src/types/PolynomialBondType.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 PolynomialBondType.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/BondType.hpp"

namespace oopse {

  /**
   * @class PolynomialBondType PolynomialBondType.hpp "types/PolynomialBondType.hpp"
   * @todo documentation
   */
  class PolynomialBondType : public BondType{

  public:
    PolynomialBondType(double r0) : BondType(r0) {}

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

    double getCoefficient(int power) {
      return polynomial_.getCoefficient(power);
    }
        
    void calcForce(double r, double & V, double & dVdr) {
      double delta = r - r0;
      V = polynomial_.evaluate(delta);
      dVdr = polynomial_.evaluateDerivative(delta);

    }

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

  std::ostream& operator <<(std::ostream& os, PolynomialBondType& pbt) {
    DoublePolynomial::const_iterator i;

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

    os << "This PolynomialBondType contains below terms:" << std::endl;    
    
    while(true){
      os << i->second << "*" << "(r - " << pbt.getEquilibriumBondLength() << ")" << "^" << i->first;

      if (++i == pbt.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 << " + ";
      }
    }
    
    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:	3927 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	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 PolynomialBondType.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
53	#include "math/Polynomial.hpp"
54	#include "types/BondType.hpp"
55
56	namespace oopse {
57
58	/**
59	* @class PolynomialBondType PolynomialBondType.hpp "types/PolynomialBondType.hpp"
60	* @todo documentation
61	*/
62	class PolynomialBondType : public BondType{
63
64	public:
65	PolynomialBondType(double r0) : BondType(r0) {}
66
67	void setCoefficient(int power, double coefficient) {
68	polynomial_.setCoefficient(power, coefficient);
69	}
70
71	double getCoefficient(int power) {
72	return polynomial_.getCoefficient(power);
73	}
74
75	void calcForce(double r, double & V, double & dVdr) {
76	double delta = r - r0;
77	V = polynomial_.evaluate(delta);
78	dVdr = polynomial_.evaluateDerivative(delta);
79
80	}
81
82	friend std::ostream& operator <<(std::ostream& os, PolynomialBondType& pbt);
83
84	private:
85
86	DoublePolynomial polynomial_;
87	};
88
89	std::ostream& operator <<(std::ostream& os, PolynomialBondType& pbt) {
90	DoublePolynomial::const_iterator i;
91
92	i = pbt.polynomial_.begin();
93
94	if (i == pbt.polynomial_.end()) {
95	os << "This PolynomialBondType contains nothing" << std::endl;
96	return os;
97	}
98
99	os << "This PolynomialBondType contains below terms:" << std::endl;
100
101	while(true){
102	os << i->second << "*" << "(r - " << pbt.getEquilibriumBondLength() << ")" << "^" << i->first;
103
104	if (++i == pbt.polynomial_.end()) {
105	//if we reach the end of the polynomial pair, write out a newline and then escape the loop
106	os << std::endl;
107	break;
108	} else {
109	//otherwise, write out a "+"
110	os << " + ";
111	}
112	}
113
114	return os;
115	}
116
117
118	} //end namespace oopse
119	#endif //TYPES_POLYNOMIALBONDTYPE_HPP