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, 234107 (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 */
    Mat3x3d  bBox;                /**< axes of a bounding box in matrix form */
    Mat3x3d  invBbox;             /**< the inverse of the bounding box */
    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 xyArea;              /**< XY area of this frame */
    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();

    /** Returns the Bounding Box */
    Mat3x3d  getBoundingBox();
    /** Sets the Bounding Box */
    void     setBoundingBox(const Mat3x3d& m);
    /** Returns the inverse Bounding Box*/
    Mat3x3d  getInvBoundingBox();
            
    RealType getVolume();
    RealType getXYarea();
    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 hasXYarea;
    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;
    bool hasBoundingBox;

  private:
    RealType orthoTolerance_;
    
  };

  typedef DataStorage (Snapshot::*DataStoragePointer); 
}
#endif //BRAINS_SNAPSHOT_HPP
Revision:	1858
Committed:	Wed Apr 3 21:32:13 2013 UTC (12 years, 7 months ago) by gezelter
File size:	11518 byte(s)
Log Message:	Some bugfixes for cell-linked-list-style neighbor lists when the simulation doesn't use periodic boundary conditions. Cleaning up some of the Hull stuff while we're in there.
#	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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#ifndef BRAINS_SNAPSHOT_HPP
44	#define BRAINS_SNAPSHOT_HPP
45
46	#include <vector>
47
48	#include "brains/DataStorage.hpp"
49	#include "nonbonded/NonBondedInteraction.hpp"
50	#include "brains/Stats.hpp"
51
52	using namespace std;
53	namespace OpenMD{
54
55	/**
56	* FrameData is a structure for holding system-wide dynamic data
57	* about the simulation.
58	*/
59
60	struct FrameData {
61	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	Mat3x3d bBox; /*< axes of a bounding box in matrix form /
66	Mat3x3d invBbox; /*< the inverse of the bounding box /
67	bool orthoRhombic; /*< is this an orthorhombic periodic box? /
68	RealType totalEnergy; /*< total energy of this frame /
69	RealType translationalKinetic; /*< translational kinetic energy of this frame /
70	RealType rotationalKinetic; /*< rotational kinetic energy of this frame /
71	RealType kineticEnergy; /*< kinetic energy of this frame /
72	RealType potentialEnergy; /*< potential energy of this frame /
73	RealType shortRangePotential; /*< short-range contributions to the potential/
74	RealType longRangePotential; /*< long-range contributions to the potential /
75	RealType bondPotential; /*< bonded contribution to the potential /
76	RealType bendPotential; /*< angle-bending contribution to the potential /
77	RealType torsionPotential; /*< dihedral (torsion angle) contribution to the potential /
78	RealType inversionPotential; /*< inversion (planarity) contribution to the potential /
79	potVec lrPotentials; /*< breakdown of long-range potentials by family /
80	potVec excludedPotentials; /*< breakdown of excluded potentials by family /
81	RealType restraintPotential; /*< potential energy of restraints /
82	RealType rawPotential; /*< unrestrained potential energy (when restraints are applied) /
83	RealType xyArea; /*< XY area of this frame /
84	RealType volume; /*< total volume of this frame /
85	RealType pressure; /*< pressure of this frame /
86	RealType temperature; /*< temperature of this frame /
87	pair<RealType, RealType> thermostat; /*< thermostat variables /
88	RealType electronicTemperature; /*< temperature of the electronic degrees of freedom /
89	pair<RealType, RealType> electronicThermostat; /*< thermostat variables for electronic degrees of freedom /
90	Mat3x3d barostat; /*< barostat matrix /
91	Vector3d COM; /*< location of system center of mass /
92	Vector3d COMvel; /*< system center of mass velocity /
93	Vector3d COMw; /*< system center of mass angular velocity /
94	Mat3x3d inertiaTensor; /*< inertia tensor for entire system /
95	RealType gyrationalVolume; /*< gyrational volume for entire system /
96	RealType hullVolume; /*< hull volume for entire system /
97	Mat3x3d stressTensor; /*< stress tensor /
98	Mat3x3d pressureTensor; /*< pressure tensor /
99	Vector3d systemDipole; /*< total system dipole moment /
100	Vector3d conductiveHeatFlux; /*< heat flux vector (conductive only) /
101	Vector3d convectiveHeatFlux; /*< heat flux vector (convective only) /
102	RealType conservedQuantity; /*< anything conserved by the integrator /
103	};
104
105
106	/**
107	* @class Snapshot
108	* @brief The Snapshot class is a repository storing dynamic data during a
109	* Simulation. Every Snapshot contains FrameData (for global information)
110	* as well as DataStorage (one for Atoms, one for RigidBodies, and one for
111	* CutoffGroups).
112	*/
113	class Snapshot {
114
115	public:
116	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups);
117	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, int storageLayout);
118	/** Returns the id of this Snapshot */
