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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
  
/**
 * @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 OpenMD{

  /**
   * @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), hasVolume_(false), volume_(0.0) {

    }

    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), hasVolume_(false),volume_(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);
            
    RealType getVolume() {
      if (hasVolume_){
        return volume_;
      }else{
        return hmat_.determinant();
      }
    }

    void setVolume(RealType volume){
      hasVolume_=true;
      volume_ = volume;
    }

    /** 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 volume_;

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

  typedef DataStorage (Snapshot::*DataStoragePointer); 
}
#endif //BRAINS_SNAPSHOT_HPP
Revision:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	6492 byte(s)
Log Message:	Creating busticated version of OpenMD
#	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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	* [4] Vardeman & Gezelter, in progress (2009).
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 OpenMD{
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), hasVolume_(false), volume_(0.0) {
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), hasVolume_(false),volume_(0.0) {
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	if (hasVolume_){
126	return volume_;
127	}else{
128	return hmat_.determinant();
129	}
130	}
131
132	void setVolume(RealType volume){
133	hasVolume_=true;
134	volume_ = volume;
135	}
136
137	/** Returns the inverse H-Matrix */
138	Mat3x3d getInvHmat() {
139	return invHmat_;
140	}
141
142	/** Wrapping the vector according to periodic boundary condition*/
143	void wrapVector(Vector3d& v);
144	Vector3d getCOM();
145	Vector3d getCOMvel();
146	Vector3d getCOMw();
147
148	RealType getTime() {
149	return currentTime_;
150	}
151
152	void increaseTime(RealType dt) {
153	setTime(getTime() + dt);
154	}
155
156	void setTime(RealType time) {
157	currentTime_ =time;
158	//time at statData is redundant
159	statData[Stats::TIME] = currentTime_;
160	}
161
162	RealType getChi() {
163	return chi_;
164	}
165
166	void setChi(RealType chi) {
167	chi_ = chi;
168	}
169
170	RealType getIntegralOfChiDt() {
171	return integralOfChiDt_;
172	}
173
174	void setIntegralOfChiDt(RealType integralOfChiDt) {
175	integralOfChiDt_ = integralOfChiDt;
176	}
177
178
179	void setOrthoTolerance(RealType orthoTolerance) {
180	orthoTolerance_ = orthoTolerance;
181	}
182
183	Mat3x3d getEta() {
184	return eta_;
185	}
186
187	void setEta(const Mat3x3d& eta) {
188	eta_ = eta;
189	}
190
191	bool hasCOM() {
192	return hasCOM_;
193	}
194
195	void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
196	COM_ = COM;
197	COMvel_ = COMvel;
198	COMw_ = COMw;
199	hasCOM_ = true;
200	}
201
202	DataStorage atomData;
203	DataStorage rigidbodyData;
204	Stats statData;
205
206	private:
207	RealType currentTime_;
208
209	Mat3x3d hmat_;
210	Mat3x3d invHmat_;
211	RealType orthoTolerance_;
212	int orthoRhombic_;
213	RealType volume_;
214
215	RealType chi_;
216	RealType integralOfChiDt_;
217	Mat3x3d eta_;
218	Vector3d COM_;
219	Vector3d COMvel_;
220	Vector3d COMw_;
221	int id_; /*< identification number of the snapshot /
222	bool hasCOM_;
223	bool hasVolume_;
224
225	};
226
227	typedef DataStorage (Snapshot::*DataStoragePointer);
228	}
229	#endif //BRAINS_SNAPSHOT_HPP