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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 1774 by gezelter, Wed Aug 8 16:03:02 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		#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	>	bool     orthoRhombic;        /**< is this an orthorhombic periodic box? */
66	>	RealType totalEnergy;         /**< total energy of this frame */
67	>	RealType translationalKinetic; /**< translational kinetic energy of this frame */
68	>	RealType rotationalKinetic;   /**< rotational kinetic energy of this frame */
69	>	RealType kineticEnergy;       /**< kinetic energy of this frame */
70	>	RealType potentialEnergy;     /**< potential energy of this frame */
71	>	RealType shortRangePotential; /**< short-range contributions to the potential*/
72	>	RealType longRangePotential;  /**< long-range contributions to the potential */
73	>	RealType bondPotential;       /**< bonded contribution to the potential */
74	>	RealType bendPotential;       /**< angle-bending contribution to the potential */
75	>	RealType torsionPotential;    /**< dihedral (torsion angle) contribution to the potential */
76	>	RealType inversionPotential;  /**< inversion (planarity) contribution to the potential */
77	>	potVec   lrPotentials;        /**< breakdown of long-range potentials by family */
78	>	potVec   excludedPotentials;  /**< breakdown of excluded potentials by family */
79	>	RealType restraintPotential;  /**< potential energy of restraints */
80	>	RealType rawPotential;        /**< unrestrained potential energy (when restraints are applied) */
81	>	RealType xyArea;              /**< XY area of this frame */
82	>	RealType volume;              /**< total volume of this frame */
83	>	RealType pressure;            /**< pressure of this frame */
84	>	RealType temperature;         /**< temperature of this frame */
85	>	pair<RealType, RealType> thermostat;    /**< thermostat variables */
86	>	RealType electronicTemperature; /**< temperature of the electronic degrees of freedom */
87	>	pair<RealType, RealType> electronicThermostat; /**< thermostat variables for electronic degrees of freedom */
88	>	Mat3x3d  barostat;            /**< barostat matrix */
89	>	Vector3d COM;                 /**< location of system center of mass */
90	>	Vector3d COMvel;              /**< system center of mass velocity */
91	>	Vector3d COMw;                /**< system center of mass angular velocity */
92	>	Mat3x3d  inertiaTensor;       /**< inertia tensor for entire system */
93	>	RealType gyrationalVolume;    /**< gyrational volume for entire system */
94	>	RealType hullVolume;          /**< hull volume for entire system */
95	>	Mat3x3d  stressTensor;        /**< stress tensor */
96	>	Mat3x3d  pressureTensor;      /**< pressure tensor */
97	>	Vector3d systemDipole;        /**< total system dipole moment */
98	>	Vector3d conductiveHeatFlux;  /**< heat flux vector (conductive only) */
99	>	Vector3d convectiveHeatFlux;  /**< heat flux vector (convective only) */
100	>	RealType conservedQuantity;   /**< anything conserved by the integrator */
101	>	};
102
46	–	//forward declaration
47	–	class Snapshot;
48	–	class SnapshotManager;
103
104	<	/**
105	<	* @struct DataStorage
106	<	* @brief
107	<	*/
108	<	class DataStorage {
109	<	public:
110	<	DataStorage() {};
111	<	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 */
104	>	/**
105	>	* @class Snapshot
106	>	* @brief The Snapshot class is a repository storing dynamic data during a
107	>	* Simulation.  Every Snapshot contains FrameData (for global information)
108	>	* as well as DataStorage (one for Atoms, one for RigidBodies, and one for
109	>	* CutoffGroups).
110	>	*/
111	>	class Snapshot {
112
113	<	};
113	>	public:
114	>	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups);
115	>	Snapshot(int nAtoms, int nRigidbodies, int nCutoffGroups, int storageLayout);
116	>	/** Returns the id of this Snapshot */
117	>	int      getID();
118	>	/** Sets the id of this Snapshot */
119	>	void     setID(int id);
120
121	<	/**
122	<	* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
123	<	* @brief Snapshot class is a repository class for storing dynamic data during
124	<	*  Simulation
125	<	* Every snapshot class will contain one DataStorage  for atoms and one DataStorage
126	<	*  for rigid bodies.
