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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 1858 by gezelter, Wed Apr 3 21:32:13 2013 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, 234107 (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;
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	>	Mat3x3d  bBox;                /**< axes of a bounding box in matrix form */
66	>	Mat3x3d  invBbox;             /**< the inverse of the bounding box */
67	>	bool     orthoRhombic;        /**< is this an orthorhombic periodic box? */
68	>	RealType totalEnergy;         /**< total energy of this frame */
69	>	RealType translationalKinetic; /**< translational kinetic energy of this frame */
70	>	RealType rotationalKinetic;   /**< rotational kinetic 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	>	potVec   excludedPotentials;  /**< breakdown of excluded potentials by family */
81	>	RealType restraintPotential;  /**< potential energy of restraints */
82	>	RealType rawPotential;        /**< unrestrained potential energy (when restraints are applied) */
83	>	RealType xyArea;              /**< XY area of this frame */
84	>	RealType volume;              /**< total volume of this frame */
85	>	RealType pressure;            /**< pressure of this frame */
86	>	RealType temperature;         /**< temperature of this frame */
87	>	pair<RealType, RealType> thermostat;    /**< thermostat variables */
88	>	RealType electronicTemperature; /**< temperature of the electronic degrees of freedom */
89	>	pair<RealType, RealType> electronicThermostat; /**< thermostat variables for electronic degrees of freedom */
90	>	Mat3x3d  barostat;            /**< barostat matrix */
91	>	Vector3d COM;                 /**< location of system center of mass */
92	>	Vector3d COMvel;              /**< system center of mass velocity */
93	>	Vector3d COMw;                /**< system center of mass angular velocity */
94	>	Mat3x3d  inertiaTensor;       /**< inertia tensor for entire system */
95	>	RealType gyrationalVolume;    /**< gyrational volume for entire system */
96	>	RealType hullVolume;          /**< hull volume for entire system */
97	>	Mat3x3d  stressTensor;        /**< stress tensor */
98	>	Mat3x3d  pressureTensor;      /**< pressure tensor */
99	>	Vector3d systemDipole;        /**< total system dipole moment */
100	>	Vector3d conductiveHeatFlux;  /**< heat flux vector (conductive only) */
101	>	Vector3d convectiveHeatFlux;  /**< heat flux vector (convective only) */
102	>	RealType conservedQuantity;   /**< anything conserved by the integrator */
103	>	};
104
46	–	//forward declaration
47	–	class Snapshot;
48	–	class SnapshotManager;
105
106	<	/**
107	<	* @struct DataStorage
108	<	* @brief
109	<	*/
110	<	class DataStorage {
111	<	public:
112	<	DataStorage() {};
113	<	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 */
106	>	/**
107	>	* @class Snapshot
108	>	* @brief The Snapshot class is a repository storing dynamic data during a
109	>	* Simulation.  Every Snapshot contains FrameData (for global information)
110	>	* as well as DataStorage (one for Atoms, one for RigidBodies, and one for
111	>	* CutoffGroups).
112	>	*/
113	>	class Snapshot {
114
115	<	};
115	>	public:
116	>	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups);
117	>	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, int storageLayout);
118	>	/** Returns the id of this Snapshot */
119	>	int      getID();
120	>	/** Sets the id of this Snapshot */
121	>	void     setID(int id);
122
123	<	/**
124	<	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
125	<	* @brief Snapshot class is a repository class for storing dynamic data during
126	<	*  Simulation
127	<	* Every snapshot class will contain one DataStorage  for atoms and one DataStorage
128	<	*  for rigid bodies.
