src/types/MorseBondType.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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
#ifndef TYPES_MORSEBONDTYPE_HPP
#define TYPES_MORSEBONDTYPE_HPP

#include "types/BondType.hpp"

namespace oopse {
  /**
   * @class MorseBondType 
   *
   * MorseBondType is a more realistic bond potential.
   *
   * The functional form is given by: \f$V(r) = D_e (1 - e^{-\beta (r
   * - r_0)})^2\f$ where \f$D_e\f$ is the bond dissociation energy (in
   * kcal / mol), \f$\beta$\f is an inverse distance parameter related
   * to the force constant. \f$\beta = \sqrt{\frac{k}{2 D_e}}\f$, and
   * \f$r_0\f$ is the equilibrium bond length.
   */
  class MorseBondType : public BondType {
    
  public:

    MorseBondType( double myR0, double myD, double myBeta) 
        : BondType(myR0), De(myD), beta(myBeta) {
    }
    
    void setWellDepth(double myD) { De = myD;}

    void setBeta(double myBeta) { beta = myBeta; }

    void setWellDepthAndForceConstant(double myD, double myK) {
      De = myD;
      beta = sqrt(myK/(2.0*De));
    }

    double getWellDepth() {return De;}

    double getBeta() {return beta;}

    double getForceConstant() {return 2.0*De*beta*beta;}

    virtual void calcForce(double r, double& V, double& dVdr) {
      double dr, eterm, eterm2;

      dr = r - r0;
      eterm = exp(-beta*dr);
      eterm2 = eterm*eterm;

      V = De*(1 - 2.0*eterm  + eterm2);
      dVdr = 2.0 * De * beta * (eterm - eterm2);
    }
                
  private:
    
    double De;
    double beta;
    
  };
}
#endif
Revision:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 5 months ago) by gezelter
File size:	3511 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	User	Rev	Content
1	gezelter	1930	/*
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. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#ifndef TYPES_MORSEBONDTYPE_HPP
43			#define TYPES_MORSEBONDTYPE_HPP
44
45			#include "types/BondType.hpp"
46
47			namespace oopse {
48			/**
49			* @class MorseBondType
50			*
51			* MorseBondType is a more realistic bond potential.
52			*
53			* The functional form is given by: \f$V(r) = D_e (1 - e^{-\beta (r
54			* - r_0)})^2\f$ where \f$D_e\f$ is the bond dissociation energy (in
55			* kcal / mol), \f$\beta$\f is an inverse distance parameter related
56			* to the force constant. \f$\beta = \sqrt{\frac{k}{2 D_e}}\f$, and
57			* \f$r_0\f$ is the equilibrium bond length.
58			*/
59			class MorseBondType : public BondType {
60
61			public:
62
63			MorseBondType( double myR0, double myD, double myBeta)
64			: BondType(myR0), De(myD), beta(myBeta) {
65			}
66
67			void setWellDepth(double myD) { De = myD;}
68
69			void setBeta(double myBeta) { beta = myBeta; }
70
71			void setWellDepthAndForceConstant(double myD, double myK) {
72			De = myD;
73			beta = sqrt(myK/(2.0*De));
74			}
75
76			double getWellDepth() {return De;}
77
78			double getBeta() {return beta;}
79
80			double getForceConstant() {return 2.0Debeta*beta;}
81
82			virtual void calcForce(double r, double& V, double& dVdr) {
83			double dr, eterm, eterm2;
84
85			dr = r - r0;
86			eterm = exp(-beta*dr);
87			eterm2 = eterm*eterm;
88
89			V = De(1 - 2.0eterm + eterm2);
90			dVdr = 2.0 * De * beta * (eterm - eterm2);
91			}
92
93			private:
94
95			double De;
96			double beta;
97
98			};
99			}
100			#endif