127	<	* @see SimData
128	<	*/
129	<	class Snapshot {
130	<	public:
121	>	/** sets the state of the computed properties to false */
122	>	void     clearDerivedProperties();
123	>
124	>	int      getSize();
125	>	/** Returns the number of atoms */
126	>	int      getNumberOfAtoms();
127	>	/** Returns the number of rigid bodies */
128	>	int      getNumberOfRigidBodies();
129	>	/** Returns the number of rigid bodies */
130	>	int      getNumberOfCutoffGroups();
131	>
132	>	/** Returns the H-Matrix */
133	>	Mat3x3d  getHmat();
134	>	/** Sets the H-Matrix */
135	>	void     setHmat(const Mat3x3d& m);
136	>	/** Returns the inverse H-Matrix */
137	>	Mat3x3d  getInvHmat();
138
139	<	Snapshot() {}
140	<	Snapshot(int i) {
139	>	RealType getVolume();
140	>	RealType getXYarea();
141	>	void     setVolume(const RealType vol);
142
143	<	}
143	>	/** Wrapping the vector according to periodic boundary condition*/
144	>	void     wrapVector(Vector3d& v);
145
146	<	Snapshot(const Snapshot& s);
146	>	/** Scaling a vector to multiples of the periodic box */
147	>	Vector3d scaleVector(Vector3d &v);
148
149	<	Snapshot& operator =(const Snapshot& s);
149	>	void     setCOM(const Vector3d &com);
150	>	void     setCOMvel(const Vector3d &comVel);
151	>	void     setCOMw(const Vector3d &comw);
152	>
153	>	Vector3d getCOM();
154	>	Vector3d getCOMvel();
155	>	Vector3d getCOMw();
156
157	<	/** Returns the id of this Snapshot */
158	<	int getID() {
159	<	return id_;
98	<	}
157	>	RealType getTime();
158	>	void     increaseTime(const RealType dt);
159	>	void     setTime(const RealType time);
160
161	<	/** Sets the id of this Snapshot */
162	<	void setID(int id) {
163	<	id_ = id;
164	<	}
161	>	void     setBondPotential(const RealType bp);
162	>	void     setBendPotential(const RealType bp);
163	>	void     setTorsionPotential(const RealType tp);
164	>	void     setInversionPotential(const RealType ip);
165	>	RealType getBondPotential();
166	>	RealType getBendPotential();
167	>	RealType getTorsionPotential();
168	>	RealType getInversionPotential();
169
170	<	//template<typename T>
106	<	//static typename T::ElemPointerType getArrayPointer(vector<T>& v) {
107	<	//    return v[0]->getArrayPointer();
108	<	//}
170	>	RealType getShortRangePotential();
171
172	<	static double* getArrayPointer(vector<Vector3d>& v) {
173	<	assert(v.size() > 0);
174	<	return v[0].getArrayPointer();
175	<	}
172	>	void     setLongRangePotential(const potVec lrPot);
173	>	RealType getLongRangePotential();
174	>	potVec   getLongRangePotentials();
175	>
176	>	void     setExcludedPotentials(const potVec exPot);
177	>	potVec   getExcludedPotentials();
178	>
179	>	void     setRestraintPotential(const RealType rp);
180	>	RealType getRestraintPotential();
181	>
182	>	void     setRawPotential(const RealType rp);
183	>	RealType getRawPotential();
184	>
185	>	RealType getPotentialEnergy();
186	>	RealType getKineticEnergy();
187	>	RealType getTranslationalKineticEnergy();
188	>	RealType getRotationalKineticEnergy();
189	>	void     setKineticEnergy(const RealType ke);
190	>	void     setTranslationalKineticEnergy(const RealType tke);
191	>	void     setRotationalKineticEnergy(const RealType rke);
