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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
  
#ifndef BRAINS_SNAPSHOT_HPP
#define BRAINS_SNAPSHOT_HPP

#include <vector>

#include "brains/DataStorage.hpp"
#include "nonbonded/NonBondedInteraction.hpp"
#include "brains/Stats.hpp"

using namespace std;
namespace OpenMD{

  /**
   * FrameData is a structure for holding system-wide dynamic data
   * about the simulation.
   */
  
  struct FrameData {
    int id;                       /**< identification number of the snapshot */
    RealType currentTime;         /**< current time */
    Mat3x3d  hmat;                /**< axes of the periodic box in matrix form */
    Mat3x3d  invHmat;             /**< the inverse of the Hmat matrix */
    bool     orthoRhombic;        /**< is this an orthorhombic periodic box? */
    RealType totalEnergy;         /**< total energy of this frame */
    RealType translationalKinetic; /**< translational kinetic energy of this frame */
    RealType rotationalKinetic;   /**< rotational kinetic energy of this frame */
    RealType kineticEnergy;       /**< kinetic energy of this frame */
    RealType potentialEnergy;     /**< potential energy of this frame */
    RealType shortRangePotential; /**< short-range contributions to the potential*/
    RealType longRangePotential;  /**< long-range contributions to the potential */
    RealType bondPotential;       /**< bonded contribution to the potential */
    RealType bendPotential;       /**< angle-bending contribution to the potential */
    RealType torsionPotential;    /**< dihedral (torsion angle) contribution to the potential */
    RealType inversionPotential;  /**< inversion (planarity) contribution to the potential */
    potVec   lrPotentials;        /**< breakdown of long-range potentials by family */
    potVec   excludedPotentials;  /**< breakdown of excluded potentials by family */
    RealType restraintPotential;  /**< potential energy of restraints */
    RealType rawPotential;        /**< unrestrained potential energy (when restraints are applied) */
    RealType volume;              /**< total volume of this frame */
    RealType pressure;            /**< pressure of this frame */
    RealType temperature;         /**< temperature of this frame */
    pair<RealType, RealType> thermostat;    /**< thermostat variables */
    RealType electronicTemperature; /**< temperature of the electronic degrees of freedom */
    pair<RealType, RealType> electronicThermostat; /**< thermostat variables for electronic degrees of freedom */
    Mat3x3d  barostat;            /**< barostat matrix */
    Vector3d COM;                 /**< location of system center of mass */
    Vector3d COMvel;              /**< system center of mass velocity */
    Vector3d COMw;                /**< system center of mass angular velocity */
    Mat3x3d  inertiaTensor;       /**< inertia tensor for entire system */
    RealType gyrationalVolume;    /**< gyrational volume for entire system */
    RealType hullVolume;          /**< hull volume for entire system */
    Mat3x3d  stressTensor;        /**< stress tensor */
    Mat3x3d  pressureTensor;      /**< pressure tensor */
    Vector3d systemDipole;        /**< total system dipole moment */
    Vector3d conductiveHeatFlux;  /**< heat flux vector (conductive only) */
    Vector3d convectiveHeatFlux;  /**< heat flux vector (convective only) */
    RealType conservedQuantity;   /**< anything conserved by the integrator */
  };


  /**
   * @class Snapshot 
   * @brief The Snapshot class is a repository storing dynamic data during a
   * Simulation.  Every Snapshot contains FrameData (for global information)
   * as well as DataStorage (one for Atoms, one for RigidBodies, and one for 
   * CutoffGroups).
   */
  class Snapshot {

  public:            
    Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups);
    Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, int storageLayout);    
    /** Returns the id of this Snapshot */
    int      getID();
    /** Sets the id of this Snapshot */
    void     setID(int id);

    /** sets the state of the computed properties to false */
    void     clearDerivedProperties();

    int      getSize();
    /** Returns the number of atoms */
    int      getNumberOfAtoms();
    /** Returns the number of rigid bodies */
    int      getNumberOfRigidBodies();
    /** Returns the number of rigid bodies */
    int      getNumberOfCutoffGroups();

