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Comparing:
trunk/src/brains/Snapshot.hpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/Snapshot.hpp (file contents), Revision 1858 by gezelter, Wed Apr 3 21:32:13 2013 UTC

#	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, 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	<	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
64	<	*  Simulation
65	<	* Every snapshot class will contain one DataStorage  for atoms and one DataStorage
66	<	*  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), rigidbodyData(nRigidbodies),
63	<	currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) {
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
74	–	}
105
106	<	Snapshot(int nAtoms, int nRigidbodies, int storageLayout)
107	<	: atomData(nAtoms, storageLayout), rigidbodyData(nRigidbodies, storageLayout),
108	<	currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0), id_(-1) {
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() {
84	<	return id_;
85	<	}
86	<
119	>	int      getID();
120		/** Sets the id of this Snapshot */
121	<	void setID(int id) {
89	<	id_ = id;
90	<	}
121	>	void     setID(int id);
122
123	<	int getSize() {
124	<	return atomData.getSize() + rigidbodyData.getSize();
94	<	}
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() {
98	<	return atomData.getSize();
99	<	}
100	<
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() {
108	<	return hmat_;
109	<	}
110	<
135	>	Mat3x3d  getHmat();
136		/** Sets the H-Matrix */
137	<	void setHmat(const Mat3x3d& m);
113	<
114	<	RealType getVolume() {
115	<	return hmat_.determinant();
116	<	}
117	<
137	>	void     setHmat(const Mat3x3d& m);
138		/** Returns the inverse H-Matrix */
139	<	Mat3x3d getInvHmat() {
120	<	return invHmat_;
121	<	}
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);
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	<	return currentTime_;
168	<	}
166	>	RealType getTime();
167	>	void     increaseTime(const RealType dt);
168	>	void     setTime(const RealType time);
169
170	<	void increaseTime(RealType dt) {
171	<	setTime(getTime() + dt);
172	<	}
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	<	void setTime(RealType time) {
136	<	currentTime_ =time;
137	<	//time at statData is redundant
138	<	statData[Stats::TIME] = currentTime_;
139	<	}
179	>	RealType getShortRangePotential();
180
181	<	RealType getChi() {
182	<	return chi_;
183	<	}
181	>	void     setLongRangePotential(const potVec lrPot);
182	>	RealType getLongRangePotential();
183	>	potVec   getLongRangePotentials();
184
185	<	void setChi(RealType chi) {
186	<	chi_ = chi;
187	<	}
185	>	void     setExcludedPotentials(const potVec exPot);
186	>	potVec   getExcludedPotentials();
187	>
188	>	void     setRestraintPotential(const RealType rp);
189	>	RealType getRestraintPotential();
190
191	<	RealType getIntegralOfChiDt() {
192	<	return integralOfChiDt_;
151	<	}
191	>	void     setRawPotential(const RealType rp);
192	>	RealType getRawPotential();
193
194	<	void setIntegralOfChiDt(RealType integralOfChiDt) {
195	<	integralOfChiDt_ = integralOfChiDt;
196	<	}
197	<
198	<	Mat3x3d getEta() {
199	<	return eta_;
200	<	}
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	<	void setEta(const Mat3x3d& eta) {
213	<	eta_ = eta;
214	<	}
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	<	Stats statData;
252	<
169	<	private:
170	<	RealType currentTime_;
251	>	DataStorage cgData;
252	>	FrameData   frameData;
253
254	<	Mat3x3d hmat_;
255	<	Mat3x3d invHmat_;
256	<	int orthoRhombic_;
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_;
179	<
180	<	int id_; /**< identification number of the snapshot */
278	>	private:
279	>	RealType orthoTolerance_;
280	>
281		};
282
283		typedef DataStorage (Snapshot::*DataStoragePointer);

Comparing:
trunk/src/brains/Snapshot.hpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 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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