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

Comparing:
trunk/src/brains/Snapshot.hpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/brains/Snapshot.hpp (file contents), Revision 1858 by gezelter, Wed Apr 3 21:32:13 2013 UTC

#	Line 35 | Line 35
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).
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
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	<
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
65	<	*  Simulation
66	<	* Every snapshot class will contain one DataStorage  for atoms and one DataStorage
67	<	*  for rigid bodies.
56	>	* FrameData is a structure for holding system-wide dynamic data
57	>	* about the simulation.
58		*/
59	<	class Snapshot {
60	<	public:
61	<
62	<	Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms),
63	<	rigidbodyData(nRigidbodies),
64	<	currentTime_(0),
65	<	orthoTolerance_(1e-6),
66	<	orthoRhombic_(0),
67	<	chi_(0.0),
68	<	integralOfChiDt_(0.0),
69	<	eta_(0.0), id_(-1),
70	<	hasCOM_(false), hasVolume_(false), volume_(0.0) {
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
82	–	}
105
106	<	Snapshot(int nAtoms, int nRigidbodies, int storageLayout)
107	<	: atomData(nAtoms, storageLayout),
108	<	rigidbodyData(nRigidbodies, storageLayout),
109	<	currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0),
110	<	integralOfChiDt_(0.0), eta_(0.0), id_(-1), hasCOM_(false), hasVolume_(false),volume_(0.0)  {
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	<	}
116	<
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() {
94	<	return id_;
95	<	}
96	<
119	>	int      getID();
120		/** Sets the id of this Snapshot */
121	<	void setID(int id) {
99	<	id_ = id;
100	<	}
121	>	void     setID(int id);
122
123	<	int getSize() {
124	<	return atomData.getSize() + rigidbodyData.getSize();
104	<	}
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() {
108	<	return atomData.getSize();
109	<	}
110	<
128	>	int      getNumberOfAtoms();
129		/** Returns the number of rigid bodies */
130	<	int getNumberOfRigidBodies() {
131	<	return rigidbodyData.getSize();
132	<	}
130	>	int      getNumberOfRigidBodies();
131	>	/** Returns the number of rigid bodies */
132	>	int      getNumberOfCutoffGroups();
133
134		/** Returns the H-Matrix */
135	<	Mat3x3d getHmat() {
118	<	return hmat_;
119	<	}
120	<
135	>	Mat3x3d  getHmat();
136		/** Sets the H-Matrix */
137	<	void setHmat(const Mat3x3d& m);
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	<	if (hasVolume_){
150	<	return volume_;
127	<	}else{
128	<	return hmat_.determinant();
129	<	}
130	<	}
148	>	RealType getVolume();
149	>	RealType getXYarea();
150	>	void     setVolume(const RealType vol);
151
152	<	void setVolume(RealType volume){
153	<	hasVolume_=true;
134	<	volume_ = volume;
135	<	}
152	>	/** Wrapping the vector according to periodic boundary condition*/
153	>	void     wrapVector(Vector3d& v);
154
155	<	/** Returns the inverse H-Matrix */
156	<	Mat3x3d getInvHmat() {
139	<	return invHmat_;
140	<	}
155	>	/** Scaling a vector to multiples of the periodic box */
156	>	Vector3d scaleVector(Vector3d &v);
157
158	<	/** Wrapping the vector according to periodic boundary condition*/
159	<	void wrapVector(Vector3d& v);
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	<	return currentTime_;
168	<	}
151	<
152	<	void increaseTime(RealType dt) {
153	<	setTime(getTime() + dt);
154	<	}
166	>	RealType getTime();
167	>	void     increaseTime(const RealType dt);
168	>	void     setTime(const RealType time);
169
170	<	void setTime(RealType time) {
171	<	currentTime_ =time;
172	<	//time at statData is redundant
173	<	statData[Stats::TIME] = currentTime_;
174	<	}
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 getChi() {
163	<	return chi_;
164	<	}
179	>	RealType getShortRangePotential();
180
181	<	void setChi(RealType chi) {
182	<	chi_ = chi;
183	<	}
181	>	void     setLongRangePotential(const potVec lrPot);
182	>	RealType getLongRangePotential();
183	>	potVec   getLongRangePotentials();
184
185	<	RealType getIntegralOfChiDt() {
186	<	return integralOfChiDt_;
187	<	}
185	>	void     setExcludedPotentials(const potVec exPot);
186	>	potVec   getExcludedPotentials();
187	>
188	>	void     setRestraintPotential(const RealType rp);
189	>	RealType getRestraintPotential();
190
191	<	void setIntegralOfChiDt(RealType integralOfChiDt) {
192	<	integralOfChiDt_ = integralOfChiDt;
176	<	}
177	<
191	>	void     setRawPotential(const RealType rp);
192	>	RealType getRawPotential();
193
194	<	void setOrthoTolerance(RealType orthoTolerance) {
195	<	orthoTolerance_ = orthoTolerance;
196	<	}
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 getEta() {
213	<	return eta_;
185	<	}
212	>	Mat3x3d  getPressureTensor();
213	>	void     setPressureTensor(const Mat3x3d& pressureTensor);
214
215	<	void setEta(const Mat3x3d& eta) {
216	<	eta_ = eta;
189	<	}
215	>	Mat3x3d  getStressTensor();
216	>	void     setStressTensor(const Mat3x3d& stressTensor);
217
218	<	bool hasCOM() {
219	<	return hasCOM_;
193	<	}
218	>	Vector3d getConductiveHeatFlux();
219	>	void     setConductiveHeatFlux(const Vector3d& chf);
220
221	<	void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
222	<	COM_ = COM;
223	<	COMvel_ = COMvel;
224	<	COMw_ = COMw;
225	<	hasCOM_ = true;
226	<	}
227	<
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	<	Stats statData;
252	<
206	<	private:
207	<	RealType currentTime_;
251	>	DataStorage cgData;
252	>	FrameData   frameData;
253
254	<	Mat3x3d hmat_;
255	<	Mat3x3d invHmat_;
256	<	RealType orthoTolerance_;
257	<	int orthoRhombic_;
258	<	RealType volume_;
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	<	RealType chi_;
279	<	RealType integralOfChiDt_;
280	<	Mat3x3d eta_;
218	<	Vector3d COM_;
219	<	Vector3d COMvel_;
220	<	Vector3d COMw_;
221	<	int id_; /**< identification number of the snapshot */
222	<	bool hasCOM_;
223	<	bool hasVolume_;
224	<
278	>	private:
279	>	RealType orthoTolerance_;
280	>
281		};
282
283		typedef DataStorage (Snapshot::*DataStoragePointer);

Comparing:
trunk/src/brains/Snapshot.hpp (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/brains/Snapshot.hpp (property svn:keywords), Revision 1858 by gezelter, Wed Apr 3 21:32:13 2013 UTC

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