    /** Returns the H-Matrix */
    Mat3x3d  getHmat();
    /** Sets the H-Matrix */
    void     setHmat(const Mat3x3d& m);
    /** Returns the inverse H-Matrix */
    Mat3x3d  getInvHmat();
            
    RealType getVolume();
    void     setVolume(const RealType vol);

    /** 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);

    void     setCOM(const Vector3d &com);
    void     setCOMvel(const Vector3d &comVel);
    void     setCOMw(const Vector3d &comw);

    Vector3d getCOM();
    Vector3d getCOMvel();
    Vector3d getCOMw();
            
    RealType getTime();
    void     increaseTime(const RealType dt);
    void     setTime(const RealType time);

    void     setBondPotential(const RealType bp);
    void     setBendPotential(const RealType bp);
    void     setTorsionPotential(const RealType tp);
    void     setInversionPotential(const RealType ip);
    RealType getBondPotential();
    RealType getBendPotential();
    RealType getTorsionPotential();
    RealType getInversionPotential();

    RealType getShortRangePotential();

    void     setLongRangePotential(const potVec lrPot);
    RealType getLongRangePotential();
    potVec   getLongRangePotentials();

    void     setExcludedPotentials(const potVec exPot);
    potVec   getExcludedPotentials();
   
    void     setRestraintPotential(const RealType rp);
    RealType getRestraintPotential();

    void     setRawPotential(const RealType rp);
    RealType getRawPotential();

    RealType getPotentialEnergy();
    RealType getKineticEnergy();
    RealType getTranslationalKineticEnergy();
    RealType getRotationalKineticEnergy();
    void     setKineticEnergy(const RealType ke);
    void     setTranslationalKineticEnergy(const RealType tke);
    void     setRotationalKineticEnergy(const RealType rke);
    RealType getTotalEnergy();
    void     setTotalEnergy(const RealType te);
    RealType getConservedQuantity();
    void     setConservedQuantity(const RealType cq);
    RealType getTemperature();
    void     setTemperature(const RealType temp);
    RealType getElectronicTemperature();
    void     setElectronicTemperature(const RealType eTemp);
    RealType getPressure();
    void     setPressure(const RealType pressure);

    Mat3x3d  getPressureTensor();
    void     setPressureTensor(const Mat3x3d& pressureTensor);

    Mat3x3d  getStressTensor();
    void     setStressTensor(const Mat3x3d& stressTensor);

    Vector3d getConductiveHeatFlux();
    void     setConductiveHeatFlux(const Vector3d& chf);

    Vector3d getConvectiveHeatFlux();
    void     setConvectiveHeatFlux(const Vector3d& chf);

    Vector3d getHeatFlux();
    
    Vector3d getSystemDipole();
    void     setSystemDipole(const Vector3d& bd);

    pair<RealType, RealType> getThermostat();
    void setThermostat(const pair<RealType, RealType>& thermostat);

    pair<RealType, RealType> getElectronicThermostat();
    void setElectronicThermostat(const pair<RealType, RealType>& eThermostat);
            
    Mat3x3d  getBarostat();
    void     setBarostat(const Mat3x3d& barostat);

    Mat3x3d  getInertiaTensor();
    void     setInertiaTensor(const Mat3x3d& inertiaTensor);

    RealType getGyrationalVolume();
    void     setGyrationalVolume(const RealType gv);

    RealType getHullVolume();
    void     setHullVolume(const RealType hv);
    
    void     setOrthoTolerance(RealType orthoTolerance);

    DataStorage atomData;
    DataStorage rigidbodyData;
    DataStorage cgData;
    FrameData   frameData;

    bool hasTotalEnergy;         
    bool hasTranslationalKineticEnergy;    
    bool hasRotationalKineticEnergy;    
    bool hasKineticEnergy;    
    bool hasShortRangePotential;
    bool hasLongRangePotential;
    bool hasPotentialEnergy;     
    bool hasVolume;         
    bool hasPressure;       
    bool hasTemperature;    
    bool hasElectronicTemperature;
    bool hasCOM;             
    bool hasCOMvel;
    bool hasCOMw;
    bool hasPressureTensor;    
    bool hasSystemDipole;    
    bool hasConvectiveHeatFlux;
    bool hasInertiaTensor;
    bool hasGyrationalVolume;
    bool hasHullVolume;
    bool hasConservedQuantity;

  private:
    RealType orthoTolerance_;
    
