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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#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 getTranslationalKinetic(); // the translational kinetic energy 
    RealType getRotationalKinetic(); // the rotational kinetic energy 
    RealType getKinetic(); // the total kinetic energy 
    RealType getPotential(); // the total potential energy
    RealType getTotalEnergy(); // gets the total energy

    RealType getTemperature(); // Gives the instant temp. in K
    RealType getElectronicTemperature(); // gives the instant electronic temperature in K

    RealType getPressure(); // gives the instant pressure in atm;

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

    /** \brief accumulate and return the simulation box dipole moment in C*m */
    Vector3d getSystemDipole(); 
    Vector3d getHeatFlux();

    /** \brief Returns the center of the mass of the whole system.*/
    Vector3d getCom();

    /** \brief Returns the velocity of center of mass of the whole system.*/
    Vector3d getComVel();

    /** \brief Returns the center of the mass and Center of Mass velocity of
        the whole system.*/ 
    void getComAll(Vector3d& com,Vector3d& comVel);

    /** \brief Returns the inertia tensor and the total angular
        momentum for for the entire system
     * \param[out] inertiaTensor the inertia tensor 
     * \param[out] angularMomentum the angular momentum vector
     * \ingroup surface
     */
    void getInertiaTensor(Mat3x3d &inertiaTensor,Vector3d &angularMomentum);
    
    /** \brief Returns the Axis-aligned bounding box for the current system.
     */
    Mat3x3d getBoundingBox();

    /** \brief Returns system angular momentum */
    Vector3d getAngularMomentum();

    /** \brief Returns volume of system as estimated by an ellipsoid defined
        by the radii of gyration */
    RealType getGyrationalVolume();

    /** \brief Overloaded version of gyrational volume that also returns
        det(I) so dV/dr can be calculated */
    void getGyrationalVolume(RealType &vol, RealType &detI);

    RealType getHullVolume();

    RealType getTaggedAtomPairDistance();
    
  private:    
    SimInfo* info_;
  };
  
} //end namespace OpenMD
#endif
Revision:	1866
Committed:	Thu Apr 25 14:32:56 2013 UTC (12 years ago) by gezelter
File size:	4669 byte(s)
Log Message:	Fixes for Qhull static build strangeness
#	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			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43			#ifndef BRAINS_THERMO_HPP
44			#define BRAINS_THERMO_HPP
45	gezelter	2
46	tim	3	#include "primitives/Atom.hpp"
47			#include "brains/SimInfo.hpp"
48	gezelter	2
49	gezelter	1390	namespace OpenMD {
50	gezelter	246
51	gezelter	507	class Thermo{
52	gezelter	2
53	gezelter	507	public:
54	gezelter	2
55	gezelter	1764	Thermo( SimInfo* info ) : info_(info) {}
56	gezelter	2
57	gezelter	507	// note: all the following energies are in kcal/mol
58	gezelter	2
59	gezelter	1764	RealType getTranslationalKinetic(); // the translational kinetic energy
60			RealType getRotationalKinetic(); // the rotational kinetic energy
61	tim	963	RealType getKinetic(); // the total kinetic energy
62			RealType getPotential(); // the total potential energy
63	gezelter	1764	RealType getTotalEnergy(); // gets the total energy
64	gezelter	2
65	gezelter	1764	RealType getTemperature(); // Gives the instant temp. in K
66	gezelter	1715	RealType getElectronicTemperature(); // gives the instant electronic temperature in K
67	gezelter	2
68	tim	963	RealType getPressure(); // gives the instant pressure in atm;
69	chrisfen	998
70	gezelter	1866	/** \brief gives the pressure tensor in amufs^-2Ang^-1 */
71	gezelter	1764	Mat3x3d getPressureTensor();
72	tim	963	RealType getVolume(); // gives the volume in Ang^3
73	chrisfen	998
74	gezelter	1866	/** \brief accumulate and return the simulation box dipole moment in Cm /
75	gezelter	1764	Vector3d getSystemDipole();
76	gezelter	1723	Vector3d getHeatFlux();
77	gezelter	1764
78	gezelter	1866	/** \brief Returns the center of the mass of the whole system.*/
79	gezelter	1764	Vector3d getCom();
80
81	gezelter	1866	/** \brief Returns the velocity of center of mass of the whole system.*/
82	gezelter	1764	Vector3d getComVel();
83
84	gezelter	1866	/** \brief Returns the center of the mass and Center of Mass velocity of
85	gezelter	1764	the whole system.*/
86			void getComAll(Vector3d& com,Vector3d& comVel);
87
88	gezelter	1866	/** \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	gezelter	945
96	gezelter	1866	/** \brief Returns the Axis-aligned bounding box for the current system.
97			*/
98			Mat3x3d getBoundingBox();
99
100			/** \brief Returns system angular momentum */
101	gezelter	1764	Vector3d getAngularMomentum();
102
103	gezelter	1866	/** \brief Returns volume of system as estimated by an ellipsoid defined
104	gezelter	1764	by the radii of gyration */
105			RealType getGyrationalVolume();
106
107	gezelter	1866	/** \brief Overloaded version of gyrational volume that also returns
108	gezelter	1764	det(I) so dV/dr can be calculated */
109			void getGyrationalVolume(RealType &vol, RealType &detI);
110
111			RealType getHullVolume();
112
113			RealType getTaggedAtomPairDistance();
114	gezelter	945
115	gezelter	1764	private:
116	gezelter	507	SimInfo* info_;
117			};
118	gezelter	945
119	gezelter	1390	} //end namespace OpenMD
120	gezelter	2	#endif