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

Comparing:
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 1757 by gezelter, Tue Jun 19 02:11:07 2012 UTC

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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	+	/**
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
53
54		#include <vector>
55
56	<	#include "math/Vector3.hpp"
57	<	#include "math/SquareMatrix3.hpp"
56	>	#include "brains/DataStorage.hpp"
57	>	#include "nonbonded/NonBondedInteraction.hpp"
58	>	#include "brains/Stats.hpp"
59
60	<	using namespace std;
60	>	namespace OpenMD{
61
62	<	namespace oopse{
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
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);
105	<	void resize(size_t size);
59	<	void reserve(size_t size);
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	<	//friend Snapshot;
108	<	//friend SnapshotManager;
109	<	//private:
110	<	vector<Vector3d> position;               /** position array */
111	<	vector<Vector3d> velocity;               /** velocity array */
112	<	vector<RotMat3x3d> Amat;            /** rotation matrix array */
113	<	vector<Vector3d> angularMomentum;/** velocity array */
114	<	vector<Vector3d> ul;                /** the lab frame unit vector array*/
115	<	vector<double> zAngle;              /** z -angle array */
116	<	vector<Vector3d> force;               /** force array */
117	<	vector<Vector3d> torque;               /** torque array */
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	<	};
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	<	/**
178	<	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
179	<	* @brief Snapshot class is a repository class for storing dynamic data during
180	<	*  Simulation
181	<	* Every snapshot class will contain one DataStorage  for atoms and one DataStorage
182	<	*  for rigid bodies.
183	<	* @see SimData
184	<	*/
185	<	class Snapshot {
186	<	public:
177	>	/** Sets the id of this Snapshot */
178	>	void setID(int id) {
179	>	frameData.id = id;
180	>	}
181	>
182	>	int getSize() {
183	>	return atomData.getSize() + rigidbodyData.getSize();
184	>	}
185	>
186	>	/** Returns the number of atoms */
187	>	int getNumberOfAtoms() {
188	>	return atomData.getSize();
189	>	}
190	>
191	>	/** Returns the number of rigid bodies */
192	>	int getNumberOfRigidBodies() {
193	>	return rigidbodyData.getSize();
194	>	}
195	>
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	<	Snapshot() {}
210	<	Snapshot(int i) {
209	>	RealType getVolume() {
210	>	if (hasVolume_){
211	>	return frameData.volume;
212	>	}else{
213	>	return frameData.hmat.determinant();
214	>	}
215	>	}
216
217	<	}
217	>	void setVolume(RealType volume){
218	>	hasVolume_=true;
219	>	frameData.volume = volume;
220	>	}
221
222	<	Snapshot(const Snapshot& s);
222	>	/** Returns the inverse H-Matrix */
223	>	Mat3x3d getInvHmat() {
224	>	return frameData.invHmat;
225	>	}
226
227	<	Snapshot& operator =(const Snapshot& s);
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	<	/** Returns the id of this Snapshot */
238	<	int getID() {
239	<	return id_;
98	<	}
237	>	RealType getTime() {
238	>	return frameData.currentTime;
239	>	}
240
241	<	/** Sets the id of this Snapshot */
242	<	void setID(int id) {
243	<	id_ = id;
103	<	}
241	>	void increaseTime(RealType dt) {
242	>	setTime(getTime() + dt);
243	>	}
244
245	<	//template<typename T>
246	<	//static typename T::ElemPointerType getArrayPointer(vector<T>& v) {
247	<	//    return v[0]->getArrayPointer();
248	<	//}
245	>	void setTime(RealType time) {
246	>	frameData.currentTime =time;
247	>	//time at statData is redundant
248	>	statData[Stats::TIME] = frameData.currentTime;
249	>	}
250
251	<	static double* getArrayPointer(vector<Vector3d>& v) {
252	<	assert(v.size() > 0);
253	<	return v[0].getArrayPointer();
254	<	}
251	>	RealType getChi() {
252	>	return frameData.chi;
253	>	}
254	>
255	>	void setChi(RealType chi) {
256	>	frameData.chi = chi;
257	>	}
258	>
259	>	RealType getIntegralOfChiDt() {
260	>	return frameData.integralOfChiDt;
261	>	}
262	>
263	>	void setIntegralOfChiDt(RealType integralOfChiDt) {
264	>	frameData.integralOfChiDt = integralOfChiDt;
265	>	}
266
267	<	static double* getArrayPointer(vector<RotMat3x3d>& v) {
268	<	assert(v.size() > 0);
269	<	return v[0].getArrayPointer();
270	<	}
267	>	RealType getChiElectronic() {
268	>	return frameData.chiQ;
269	>	}
270	>
271	>	void setChiElectronic(RealType chiQ) {
272	>	frameData.chiQ = chiQ;
273	>	}
274	>
275	>	RealType getIntegralOfChiElectronicDt() {
276	>	return frameData.integralOfChiQDt;
277	>	}
278	>
279	>	void setIntegralOfChiElectronicDt(RealType integralOfChiQDt) {
280	>	frameData.integralOfChiQDt = integralOfChiQDt;
281	>	}
282
120	–	static double* getArrayPointer(vector<double>& v) {
121	–	assert(v.size() > 0);
122	–	return &(v[0]);
123	–	}
124	–
125	–	/** */
126	–	void resize(size_t size);
283
284	+	void setOrthoTolerance(RealType orthoTolerance) {
285	+	orthoTolerance_ = orthoTolerance;
286	+	}
287
288	<	/** */
289	<	void reserve(size_t size);
288	>	Mat3x3d getEta() {
289	>	return frameData.eta;
290	>	}
291
292	<	DataStorage atomData;
293	<	DataStorage rigidbodyData;
292	>	void setEta(const Mat3x3d& eta) {
293	>	frameData.eta = eta;
294	>	}
295
296	<	friend class SnapshotManager;
297	<	private:
296	>	Mat3x3d getStressTensor() {
297	>	return frameData.stressTensor;
298	>	}
299	>
300	>	void setStressTensor(const Mat3x3d& stressTensor) {
301	>	frameData.stressTensor = stressTensor;
302	>	}
303
304	<	int id_; /**< identification number of the snapshot */
305	<	};
304	>	Vector3d getConductiveHeatFlux() {
305	>	return frameData.conductiveHeatFlux;
306	>	}
307	>
308	>	void setConductiveHeatFlux(const Vector3d& heatFlux) {
309	>	frameData.conductiveHeatFlux = heatFlux;
310	>	}
311
312	<	typedef DataStorage* (Snapshot::*DataStoragePointer);
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 146 by tim, Fri Oct 22 23:09:57 2004 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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