  };

  typedef DataStorage (Snapshot::*DataStoragePointer); 
}
#endif //BRAINS_SNAPSHOT_HPP
Revision:	1764
Committed:	Tue Jul 3 18:32:27 2012 UTC (12 years, 10 months ago) by gezelter
File size:	11004 byte(s)
Log Message:	Refactored Snapshot and Stats to use the Accumulator classes. Collected a number of methods into Thermo that belonged there.
#	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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	122	*/
42	gezelter	246
43	tim	122	#ifndef BRAINS_SNAPSHOT_HPP
44			#define BRAINS_SNAPSHOT_HPP
45	tim	137
46			#include <vector>
47
48	tim	155	#include "brains/DataStorage.hpp"
49	gezelter	1757	#include "nonbonded/NonBondedInteraction.hpp"
50	gezelter	246	#include "brains/Stats.hpp"
51	tim	137
52	gezelter	1764	using namespace std;
53	gezelter	1390	namespace OpenMD{
54	tim	122
55	gezelter	1760	/**
56			* FrameData is a structure for holding system-wide dynamic data
57			* about the simulation.
58			*/
59
60	gezelter	1715	struct FrameData {
61	gezelter	1760	int id; /*< identification number of the snapshot /
62			RealType currentTime; /*< current time /
63			Mat3x3d hmat; /*< axes of the periodic box in matrix form /
64			Mat3x3d invHmat; /*< the inverse of the Hmat matrix /
65			bool orthoRhombic; /*< is this an orthorhombic periodic box? /
66			RealType totalEnergy; /*< total energy of this frame /
67	gezelter	1764	RealType translationalKinetic; /*< translational kinetic energy of this frame /
68			RealType rotationalKinetic; /*< rotational kinetic energy of this frame /
69	gezelter	1760	RealType kineticEnergy; /*< kinetic energy of this frame /
70			RealType potentialEnergy; /*< potential energy of this frame /
71	gezelter	1757	RealType shortRangePotential; /*< short-range contributions to the potential/
72	gezelter	1760	RealType longRangePotential; /*< long-range contributions to the potential /
73			RealType bondPotential; /*< bonded contribution to the potential /
74			RealType bendPotential; /*< angle-bending contribution to the potential /
75			RealType torsionPotential; /*< dihedral (torsion angle) contribution to the potential /
76			RealType inversionPotential; /*< inversion (planarity) contribution to the potential /
77			potVec lrPotentials; /*< breakdown of long-range potentials by family /
78			potVec excludedPotentials; /*< breakdown of excluded potentials by family /
79			RealType restraintPotential; /*< potential energy of restraints /
80			RealType rawPotential; /*< unrestrained potential energy (when restraints are applied) /
81	gezelter	1764	RealType volume; /*< total volume of this frame /
82			RealType pressure; /*< pressure of this frame /
83	gezelter	1760	RealType temperature; /*< temperature of this frame /
84	gezelter	1764	pair<RealType, RealType> thermostat; /*< thermostat variables /
85	gezelter	1715	RealType electronicTemperature; /*< temperature of the electronic degrees of freedom /
86	gezelter	1764	pair<RealType, RealType> electronicThermostat; /*< thermostat variables for electronic degrees of freedom /
87			Mat3x3d barostat; /*< barostat matrix /
88	gezelter	1760	Vector3d COM; /*< location of system center of mass /
89			Vector3d COMvel; /*< system center of mass velocity /
90			Vector3d COMw; /*< system center of mass angular velocity /
91	gezelter	1764	Mat3x3d inertiaTensor; /*< inertia tensor for entire system /
92			RealType gyrationalVolume; /*< gyrational volume for entire system /
93			RealType hullVolume; /*< hull volume for entire system /
