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 |
/** |
43 |
* @file PolynomialTorsionType.hpp |
44 |
* @author teng lin |
45 |
* @date 11/16/2004 |
46 |
* @version 1.0 |
47 |
*/ |
48 |
|
49 |
#ifndef TYPES_POLYNOMIALBONDTYPE_HPP |
50 |
#define TYPES_POLYNOMIALBONDTYPE_HPP |
51 |
|
52 |
#include "math/Polynomial.hpp" |
53 |
#include "types/TorsionType.hpp" |
54 |
|
55 |
namespace oopse { |
56 |
|
57 |
/** |
58 |
* @class PolynomialTorsionType PolynomialTorsionType.hpp "types/PolynomialTorsionType.hpp" |
59 |
* @todo documentation |
60 |
*/ |
61 |
class PolynomialTorsionType : public TorsionType{ |
62 |
|
63 |
public: |
64 |
PolynomialTorsionType() {} |
65 |
|
66 |
double getCoefficient(int power) { |
67 |
return polynomial_.getCoefficient(power); |
68 |
} |
69 |
|
70 |
void addCoefficient(int power, double coefficient) { |
71 |
polynomial_.addCoefficient(power, coefficient); |
72 |
} |
73 |
|
74 |
void setCoefficient(int power, double coefficient) { |
75 |
polynomial_.setCoefficient(power, coefficient); |
76 |
} |
77 |
|
78 |
void setPolynomial(const DoublePolynomial& p) { |
79 |
polynomial_ = p; |
80 |
} |
81 |
|
82 |
virtual void calcForce(double cosPhi, double sinPhi, double& V, double& dVdPhi) { |
83 |
V = polynomial_.evaluate(cosPhi); |
84 |
double dVdcosPhi = polynomial_.evaluateDerivative(cosPhi); |
85 |
dVdPhi = - dVdcosPhi * sinPhi; |
86 |
} |
87 |
|
88 |
friend std::ostream& operator <<(std::ostream& os, PolynomialTorsionType& pbt); |
89 |
|
90 |
private: |
91 |
|
92 |
DoublePolynomial polynomial_; |
93 |
}; |
94 |
|
95 |
std::ostream& operator <<(std::ostream& os, PolynomialTorsionType& ptt) { |
96 |
DoublePolynomial::const_iterator i; |
97 |
|
98 |
i = ptt.polynomial_.begin(); |
99 |
|
100 |
if (i == ptt.polynomial_.end()) { |
101 |
os << "This Polynomial contains nothing" << std::endl; |
102 |
return os; |
103 |
} |
104 |
|
105 |
os << "This Polynomial contains below terms:" << std::endl; |
106 |
|
107 |
while(true){ |
108 |
os << i->second << "*" << "(cosPhi)" << "^" << i->first; |
109 |
|
110 |
if (++i == ptt.polynomial_.end()) { |
111 |
//if we reach the end of the polynomial pair, write out a newline and then escape the loop |
112 |
os << std::endl; |
113 |
break; |
114 |
} else { |
115 |
//otherwise, write out a "+" |
116 |
os << " + "; |
117 |
} |
118 |
} |
119 |
|
120 |
os << std::endl; |
121 |
return os; |
122 |
} |
123 |
|
124 |
|
125 |
} //end namespace oopse |
126 |
#endif //TYPES_POLYNOMIALBONDTYPE_HPP |
127 |
|