129	<	* @see SimData
130	<	*/
131	<	class Snapshot {
132	<	public:
123	>	/** sets the state of the computed properties to false */
124	>	void     clearDerivedProperties();
125	>
126	>	int      getSize();
127	>	/** Returns the number of atoms */
128	>	int      getNumberOfAtoms();
129	>	/** Returns the number of rigid bodies */
130	>	int      getNumberOfRigidBodies();
131	>	/** Returns the number of rigid bodies */
132	>	int      getNumberOfCutoffGroups();
133	>
134	>	/** Returns the H-Matrix */
135	>	Mat3x3d  getHmat();
136	>	/** Sets the H-Matrix */
137	>	void     setHmat(const Mat3x3d& m);
138	>	/** Returns the inverse H-Matrix */
139	>	Mat3x3d  getInvHmat();
140	>
141	>	/** Returns the Bounding Box */
142	>	Mat3x3d  getBoundingBox();
143	>	/** Sets the Bounding Box */
144	>	void     setBoundingBox(const Mat3x3d& m);
145	>	/** Returns the inverse Bounding Box*/
146	>	Mat3x3d  getInvBoundingBox();
147
148	<	Snapshot() {}
149	<	Snapshot(int i) {
148	>	RealType getVolume();
149	>	RealType getXYarea();
150	>	void     setVolume(const RealType vol);
151
152	<	}
152	>	/** Wrapping the vector according to periodic boundary condition*/
153	>	void     wrapVector(Vector3d& v);
154
155	<	Snapshot(const Snapshot& s);
155	>	/** Scaling a vector to multiples of the periodic box */
156	>	Vector3d scaleVector(Vector3d &v);
157
158	<	Snapshot& operator =(const Snapshot& s);
158	>	void     setCOM(const Vector3d &com);
159	>	void     setCOMvel(const Vector3d &comVel);
160	>	void     setCOMw(const Vector3d &comw);
161	>
162	>	Vector3d getCOM();
163	>	Vector3d getCOMvel();
164	>	Vector3d getCOMw();
165
166	<	/** Returns the id of this Snapshot */
167	<	int getID() {
168	<	return id_;
98	<	}
166	>	RealType getTime();
167	>	void     increaseTime(const RealType dt);
168	>	void     setTime(const RealType time);
169
170	<	/** Sets the id of this Snapshot */
171	<	void setID(int id) {
172	<	id_ = id;
173	<	}
170	>	void     setBondPotential(const RealType bp);
171	>	void     setBendPotential(const RealType bp);
172	>	void     setTorsionPotential(const RealType tp);
173	>	void     setInversionPotential(const RealType ip);
174	>	RealType getBondPotential();
175	>	RealType getBendPotential();
176	>	RealType getTorsionPotential();
177	>	RealType getInversionPotential();
178
179	<	//template<typename T>
106	<	//static typename T::ElemPointerType getArrayPointer(vector<T>& v) {
107	<	//    return v[0]->getArrayPointer();
108	<	//}
179	>	RealType getShortRangePotential();
180
181	<	static double* getArrayPointer(vector<Vector3d>& v) {
182	<	assert(v.size() > 0);
183	<	return v[0].getArrayPointer();
184	<	}
181	>	void     setLongRangePotential(const potVec lrPot);
182	>	RealType getLongRangePotential();
183	>	potVec   getLongRangePotentials();
184	>
185	>	void     setExcludedPotentials(const potVec exPot);
186	>	potVec   getExcludedPotentials();
187	>
188	>	void     setRestraintPotential(const RealType rp);
189	>	RealType getRestraintPotential();
190	>
191	>	void     setRawPotential(const RealType rp);
192	>	RealType getRawPotential();
193	>
194	>	RealType getPotentialEnergy();
195	>	RealType getKineticEnergy();
196	>	RealType getTranslationalKineticEnergy();
197	>	RealType getRotationalKineticEnergy();
198	>	void     setKineticEnergy(const RealType ke);
199	>	void     setTranslationalKineticEnergy(const RealType tke);
