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, 
             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 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;
    }

    Vector3d getAtomPosByIindex(int iIndex) {
#ifdef IS_MPI
      return atomIData.position[iIndex];
#else
      return atomData.position[iIndex];
#endif
    }
    Vector3d getAtomPosByJindex(int jIndex) {
#ifdef IS_MPI
      return atomJData.position[jIndex];
#else
      return atomData.position[jIndex];
#endif
    }

    Vector3d getCutoffGroupPosByIindex(int iIndex) {
#ifdef IS_MPI
      return cgIData.position[iIndex];
#else
      return cgData.position[iIndex];
#endif
    }
    Vector3d getCutoffGroupPosByJindex(int jIndex) {
#ifdef IS_MPI
      return cgJData.position[jIndex];
#else
      return cgData.position[jIndex];
#endif
    }

    DataStorage atomData;
    DataStorage rigidbodyData;
    DataStorage cgData;
    Stats statData;

#ifdef IS_MPI
    DataStorage atomIData;
    DataStorage atomJData;
    DataStorage cgIData;
    DataStorage cgJData;
#endif
   
            
  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:	1541
Committed:	Fri Feb 4 20:04:56 2011 UTC (14 years, 3 months ago) by gezelter
File size:	7626 byte(s)
Log Message:	working on communicators
#	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			#include "UseTheForce/DarkSide/simulation_interface.h"
58	tim	137
59	chuckv	1112
60	gezelter	1390	namespace OpenMD{
61	tim	122
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	gezelter	1540	* Every snapshot class will contain one DataStorage for atoms and one DataStorage
67	gezelter	507	* for rigid bodies.
68			*/
69			class Snapshot {
70			public:
71	tim	146
72	gezelter	1540	Snapshot(int nAtoms, int nRigidbodies,
73			int nCutoffGroups) : atomData(nAtoms),
74			rigidbodyData(nRigidbodies),
75			cgData(nCutoffGroups, DataStorage::dslPosition),
76			currentTime_(0),
77			orthoTolerance_(1e-6),
78			orthoRhombic_(0),
79			chi_(0.0),
80			integralOfChiDt_(0.0),
81			eta_(0.0), id_(-1), hasCOM_(false),
82			hasVolume_(false), volume_(0.0) {
83	gezelter	246
84	gezelter	507	}
85	tim	137
86	gezelter	1540	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
87			int storageLayout) : atomData(nAtoms, storageLayout),
88			rigidbodyData(nRigidbodies, storageLayout),
89			cgData(nCutoffGroups, DataStorage::dslPosition),
90			currentTime_(0), orthoTolerance_(1e-6),
91			orthoRhombic_(0), chi_(0.0),
92			integralOfChiDt_(0.0), eta_(0.0), id_(-1),
93			hasCOM_(false), hasVolume_(false),
94			volume_(0.0) {
95			}
96
97	gezelter	507	/** Returns the id of this Snapshot */
98			int getID() {
99			return id_;
100			}
101	tim	137
102	gezelter	507	/** Sets the id of this Snapshot */
103			void setID(int id) {
104			id_ = id;
105			}
106	tim	137
107	gezelter	507	int getSize() {
108			return atomData.getSize() + rigidbodyData.getSize();
109			}
110	tim	152
111	gezelter	507	/** Returns the number of atoms */
112			int getNumberOfAtoms() {
113			return atomData.getSize();
114			}
115	tim	152
116	gezelter	507	/** Returns the number of rigid bodies */
117			int getNumberOfRigidBodies() {
118			return rigidbodyData.getSize();
119			}
120	tim	152
121	gezelter	507	/** Returns the H-Matrix */
122			Mat3x3d getHmat() {
123			return hmat_;
124			}
125	tim	152
126	gezelter	507	/** Sets the H-Matrix */
127			void setHmat(const Mat3x3d& m);
128	gezelter	246
129	tim	963	RealType getVolume() {
130	chuckv	1302	if (hasVolume_){
131			return volume_;
132			}else{
133			return hmat_.determinant();
134			}
135	gezelter	507	}
136	tim	152
