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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

 /* 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, long long int memSize);   
        
  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:	1850
Committed:	Wed Feb 20 15:39:39 2013 UTC (12 years, 3 months ago) by gezelter
File size:	3586 byte(s)
Log Message:	Fixed a widespread typo in the license
#	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	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	chuckv	1246	*/
42
43			/* Uses the Helfand-moment method for calculating thermal
44			* conductivity using the relation kappa = (N,V)lim(t)->inf 1/(2k_BT^2Vt) <[G_K(t)-G_K(0)]^2>
45			* where G_K is the Helfand moment for thermal conductivity definded as
46			* G_K(t) = sum_{a=1}{^N} x_a(E_a-<E_a>) and E_a is defined to be
47			* 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
48			* particle pair a-b. This routine calculates E_a, <E_a> and does the correlation
49			* <[G_K(t)-G_K(0)]^2>.
50			* See Viscardy et al. JCP 126, 184513 (2007)
51			*/
52
53
54			#ifndef APPLICATIONS_DYNAMICPROPS_ENERGYCORRFUNC_HPP
55			#define APPLICATIONS_DYNAMICPROPS_ENERGYCORRFUNC_HPP
56
57			#include "applications/dynamicProps/FrameTimeCorrFunc.hpp"
58
59	gezelter	1390	namespace OpenMD {
60	chuckv	1246
61			class EnergyCorrFunc : public FrameTimeCorrFunc {
62			public:
63	gezelter	1629	EnergyCorrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, long long int memSize);
64	chuckv	1246
65			private:
66			virtual void correlateFrames(int frame1, int frame2);
67			virtual RealType calcCorrVal(int frame1, int frame2) { return 0.0; }
68			virtual void writeCorrelate();
69
70			protected:
71			virtual void preCorrelate();
72			virtual void postCorrelate();
73	gezelter	1249	std::vector<Vector3d> histogram_;
74	chuckv	1246
75	gezelter	1249	std::vector<std::vector<RealType> > E_a_;
76			std::vector<RealType> AvgE_a_;
77			std::vector<Vector3d> G_t_;
78	chuckv	1246	};
79
80			}
81			#endif //ENERGYCORRFUNC
82