/*
* 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