94	gezelter	1760	Mat3x3d stressTensor; /*< stress tensor /
95			Mat3x3d pressureTensor; /*< pressure tensor /
96			Vector3d systemDipole; /*< total system dipole moment /
97			Vector3d conductiveHeatFlux; /*< heat flux vector (conductive only) /
98	gezelter	1764	Vector3d convectiveHeatFlux; /*< heat flux vector (convective only) /
99			RealType conservedQuantity; /*< anything conserved by the integrator /
100	gezelter	1715	};
101
102
103	gezelter	507	/**
104	gezelter	1760	* @class Snapshot
105			* @brief The Snapshot class is a repository storing dynamic data during a
106			* Simulation. Every Snapshot contains FrameData (for global information)
107			* as well as DataStorage (one for Atoms, one for RigidBodies, and one for
108			* CutoffGroups).
109	gezelter	507	*/
110			class Snapshot {
111	gezelter	1760
112			public:
113	gezelter	1764	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups);
114			Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, int storageLayout);
115	gezelter	507	/** Returns the id of this Snapshot */
116	gezelter	1764	int getID();
117	gezelter	507	/** Sets the id of this Snapshot */
118	gezelter	1764	void setID(int id);
119	tim	137
120	gezelter	1764	/** sets the state of the computed properties to false */
121			void clearDerivedProperties();
122	tim	152
123	gezelter	1764	int getSize();
124	gezelter	507	/** Returns the number of atoms */
125	gezelter	1764	int getNumberOfAtoms();
126	gezelter	507	/** Returns the number of rigid bodies */
127	gezelter	1764	int getNumberOfRigidBodies();
128	gezelter	1544	/** Returns the number of rigid bodies */
129	gezelter	1764	int getNumberOfCutoffGroups();
130	gezelter	1544
131	gezelter	507	/** Returns the H-Matrix */
132	gezelter	1764	Mat3x3d getHmat();
133	gezelter	507	/** Sets the H-Matrix */
134	gezelter	1764	void setHmat(const Mat3x3d& m);
135			/** Returns the inverse H-Matrix */
136			Mat3x3d getInvHmat();
137	gezelter	246
138	gezelter	1764	RealType getVolume();
139			void setVolume(const RealType vol);
140	tim	152
141	gezelter	1764	/** Wrapping the vector according to periodic boundary condition*/
142			void wrapVector(Vector3d& v);
143	chuckv	1302
144	gezelter	1562	/** Scaling a vector to multiples of the periodic box */
145			Vector3d scaleVector(Vector3d &v);
146
147	gezelter	1764	void setCOM(const Vector3d &com);
148			void setCOMvel(const Vector3d &comVel);
149			void setCOMw(const Vector3d &comw);
150	gezelter	1562
151	gezelter	1104	Vector3d getCOM();
152			Vector3d getCOMvel();
153			Vector3d getCOMw();
154	gezelter	246
155	gezelter	1764	RealType getTime();
156			void increaseTime(const RealType dt);
157			void setTime(const RealType time);
158	tim	152
159	gezelter	1764	void setBondPotential(const RealType bp);
160			void setBendPotential(const RealType bp);
161			void setTorsionPotential(const RealType tp);
162			void setInversionPotential(const RealType ip);
163			RealType getBondPotential();
164			RealType getBendPotential();
165			RealType getTorsionPotential();
166			RealType getInversionPotential();
167	tim	152
168	gezelter	1764	RealType getShortRangePotential();
169	tim	152
170	gezelter	1764	void setLongRangePotential(const potVec lrPot);
171			RealType getLongRangePotential();
172			potVec getLongRangePotentials();
173	gezelter	1760
174	gezelter	1764	void setExcludedPotentials(const potVec exPot);
175			potVec getExcludedPotentials();
176
177			void setRestraintPotential(const RealType rp);
178			RealType getRestraintPotential();
