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trunk/src/brains/Snapshot.hpp (file contents), Revision 146 by tim, Fri Oct 22 23:09:57 2004 UTC vs.
branches/development/src/brains/Snapshot.hpp (file contents), Revision 1760 by gezelter, Thu Jun 21 19:26:46 2012 UTC

#	Line 1 | Line 1
1		/*
2	<	* Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
3	<	*
4	<	* Contact: oopse@oopse.org
5	<	*
6	<	* This program is free software; you can redistribute it and/or
7	<	* modify it under the terms of the GNU Lesser General Public License
8	<	* as published by the Free Software Foundation; either version 2.1
9	<	* of the License, or (at your option) any later version.
10	<	* All we ask is that proper credit is given for our work, which includes
11	<	* - but is not limited to - adding the above copyright notice to the beginning
12	<	* of your source code files, and to any copyright notice that you may distribute
13	<	* with programs based on this work.
14	<	*
15	<	* This program is distributed in the hope that it will be useful,
16	<	* but WITHOUT ANY WARRANTY; without even the implied warranty of
17	<	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18	<	* GNU Lesser General Public License for more details.
19	<	*
20	<	* You should have received a copy of the GNU Lesser General Public License
21	<	* along with this program; if not, write to the Free Software
22	<	* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4	+	* The University of Notre Dame grants you ("Licensee") a
5	+	* non-exclusive, royalty free, license to use, modify and
6	+	* redistribute this software in source and binary code form, provided
7	+	* that the following conditions are met:
8	+	*
9	+	* 1. Redistributions of source code must retain the above copyright
10	+	*    notice, this list of conditions and the following disclaimer.
11	+	*
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.
16	+	*
17	+	* This software is provided "AS IS," without a warranty of any
18	+	* kind. All express or implied conditions, representations and
19	+	* warranties, including any implied warranty of merchantability,
20	+	* fitness for a particular purpose or non-infringement, are hereby
21	+	* excluded.  The University of Notre Dame and its licensors shall not
22	+	* be liable for any damages suffered by licensee as a result of
23	+	* using, modifying or distributing the software or its
24	+	* derivatives. In no event will the University of Notre Dame or its
25	+	* licensors be liable for any lost revenue, profit or data, or for
26	+	* direct, indirect, special, consequential, incidental or punitive
27	+	* damages, however caused and regardless of the theory of liability,
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		*/
25	–
26	–	/**
27	–	* @file Snapshot.hpp
28	–	* @author tlin
29	–	* @date 10/20/2004
30	–	* @time 23:56am
31	–	* @version 1.0
32	–	*/
42
43		#ifndef BRAINS_SNAPSHOT_HPP
44		#define BRAINS_SNAPSHOT_HPP
45
46		#include <vector>
47
48	<	#include "math/Vector3.hpp"
49	<	#include "math/SquareMatrix3.hpp"
48	>	#include "brains/DataStorage.hpp"
49	>	#include "nonbonded/NonBondedInteraction.hpp"
50	>	#include "brains/Stats.hpp"
51
52	<	using namespace std;
52	>	namespace OpenMD{
53
54	<	namespace oopse{
54	>	/**
55	>	* FrameData is a structure for holding system-wide dynamic data
56	>	* about the simulation.
