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root/OpenMD/branches/development/src/brains/Snapshot.hpp

Comparing:
trunk/src/brains/Snapshot.hpp (file contents), Revision 316 by tim, Fri Feb 11 22:41:02 2005 UTC vs.
branches/development/src/brains/Snapshot.hpp (file contents), Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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, 24107 (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
42	–	/**
43	–	* @file Snapshot.hpp
44	–	* @author tlin
45	–	* @date 10/20/2004
46	–	* @time 23:56am
47	–	* @version 1.0
48	–	*/
49	–
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"
57	–	#include "UseTheForce/DarkSide/simulation_interface.h"
51
52	<	namespace oopse{
52	>	using namespace std;
53	>	namespace OpenMD{
54
55	<	/**
56	<	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
57	<	* @brief Snapshot class is a repository class for storing dynamic data during
58	<	*  Simulation
59	<	* Every snapshot class will contain one DataStorage  for atoms and one DataStorage
60	<	*  for rigid bodies.
61	<	*/
62	<	class Snapshot {
63	<	public:
64	<
65	<	Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies),
66	<	currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0) {
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	>	bool     orthoRhombic;        /**< is this an orthorhombic periodic box? */
66	>	RealType totalEnergy;         /**< total energy of this frame */
67	>	RealType translationalKinetic; /**< translational kinetic energy of this frame */
68	>	RealType rotationalKinetic;   /**< rotational kinetic energy of this frame */
69	>	RealType kineticEnergy;       /**< kinetic energy of this frame */
70	>	RealType potentialEnergy;     /**< potential energy of this frame */
71	>	RealType shortRangePotential; /**< short-range contributions to the potential*/
72	>	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	>	RealType volume;              /**< total volume of this frame */
82	>	RealType pressure;            /**< pressure of this frame */
83	>	RealType temperature;         /**< temperature of this frame */
84	>	pair<RealType, RealType> thermostat;    /**< thermostat variables */
85	>	RealType electronicTemperature; /**< temperature of the electronic degrees of freedom */
86	>	pair<RealType, RealType> electronicThermostat; /**< thermostat variables for electronic degrees of freedom */
87	>	Mat3x3d  barostat;            /**< barostat matrix */
88	>	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	>	Mat3x3d  inertiaTensor;       /**< inertia tensor for entire system */
92	>	RealType gyrationalVolume;    /**< gyrational volume for entire system */
93	>	RealType hullVolume;          /**< hull volume for entire system */
94	>	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	>	Vector3d convectiveHeatFlux;  /**< heat flux vector (convective only) */
99	>	RealType conservedQuantity;   /**< anything conserved by the integrator */
100	>	};
101
74	–	}
102
103	<	Snapshot(int nAtoms, int nRigidbodies, int storageLayout)
104	<	: atomData(nAtoms, storageLayout), rigidbodyData(nRigidbodies, storageLayout),
105	<	currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0) {
103	>	/**
104	>	* @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	>	*/
110	>	class Snapshot {
111
112	<	}
113	<
114	<	/** Returns the id of this Snapshot */
115	<	int getID() {
116	<	return id_;
117	<	}
112	>	public:
113	>	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups);
114	>	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, int storageLayout);
115	>	/** Returns the id of this Snapshot */
116	>	int      getID();
117	>	/** Sets the id of this Snapshot */
118	>	void     setID(int id);
119
120	<	/** Sets the id of this Snapshot */
121	<	void setID(int id) {
89	<	id_ = id;
90	<	}
120	>	/** sets the state of the computed properties to false */
121	>	void     clearDerivedProperties();
122
123	<	int getSize() {
124	<	return atomData.getSize() + rigidbodyData.getSize();
125	<	}
123	>	int      getSize();
124	>	/** Returns the number of atoms */
125	>	int      getNumberOfAtoms();
126	>	/** Returns the number of rigid bodies */
127	>	int      getNumberOfRigidBodies();
128	>	/** Returns the number of rigid bodies */
129	>	int      getNumberOfCutoffGroups();
130
131	<	/** Returns the number of atoms */
132	<	int getNumberOfAtoms() {
133	<	return atomData.getSize();
134	<	}
131	>	/** Returns the H-Matrix */
132	>	Mat3x3d  getHmat();
133	>	/** Sets the H-Matrix */
134	>	void     setHmat(const Mat3x3d& m);
135	>	/** Returns the inverse H-Matrix */
136	>	Mat3x3d  getInvHmat();
137	>
138	>	RealType getVolume();
139	>	void     setVolume(const RealType vol);
140
141	<	/** Returns the number of rigid bodies */
