return atomData.getSize() + rigidbodyData.getSize();
104	}
105
106	/** Returns the number of atoms */
107	int getNumberOfAtoms() {
108	return atomData.getSize();
109	}
110
111	/** Returns the number of rigid bodies */
112	int getNumberOfRigidBodies() {
113	return rigidbodyData.getSize();
114	}
115
116	/** Returns the H-Matrix */
117	Mat3x3d getHmat() {
118	return hmat_;
119	}
120
121	/** Sets the H-Matrix */
122	void setHmat(const Mat3x3d& m);
123
124	RealType getVolume() {
125	return hmat_.determinant();
126	}
127
128	/** Returns the inverse H-Matrix */
129	Mat3x3d getInvHmat() {
130	return invHmat_;
131	}
132
133	/** Wrapping the vector according to periodic boundary condition*/
134	void wrapVector(Vector3d& v);
135	Vector3d getCOM();
136	Vector3d getCOMvel();
137	Vector3d getCOMw();
138
139	RealType getTime() {
140	return currentTime_;
141	}
142
143	void increaseTime(RealType dt) {
144	setTime(getTime() + dt);
145	}
146
147	void setTime(RealType time) {
148	currentTime_ =time;
149	//time at statData is redundant
150	statData[Stats::TIME] = currentTime_;
151	}
152
153	RealType getChi() {
154	return chi_;
155	}
156
157	void setChi(RealType chi) {
158	chi_ = chi;
159	}
160
161	RealType getIntegralOfChiDt() {
162	return integralOfChiDt_;
163	}
164
165	void setIntegralOfChiDt(RealType integralOfChiDt) {
166	integralOfChiDt_ = integralOfChiDt;
167	}
168
169
170	void setOrthoTolerance(RealType orthoTolerance) {
171	orthoTolerance_ = orthoTolerance;
172	}
173
174	Mat3x3d getEta() {
175	return eta_;
176	}
177
178	void setEta(const Mat3x3d& eta) {
179	eta_ = eta;
180	}
181
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	DataStorage atomData;
194	DataStorage rigidbodyData;
195	Stats statData;
196
197	private:
198	RealType currentTime_;
199
200	Mat3x3d hmat_;
201	Mat3x3d invHmat_;
202	RealType orthoTolerance_;
203	int orthoRhombic_;
204
205	RealType chi_;
206	RealType integralOfChiDt_;
207	Mat3x3d eta_;
208	Vector3d COM_;
209	Vector3d COMvel_;
210	Vector3d COMw_;
211	bool hasCOM_;
212
213	int id_; /*< identification number of the snapshot /
214	};
215
216	typedef DataStorage (Snapshot::*DataStoragePointer);
217	}
218	#endif //BRAINS_SNAPSHOT_HPP