200	>	void     setRotationalKineticEnergy(const RealType rke);
201	>	RealType getTotalEnergy();
202	>	void     setTotalEnergy(const RealType te);
203	>	RealType getConservedQuantity();
204	>	void     setConservedQuantity(const RealType cq);
205	>	RealType getTemperature();
206	>	void     setTemperature(const RealType temp);
207	>	RealType getElectronicTemperature();
208	>	void     setElectronicTemperature(const RealType eTemp);
209	>	RealType getPressure();
210	>	void     setPressure(const RealType pressure);
211	>
212	>	Mat3x3d  getPressureTensor();
213	>	void     setPressureTensor(const Mat3x3d& pressureTensor);
214	>
215	>	Mat3x3d  getStressTensor();
216	>	void     setStressTensor(const Mat3x3d& stressTensor);
217	>
218	>	Vector3d getConductiveHeatFlux();
219	>	void     setConductiveHeatFlux(const Vector3d& chf);
220	>
221	>	Vector3d getConvectiveHeatFlux();
222	>	void     setConvectiveHeatFlux(const Vector3d& chf);
223	>
224	>	Vector3d getHeatFlux();
225	>
226	>	Vector3d getSystemDipole();
227	>	void     setSystemDipole(const Vector3d& bd);
228	>
229	>	pair<RealType, RealType> getThermostat();
230	>	void setThermostat(const pair<RealType, RealType>& thermostat);
231	>
232	>	pair<RealType, RealType> getElectronicThermostat();
233	>	void setElectronicThermostat(const pair<RealType, RealType>& eThermostat);
234
235	<	static double* getArrayPointer(vector<RotMat3x3d>& v) {
236	<	assert(v.size() > 0);
117	<	return v[0].getArrayPointer();
118	<	}
119	<
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);
235	>	Mat3x3d  getBarostat();
236	>	void     setBarostat(const Mat3x3d& barostat);
237
238	+	Mat3x3d  getInertiaTensor();
239	+	void     setInertiaTensor(const Mat3x3d& inertiaTensor);
240
241	<	/** */
242	<	void reserve(size_t size);
241	>	RealType getGyrationalVolume();
242	>	void     setGyrationalVolume(const RealType gv);
243
244	<	DataStorage atomData;
245	<	DataStorage rigidbodyData;
244	>	RealType getHullVolume();
245	>	void     setHullVolume(const RealType hv);
246	>
247	>	void     setOrthoTolerance(RealType orthoTolerance);
248
249	<	friend class SnapshotManager;
250	<	private:
249	>	DataStorage atomData;
250	>	DataStorage rigidbodyData;
251	>	DataStorage cgData;
252	>	FrameData   frameData;
253
254	<	int id_; /**< identification number of the snapshot */
255	<	};
254	>	bool hasTotalEnergy;
255	>	bool hasTranslationalKineticEnergy;
256	>	bool hasRotationalKineticEnergy;
257	>	bool hasKineticEnergy;
258	>	bool hasShortRangePotential;
259	>	bool hasLongRangePotential;
260	>	bool hasPotentialEnergy;
261	>	bool hasXYarea;
262	>	bool hasVolume;
263	>	bool hasPressure;
264	>	bool hasTemperature;
265	>	bool hasElectronicTemperature;
266	>	bool hasCOM;
267	>	bool hasCOMvel;
268	>	bool hasCOMw;
269	>	bool hasPressureTensor;
270	>	bool hasSystemDipole;
271	>	bool hasConvectiveHeatFlux;
272	>	bool hasInertiaTensor;
273	>	bool hasGyrationalVolume;
274	>	bool hasHullVolume;
275	>	bool hasConservedQuantity;
276	>	bool hasBoundingBox;
277
278	<	typedef DataStorage* (Snapshot::*DataStoragePointer);
278	>	private:
279	>	RealType orthoTolerance_;
280	>
281	>	};
282	>
283	>	typedef DataStorage (Snapshot::*DataStoragePointer);
284		}
285		#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 1858 by gezelter, Wed Apr 3 21:32:13 2013 UTC

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