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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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#include <fstream> |
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#include <algorithm> |
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#include <cmath> |
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#include "types/CharmmTorsionType.hpp" |
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#include "utils/NumericConstant.hpp" |
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#include "math/ChebyshevT.hpp" |
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#include "math/ChebyshevU.hpp" |
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|
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|
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namespace oopse { |
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|
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CharmmTorsionType::CharmmTorsionType(std::vector<CharmmTorsionParameter>& parameters) { |
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std::vector<CharmmTorsionParameter>::iterator i; |
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i = std::max_element(parameters.begin(), parameters.end(), |
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LessThanPeriodicityFunctor()); |
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if (i != parameters.end()) { |
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int maxPower = i->n; |
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ChebyshevT T(maxPower); |
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ChebyshevU U(maxPower); |
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|
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// convert parameters of charmm type torsion into |
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// PolynomialTorsion's parameters |
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DoublePolynomial finalPolynomial; |
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for (i = parameters.begin(); i != parameters.end(); ++i) { |
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DoublePolynomial cosTerm = T.getChebyshevPolynomial(i->n); |
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cosTerm.operator*=(cos(i->delta) * i->kchi * 0.5); |
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|
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DoublePolynomial sinTerm = U.getChebyshevPolynomial(i->n); |
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sinTerm *= -sin(i->delta) * i->kchi * 0.5; |
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|
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finalPolynomial += cosTerm + sinTerm; |
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|
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finalPolynomial += (i->kchi * 0.5); |
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} |
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this->setPolynomial(finalPolynomial); |
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|
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/*std::ofstream myfile; |
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myfile.open("MyParameters", std::ios::app); |
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myfile << "The Polynomial contains below terms:" << std::endl;*/ |
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|
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} |
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} |
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} //end namespace oopse |