57	>	*/
58	>
59	>	struct FrameData {
60	>	int id;                       /**< identification number of the snapshot */
61	>	RealType currentTime;         /**< current time */
62	>	Mat3x3d  hmat;                /**< axes of the periodic box in matrix form */
63	>	Mat3x3d  invHmat;             /**< the inverse of the Hmat matrix */
64	>	bool     orthoRhombic;        /**< is this an orthorhombic periodic box? */
65	>	RealType volume;              /**< total volume of this frame */
66	>	RealType pressure;            /**< pressure of this frame */
67	>	RealType totalEnergy;         /**< total energy of this frame */
68	>	RealType kineticEnergy;       /**< kinetic energy of this frame */
69	>	RealType potentialEnergy;     /**< potential energy of this frame */
70	>	RealType shortRangePotential; /**< short-range contributions to the potential*/
71	>	RealType longRangePotential;  /**< long-range contributions to the potential */
72	>	RealType bondPotential;       /**< bonded contribution to the potential */
73	>	RealType bendPotential;       /**< angle-bending contribution to the potential */
74	>	RealType torsionPotential;    /**< dihedral (torsion angle) contribution to the potential */
75	>	RealType inversionPotential;  /**< inversion (planarity) contribution to the potential */
76	>	potVec   lrPotentials;        /**< breakdown of long-range potentials by family */
77	>	potVec   excludedPotentials;  /**< breakdown of excluded potentials by family */
78	>	RealType restraintPotential;  /**< potential energy of restraints */
79	>	RealType rawPotential;        /**< unrestrained potential energy (when restraints are applied) */
80	>	RealType temperature;         /**< temperature of this frame */
81	>	RealType chi;                 /**< thermostat velocity */
82	>	RealType integralOfChiDt;     /**< thermostat position */
83	>	RealType electronicTemperature; /**< temperature of the electronic degrees of freedom */
84	>	RealType chiQ;                /**< fluctuating charge thermostat velocity */
85	>	RealType integralOfChiQDt;    /**< fluctuating charge thermostat position */
86	>	Mat3x3d  eta;                 /**< barostat matrix */
87	>	Vector3d COM;                 /**< location of system 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
46	–	//forward declaration
47	–	class Snapshot;
48	–	class SnapshotManager;
96
97	<	/**
98	<	* @struct DataStorage
99	<	* @brief
100	<	*/
101	<	class DataStorage {
102	<	public:
103	<	DataStorage() {};
104	<	DataStorage(size_t size);
58	<	void resize(size_t size);
59	<	void reserve(size_t size);
60	<
61	<	//friend Snapshot;
62	<	//friend SnapshotManager;
63	<	//private:
64	<	vector<Vector3d> position;               /** position array */
65	<	vector<Vector3d> velocity;               /** velocity array */
66	<	vector<RotMat3x3d> Amat;            /** rotation matrix array */
67	<	vector<Vector3d> angularMomentum;/** velocity array */
68	<	vector<Vector3d> ul;                /** the lab frame unit vector array*/
69	<	vector<double> zAngle;              /** z -angle array */
70	<	vector<Vector3d> force;               /** force array */
71	<	vector<Vector3d> torque;               /** torque array */
97	>	/**
98	>	* @class Snapshot
99	>	* @brief The Snapshot class is a repository storing dynamic data during a
100	>	* Simulation.  Every Snapshot contains FrameData (for global information)
101	>	* as well as DataStorage (one for Atoms, one for RigidBodies, and one for
102	>	* CutoffGroups).
103	>	*/
104	>	class Snapshot {
105
106	<	};
106	>	public:
107	>	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups) :
108	>	atomData(nAtoms), rigidbodyData(nRigidbodies),
109	>	cgData(nCutoffGroups, DataStorage::dslPosition),
110	>	orthoTolerance_(1e-6), hasCOM_(false), hasVolume_(false),
111	>	hasShortRangePotential_(false),
112	>	hasBondPotential_(false), hasBendPotential_(false),
113	>	hasTorsionPotential_(false), hasInversionPotential_(false),
114	>	hasLongRangePotential_(false), hasLongRangePotentialFamilies_(false),
115	>	hasRestraintPotential_(false), hasRawPotential_(false),
116	>	hasExcludedPotentials_(false)
117	>	{
118	>
119	>	frameData.id = -1;
120	>	frameData.currentTime = 0;
121	>	frameData.hmat = Mat3x3d(0.0);
122	>	frameData.invHmat = Mat3x3d(0.0);
123	>	frameData.orthoRhombic = false;
124	>	frameData.volume = 0.0;
125	>	frameData.pressure = 0.0;
126	>	frameData.totalEnergy = 0.0;
127	>	frameData.kineticEnergy = 0.0;
128	>	frameData.potentialEnergy = 0.0;
129	>	frameData.temperature = 0.0;
130	>	frameData.chi = 0.0;
131	>	frameData.integralOfChiDt = 0.0;
132	>	frameData.electronicTemperature = 0.0;
133	>	frameData.chiQ = 0.0;
134	>	frameData.integralOfChiQDt = 0.0;
135	>	frameData.eta = Mat3x3d(0.0);
136	>	frameData.COM = V3Zero;
137	>	frameData.COMvel = V3Zero;
138	>	frameData.COMw = V3Zero;
139	>	frameData.stressTensor = Mat3x3d(0.0);
140	>	frameData.pressureTensor = Mat3x3d(0.0);
141	>	frameData.systemDipole = Vector3d(0.0);
142	>	frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
143	>	}
144
145	<	/**
146	<	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
147	<	* @brief Snapshot class is a repository class for storing dynamic data during
148	<	*  Simulation
149	<	* Every snapshot class will contain one DataStorage  for atoms and one DataStorage
150	<	*  for rigid bodies.
