src/types/CharmmTorsionType.cpp

/*
 * 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.
 */
#include <algorithm>
#include <cmath> 
#include "types/CharmmTorsionType.hpp"
#include "utils/NumericConstant.hpp"
#include "math/ChebyshevT.hpp"
#include "math/ChebyshevU.hpp"

namespace oopse {
  CharmmTorsionType::CharmmTorsionType(std::vector<CharmmTorsionParameter>& parameters) {
    std::vector<CharmmTorsionParameter>::iterator i;
    i = std::max_element(parameters.begin(), parameters.end(), 
                         LessThanPeriodicityFunctor());
    if (i != parameters.end()) {
      int maxPower = i->n;
      ChebyshevT T(maxPower);
      ChebyshevU U(maxPower);
      
      // convert parameters of charmm type torsion into 
      // PolynomialTorsion's parameters
      DoublePolynomial finalPolynomial;
      for (i = parameters.begin(); i != parameters.end(); ++i) {
        DoublePolynomial cosTerm = T.getChebyshevPolynomial(i->n);
        cosTerm *= cos(i->delta) * i->kchi;
        DoublePolynomial sinTerm = U.getChebyshevPolynomial(i->n);
        sinTerm *= -sin(i->delta) * i->kchi;
        finalPolynomial = cosTerm + sinTerm;
        finalPolynomial += i->kchi;
      }
      this->setPolynomial(finalPolynomial);
    }
  }
} //end namespace oopse
Revision:	3286
Committed:	Thu Dec 6 20:04:02 2007 UTC (16 years, 7 months ago) by cpuglis
File size:	3189 byte(s)
Log Message:	Many fixes for Charmm-type torsions.
#	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	tim	2448	#include <algorithm>
42	tim	1937	#include <cmath>
43	gezelter	1930	#include "types/CharmmTorsionType.hpp"
44			#include "utils/NumericConstant.hpp"
45	cpuglis	3286	#include "math/ChebyshevT.hpp"
46			#include "math/ChebyshevU.hpp"
47
48	gezelter	1930	namespace oopse {
49	gezelter	3173	CharmmTorsionType::CharmmTorsionType(std::vector<CharmmTorsionParameter>& parameters) {
50	gezelter	1930	std::vector<CharmmTorsionParameter>::iterator i;
51	gezelter	3173	i = std::max_element(parameters.begin(), parameters.end(),
52	cpuglis	3286	LessThanPeriodicityFunctor());
53	tim	2448	if (i != parameters.end()) {
54	gezelter	3173	int maxPower = i->n;
55			ChebyshevT T(maxPower);
56			ChebyshevU U(maxPower);
57
58	cpuglis	3286	// convert parameters of charmm type torsion into
59	gezelter	3173	// PolynomialTorsion's parameters
60			DoublePolynomial finalPolynomial;
61			for (i = parameters.begin(); i != parameters.end(); ++i) {
62	cpuglis	3286	DoublePolynomial cosTerm = T.getChebyshevPolynomial(i->n);
63			cosTerm = cos(i->delta) i->kchi;
64			DoublePolynomial sinTerm = U.getChebyshevPolynomial(i->n);
65			sinTerm = -sin(i->delta) i->kchi;
66			finalPolynomial = cosTerm + sinTerm;
67			finalPolynomial += i->kchi;
68	gezelter	3173	}
69	cpuglis	3286	this->setPolynomial(finalPolynomial);
70	tim	2448	}
71	cpuglis	3286	}
72	gezelter	1930	} //end namespace oopse