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Comparing:
trunk/src/brains/Snapshot.hpp (file contents), Revision 1302 by chuckv, Tue Oct 7 17:12:48 2008 UTC vs.
branches/development/src/brains/Snapshot.hpp (file contents), Revision 1774 by gezelter, Wed Aug 8 16:03:02 2012 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, 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	+	using namespace std;
53	+	namespace OpenMD{
54
55	<	namespace oopse{
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 xyArea;              /**< XY area of this frame */
82	>	RealType volume;              /**< total volume of this frame */
83	>	RealType pressure;            /**< pressure of this frame */
84	>	RealType temperature;         /**< temperature of this frame */
85	>	pair<RealType, RealType> thermostat;    /**< thermostat variables */
86	>	RealType electronicTemperature; /**< temperature of the electronic degrees of freedom */
87	>	pair<RealType, RealType> electronicThermostat; /**< thermostat variables for electronic degrees of freedom */
88	>	Mat3x3d  barostat;            /**< barostat matrix */
89	>	Vector3d COM;                 /**< location of system center of mass */
90	>	Vector3d COMvel;              /**< system center of mass velocity */
91	>	Vector3d COMw;                /**< system center of mass angular velocity */
92	>	Mat3x3d  inertiaTensor;       /**< inertia tensor for entire system */
93	>	RealType gyrationalVolume;    /**< gyrational volume for entire system */
94	>	RealType hullVolume;          /**< hull volume for entire system */
95	>	Mat3x3d  stressTensor;        /**< stress tensor */
96	>	Mat3x3d  pressureTensor;      /**< pressure tensor */
97	>	Vector3d systemDipole;        /**< total system dipole moment */
98	>	Vector3d conductiveHeatFlux;  /**< heat flux vector (conductive only) */
99	>	Vector3d convectiveHeatFlux;  /**< heat flux vector (convective only) */
100	>	RealType conservedQuantity;   /**< anything conserved by the integrator */
101	>	};
102
103	+
104		/**
105	<	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
106	<	* @brief Snapshot class is a repository class for storing dynamic data during
107	<	*  Simulation
108	<	* Every snapshot class will contain one DataStorage  for atoms and one DataStorage
109	<	*  for rigid bodies.
105	>	* @class Snapshot
106	>	* @brief The Snapshot class is a repository storing dynamic data during a
107	>	* Simulation.  Every Snapshot contains FrameData (for global information)
108	>	* as well as DataStorage (one for Atoms, one for RigidBodies, and one for
109	>	* CutoffGroups).
110		*/
111		class Snapshot {
70	–	public:
71	–
72	–	Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms),
73	–	rigidbodyData(nRigidbodies),
74	–	currentTime_(0),
75	–	orthoTolerance_(1e-6),
76	–	orthoRhombic_(0),
77	–	chi_(0.0),
78	–	integralOfChiDt_(0.0),
79	–	eta_(0.0), id_(-1),
80	–	hasCOM_(false), hasVolume_(false), volume_(0.0) {
112
113	<	}
114	<
115	<	Snapshot(int nAtoms, int nRigidbodies, int storageLayout)
85	<	: atomData(nAtoms, storageLayout),
86	<	rigidbodyData(nRigidbodies, storageLayout),
87	<	currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0),
88	<	integralOfChiDt_(0.0), eta_(0.0), id_(-1), hasCOM_(false), hasVolume_(false),volume_(0.0)  {
89	<
90	<	}
91	<
113	>	public:
114	>	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups);
115	>	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, int storageLayout);
116		/** Returns the id of this Snapshot */
117	<	int getID() {
94	<	return id_;
95	<	}
96	<
117	>	int      getID();
118		/** Sets the id of this Snapshot */
119	<	void setID(int id) {
99	<	id_ = id;
100	<	}
119	>	void     setID(int id);
120
121	<	int getSize() {