151	<	* @see SimData
152	<	*/
153	<	class Snapshot {
154	<	public:
155	<
156	<	Snapshot() {}
87	<	Snapshot(int i) {
145	>	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, int storageLayout) :
146	>	atomData(nAtoms, storageLayout),
147	>	rigidbodyData(nRigidbodies, storageLayout),
148	>	cgData(nCutoffGroups, DataStorage::dslPosition),
149	>	orthoTolerance_(1e-6), hasCOM_(false), hasVolume_(false),
150	>	hasShortRangePotential_(false),
151	>	hasBondPotential_(false), hasBendPotential_(false),
152	>	hasTorsionPotential_(false), hasInversionPotential_(false),
153	>	hasLongRangePotential_(false), hasLongRangePotentialFamilies_(false),
154	>	hasRestraintPotential_(false), hasRawPotential_(false),
155	>	hasExcludedPotentials_(false)
156	>	{
157
158	<	}
158	>	frameData.id = -1;
159	>	frameData.currentTime = 0;
160	>	frameData.hmat = Mat3x3d(0.0);
161	>	frameData.invHmat = Mat3x3d(0.0);
162	>	frameData.orthoRhombic = false;
163	>	frameData.volume = 0.0;
164	>	frameData.pressure = 0.0;
165	>	frameData.totalEnergy = 0.0;
166	>	frameData.kineticEnergy = 0.0;
167	>	frameData.potentialEnergy = 0.0;
168	>	frameData.temperature = 0.0;
169	>	frameData.chi = 0.0;
170	>	frameData.integralOfChiDt = 0.0;
171	>	frameData.electronicTemperature = 0.0;
172	>	frameData.chiQ = 0.0;
173	>	frameData.integralOfChiQDt = 0.0;
174	>	frameData.eta = Mat3x3d(0.0);
175	>	frameData.COM = V3Zero;
176	>	frameData.COMvel = V3Zero;
177	>	frameData.COMw = V3Zero;
178	>	frameData.stressTensor = Mat3x3d(0.0);
179	>	frameData.pressureTensor = Mat3x3d(0.0);
180	>	frameData.systemDipole = V3Zero;
181	>	frameData.conductiveHeatFlux = Vector3d(0.0, 0.0, 0.0);
182	>	}
183	>
184	>	/** Returns the id of this Snapshot */
185	>	int getID() {
186	>	return frameData.id;
187	>	}
188
189	<	Snapshot(const Snapshot& s);
189	>	/** Sets the id of this Snapshot */
190	>	void setID(int id) {
191	>	frameData.id = id;
192	>	}
193
194	<	Snapshot& operator =(const Snapshot& s);
195	<
196	<	/** Returns the id of this Snapshot */
96	<	int getID() {
97	<	return id_;
98	<	}
194	>	int getSize() {
195	>	return atomData.getSize() + rigidbodyData.getSize();
196	>	}
197
198	<	/** Sets the id of this Snapshot */
199	<	void setID(int id) {
200	<	id_ = id;
201	<	}
198	>	/** Returns the number of atoms */
199	>	int getNumberOfAtoms() {
200	>	return atomData.getSize();
201	>	}
202
203	<	//template<typename T>
204	<	//static typename T::ElemPointerType getArrayPointer(vector<T>& v) {
205	<	//    return v[0]->getArrayPointer();
206	<	//}
203	>	/** Returns the number of rigid bodies */
204	>	int getNumberOfRigidBodies() {
205	>	return rigidbodyData.getSize();
206	>	}
207
208	<	static double* getArrayPointer(vector<Vector3d>& v) {
209	<	assert(v.size() > 0);
210	<	return v[0].getArrayPointer();
211	<	}
208	>	/** Returns the number of rigid bodies */
209	>	int getNumberOfCutoffGroups() {
210	>	return cgData.getSize();
211	>	}
212	>
213	>	/** Returns the H-Matrix */
214	>	Mat3x3d getHmat() {
215	>	return frameData.hmat;
216	>	}
217	>
218	>	/** Sets the H-Matrix */
219	>	void setHmat(const Mat3x3d& m);
220
221	<	static double* getArrayPointer(vector<RotMat3x3d>& v) {
222	<	assert(v.size() > 0);
223	<	return v[0].getArrayPointer();
224	<	}
221	>	RealType getVolume() {
222	>	if (!hasVolume_) {
223	>	frameData.volume = frameData.hmat.determinant();
224	>	hasVolume_ = true;
225	>	}
226	>	return frameData.volume;
227	>	}
228	>
229	>	void setVolume(RealType volume){
