/* * Project: MoleCuilder * Description: creates and alters molecular systems * Copyright (C) 2012 University of Bonn. All rights reserved. * Copyright (C) 2013 Frederik Heber. All rights reserved. * Please see the COPYING file or "Copyright notice" in builder.cpp for details. * * * This file is part of MoleCuilder. * * MoleCuilder is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * MoleCuilder is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with MoleCuilder. If not, see . */ /* * PairPotential_Harmonic.cpp * * Created on: Sep 26, 2012 * Author: heber */ // include config.h #ifdef HAVE_CONFIG_H #include #endif #include "CodePatterns/MemDebug.hpp" #include "PairPotential_Harmonic.hpp" #include // for 'map_list_of()' #include #include #include #include "CodePatterns/Assert.hpp" #include "FunctionApproximation/Extractors.hpp" #include "FunctionApproximation/TrainingData.hpp" #include "Potentials/helpers.hpp" #include "Potentials/InternalCoordinates/TwoBody_Length.hpp" #include "Potentials/ParticleTypeCheckers.hpp" #include "RandomNumbers/RandomNumberGeneratorFactory.hpp" #include "RandomNumbers/RandomNumberGenerator.hpp" class Fragment; // static definitions const PairPotential_Harmonic::ParameterNames_t PairPotential_Harmonic::ParameterNames = boost::assign::list_of ("spring_constant") ("equilibrium_distance") ; const std::string PairPotential_Harmonic::potential_token("harmonic_bond"); Coordinator::ptr PairPotential_Harmonic::coordinator(Memory::ignore(new TwoBody_Length())); static HomologyGraph generateBindingModel(const EmpiricalPotential::ParticleTypes_t &_ParticleTypes) { // fill nodes HomologyGraph::nodes_t nodes; { ASSERT( _ParticleTypes.size() == (size_t)2, "generateBindingModel() - PairPotential_Harmonic needs two types."); std::pair inserter; inserter = nodes.insert( std::make_pair(FragmentNode(_ParticleTypes[0], 1), 1) ); if (!inserter.second) ++(inserter.first->second); inserter = nodes.insert( std::make_pair(FragmentNode(_ParticleTypes[1], 1), 1) ); if (!inserter.second) ++(inserter.first->second); } // there are no edges HomologyGraph::edges_t edges; { edges.insert( std::make_pair( FragmentEdge(_ParticleTypes[0], _ParticleTypes[1]), 1) ); } return HomologyGraph(nodes, edges); } PairPotential_Harmonic::PairPotential_Harmonic() : EmpiricalPotential(), params(parameters_t(MAXPARAMS, 0.)), bindingmodel(HomologyGraph()) { // have some decent defaults for parameter_derivative checking params[spring_constant] = 1.; params[equilibrium_distance] = 1.; } PairPotential_Harmonic::PairPotential_Harmonic( const ParticleTypes_t &_ParticleTypes) : EmpiricalPotential(_ParticleTypes), params(parameters_t(MAXPARAMS, 0.)), bindingmodel(generateBindingModel(_ParticleTypes)) { // have some decent defaults for parameter_derivative checking params[spring_constant] = 1.; params[equilibrium_distance] = 1.; } PairPotential_Harmonic::PairPotential_Harmonic( const ParticleTypes_t &_ParticleTypes, const double _spring_constant, const double _equilibrium_distance) : EmpiricalPotential(_ParticleTypes), params(parameters_t(MAXPARAMS, 0.)), bindingmodel(generateBindingModel(_ParticleTypes)) { params[spring_constant] = _spring_constant; params[equilibrium_distance] = _equilibrium_distance; } void PairPotential_Harmonic::setParameters(const parameters_t &_params) { const size_t paramsDim = _params.size(); ASSERT( paramsDim <= getParameterDimension(), "PairPotential_Harmonic::setParameters() - we need not more than " +toString(getParameterDimension())+" parameters."); for(size_t i=0;i