122	<	return atomData.getSize() + rigidbodyData.getSize();
104	<	}
121	>	/** sets the state of the computed properties to false */
122	>	void     clearDerivedProperties();
123
124	+	int      getSize();
125		/** Returns the number of atoms */
126	<	int getNumberOfAtoms() {
108	<	return atomData.getSize();
109	<	}
110	<
126	>	int      getNumberOfAtoms();
127		/** Returns the number of rigid bodies */
128	<	int getNumberOfRigidBodies() {
129	<	return rigidbodyData.getSize();
130	<	}
128	>	int      getNumberOfRigidBodies();
129	>	/** Returns the number of rigid bodies */
130	>	int      getNumberOfCutoffGroups();
131
132		/** Returns the H-Matrix */
133	<	Mat3x3d getHmat() {
118	<	return hmat_;
119	<	}
120	<
133	>	Mat3x3d  getHmat();
134		/** Sets the H-Matrix */
135	<	void setHmat(const Mat3x3d& m);
135	>	void     setHmat(const Mat3x3d& m);
136	>	/** Returns the inverse H-Matrix */
137	>	Mat3x3d  getInvHmat();
138
139	<	RealType getVolume() {
140	<	if (hasVolume_){
141	<	return volume_;
127	<	}else{
128	<	return hmat_.determinant();
129	<	}
130	<	}
139	>	RealType getVolume();
140	>	RealType getXYarea();
141	>	void     setVolume(const RealType vol);
142
143	<	void setVolume(RealType volume){
144	<	hasVolume_=true;
134	<	volume_ = volume;
135	<	}
143	>	/** Wrapping the vector according to periodic boundary condition*/
144	>	void     wrapVector(Vector3d& v);
145
146	<	/** Returns the inverse H-Matrix */
147	<	Mat3x3d getInvHmat() {
139	<	return invHmat_;
140	<	}
146	>	/** Scaling a vector to multiples of the periodic box */
147	>	Vector3d scaleVector(Vector3d &v);
148
149	<	/** Wrapping the vector according to periodic boundary condition*/
150	<	void wrapVector(Vector3d& v);
149	>	void     setCOM(const Vector3d &com);
150	>	void     setCOMvel(const Vector3d &comVel);
151	>	void     setCOMw(const Vector3d &comw);
152	>
153		Vector3d getCOM();
154		Vector3d getCOMvel();
155		Vector3d getCOMw();
156
157	<	RealType getTime() {
158	<	return currentTime_;
159	<	}
157	>	RealType getTime();
158	>	void     increaseTime(const RealType dt);
159	>	void     setTime(const RealType time);
160
161	<	void increaseTime(RealType dt) {
162	<	setTime(getTime() + dt);
163	<	}
161	>	void     setBondPotential(const RealType bp);
162	>	void     setBendPotential(const RealType bp);
163	>	void     setTorsionPotential(const RealType tp);
164	>	void     setInversionPotential(const RealType ip);
165	>	RealType getBondPotential();
166	>	RealType getBendPotential();
167	>	RealType getTorsionPotential();
168	>	RealType getInversionPotential();
169
170	<	void setTime(RealType time) {
157	<	currentTime_ =time;
158	<	//time at statData is redundant
159	<	statData[Stats::TIME] = currentTime_;
160	<	}
170	>	RealType getShortRangePotential();
171
172	<	RealType getChi() {
173	<	return chi_;
174	<	}
172	>	void     setLongRangePotential(const potVec lrPot);
173	>	RealType getLongRangePotential();
174	>	potVec   getLongRangePotentials();
175
176	<	void setChi(RealType chi) {
177	<	chi_ = chi;
178	<	}
176	>	void     setExcludedPotentials(const potVec exPot);
177	>	potVec   getExcludedPotentials();
178	>
179	>	void     setRestraintPotential(const RealType rp);
180	>	RealType getRestraintPotential();
181
182	<	RealType getIntegralOfChiDt() {
183	<	return integralOfChiDt_;
172	<	}
182	>	void     setRawPotential(const RealType rp);
183	>	RealType getRawPotential();
184
185	<	void setIntegralOfChiDt(RealType integralOfChiDt) {
186	<	integralOfChiDt_ = integralOfChiDt;
187	<	}
188	<
185	>	RealType getPotentialEnergy();
186	>	RealType getKineticEnergy();
187	>	RealType getTranslationalKineticEnergy();
188	>	RealType getRotationalKineticEnergy();
189	>	void     setKineticEnergy(const RealType ke);
190	>	void     setTranslationalKineticEnergy(const RealType tke);