142	<	int getNumberOfRigidBodies() {
103	<	return rigidbodyData.getSize();
104	<	}
141	>	/** Wrapping the vector according to periodic boundary condition*/
142	>	void     wrapVector(Vector3d& v);
143
144	<	/** Returns the H-Matrix */
145	<	Mat3x3d getHmat() {
108	<	return hmat_;
109	<	}
144	>	/** Scaling a vector to multiples of the periodic box */
145	>	Vector3d scaleVector(Vector3d &v);
146
147	<	/** Sets the H-Matrix */
148	<	void setHmat(const Mat3x3d& m);
147	>	void     setCOM(const Vector3d &com);
148	>	void     setCOMvel(const Vector3d &comVel);
149	>	void     setCOMw(const Vector3d &comw);
150	>
151	>	Vector3d getCOM();
152	>	Vector3d getCOMvel();
153	>	Vector3d getCOMw();
154
155	<	double getVolume() {
156	<	return hmat_.determinant();
157	<	}
155	>	RealType getTime();
156	>	void     increaseTime(const RealType dt);
157	>	void     setTime(const RealType time);
158
159	<	/** Returns the inverse H-Matrix */
160	<	Mat3x3d getInvHmat() {
161	<	return invHmat_;
162	<	}
159	>	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
168	<	/** Wrapping the vector according to periodic boundary condition*/
124	<	void wrapVector(Vector3d& v);
168	>	RealType getShortRangePotential();
169
170	<
171	<	double getTime() {
172	<	return currentTime_;
129	<	}
170	>	void     setLongRangePotential(const potVec lrPot);
171	>	RealType getLongRangePotential();
172	>	potVec   getLongRangePotentials();
173
174	<	void increaseTime(double dt) {
175	<	setTime(getTime() + dt);
176	<	}
174	>	void     setExcludedPotentials(const potVec exPot);
175	>	potVec   getExcludedPotentials();
176	>
177	>	void     setRestraintPotential(const RealType rp);
178	>	RealType getRestraintPotential();
179
180	<	void setTime(double time) {
181	<	currentTime_ =time;
137	<	//time at statData is redundant
138	<	statData[Stats::TIME] = currentTime_;
139	<	}
180	>	void     setRawPotential(const RealType rp);
181	>	RealType getRawPotential();
182
183	<	double getChi() {
184	<	return chi_;
185	<	}
183	>	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
201	<	void setChi(double chi) {
202	<	chi_ = chi;
147	<	}
201	>	Mat3x3d  getPressureTensor();
202	>	void     setPressureTensor(const Mat3x3d& pressureTensor);
203
204	<	double getIntegralOfChiDt() {
205	<	return integralOfChiDt_;
151	<	}
204	>	Mat3x3d  getStressTensor();
205	>	void     setStressTensor(const Mat3x3d& stressTensor);
206
207	<	void setIntegralOfChiDt(double integralOfChiDt) {
208	<	integralOfChiDt_ = integralOfChiDt;
155	<	}
156	<
157	<	Mat3x3d getEta() {
158	<	return eta_;
159	<	}
207	>	Vector3d getConductiveHeatFlux();
208	>	void     setConductiveHeatFlux(const Vector3d& chf);
209
210	<	void setEta(const Mat3x3d& eta) {
211	<	eta_ = eta;
163	<	}
164	<
165	<	DataStorage atomData;
166	<	DataStorage rigidbodyData;
167	<	Stats statData;
168	<
169	<	private:
170	<	double currentTime_;
210	>	Vector3d getConvectiveHeatFlux();
211	>	void     setConvectiveHeatFlux(const Vector3d& chf);
212
213	<	Mat3x3d hmat_;
214	<	Mat3x3d invHmat_;
215	<	int orthoRhombic_;
213	>	Vector3d getHeatFlux();
214	>
215	>	Vector3d getSystemDipole();
216	>	void     setSystemDipole(const Vector3d& bd);
217
218	<	double chi_;
219	<	double integralOfChiDt_;
220	<	Mat3x3d eta_;
218	>	pair<RealType, RealType> getThermostat();
219	>	void setThermostat(const pair<RealType, RealType>& thermostat);
220	>
221	>	pair<RealType, RealType> getElectronicThermostat();
222	>	void setElectronicThermostat(const pair<RealType, RealType>& eThermostat);
223
224	<	int id_; /**< identification number of the snapshot */
225	<	};
224	>	Mat3x3d  getBarostat();
225	>	void     setBarostat(const Mat3x3d& barostat);
226
227	<	typedef DataStorage (Snapshot::*DataStoragePointer);
227	>	Mat3x3d  getInertiaTensor();
228	>	void     setInertiaTensor(const Mat3x3d& inertiaTensor);
229	>
230	>	RealType getGyrationalVolume();
231	>	void     setGyrationalVolume(const RealType gv);
232	>
233	>	RealType getHullVolume();
234	>	void     setHullVolume(const RealType hv);
235	>
236	>	void     setOrthoTolerance(RealType orthoTolerance);
237	>
238	>	DataStorage atomData;
239	>	DataStorage rigidbodyData;
240	>	DataStorage cgData;
241	>	FrameData   frameData;
242	>
243	>	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	>	private:
266	>	RealType orthoTolerance_;
267	>
268	>	};
269	>
270	>	typedef DataStorage (Snapshot::*DataStoragePointer);
271		}
272		#endif //BRAINS_SNAPSHOT_HPP

Comparing:
trunk/src/brains/Snapshot.hpp (property svn:keywords), Revision 316 by tim, Fri Feb 11 22:41:02 2005 UTC vs.
branches/development/src/brains/Snapshot.hpp (property svn:keywords), Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

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