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

Comparing:
trunk/src/brains/Snapshot.hpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/Snapshot.hpp (file contents), Revision 1757 by gezelter, Tue Jun 19 02:11:07 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
43	<	/**
44	<	* @file Snapshot.hpp
45	<	* @author tlin
46	<	* @date 10/20/2004
47	<	* @time 23:56am
48	<	* @version 1.0
49	<	*/
43	>	/**
44	>	* @file Snapshot.hpp
45	>	* @author tlin
46	>	* @date 10/20/2004
47	>	* @time 23:56am
48	>	* @version 1.0
49	>	*/
50
51		#ifndef BRAINS_SNAPSHOT_HPP
52		#define BRAINS_SNAPSHOT_HPP
#	Line 53 | Line 54
54		#include <vector>
55
56		#include "brains/DataStorage.hpp"
57	+	#include "nonbonded/NonBondedInteraction.hpp"
58		#include "brains/Stats.hpp"
57	–	#include "UseTheForce/DarkSide/simulation_interface.h"
59
60	<	namespace oopse{
60	>	namespace OpenMD{
61
62	<	/**
63	<	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
64	<	* @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.
68	<	*/
69	<	class Snapshot {
70	<	public:
71	<
72	<	Snapshot(int nAtoms, int nRigidbodies) : atomData(nAtoms), rigidbodyData(nRigidbodies),
73	<	currentTime_(0), orthoRhombic_(0), chi_(0.0), integralOfChiDt_(0.0), eta_(0.0) {
62	>	struct FrameData {
63	>	int id;                   /**< identification number of the snapshot */
64	>	RealType currentTime;     /**< current time */
65	>	Mat3x3d hmat;             /**< axes of the periodic box in matrix form */
66	>	Mat3x3d invHmat;          /**< the inverse of the Hmat matrix */
67	>	bool orthoRhombic;        /**< is this an orthorhombic periodic box? */
68	>	RealType volume;          /**< total volume of this frame */
69	>	RealType pressure;        /**< pressure of this frame */
70	>	RealType totalEnergy;     /**< total 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	>	RealType temperature;     /**< temperature of this frame */
81	>	RealType chi;             /**< thermostat velocity */
82	>	RealType integralOfChiDt; /**< the actual thermostat */
83	>	RealType electronicTemperature; /**< temperature of the electronic degrees of freedom */
84	>	RealType chiQ;            /**< fluctuating charge thermostat velocity */
85	>	RealType integralOfChiQDt; /**< the actual fluctuating charge thermostat */
86	>	Mat3x3d eta;              /**< barostat matrix */
87	>	Vector3d COM;             /**< location of center of mass */
88	>	Vector3d COMvel;          /**< system center of mass velocity */
89	>	Vector3d COMw;            /**< system center of mass angular velocity */
90	>	Mat3x3d stressTensor;     /**< stress tensor */
91	>	Mat3x3d pressureTensor;   /**< pressure tensor */
92	>	Vector3d systemDipole;    /**< total system dipole moment */
93	>	Vector3d conductiveHeatFlux; /**< heat flux vector (conductive only) */
94	>	};
95
74	–	}
96
97	+	/**
98	+	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
99	+	* @brief Snapshot class is a repository class for storing dynamic data during
100	+	*  Simulation
101	+	* Every snapshot class will contain one DataStorage for atoms and one DataStorage
102	+	*  for rigid bodies.
103	+	*/
104	+	class Snapshot {
105	+	public:
106
107	<	/** Returns the id of this Snapshot */
108	<	int getID() {
109	<	return id_;
110	<	}
107	>	Snapshot(int nAtoms, int nRigidbodies,
108	>	int nCutoffGroups) : atomData(nAtoms),
109	>	rigidbodyData(nRigidbodies),
110	>	cgData(nCutoffGroups, DataStorage::dslPosition),
111	>	orthoTolerance_(1e-6), hasCOM_(false), hasVolume_(false){
112	>
113	>	frameData.id = -1;
114	>	frameData.currentTime = 0;
115	>	frameData.hmat = Mat3x3d(0.0);
116	>	frameData.invHmat = Mat3x3d(0.0);
117	>	frameData.orthoRhombic = false;
118	>	frameData.volume = 0.0;
119	>	frameData.pressure = 0.0;
120	>	frameData.totalEnergy = 0.0;
121	>	frameData.kineticEnergy = 0.0;
122	>	frameData.potentialEnergy = 0.0;
123	>	frameData.temperature = 0.0;
124	>	frameData.chi = 0.0;