191	>	void     setRotationalKineticEnergy(const RealType rke);
192	>	RealType getTotalEnergy();
193	>	void     setTotalEnergy(const RealType te);
194	>	RealType getConservedQuantity();
195	>	void     setConservedQuantity(const RealType cq);
196	>	RealType getTemperature();
197	>	void     setTemperature(const RealType temp);
198	>	RealType getElectronicTemperature();
199	>	void     setElectronicTemperature(const RealType eTemp);
200	>	RealType getPressure();
201	>	void     setPressure(const RealType pressure);
202
203	<	void setOrthoTolerance(RealType orthoTolerance) {
204	<	orthoTolerance_ = orthoTolerance;
181	<	}
203	>	Mat3x3d  getPressureTensor();
204	>	void     setPressureTensor(const Mat3x3d& pressureTensor);
205
206	<	Mat3x3d getEta() {
207	<	return eta_;
185	<	}
206	>	Mat3x3d  getStressTensor();
207	>	void     setStressTensor(const Mat3x3d& stressTensor);
208
209	<	void setEta(const Mat3x3d& eta) {
210	<	eta_ = eta;
189	<	}
209	>	Vector3d getConductiveHeatFlux();
210	>	void     setConductiveHeatFlux(const Vector3d& chf);
211
212	<	bool hasCOM() {
213	<	return hasCOM_;
193	<	}
212	>	Vector3d getConvectiveHeatFlux();
213	>	void     setConvectiveHeatFlux(const Vector3d& chf);
214
215	<	void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
216	<	COM_ = COM;
217	<	COMvel_ = COMvel;
218	<	COMw_ = COMw;
219	<	hasCOM_ = true;
220	<	}
221	<
215	>	Vector3d getHeatFlux();
216	>
217	>	Vector3d getSystemDipole();
218	>	void     setSystemDipole(const Vector3d& bd);
219	>
220	>	pair<RealType, RealType> getThermostat();
221	>	void setThermostat(const pair<RealType, RealType>& thermostat);
222	>
223	>	pair<RealType, RealType> getElectronicThermostat();
224	>	void setElectronicThermostat(const pair<RealType, RealType>& eThermostat);
225	>
226	>	Mat3x3d  getBarostat();
227	>	void     setBarostat(const Mat3x3d& barostat);
228	>
229	>	Mat3x3d  getInertiaTensor();
230	>	void     setInertiaTensor(const Mat3x3d& inertiaTensor);
231	>
232	>	RealType getGyrationalVolume();
233	>	void     setGyrationalVolume(const RealType gv);
234	>
235	>	RealType getHullVolume();
236	>	void     setHullVolume(const RealType hv);
237	>
238	>	void     setOrthoTolerance(RealType orthoTolerance);
239	>
240		DataStorage atomData;
241		DataStorage rigidbodyData;
242	<	Stats statData;
243	<
206	<	private:
207	<	RealType currentTime_;
242	>	DataStorage cgData;
243	>	FrameData   frameData;
244
245	<	Mat3x3d hmat_;
246	<	Mat3x3d invHmat_;
247	<	RealType orthoTolerance_;
248	<	int orthoRhombic_;
249	<	RealType volume_;
245	>	bool hasTotalEnergy;
246	>	bool hasTranslationalKineticEnergy;
247	>	bool hasRotationalKineticEnergy;
248	>	bool hasKineticEnergy;
249	>	bool hasShortRangePotential;
250	>	bool hasLongRangePotential;
251	>	bool hasPotentialEnergy;
252	>	bool hasXYarea;
253	>	bool hasVolume;
254	>	bool hasPressure;
255	>	bool hasTemperature;
256	>	bool hasElectronicTemperature;
257	>	bool hasCOM;
258	>	bool hasCOMvel;
259	>	bool hasCOMw;
260	>	bool hasPressureTensor;
261	>	bool hasSystemDipole;
262	>	bool hasConvectiveHeatFlux;
263	>	bool hasInertiaTensor;
264	>	bool hasGyrationalVolume;
265	>	bool hasHullVolume;
266	>	bool hasConservedQuantity;
267
268	<	RealType chi_;
269	<	RealType integralOfChiDt_;
270	<	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	<
268	>	private:
269	>	RealType orthoTolerance_;
270	>
271		};
272
273		typedef DataStorage (Snapshot::*DataStoragePointer);

Comparing:
trunk/src/brains/Snapshot.hpp (property svn:keywords), Revision 1302 by chuckv, Tue Oct 7 17:12:48 2008 UTC vs.
branches/development/src/brains/Snapshot.hpp (property svn:keywords), Revision 1774 by gezelter, Wed Aug 8 16:03:02 2012 UTC

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