applications/dynamicProps/EnergyCorrFunc.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).                        
 */

 /* Uses the Helfand-moment method for calculating thermal
  * conductivity using the relation kappa = (N,V)lim(t)->inf 1/(2*k_B*T^2*V*t) <[G_K(t)-G_K(0)]^2>
  * where G_K is the Helfand moment for thermal conductivity definded as
  * G_K(t) = sum_{a=1}{^N} x_a(E_a-<E_a>) and E_a is defined to be
  *     E_a = p_2^2/(2*m)+1/2 sum_{b.ne.a} u(r_ab) where p is momentum and u is pot energy for the 
  * particle pair a-b. This routine calculates E_a, <E_a> and does the correlation
  * <[G_K(t)-G_K(0)]^2>.
  * See Viscardy et al. JCP 126, 184513 (2007)
  */


#ifndef APPLICATIONS_DYNAMICPROPS_ENERGYCORRFUNC_HPP
#define APPLICATIONS_DYNAMICPROPS_ENERGYCORRFUNC_HPP

#include "applications/dynamicProps/FrameTimeCorrFunc.hpp"

namespace OpenMD {

  class EnergyCorrFunc : public FrameTimeCorrFunc {
  public:
    EnergyCorrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2);   
        
  private:
    virtual void correlateFrames(int frame1, int frame2);
    virtual RealType calcCorrVal(int frame1, int frame2) { return 0.0; }
    virtual void writeCorrelate();

  protected:
    virtual void preCorrelate();
    virtual void postCorrelate();
    std::vector<Vector3d> histogram_;
    
    std::vector<std::vector<RealType> > E_a_;
    std::vector<RealType> AvgE_a_;
    std::vector<Vector3d> G_t_;
  };

}
#endif //ENERGYCORRFUNC

Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 6 months ago) by gezelter
Original Path:	*trunk/src/applications/dynamicProps/EnergyCorrFunc.hpp*
File size:	3496 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	User	Rev	Content
1	chuckv	1246	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	chuckv	1246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	chuckv	1246	* 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			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	chuckv	1246	*/
41
42			/* Uses the Helfand-moment method for calculating thermal
43			* conductivity using the relation kappa = (N,V)lim(t)->inf 1/(2k_BT^2Vt) <[G_K(t)-G_K(0)]^2>
44			* where G_K is the Helfand moment for thermal conductivity definded as
45			* G_K(t) = sum_{a=1}{^N} x_a(E_a-<E_a>) and E_a is defined to be
46			* E_a = p_2^2/(2*m)+1/2 sum_{b.ne.a} u(r_ab) where p is momentum and u is pot energy for the
47			* particle pair a-b. This routine calculates E_a, <E_a> and does the correlation
48			* <[G_K(t)-G_K(0)]^2>.
49			* See Viscardy et al. JCP 126, 184513 (2007)
50			*/
51
52
53			#ifndef APPLICATIONS_DYNAMICPROPS_ENERGYCORRFUNC_HPP
54			#define APPLICATIONS_DYNAMICPROPS_ENERGYCORRFUNC_HPP
55
56			#include "applications/dynamicProps/FrameTimeCorrFunc.hpp"
57
58	gezelter	1390	namespace OpenMD {
59	chuckv	1246
60			class EnergyCorrFunc : public FrameTimeCorrFunc {
61			public:
62			EnergyCorrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2);
63
64			private:
65			virtual void correlateFrames(int frame1, int frame2);
66			virtual RealType calcCorrVal(int frame1, int frame2) { return 0.0; }
67			virtual void writeCorrelate();
68
69			protected:
70			virtual void preCorrelate();
71			virtual void postCorrelate();
72	gezelter	1249	std::vector<Vector3d> histogram_;
73	chuckv	1246
74	gezelter	1249	std::vector<std::vector<RealType> > E_a_;
75			std::vector<RealType> AvgE_a_;
76			std::vector<Vector3d> G_t_;
77	chuckv	1246	};
78
79			}
80			#endif //ENERGYCORRFUNC
81