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Comparing trunk/src/brains/Thermo.hpp (file contents):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 1 | Line 1
1	<	#ifndef __THERMO_H__
2	<	#define __THERMO_H__
1	>	/*
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	>	*/
42	>
43	>	#ifndef BRAINS_THERMO_HPP
44	>	#define BRAINS_THERMO_HPP
45
46		#include "primitives/Atom.hpp"
5	–	#include "primitives/SRI.hpp"
47		#include "brains/SimInfo.hpp"
7	–	#include "math/randomSPRNG.hpp"
48
49	<	class Thermo{
49	>	namespace OpenMD {
50
51	<	public:
12	<
13	<	Thermo( SimInfo* the_info );
14	<	~Thermo();
51	>	class Thermo{
52
53	<	// note: all the following energies are in kcal/mol
53	>	public:
54
55	<	double getKinetic(); // the total kinetic energy
19	<	double getPotential(); // the total potential energy
20	<	double getTotalE(); // gets the total energy
55	>	Thermo( SimInfo* info ) : info_(info) {}
56
57	<	double getTemperature(); // gives the instant temp. in K
57	>	// note: all the following energies are in kcal/mol
58
59	<	double getPressure(); // gives the instant pressure in atm;
60	<	double getPressureX(); // gives the instant pressure in atm;
61	<	double getPressureY(); // gives the instant pressure in atm;
62	<	double getPressureZ(); // gives the instant pressure in atm;
59	>	RealType getTranslationalKinetic(); // the translational kinetic energy
60	>	RealType getRotationalKinetic(); // the rotational kinetic energy
61	>	RealType getKinetic(); // the total kinetic energy
62	>	RealType getPotential(); // the total potential energy
63	>	RealType getTotalEnergy(); // gets the total energy
64
65	<	void   getPressureTensor(double press[3][3]); // gives the pressure
66	<	// tensor in
31	<	// amu*fs^-2*Ang^-1
32	<	double getVolume();   // gives the volume in Ang^3
65	>	RealType getTemperature(); // Gives the instant temp. in K
66	>	RealType getElectronicTemperature(); // gives the instant electronic temperature in K
67
68	<	int getNDF();    // get the number of degrees of freedom in the system
35	<	int getNDFraw(); // get the number of raw degrees of freedom in the system
36	<	// i.e. don't subtract constraints or system COM.
37	<
38	<	void velocitize(); // set the temperature to the target temp in SimInfo
39	<	// NOTE: srand48 should be seeded before calling.
40	<	void getCOMVel(double vdrift[3]);
41	<	void getCOM(double COM[3]);
42	<	void removeCOMdrift();
68	>	RealType getPressure(); // gives the instant pressure in atm;
69
70	<	private:
71	<	SimInfo* info;
72	<	gaussianSPRNG *gaussStream;
73	<	};
70	>	/** \brief gives the pressure tensor in amu*fs^-2*Ang^-1 */
71	>	Mat3x3d  getPressureTensor();
72	>	RealType getVolume();   // gives the volume in Ang^3
73	>
74	>	/** \brief accumulate and return the simulation box dipole moment in C*m */
75	>	Vector3d getSystemDipole();
76	>	Vector3d getHeatFlux();
77	>
78	>	/** \brief Returns the center of the mass of the whole system.*/
79	>	Vector3d getCom();
80	>
81	>	/** \brief Returns the velocity of center of mass of the whole system.*/
82	>	Vector3d getComVel();
83	>
84	>	/** \brief Returns the center of the mass and Center of Mass velocity of
85	>	the whole system.*/
86	>	void getComAll(Vector3d& com,Vector3d& comVel);
87	>
88	>	/** \brief Returns the inertia tensor and the total angular
89	>	momentum for for the entire system
90	>	* \param[out] inertiaTensor the inertia tensor
91	>	* \param[out] angularMomentum the angular momentum vector
92	>	* \ingroup surface
93	>	*/
94	>	void getInertiaTensor(Mat3x3d &inertiaTensor,Vector3d &angularMomentum);
95	>
96	>	/** \brief Returns the Axis-aligned bounding box for the current system.
97	>	*/
98	>	Mat3x3d getBoundingBox();
99	>
100	>	/** \brief Returns system angular momentum */
101	>	Vector3d getAngularMomentum();
102	>
103	>	/** \brief Returns volume of system as estimated by an ellipsoid defined
104	>	by the radii of gyration */
105	>	RealType getGyrationalVolume();
106	>
107	>	/** \brief Overloaded version of gyrational volume that also returns
108	>	det(I) so dV/dr can be calculated */
109	>	void getGyrationalVolume(RealType &vol, RealType &detI);
110	>
111	>	RealType getHullVolume();
112	>
113	>	RealType getTaggedAtomPairDistance();
114	>
115	>	private:
116	>	SimInfo* info_;
117	>	};
118	>
119	>	} //end namespace OpenMD
120		#endif

Comparing trunk/src/brains/Thermo.hpp (property svn:keywords):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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