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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.
branches/development/src/brains/Thermo.hpp (file contents), Revision 1723 by gezelter, Thu May 24 20:59:54 2012 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, 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	>	#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;
27	<	double getPressureZ(); // gives the instant pressure in atm;
59	>	RealType getKinetic(); // the total kinetic energy
60	>	RealType getPotential(); // the total potential energy
61	>	RealType getTotalE(); // gets the total energy
62
63	<	void   getPressureTensor(double press[3][3]); // gives the pressure
64	<	// tensor in
31	<	// amu*fs^-2*Ang^-1
32	<	double getVolume();   // gives the volume in Ang^3
63	>	RealType getTemperature(); // gives the instant temp. in K
64	>	RealType getElectronicTemperature(); // gives the instant electronic temperature in K
65
66	<	int getNDF();    // get the number of degrees of freedom in the system
67	<	int getNDFraw(); // get the number of raw degrees of freedom in the system
68	<	// i.e. don't subtract constraints or system COM.
69	<
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();
66	>	RealType getPressure(); // gives the instant pressure in atm;
67	>	RealType getPressureX() { return getPressure(0); }
68	>	RealType getPressureY() { return getPressure(1); }
69	>	RealType getPressureZ() { return getPressure(2); }
70
71	<	private:
72	<	SimInfo* info;
73	<	gaussianSPRNG *gaussStream;
74	<	};
71	>	// gives the pressure tensor in amu*fs^-2*Ang^-1
72	>	Mat3x3d getPressureTensor();
73	>	RealType getVolume();   // gives the volume in Ang^3
74	>
75	>	// accumulate and return the simulation box dipole moment in C*m
76	>	Vector3d getBoxDipole();
77	>	Vector3d getHeatFlux();
78	>	void saveStat();
79	>
80	>	private:
81	>	RealType getPressure(int direction);
82	>
83	>	SimInfo* info_;
84	>	};
85	>
86	>	} //end namespace OpenMD
87		#endif

Comparing:
trunk/src/brains/Thermo.hpp (property svn:keywords), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/brains/Thermo.hpp (property svn:keywords), Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC

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