179	gezelter	1760
180	gezelter	1764	void setRawPotential(const RealType rp);
181			RealType getRawPotential();
182	gezelter	1760
183	gezelter	1764	RealType getPotentialEnergy();
184			RealType getKineticEnergy();
185			RealType getTranslationalKineticEnergy();
186			RealType getRotationalKineticEnergy();
187			void setKineticEnergy(const RealType ke);
188			void setTranslationalKineticEnergy(const RealType tke);
189			void setRotationalKineticEnergy(const RealType rke);
190			RealType getTotalEnergy();
191			void setTotalEnergy(const RealType te);
192			RealType getConservedQuantity();
193			void setConservedQuantity(const RealType cq);
194			RealType getTemperature();
195			void setTemperature(const RealType temp);
196			RealType getElectronicTemperature();
197			void setElectronicTemperature(const RealType eTemp);
198			RealType getPressure();
199			void setPressure(const RealType pressure);
200	gezelter	1760
201	gezelter	1764	Mat3x3d getPressureTensor();
202			void setPressureTensor(const Mat3x3d& pressureTensor);
203	gezelter	1760
204	gezelter	1764	Mat3x3d getStressTensor();
205			void setStressTensor(const Mat3x3d& stressTensor);
206	gezelter	1760
207	gezelter	1764	Vector3d getConductiveHeatFlux();
208			void setConductiveHeatFlux(const Vector3d& chf);
209	gezelter	1760
210	gezelter	1764	Vector3d getConvectiveHeatFlux();
211			void setConvectiveHeatFlux(const Vector3d& chf);
212	gezelter	1760
213	gezelter	1764	Vector3d getHeatFlux();
214	gezelter	1760
215	gezelter	1764	Vector3d getSystemDipole();
216			void setSystemDipole(const Vector3d& bd);
217	gezelter	1760
218	gezelter	1764	pair<RealType, RealType> getThermostat();
219			void setThermostat(const pair<RealType, RealType>& thermostat);
220	gezelter	1760
221	gezelter	1764	pair<RealType, RealType> getElectronicThermostat();
222			void setElectronicThermostat(const pair<RealType, RealType>& eThermostat);
223	gezelter	246
224	gezelter	1764	Mat3x3d getBarostat();
225			void setBarostat(const Mat3x3d& barostat);
226	gezelter	1021
227	gezelter	1764	Mat3x3d getInertiaTensor();
228			void setInertiaTensor(const Mat3x3d& inertiaTensor);
229	gezelter	1715
230	gezelter	1764	RealType getGyrationalVolume();
231			void setGyrationalVolume(const RealType gv);
232	gezelter	1715
233	gezelter	1764	RealType getHullVolume();
234			void setHullVolume(const RealType hv);
235
236			void setOrthoTolerance(RealType orthoTolerance);
237	gezelter	1715
238	gezelter	507	DataStorage atomData;
239			DataStorage rigidbodyData;
240	gezelter	1540	DataStorage cgData;
241	gezelter	1764	FrameData frameData;
242	gezelter	1540
243	gezelter	1764	bool hasTotalEnergy;
244			bool hasTranslationalKineticEnergy;
245			bool hasRotationalKineticEnergy;
246			bool hasKineticEnergy;
247			bool hasShortRangePotential;
248			bool hasLongRangePotential;
249			bool hasPotentialEnergy;
250			bool hasVolume;
251			bool hasPressure;
252			bool hasTemperature;
253			bool hasElectronicTemperature;
254			bool hasCOM;
255			bool hasCOMvel;
256			bool hasCOMw;
257			bool hasPressureTensor;
258			bool hasSystemDipole;
259			bool hasConvectiveHeatFlux;
260			bool hasInertiaTensor;
261			bool hasGyrationalVolume;
262			bool hasHullVolume;
263			bool hasConservedQuantity;
264
265	gezelter	507	private:
266	gezelter	1021	RealType orthoTolerance_;
267	gezelter	1764
268	gezelter	507	};
269	tim	122
270	gezelter	507	typedef DataStorage (Snapshot::*DataStoragePointer);
271	tim	122	}
272			#endif //BRAINS_SNAPSHOT_HPP