137	chuckv	1302	void setVolume(RealType volume){
138			hasVolume_=true;
139			volume_ = volume;
140			}
141
142	gezelter	507	/** Returns the inverse H-Matrix */
143			Mat3x3d getInvHmat() {
144			return invHmat_;
145			}
146	tim	152
147	gezelter	507	/** Wrapping the vector according to periodic boundary condition*/
148			void wrapVector(Vector3d& v);
149	gezelter	1104	Vector3d getCOM();
150			Vector3d getCOMvel();
151			Vector3d getCOMw();
152	gezelter	246
153	tim	963	RealType getTime() {
154	gezelter	507	return currentTime_;
155			}
156	tim	152
157	tim	963	void increaseTime(RealType dt) {
158	gezelter	507	setTime(getTime() + dt);
159			}
160	tim	152
161	tim	963	void setTime(RealType time) {
162	gezelter	507	currentTime_ =time;
163			//time at statData is redundant
164			statData[Stats::TIME] = currentTime_;
165			}
166	tim	152
167	tim	963	RealType getChi() {
168	gezelter	507	return chi_;
169			}
170	gezelter	246
171	tim	963	void setChi(RealType chi) {
172	gezelter	507	chi_ = chi;
173			}
174	gezelter	246
175	tim	963	RealType getIntegralOfChiDt() {
176	gezelter	507	return integralOfChiDt_;
177			}
178	gezelter	246
179	tim	963	void setIntegralOfChiDt(RealType integralOfChiDt) {
180	gezelter	507	integralOfChiDt_ = integralOfChiDt;
181			}
182	gezelter	246
183	gezelter	1021
184			void setOrthoTolerance(RealType orthoTolerance) {
185			orthoTolerance_ = orthoTolerance;
186			}
187
188	gezelter	507	Mat3x3d getEta() {
189			return eta_;
190			}
191	gezelter	246
192	gezelter	507	void setEta(const Mat3x3d& eta) {
193			eta_ = eta;
194			}
195	gezelter	1104
196			bool hasCOM() {
197			return hasCOM_;
198			}
199
200			void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
201			COM_ = COM;
202			COMvel_ = COMvel;
203			COMw_ = COMw;
204			hasCOM_ = true;
205			}
206	gezelter	1540
207			Vector3d getAtomPosByIindex(int iIndex) {
208			#ifdef IS_MPI
209			return atomIData.position[iIndex];
210			#else
211			return atomData.position[iIndex];
212			#endif
213			}
214			Vector3d getAtomPosByJindex(int jIndex) {
215			#ifdef IS_MPI
216			return atomJData.position[jIndex];
217			#else
218			return atomData.position[jIndex];
219			#endif
220			}
221
222			Vector3d getCutoffGroupPosByIindex(int iIndex) {
223			#ifdef IS_MPI
224			return cgIData.position[iIndex];
225			#else
226			return cgData.position[iIndex];
227			#endif
228			}
229			Vector3d getCutoffGroupPosByJindex(int jIndex) {
230			#ifdef IS_MPI
231			return cgJData.position[jIndex];
232			#else
233			return cgData.position[jIndex];
234			#endif
235			}
236
237	gezelter	507	DataStorage atomData;
238			DataStorage rigidbodyData;
239	gezelter	1540	DataStorage cgData;
240	gezelter	1541	Stats statData;
241	gezelter	1540
242			#ifdef IS_MPI
243			DataStorage atomIData;
244			DataStorage atomJData;
245			DataStorage cgIData;
246			DataStorage cgJData;
247			#endif
248	gezelter	1541
249	tim	152
250	gezelter	507	private:
251	tim	963	RealType currentTime_;
252	gezelter	246
253	gezelter	507	Mat3x3d hmat_;
254			Mat3x3d invHmat_;
255	gezelter	1021	RealType orthoTolerance_;
256	gezelter	507	int orthoRhombic_;
257	chuckv	1302	RealType volume_;
258	gezelter	246
259	tim	963	RealType chi_;
260			RealType integralOfChiDt_;
261	gezelter	507	Mat3x3d eta_;
262	gezelter	1104	Vector3d COM_;
263			Vector3d COMvel_;
264			Vector3d COMw_;
265	gezelter	1287	int id_; /*< identification number of the snapshot /
266	gezelter	1104	bool hasCOM_;
267	chuckv	1302	bool hasVolume_;
268	gezelter	246
269	gezelter	507	};
270	tim	122
271	gezelter	507	typedef DataStorage (Snapshot::*DataStoragePointer);
272	tim	122	}
273			#endif //BRAINS_SNAPSHOT_HPP