125	>	frameData.integralOfChiDt = 0.0;
126	>	frameData.electronicTemperature = 0.0;
127	>	frameData.chiQ = 0.0;
128	>	frameData.integralOfChiQDt = 0.0;
129	>	frameData.eta = Mat3x3d(0.0);
130	>	frameData.COM = V3Zero;
131	>	frameData.COMvel = V3Zero;
132	>	frameData.COMw = V3Zero;
133	>	frameData.stressTensor = Mat3x3d(0.0);
134	>	frameData.pressureTensor = Mat3x3d(0.0);
135	>	frameData.systemDipole = Vector3d(0.0);
136	>	frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
137	>	}
138
139	<	/** Sets the id of this Snapshot */
140	<	void setID(int id) {
141	<	id_ = id;
142	<	}
139	>	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups,
140	>	int storageLayout) : atomData(nAtoms, storageLayout),
141	>	rigidbodyData(nRigidbodies, storageLayout),
142	>	cgData(nCutoffGroups, DataStorage::dslPosition),
143	>	orthoTolerance_(1e-6),
144	>	hasCOM_(false),
145	>	hasVolume_(false) {
146	>	frameData.id = -1;
147	>	frameData.currentTime = 0;
148	>	frameData.hmat = Mat3x3d(0.0);
149	>	frameData.invHmat = Mat3x3d(0.0);
150	>	frameData.orthoRhombic = false;
151	>	frameData.volume = 0.0;
152	>	frameData.pressure = 0.0;
153	>	frameData.totalEnergy = 0.0;
154	>	frameData.kineticEnergy = 0.0;
155	>	frameData.potentialEnergy = 0.0;
156	>	frameData.temperature = 0.0;
157	>	frameData.chi = 0.0;
158	>	frameData.integralOfChiDt = 0.0;
159	>	frameData.electronicTemperature = 0.0;
160	>	frameData.chiQ = 0.0;
161	>	frameData.integralOfChiQDt = 0.0;
162	>	frameData.eta = Mat3x3d(0.0);
163	>	frameData.COM = V3Zero;
164	>	frameData.COMvel = V3Zero;
165	>	frameData.COMw = V3Zero;
166	>	frameData.stressTensor = Mat3x3d(0.0);
167	>	frameData.pressureTensor = Mat3x3d(0.0);
168	>	frameData.systemDipole = V3Zero;
169	>	frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
170	>	}
171	>
172	>	/** Returns the id of this Snapshot */
173	>	int getID() {
174	>	return frameData.id;
175	>	}
176
177	<	int getSize() {
178	<	return atomData.getSize() + rigidbodyData.getSize();
179	<	}
177	>	/** Sets the id of this Snapshot */
178	>	void setID(int id) {
179	>	frameData.id = id;
180	>	}
181
182	<	/** Returns the number of atoms */
183	<	int getNumberOfAtoms() {
184	<	return atomData.getSize();
94	<	}
182	>	int getSize() {
183	>	return atomData.getSize() + rigidbodyData.getSize();
184	>	}
185
186	<	/** Returns the number of rigid bodies */
187	<	int getNumberOfRigidBodies() {
188	<	return rigidbodyData.getSize();
189	<	}
186	>	/** Returns the number of atoms */
187	>	int getNumberOfAtoms() {
188	>	return atomData.getSize();
189	>	}
190
191	<	/** Returns the H-Matrix */
192	<	Mat3x3d getHmat() {
193	<	return hmat_;
194	<	}
191	>	/** Returns the number of rigid bodies */
192	>	int getNumberOfRigidBodies() {
193	>	return rigidbodyData.getSize();
194	>	}
195
196	<	/** Sets the H-Matrix */
197	<	void setHmat(const Mat3x3d& m);
196	>	/** Returns the number of rigid bodies */
197	>	int getNumberOfCutoffGroups() {
198	>	return cgData.getSize();
199	>	}
200	>
201	>	/** Returns the H-Matrix */
202	>	Mat3x3d getHmat() {
203	>	return frameData.hmat;
204	>	}
205	>
206	>	/** Sets the H-Matrix */
207	>	void setHmat(const Mat3x3d& m);
208
209	<	double getVolume() {
210	<	return hmat_.determinant();
211	<	}
209	>	RealType getVolume() {
210	>	if (hasVolume_){
211	>	return frameData.volume;
212	>	}else{
213	>	return frameData.hmat.determinant();
214	>	}
215	>	}
216
217	<	/** Returns the inverse H-Matrix */
218	<	Mat3x3d getInvHmat() {
219	<	return invHmat_;
220	<	}
217	>	void setVolume(RealType volume){
218	>	hasVolume_=true;
219	>	frameData.volume = volume;
220	>	}
221
222	<	/** Wrapping the vector according to periodic boundary condition*/
223	<	void wrapVector(Vector3d& v);
222	>	/** Returns the inverse H-Matrix */
223	>	Mat3x3d getInvHmat() {
224	>	return frameData.invHmat;
225	>	}
226
227	+	/** Wrapping the vector according to periodic boundary condition*/
228	+	void wrapVector(Vector3d& v);