192	>	RealType getTotalEnergy();
193	>	void     setTotalEnergy(const RealType te);
194	>	RealType getConservedQuantity();
195	>	void     setConservedQuantity(const RealType cq);
196	>	RealType getTemperature();
197	>	void     setTemperature(const RealType temp);
198	>	RealType getElectronicTemperature();
199	>	void     setElectronicTemperature(const RealType eTemp);
200	>	RealType getPressure();
201	>	void     setPressure(const RealType pressure);
202	>
203	>	Mat3x3d  getPressureTensor();
204	>	void     setPressureTensor(const Mat3x3d& pressureTensor);
205	>
206	>	Mat3x3d  getStressTensor();
207	>	void     setStressTensor(const Mat3x3d& stressTensor);
208	>
209	>	Vector3d getConductiveHeatFlux();
210	>	void     setConductiveHeatFlux(const Vector3d& chf);
211	>
212	>	Vector3d getConvectiveHeatFlux();
213	>	void     setConvectiveHeatFlux(const Vector3d& chf);
214	>
215	>	Vector3d getHeatFlux();
216	>
217	>	Vector3d getSystemDipole();
218	>	void     setSystemDipole(const Vector3d& bd);
219	>
220	>	pair<RealType, RealType> getThermostat();
221	>	void setThermostat(const pair<RealType, RealType>& thermostat);
222	>
223	>	pair<RealType, RealType> getElectronicThermostat();
224	>	void setElectronicThermostat(const pair<RealType, RealType>& eThermostat);
225
226	<	static double* getArrayPointer(vector<RotMat3x3d>& v) {
227	<	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);
226	>	Mat3x3d  getBarostat();
227	>	void     setBarostat(const Mat3x3d& barostat);
228
229	+	Mat3x3d  getInertiaTensor();
230	+	void     setInertiaTensor(const Mat3x3d& inertiaTensor);
231
232	<	/** */
233	<	void reserve(size_t size);
232	>	RealType getGyrationalVolume();
233	>	void     setGyrationalVolume(const RealType gv);
234
235	<	DataStorage atomData;
236	<	DataStorage rigidbodyData;
235	>	RealType getHullVolume();
236	>	void     setHullVolume(const RealType hv);
237	>
238	>	void     setOrthoTolerance(RealType orthoTolerance);
239
240	<	friend class SnapshotManager;
241	<	private:
240	>	DataStorage atomData;
241	>	DataStorage rigidbodyData;
242	>	DataStorage cgData;
243	>	FrameData   frameData;
244
245	<	int id_; /**< identification number of the snapshot */
246	<	};
245	>	bool hasTotalEnergy;
246	>	bool hasTranslationalKineticEnergy;
247	>	bool hasRotationalKineticEnergy;
248	>	bool hasKineticEnergy;
249	>	bool hasShortRangePotential;
250	>	bool hasLongRangePotential;
251	>	bool hasPotentialEnergy;
252	>	bool hasXYarea;
253	>	bool hasVolume;
254	>	bool hasPressure;
255	>	bool hasTemperature;
256	>	bool hasElectronicTemperature;
257	>	bool hasCOM;
258	>	bool hasCOMvel;
259	>	bool hasCOMw;
260	>	bool hasPressureTensor;
261	>	bool hasSystemDipole;
262	>	bool hasConvectiveHeatFlux;
263	>	bool hasInertiaTensor;
264	>	bool hasGyrationalVolume;
265	>	bool hasHullVolume;
266	>	bool hasConservedQuantity;
267
268	<	typedef DataStorage* (Snapshot::*DataStoragePointer);
268	>	private:
269	>	RealType orthoTolerance_;
270	>
271	>	};
272	>
273	>	typedef DataStorage (Snapshot::*DataStoragePointer);
274		}
275		#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 1774 by gezelter, Wed Aug 8 16:03:02 2012 UTC

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