230	>	hasVolume_=true;
231	>	frameData.volume = volume;
232	>	}
233	>
234	>	/** Returns the inverse H-Matrix */
235	>	Mat3x3d getInvHmat() {
236	>	return frameData.invHmat;
237	>	}
238	>
239	>	/** Wrapping the vector according to periodic boundary condition*/
240	>	void wrapVector(Vector3d& v);
241	>	/** Scaling a vector to multiples of the periodic box */
242	>	Vector3d scaleVector(Vector3d &v);
243	>
244	>
245	>	Vector3d getCOM();
246	>	Vector3d getCOMvel();
247	>	Vector3d getCOMw();
248
249	<	static double* getArrayPointer(vector<double>& v) {
250	<	assert(v.size() > 0);
251	<	return &(v[0]);
252	<	}
249	>	RealType getTime() {
250	>	return frameData.currentTime;
251	>	}
252	>
253	>	void increaseTime(RealType dt) {
254	>	setTime(getTime() + dt);
255	>	}
256	>
257	>	void setTime(RealType time) {
258	>	frameData.currentTime =time;
259	>	//time at statData is redundant
260	>	statData[Stats::TIME] = frameData.currentTime;
261	>	}
262	>
263	>	void setShortRangePotential(RealType srp) {
264	>	frameData.shortRangePotential = srp;
265	>	hasShortRangePotential_ = true;
266	>	statData[Stats::SHORT_RANGE_POTENTIAL] = frameData.shortRangePotential;
267	>	}
268	>
269	>	RealType getShortRangePotential() {
270	>	return frameData.shortRangePotential;
271	>	}
272	>
273	>	void setBondPotential(RealType bp) {
274	>	frameData.bondPotential = bp;
275	>	hasBondPotential_ = true;
276	>	statData[Stats::BOND_POTENTIAL] = frameData.bondPotential;
277	>	}
278	>
279	>	void setBendPotential(RealType bp) {
280	>	frameData.bendPotential = bp;
281	>	hasBendPotential_ = true;
282	>	statData[Stats::BEND_POTENTIAL] = frameData.bendPotential;
283	>	}
284	>
285	>	void setTorsionPotential(RealType tp) {
286	>	frameData.torsionPotential = tp;
287	>	hasTorsionPotential_ = true;
288	>	statData[Stats::DIHEDRAL_POTENTIAL] = frameData.torsionPotential;
289	>	}
290	>
291	>	void setInversionPotential(RealType ip) {
292	>	frameData.inversionPotential = ip;
293	>	hasInversionPotential_ = true;
294	>	statData[Stats::INVERSION_POTENTIAL] = frameData.inversionPotential;
295	>	}
296	>
297	>	void setLongRangePotential(RealType lrp) {
298	>	frameData.longRangePotential = lrp;
299	>	hasLongRangePotential_ = true;
300	>	statData[Stats::LONG_RANGE_POTENTIAL] = frameData.longRangePotential;
301	>	}
302	>
303	>	RealType getLongRangePotential() {
304	>	return frameData.longRangePotential;
305	>	}
306	>
307	>	void setLongRangePotentialFamilies(potVec lrPot) {
308	>	frameData.lrPotentials = lrPot;
309	>	hasLongRangePotentialFamilies_ = true;
310	>	statData[Stats::VANDERWAALS_POTENTIAL] = frameData.lrPotentials[VANDERWAALS_FAMILY];
311	>	statData[Stats::ELECTROSTATIC_POTENTIAL] = frameData.lrPotentials[ELECTROSTATIC_FAMILY];
312	>	statData[Stats::METALLIC_POTENTIAL] = frameData.lrPotentials[METALLIC_FAMILY];
313	>	statData[Stats::HYDROGENBONDING_POTENTIAL] = frameData.lrPotentials[HYDROGENBONDING_FAMILY];
314	>	}
315	>
316	>	potVec getLongRangePotentials() {
317	>	return frameData.lrPotentials;
318	>	}
319	>
320	>	void setExcludedPotentials(potVec exPot) {
321	>	frameData.excludedPotentials = exPot;
322	>	hasExcludedPotentials_ = true;
323	>	}
324	>
325	>	potVec getExcludedPotentials() {
326	>	return frameData.excludedPotentials;
327	>	}
328	>
329	>
330	>	void setRestraintPotential(RealType rp) {
331	>	frameData.restraintPotential = rp;
332	>	hasRestraintPotential_ = true;
333	>	statData[Stats::RESTRAINT_POTENTIAL] = frameData.restraintPotential;