119	int getID();
120	/** Sets the id of this Snapshot */
121	void setID(int id);
122
123	/** sets the state of the computed properties to false */
124	void clearDerivedProperties();
125
126	int getSize();
127	/** Returns the number of atoms */
128	int getNumberOfAtoms();
129	/** Returns the number of rigid bodies */
130	int getNumberOfRigidBodies();
131	/** Returns the number of rigid bodies */
132	int getNumberOfCutoffGroups();
133
134	/** Returns the H-Matrix */
135	Mat3x3d getHmat();
136	/** Sets the H-Matrix */
137	void setHmat(const Mat3x3d& m);
138	/** Returns the inverse H-Matrix */
139	Mat3x3d getInvHmat();
140
141	/** Returns the Bounding Box */
142	Mat3x3d getBoundingBox();
143	/** Sets the Bounding Box */
144	void setBoundingBox(const Mat3x3d& m);
145	/** Returns the inverse Bounding Box*/
146	Mat3x3d getInvBoundingBox();
147
148	RealType getVolume();
149	RealType getXYarea();
150	void setVolume(const RealType vol);
151
152	/** Wrapping the vector according to periodic boundary condition*/
153	void wrapVector(Vector3d& v);
154
155	/** Scaling a vector to multiples of the periodic box */
156	Vector3d scaleVector(Vector3d &v);
157
158	void setCOM(const Vector3d &com);
159	void setCOMvel(const Vector3d &comVel);
160	void setCOMw(const Vector3d &comw);
161
162	Vector3d getCOM();
163	Vector3d getCOMvel();
164	Vector3d getCOMw();
165
166	RealType getTime();
167	void increaseTime(const RealType dt);
168	void setTime(const RealType time);
169
170	void setBondPotential(const RealType bp);
171	void setBendPotential(const RealType bp);
172	void setTorsionPotential(const RealType tp);
173	void setInversionPotential(const RealType ip);
174	RealType getBondPotential();
175	RealType getBendPotential();
176	RealType getTorsionPotential();
177	RealType getInversionPotential();
178
179	RealType getShortRangePotential();
180
181	void setLongRangePotential(const potVec lrPot);
182	RealType getLongRangePotential();
183	potVec getLongRangePotentials();
184
185	void setExcludedPotentials(const potVec exPot);
186	potVec getExcludedPotentials();
187
188	void setRestraintPotential(const RealType rp);
189	RealType getRestraintPotential();
190
191	void setRawPotential(const RealType rp);
192	RealType getRawPotential();
193
194	RealType getPotentialEnergy();
195	RealType getKineticEnergy();
196	RealType getTranslationalKineticEnergy();
197	RealType getRotationalKineticEnergy();
198	void setKineticEnergy(const RealType ke);
199	void setTranslationalKineticEnergy(const RealType tke);
200	void setRotationalKineticEnergy(const RealType rke);
201	RealType getTotalEnergy();
202	void setTotalEnergy(const RealType te);
203	RealType getConservedQuantity();
204	void setConservedQuantity(const RealType cq);
205	RealType getTemperature();
206	void setTemperature(const RealType temp);
207	RealType getElectronicTemperature();
208	void setElectronicTemperature(const RealType eTemp);
209	RealType getPressure();
210	void setPressure(const RealType pressure);
211
212	Mat3x3d getPressureTensor();
213	void setPressureTensor(const Mat3x3d& pressureTensor);
214
215	Mat3x3d getStressTensor();
216	void setStressTensor(const Mat3x3d& stressTensor);
217
218	Vector3d getConductiveHeatFlux();
219	void setConductiveHeatFlux(const Vector3d& chf);
220
221	Vector3d getConvectiveHeatFlux();
222	void setConvectiveHeatFlux(const Vector3d& chf);
223
224	Vector3d getHeatFlux();
225
226	Vector3d getSystemDipole();
227	void setSystemDipole(const Vector3d& bd);
228
229	pair<RealType, RealType> getThermostat();
230	void setThermostat(const pair<RealType, RealType>& thermostat);
231
232	pair<RealType, RealType> getElectronicThermostat();
233	void setElectronicThermostat(const pair<RealType, RealType>& eThermostat);
234
235	Mat3x3d getBarostat();
236	void setBarostat(const Mat3x3d& barostat);
237
238	Mat3x3d getInertiaTensor();
239	void setInertiaTensor(const Mat3x3d& inertiaTensor);
240
241	RealType getGyrationalVolume();
242	void setGyrationalVolume(const RealType gv);
243
244	RealType getHullVolume();
245	void setHullVolume(const RealType hv);
246
247	void setOrthoTolerance(RealType orthoTolerance);
248
249	DataStorage atomData;
250	DataStorage rigidbodyData;
251	DataStorage cgData;
252	FrameData frameData;
253
254	bool hasTotalEnergy;
255	bool hasTranslationalKineticEnergy;
256	bool hasRotationalKineticEnergy;
257	bool hasKineticEnergy;
258	bool hasShortRangePotential;
259	bool hasLongRangePotential;
260	bool hasPotentialEnergy;
261	bool hasXYarea;
262	bool hasVolume;
263	bool hasPressure;
264	bool hasTemperature;
265	bool hasElectronicTemperature;
266	bool hasCOM;
267	bool hasCOMvel;
268	bool hasCOMw;
269	bool hasPressureTensor;
270	bool hasSystemDipole;
271	bool hasConvectiveHeatFlux;
272	bool hasInertiaTensor;
273	bool hasGyrationalVolume;
274	bool hasHullVolume;
275	bool hasConservedQuantity;
276	bool hasBoundingBox;
277
278	private:
279	RealType orthoTolerance_;
280
281	};
282
283	typedef DataStorage (Snapshot::*DataStoragePointer);
284	}
285	#endif //BRAINS_SNAPSHOT_HPP