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

Comparing:
trunk/src/brains/Snapshot.hpp (file contents), Revision 122 by tim, Wed Oct 20 05:52:25 2004 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		/*
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		*/
42	<
43	<	/**
44	<	* @file Snapshot.hpp
45	<	* @author tlin
46	<	* @date 10/20/2004
47	<	* @time 23:56am
48	<	* @version 1.0
49	<	*/
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
35	–	namespace oopse{
53
54	<	/**
55	<	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
56	<	* @brief Snapshot class is a repository class for storing dynamic data during
57	<	*  Simulation
58	<	* @see SimData
59	<	*/
60	<	class Snapshot {
61	<	public:
54	>	#include <vector>
55	>
56	>	#include "brains/DataStorage.hpp"
57	>	#include "nonbonded/NonBondedInteraction.hpp"
58	>	#include "brains/Stats.hpp"
59	>
60	>	namespace OpenMD{
61	>
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	>
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	<	PropertyMap properties_;
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	>	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	>	/** 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	<	private:
209	>	RealType getVolume() {
210	>	if (hasVolume_){
211	>	return frameData.volume;
212	>	}else{
213	>	return frameData.hmat.determinant();
214	>	}
215	>	}
216	>
217	>	void setVolume(RealType volume){
218	>	hasVolume_=true;
219	>	frameData.volume = volume;
220	>	}
221	>
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	<	};
237	>	RealType getTime() {
238	>	return frameData.currentTime;
239	>	}
240
241	+	void increaseTime(RealType dt) {
242	+	setTime(getTime() + dt);
243	+	}
244	+
245	+	void setTime(RealType time) {
246	+	frameData.currentTime =time;
247	+	//time at statData is redundant
248	+	statData[Stats::TIME] = frameData.currentTime;
249	+	}
250	+
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	+	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	+
283	+
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 122 by tim, Wed Oct 20 05:52:25 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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