1 |
/* |
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 2.0*De*beta*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 - 2.0*eterm + 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 |