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:	2204
Committed:	Fri Apr 15 22:04:00 2005 UTC (19 years, 2 months ago) by gezelter
File size:	4147 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	gezelter	2204	/**
58			* @class PolynomialTorsionType PolynomialTorsionType.hpp "types/PolynomialTorsionType.hpp"
59			* @todo documentation
60			*/
61			class PolynomialTorsionType : public TorsionType{
62	gezelter	1930
63	gezelter	2204	public:
64			PolynomialTorsionType() {}
65	gezelter	1930
66	gezelter	2204	double getCoefficient(int power) {
67			return polynomial_.getCoefficient(power);
68			}
69	gezelter	1930
70	gezelter	2204	void addCoefficient(int power, double coefficient) {
71			polynomial_.addCoefficient(power, coefficient);
72			}
73	gezelter	1930
74	gezelter	2204	void setCoefficient(int power, double coefficient) {
75			polynomial_.setCoefficient(power, coefficient);
76			}
77	gezelter	1930
78	gezelter	2204	void setPolynomial(const DoublePolynomial& p) {
79			polynomial_ = p;
80			}
81	gezelter	1930
82	gezelter	2204	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	gezelter	1930
88	gezelter	2204	friend std::ostream& operator <<(std::ostream& os, PolynomialTorsionType& pbt);
89	gezelter	1930
90	gezelter	2204	private:
91	gezelter	1930
92	gezelter	2204	DoublePolynomial polynomial_;
93			};
94	gezelter	1930
95	gezelter	2204	std::ostream& operator <<(std::ostream& os, PolynomialTorsionType& ptt) {
96	gezelter	1930	DoublePolynomial::const_iterator i;
97
98			i = ptt.polynomial_.begin();
99
100			if (i == ptt.polynomial_.end()) {
101	gezelter	2204	os << "This Polynomial contains nothing" << std::endl;
102			return os;
103	gezelter	1930	}
104
105			os << "This Polynomial contains below terms:" << std::endl;
106
107			while(true){
108	gezelter	2204	os << i->second << "*" << "(cosPhi)" << "^" << i->first;
109	gezelter	1930
110	gezelter	2204	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	gezelter	1930	}
119
120			os << std::endl;
121			return os;
122	gezelter	2204	}
123	gezelter	1930
124
125			} //end namespace oopse
126			#endif //TYPES_POLYNOMIALBONDTYPE_HPP
127