334	>	}
335	>
336	>	RealType getRestraintPotential() {
337	>	return frameData.restraintPotential;
338	>	}
339	>
340	>	void setRawPotential(RealType rp) {
341	>	frameData.rawPotential = rp;
342	>	hasRawPotential_ = true;
343	>	statData[Stats::RAW_POTENTIAL] = frameData.rawPotential;
344	>	}
345	>
346	>	RealType getRawPotential() {
347	>	return frameData.rawPotential;
348	>	}
349	>
350	>	RealType getChi() {
351	>	return frameData.chi;
352	>	}
353	>
354	>	void setChi(RealType chi) {
355	>	frameData.chi = chi;
356	>	}
357	>
358	>	RealType getIntegralOfChiDt() {
359	>	return frameData.integralOfChiDt;
360	>	}
361	>
362	>	void setIntegralOfChiDt(RealType integralOfChiDt) {
363	>	frameData.integralOfChiDt = integralOfChiDt;
364	>	}
365
366	<	/** */
367	<	void resize(size_t size);
366	>	RealType getChiElectronic() {
367	>	return frameData.chiQ;
368	>	}
369
370	+	void setChiElectronic(RealType chiQ) {
371	+	frameData.chiQ = chiQ;
372	+	}
373
374	<	/** */
375	<	void reserve(size_t size);
374	>	RealType getIntegralOfChiElectronicDt() {
375	>	return frameData.integralOfChiQDt;
376	>	}
377
378	<	DataStorage atomData;
379	<	DataStorage rigidbodyData;
378	>	void setIntegralOfChiElectronicDt(RealType integralOfChiQDt) {
379	>	frameData.integralOfChiQDt = integralOfChiQDt;
380	>	}
381
382	<	friend class SnapshotManager;
383	<	private:
382	>	void setOrthoTolerance(RealType orthoTolerance) {
383	>	orthoTolerance_ = orthoTolerance;
384	>	}
385
386	<	int id_; /**< identification number of the snapshot */
387	<	};
386	>	Mat3x3d getEta() {
387	>	return frameData.eta;
388	>	}
389
390	<	typedef DataStorage* (Snapshot::*DataStoragePointer);
390	>	void setEta(const Mat3x3d& eta) {
391	>	frameData.eta = eta;
392	>	}
393	>
394	>	Mat3x3d getStressTensor() {
395	>	return frameData.stressTensor;
396	>	}
397	>
398	>	void setStressTensor(const Mat3x3d& stressTensor) {
399	>	frameData.stressTensor = stressTensor;
400	>	}
401	>
402	>	Vector3d getConductiveHeatFlux() {
403	>	return frameData.conductiveHeatFlux;
404	>	}
405	>
406	>	void setConductiveHeatFlux(const Vector3d& heatFlux) {
407	>	frameData.conductiveHeatFlux = heatFlux;
408	>	}
409	>
410	>	bool hasCOM() {
411	>	return hasCOM_;
412	>	}
413	>
414	>	void setCOMprops(const Vector3d& COM, const Vector3d& COMvel, const Vector3d& COMw) {
415	>	frameData.COM = COM;
416	>	frameData.COMvel = COMvel;
417	>	frameData.COMw = COMw;
418	>	hasCOM_ = true;
419	>	}
420	>
421	>	DataStorage atomData;
422	>	DataStorage rigidbodyData;
423	>	DataStorage cgData;
424	>	FrameData frameData;
425	>	Stats statData;
426	>
427	>	private:
428	>	RealType orthoTolerance_;
429	>	bool hasCOM_;
430	>	bool hasVolume_;
431	>	bool hasShortRangePotential_;
432	>	bool hasBondPotential_;
433	>	bool hasBendPotential_;
434	>	bool hasTorsionPotential_;
435	>	bool hasInversionPotential_;
436	>	bool hasLongRangePotential_;
437	>	bool hasLongRangePotentialFamilies_;
438	>	bool hasRestraintPotential_;
439	>	bool hasRawPotential_;
440	>	bool hasExcludedPotentials_;
441	>	};
442	>
443	>	typedef DataStorage (Snapshot::*DataStoragePointer);
444		}
445		#endif //BRAINS_SNAPSHOT_HPP

Comparing:
trunk/src/brains/Snapshot.hpp (property svn:keywords), Revision 146 by tim, Fri Oct 22 23:09:57 2004 UTC vs.
branches/development/src/brains/Snapshot.hpp (property svn:keywords), Revision 1760 by gezelter, Thu Jun 21 19:26:46 2012 UTC

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