src/brains/Thermo.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
 * [4]  Vardeman & Gezelter, in progress (2009).
 */

#ifndef BRAINS_THERMO_HPP
#define BRAINS_THERMO_HPP

#include "primitives/Atom.hpp"
#include "brains/SimInfo.hpp"

namespace OpenMD {

  class Thermo{

  public:

    Thermo( SimInfo* info) : info_(info) {}

    // note: all the following energies are in kcal/mol

    RealType getKinetic(); // the total kinetic energy
    RealType getPotential(); // the total potential energy
    RealType getTotalE(); // gets the total energy

    RealType getTemperature(); // gives the instant temp. in K

    RealType getPressure(); // gives the instant pressure in atm;
    RealType getPressureX() { return getPressure(0); }
    RealType getPressureY() { return getPressure(1); }
    RealType getPressureZ() { return getPressure(2); }

    // gives the pressure tensor in amu*fs^-2*Ang^-1
    Mat3x3d getPressureTensor();
    RealType getVolume();   // gives the volume in Ang^3

    // accumulate and return the simulation box dipole moment in C*m
    Vector3d getBoxDipole();
    // accumulate and return helfand thermal momoment
    Vector3d getThermalHelfand();
      // Return the heat flux S
    Vector3d getHeatFlux();

    void saveStat();

  private:
    RealType getPressure(int direction);

    SimInfo* info_;
  };

} //end namespace OpenMD
#endif
Revision:	1671
Committed:	Mon Jan 30 21:31:09 2012 UTC (13 years, 7 months ago) by chuckv
File size:	3240 byte(s)
Log Message:	Adding support for atomic heat flux. Is broken w/ group based cuttoffs. Units need to be corrected and their may be a sign error in Jv.
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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	chuckv	1671	*
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] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
41	chuckv	1671
42	gezelter	246	#ifndef BRAINS_THERMO_HPP
43			#define BRAINS_THERMO_HPP
44	gezelter	2
45	tim	3	#include "primitives/Atom.hpp"
46			#include "brains/SimInfo.hpp"
47	gezelter	2
48	gezelter	1390	namespace OpenMD {
49	gezelter	246
50	gezelter	507	class Thermo{
51	gezelter	2
52	gezelter	507	public:
53	gezelter	2
54	gezelter	507	Thermo( SimInfo* info) : info_(info) {}
55	gezelter	2
56	gezelter	507	// note: all the following energies are in kcal/mol
57	gezelter	2
58	chuckv	1671	RealType getKinetic(); // the total kinetic energy
59	tim	963	RealType getPotential(); // the total potential energy
60			RealType getTotalE(); // gets the total energy
61	gezelter	2
62	tim	963	RealType getTemperature(); // gives the instant temp. in K
63	gezelter	2
64	tim	963	RealType getPressure(); // gives the instant pressure in atm;
65			RealType getPressureX() { return getPressure(0); }
66			RealType getPressureY() { return getPressure(1); }
67			RealType getPressureZ() { return getPressure(2); }
68	chrisfen	998
69			// gives the pressure tensor in amufs^-2Ang^-1
70	chuckv	1671	Mat3x3d getPressureTensor();
71			RealType getVolume(); // gives the volume in Ang^3
72	chrisfen	998
73			// accumulate and return the simulation box dipole moment in C*m
74	chuckv	1671	Vector3d getBoxDipole();
75	chuckv	1638	// accumulate and return helfand thermal momoment
76			Vector3d getThermalHelfand();
77	chuckv	1671	// Return the heat flux S
78			Vector3d getHeatFlux();
79
80	gezelter	507	void saveStat();
81	chuckv	1671
82	gezelter	507	private:
83	tim	963	RealType getPressure(int direction);
84	chuckv	1671
85	gezelter	507	SimInfo* info_;
86			};
87	chuckv	1671
88	gezelter	1390	} //end namespace OpenMD
89	gezelter	2	#endif