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 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);
    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:	1544
Committed:	Fri Mar 18 19:31:52 2011 UTC (14 years, 1 month ago) by gezelter
File size:	7746 byte(s)
Log Message:	More modifications for paralllel rewrite
#	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	1544	/** Returns the number of rigid bodies */
122			int getNumberOfCutoffGroups() {
123			return cgData.getSize();
124			}
125
126	gezelter	507	/** Returns the H-Matrix */
127			Mat3x3d getHmat() {
128			return hmat_;
129			}
130	tim	152
131	gezelter	507	/** Sets the H-Matrix */
132			void setHmat(const Mat3x3d& m);
133	gezelter	246
134	tim	963	RealType getVolume() {
135	chuckv	1302	if (hasVolume_){
136			return volume_;
137			}else{
138			return hmat_.determinant();
139			}
140	gezelter	507	}
141	tim	152
142	chuckv	1302	void setVolume(RealType volume){
143			hasVolume_=true;
144			volume_ = volume;
145			}
146
147	gezelter	507	/** Returns the inverse H-Matrix */
148			Mat3x3d getInvHmat() {
149			return invHmat_;
150			}
151	tim	152
152	gezelter	507	/** Wrapping the vector according to periodic boundary condition*/
153			void wrapVector(Vector3d& v);
154	gezelter	1104	Vector3d getCOM();
155			Vector3d getCOMvel();
156			Vector3d getCOMw();
157	gezelter	246
158	tim	963	RealType getTime() {
159	gezelter	507	return currentTime_;
160			}
161	tim	152
162	tim	963	void increaseTime(RealType dt) {
163	gezelter	507	setTime(getTime() + dt);
164			}
165	tim	152
166	tim	963	void setTime(RealType time) {
167	gezelter	507	currentTime_ =time;
168			//time at statData is redundant
169			statData[Stats::TIME] = currentTime_;
170			}
171	tim	152
172	tim	963	RealType getChi() {
173	gezelter	507	return chi_;
174			}
175	gezelter	246
176	tim	963	void setChi(RealType chi) {
177	gezelter	507	chi_ = chi;
178			}
179	gezelter	246
180	tim	963	RealType getIntegralOfChiDt() {
181	gezelter	507	return integralOfChiDt_;
182			}
183	gezelter	246
184	tim	963	void setIntegralOfChiDt(RealType integralOfChiDt) {
185	gezelter	507	integralOfChiDt_ = integralOfChiDt;
186			}
187	gezelter	246
188	gezelter	1021
189			void setOrthoTolerance(RealType orthoTolerance) {
190			orthoTolerance_ = orthoTolerance;
191			}
192
193	gezelter	507	Mat3x3d getEta() {
194			return eta_;
195			}
196	gezelter	246
197	gezelter	507	void setEta(const Mat3x3d& eta) {
198			eta_ = eta;
199			}
200	gezelter	1104
201			bool hasCOM() {
202			return hasCOM_;
203			}
204
205			void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
206			COM_ = COM;
207			COMvel_ = COMvel;
208			COMw_ = COMw;
209			hasCOM_ = true;
210			}
211	gezelter	1540
212			Vector3d getAtomPosByIindex(int iIndex) {
213			#ifdef IS_MPI
214			return atomIData.position[iIndex];
215			#else
216			return atomData.position[iIndex];
217			#endif
218			}
219			Vector3d getAtomPosByJindex(int jIndex) {
220			#ifdef IS_MPI
221			return atomJData.position[jIndex];
222			#else
223			return atomData.position[jIndex];
224			#endif
225			}
226
227			Vector3d getCutoffGroupPosByIindex(int iIndex) {
228			#ifdef IS_MPI
229			return cgIData.position[iIndex];
230			#else
231			return cgData.position[iIndex];
232			#endif
233			}
234			Vector3d getCutoffGroupPosByJindex(int jIndex) {
235			#ifdef IS_MPI
236			return cgJData.position[jIndex];
237			#else
238			return cgData.position[jIndex];
239			#endif
240			}
241
242	gezelter	507	DataStorage atomData;
243			DataStorage rigidbodyData;
244	gezelter	1540	DataStorage cgData;
245	gezelter	1541	Stats statData;
246	gezelter	1540
247			#ifdef IS_MPI
248			DataStorage atomIData;
249			DataStorage atomJData;
250			DataStorage cgIData;
251			DataStorage cgJData;
252			#endif
253	gezelter	1541
254	tim	152
255	gezelter	507	private:
256	tim	963	RealType currentTime_;
257	gezelter	246
258	gezelter	507	Mat3x3d hmat_;
259			Mat3x3d invHmat_;
260	gezelter	1021	RealType orthoTolerance_;
261	gezelter	507	int orthoRhombic_;
262	chuckv	1302	RealType volume_;
263	gezelter	246
264	tim	963	RealType chi_;
265			RealType integralOfChiDt_;
266	gezelter	507	Mat3x3d eta_;
267	gezelter	1104	Vector3d COM_;
268			Vector3d COMvel_;
269			Vector3d COMw_;
270	gezelter	1287	int id_; /*< identification number of the snapshot /
271	gezelter	1104	bool hasCOM_;
272	chuckv	1302	bool hasVolume_;
273	gezelter	246
274	gezelter	507	};
275	tim	122
276	gezelter	507	typedef DataStorage (Snapshot::*DataStoragePointer);
277	tim	122	}
278			#endif //BRAINS_SNAPSHOT_HPP