229	+	/** Scaling a vector to multiples of the periodic box */
230	+	Vector3d scaleVector(Vector3d &v);
231	+
232	+
233	+	Vector3d getCOM();
234	+	Vector3d getCOMvel();
235	+	Vector3d getCOMw();
236
237	<	double getTime() {
238	<	return currentTime_;
239	<	}
237	>	RealType getTime() {
238	>	return frameData.currentTime;
239	>	}
240
241	<	void increaseTime(double dt) {
242	<	setTime(getTime() + dt);
243	<	}
241	>	void increaseTime(RealType dt) {
242	>	setTime(getTime() + dt);
243	>	}
244
245	<	void setTime(double time) {
246	<	currentTime_ =time;
247	<	//time at statData is redundant
248	<	statData[Stats::TIME] = currentTime_;
249	<	}
245	>	void setTime(RealType time) {
246	>	frameData.currentTime =time;
247	>	//time at statData is redundant
248	>	statData[Stats::TIME] = frameData.currentTime;
249	>	}
250
251	<	double getChi() {
252	<	return chi_;
253	<	}
251	>	RealType getChi() {
252	>	return frameData.chi;
253	>	}
254
255	<	void setChi(double chi) {
256	<	chi_ = chi;
257	<	}
255	>	void setChi(RealType chi) {
256	>	frameData.chi = chi;
257	>	}
258
259	<	double getIntegralOfChiDt() {
260	<	return integralOfChiDt_;
261	<	}
259	>	RealType getIntegralOfChiDt() {
260	>	return frameData.integralOfChiDt;
261	>	}
262
263	<	void setIntegralOfChiDt(double integralOfChiDt) {
264	<	integralOfChiDt_ = integralOfChiDt;
265	<	}
263	>	void setIntegralOfChiDt(RealType integralOfChiDt) {
264	>	frameData.integralOfChiDt = integralOfChiDt;
265	>	}
266
267	<	Mat3x3d getEta() {
268	<	return eta_;
269	<	}
267	>	RealType getChiElectronic() {
268	>	return frameData.chiQ;
269	>	}
270
271	<	void setEta(const Mat3x3d& eta) {
272	<	eta_ = eta;
273	<	}
159	<
160	<	DataStorage atomData;
161	<	DataStorage rigidbodyData;
162	<	Stats statData;
163	<
164	<	private:
165	<	double currentTime_;
271	>	void setChiElectronic(RealType chiQ) {
272	>	frameData.chiQ = chiQ;
273	>	}
274
275	<	Mat3x3d hmat_;
276	<	Mat3x3d invHmat_;
277	<	int orthoRhombic_;
275	>	RealType getIntegralOfChiElectronicDt() {
276	>	return frameData.integralOfChiQDt;
277	>	}
278
279	<	double chi_;
280	<	double integralOfChiDt_;
281	<	Mat3x3d eta_;
279	>	void setIntegralOfChiElectronicDt(RealType integralOfChiQDt) {
280	>	frameData.integralOfChiQDt = integralOfChiQDt;
281	>	}
282
175	–	int id_; /**< identification number of the snapshot */
176	–	};
283
284	<	typedef DataStorage (Snapshot::*DataStoragePointer);
284	>	void setOrthoTolerance(RealType orthoTolerance) {
285	>	orthoTolerance_ = orthoTolerance;
286	>	}
287	>
288	>	Mat3x3d getEta() {
289	>	return frameData.eta;
290	>	}
291	>
292	>	void setEta(const Mat3x3d& eta) {
293	>	frameData.eta = eta;
294	>	}
295	>
296	>	Mat3x3d getStressTensor() {
297	>	return frameData.stressTensor;
298	>	}
299	>
300	>	void setStressTensor(const Mat3x3d& stressTensor) {
301	>	frameData.stressTensor = stressTensor;
302	>	}
303	>
304	>	Vector3d getConductiveHeatFlux() {
305	>	return frameData.conductiveHeatFlux;
306	>	}
307	>
308	>	void setConductiveHeatFlux(const Vector3d& heatFlux) {
309	>	frameData.conductiveHeatFlux = heatFlux;
310	>	}
311	>
312	>	bool hasCOM() {
313	>	return hasCOM_;
314	>	}
315	>
316	>	void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
317	>	frameData.COM = COM;
318	>	frameData.COMvel = COMvel;
319	>	frameData.COMw = COMw;
320	>	hasCOM_ = true;
321	>	}
322	>
323	>	DataStorage atomData;
324	>	DataStorage rigidbodyData;
325	>	DataStorage cgData;
326	>	FrameData frameData;
327	>	Stats statData;
328	>
329	>	private:
330	>	RealType orthoTolerance_;
331	>	bool hasCOM_;
332	>	bool hasVolume_;
333	>	};
334	>
335	>	typedef DataStorage (Snapshot::*DataStoragePointer);
336		}
337		#endif //BRAINS_SNAPSHOT_HPP

Comparing:
trunk/src/brains/Snapshot.hpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/Snapshot.hpp (property svn:keywords), Revision 1757 by gezelter, Tue Jun 19 02:11:07 2012 UTC

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