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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: electrostaticPotentialCalculator.C,v 1.4 2004/05/10 11:47:17 amoll Exp $
#include <BALL/SOLVATION/electrostaticPotentialCalculator.h>
#include <BALL/STRUCTURE/fragmentDB.h>
namespace BALL
{
const char* ElectrostaticPotentialCalculator::Option::LOCALITY = "locality";
const bool ElectrostaticPotentialCalculator::Default::LOCALITY = true;
ElectrostaticPotentialCalculator::ElectrostaticPotentialCalculator()
: mySys_(),
frag_db_(0)
{
options.setDefaultBool(Option::LOCALITY, Default::LOCALITY);
}
ElectrostaticPotentialCalculator::ElectrostaticPotentialCalculator(const ElectrostaticPotentialCalculator& epc)
: mySys_(epc.mySys_),
frag_db_(epc.frag_db_)
{
options.setDefaultBool(Option::LOCALITY, Default::LOCALITY);
// TODO...
}
ElectrostaticPotentialCalculator::~ElectrostaticPotentialCalculator()
{
}
void ElectrostaticPotentialCalculator::apply(System &S)
throw(Exception::NullPointer)
{
if (frag_db_ == 0)
{
throw(Exception::NullPointer(__FILE__, __LINE__));
}
mySys_ = S;
mySys_.apply(frag_db_->normalize_names);
radii_.setFilename("PARSE.siz");
charges_.setFilename("PARSE.crg");
mySys_.apply(radii_);
mySys_.apply(charges_);
}
float ElectrostaticPotentialCalculator::operator() (const Vector3& pos)
{
float phi_nonloc=0.;
float length;
static float eps=78.;
if (options.getBool(Option::LOCALITY)==true)
{
AtomIterator atIt;
for (atIt=mySys_.beginAtom();+atIt;++atIt)
{
length = (pos-(*atIt).getPosition()).getLength();
phi_nonloc += (*atIt).getCharge()/length;
}
phi_nonloc*=1./(4*M_PI*8.85e-22*eps)*1.6e-19;
}
else
{
static double lambda = 20.;
static double eps_inf = 1.8;
static double xi = sqrt(eps/eps_inf);
static double xiol = xi/lambda;
static double weight = (eps - eps_inf)/eps_inf;
float length;
AtomIterator atIt;
for (atIt=mySys_.beginAtom();+atIt;++atIt)
{
length = (pos-(*atIt).getPosition()).getLength();
phi_nonloc += (*atIt).getCharge()/length * (1.+weight*sinh((*atIt).getRadius() * xiol)/((*atIt).getRadius() * xiol)
* exp(-xiol*length));
}
phi_nonloc*=1./(4*M_PI*8.85e-22*eps)*1.6e-19;
}
return phi_nonloc;
}
void ElectrostaticPotentialCalculator::setFragmentDB(const FragmentDB* db)
{
frag_db_ = (FragmentDB*) db;
}
const FragmentDB* ElectrostaticPotentialCalculator::getFragmentDB() const
{
return frag_db_;
}
} // namespace
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