src/types/PolynomialTorsionType.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.
 */
 
/**
 * @file PolynomialTorsionType.hpp
 * @author teng lin
 * @date  11/16/2004
 * @version 1.0
 */ 

#ifndef TYPES_POLYNOMIALBONDTYPE_HPP
#define TYPES_POLYNOMIALBONDTYPE_HPP

#include "math/Polynomial.hpp"
#include "types/TorsionType.hpp"

namespace oopse {

/**
 * @class PolynomialTorsionType PolynomialTorsionType.hpp "types/PolynomialTorsionType.hpp"
 * @todo documentation
 */
class PolynomialTorsionType : public TorsionType{

    public:
        PolynomialTorsionType() {}

        double getCoefficient(int power) {
            return polynomial_.getCoefficient(power);
        }

        void addCoefficient(int power, double coefficient) {
            polynomial_.addCoefficient(power, coefficient);
        }

        void setCoefficient(int power, double coefficient) {
            polynomial_.setCoefficient(power, coefficient);
        }

        void setPolynomial(const DoublePolynomial& p) {
            polynomial_ = p;
        }
        
        virtual void calcForce(double cosPhi, double sinPhi, double& V, double& dVdPhi) {
            V = polynomial_.evaluate(cosPhi);
            double dVdcosPhi = polynomial_.evaluateDerivative(cosPhi); 
            dVdPhi = - dVdcosPhi * sinPhi;
        }

        friend std::ostream& operator <<(std::ostream& os, PolynomialTorsionType& pbt);
        
    private:
        
        DoublePolynomial polynomial_;
};

std::ostream& operator <<(std::ostream& os, PolynomialTorsionType& ptt) {
    DoublePolynomial::const_iterator i;

    i = ptt.polynomial_.begin();
    
    if (i == ptt.polynomial_.end()) {
        os << "This Polynomial contains nothing" << std::endl;
        return os;
    }

    os << "This Polynomial contains below terms:" << std::endl;    
    
    while(true){
        os << i->second << "*" << "(cosPhi)" << "^" << i->first;

        if (++i == ptt.polynomial_.end()) {
            //if we reach the end of the polynomial pair, write out a newline and then escape the loop
            os << std::endl;
            break;
        } else {
            //otherwise, write out a "+"
            os << " + ";
        }
    }
    
    os << std::endl;
    return os;
}


} //end namespace oopse
#endif //TYPES_POLYNOMIALBONDTYPE_HPP

Revision:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 5 months ago) by gezelter
File size:	4297 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	Content
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