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"

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, 
             int nCutoffGroups) : atomData(nAtoms), 
                                  rigidbodyData(nRigidbodies),
                                  cgData(nCutoffGroups, DataStorage::dslPosition),
                                  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 nCutoffGroups, 
             int storageLayout) : atomData(nAtoms, storageLayout), 
                                  rigidbodyData(nRigidbodies, storageLayout),
                                  cgData(nCutoffGroups, DataStorage::dslPosition),
                                  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 number of rigid bodies */
    int getNumberOfCutoffGroups() {
      return cgData.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);
    /** Scaling a vector to multiples of the periodic box */
    Vector3d scaleVector(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;
    DataStorage cgData;
    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:	1562
Committed:	Thu May 12 17:00:14 2011 UTC (13 years, 11 months ago) by gezelter
File size:	7002 byte(s)
Log Message:	changes for cell linked lists
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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	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	tim	137
58	gezelter	1390	namespace OpenMD{
59	tim	122
60	gezelter	507	/**
61			* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
62			* @brief Snapshot class is a repository class for storing dynamic data during
63			* Simulation
64	gezelter	1540	* Every snapshot class will contain one DataStorage for atoms and one DataStorage
65	gezelter	507	* for rigid bodies.
66			*/
67			class Snapshot {
68			public:
69	tim	146
70	gezelter	1540	Snapshot(int nAtoms, int nRigidbodies,
71			int nCutoffGroups) : atomData(nAtoms),
72			rigidbodyData(nRigidbodies),
73			cgData(nCutoffGroups, DataStorage::dslPosition),
74			currentTime_(0),
75			orthoTolerance_(1e-6),
76			orthoRhombic_(0),
77			chi_(0.0),
78			integralOfChiDt_(0.0),
79			eta_(0.0), id_(-1), hasCOM_(false),
80			hasVolume_(false), volume_(0.0) {
81	gezelter	246
82	gezelter	507	}
83	tim	137
84	gezelter	1540	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
85			int storageLayout) : atomData(nAtoms, storageLayout),
86			rigidbodyData(nRigidbodies, storageLayout),
87			cgData(nCutoffGroups, DataStorage::dslPosition),
88			currentTime_(0), orthoTolerance_(1e-6),
89			orthoRhombic_(0), chi_(0.0),
90			integralOfChiDt_(0.0), eta_(0.0), id_(-1),
91			hasCOM_(false), hasVolume_(false),
92			volume_(0.0) {
93			}
94
95	gezelter	507	/** Returns the id of this Snapshot */
96			int getID() {
97			return id_;
98			}
99	tim	137
100	gezelter	507	/** Sets the id of this Snapshot */
101			void setID(int id) {
102			id_ = id;
103			}
104	tim	137
105	gezelter	507	int getSize() {
106			return atomData.getSize() + rigidbodyData.getSize();
107			}
108	tim	152
109	gezelter	507	/** Returns the number of atoms */
110			int getNumberOfAtoms() {
111			return atomData.getSize();
112			}
113	tim	152
114	gezelter	507	/** Returns the number of rigid bodies */
115			int getNumberOfRigidBodies() {
116			return rigidbodyData.getSize();
117			}
118	tim	152
119	gezelter	1544	/** Returns the number of rigid bodies */
120			int getNumberOfCutoffGroups() {
121			return cgData.getSize();
122			}
123
124	gezelter	507	/** Returns the H-Matrix */
125			Mat3x3d getHmat() {
126			return hmat_;
127			}
128	tim	152
129	gezelter	507	/** Sets the H-Matrix */
130			void setHmat(const Mat3x3d& m);
131	gezelter	246
132	tim	963	RealType getVolume() {
133	chuckv	1302	if (hasVolume_){
134			return volume_;
135			}else{
136			return hmat_.determinant();
137			}
138	gezelter	507	}
139	tim	152
140	chuckv	1302	void setVolume(RealType volume){
141			hasVolume_=true;
142			volume_ = volume;
143			}
144
145	gezelter	507	/** Returns the inverse H-Matrix */
146			Mat3x3d getInvHmat() {
147			return invHmat_;
148			}
149	tim	152
150	gezelter	507	/** Wrapping the vector according to periodic boundary condition*/
151			void wrapVector(Vector3d& v);
152	gezelter	1562	/** Scaling a vector to multiples of the periodic box */
153			Vector3d scaleVector(Vector3d &v);
154
155
156	gezelter	1104	Vector3d getCOM();
157			Vector3d getCOMvel();
158			Vector3d getCOMw();
159	gezelter	246
160	tim	963	RealType getTime() {
161	gezelter	507	return currentTime_;
162			}
163	tim	152
164	tim	963	void increaseTime(RealType dt) {
165	gezelter	507	setTime(getTime() + dt);
166			}
167	tim	152
168	tim	963	void setTime(RealType time) {
169	gezelter	507	currentTime_ =time;
170			//time at statData is redundant
171			statData[Stats::TIME] = currentTime_;
172			}
173	tim	152
174	tim	963	RealType getChi() {
175	gezelter	507	return chi_;
176			}
177	gezelter	246
178	tim	963	void setChi(RealType chi) {
179	gezelter	507	chi_ = chi;
180			}
181	gezelter	246
182	tim	963	RealType getIntegralOfChiDt() {
183	gezelter	507	return integralOfChiDt_;
184			}
185	gezelter	246
186	tim	963	void setIntegralOfChiDt(RealType integralOfChiDt) {
187	gezelter	507	integralOfChiDt_ = integralOfChiDt;
188			}
189	gezelter	246
190	gezelter	1021
191			void setOrthoTolerance(RealType orthoTolerance) {
192			orthoTolerance_ = orthoTolerance;
193			}
194
195	gezelter	507	Mat3x3d getEta() {
196			return eta_;
197			}
198	gezelter	246
199	gezelter	507	void setEta(const Mat3x3d& eta) {
200			eta_ = eta;
201			}
202	gezelter	1104
203			bool hasCOM() {
204			return hasCOM_;
205			}
206
207			void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
208			COM_ = COM;
209			COMvel_ = COMvel;
210			COMw_ = COMw;
211			hasCOM_ = true;
212			}
213	gezelter	1540
214	gezelter	507	DataStorage atomData;
215			DataStorage rigidbodyData;
216	gezelter	1540	DataStorage cgData;
217	gezelter	1541	Stats statData;
218	gezelter	1540
219	gezelter	507	private:
220	tim	963	RealType currentTime_;
221	gezelter	246
222	gezelter	507	Mat3x3d hmat_;
223			Mat3x3d invHmat_;
224	gezelter	1021	RealType orthoTolerance_;
225	gezelter	507	int orthoRhombic_;
226	chuckv	1302	RealType volume_;
227	gezelter	246
228	tim	963	RealType chi_;
229			RealType integralOfChiDt_;
230	gezelter	507	Mat3x3d eta_;
231	gezelter	1104	Vector3d COM_;
232			Vector3d COMvel_;
233			Vector3d COMw_;
234	gezelter	1287	int id_; /*< identification number of the snapshot /
235	gezelter	1104	bool hasCOM_;
236	chuckv	1302	bool hasVolume_;
237	gezelter	246
238	gezelter	507	};
239	tim	122
240	gezelter	507	typedef DataStorage (Snapshot::*DataStoragePointer);
241	tim	122	}
242			#endif //BRAINS_SNAPSHOT_HPP