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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/MOLMEC/PARAMETER/quadraticBondStretch.h>
#include <BALL/MOLMEC/PARAMETER/forceFieldParameters.h>
using namespace std;
namespace BALL
{
QuadraticBondStretch::QuadraticBondStretch()
: ParameterSection(),
k_(0),
r0_(0),
is_defined_(0)
{
}
QuadraticBondStretch::~QuadraticBondStretch()
{
clear();
}
void QuadraticBondStretch::clear()
{
// clear allocated parameter fields
delete [] k_;
delete [] r0_;
delete [] is_defined_;
k_ = 0;
r0_ = 0;
is_defined_ = 0;
ParameterSection::clear();
}
bool QuadraticBondStretch::extractSection
(Parameters& parameters, const String& section_name)
{
return ParameterSection::extractSection(parameters, section_name);
}
bool QuadraticBondStretch::extractSection
(ForceFieldParameters& parameters, const String& section_name)
{
// check whether the parameters are valid
if (!parameters.isValid())
{
return false;
}
// extract the basis information
ParameterSection::extractSection(parameters, section_name);
// check whether all variables we need are defined, terminate otherwise
if (!hasVariable("r0") || !hasVariable("k"))
{
return false;
}
// build a two dimensional array of the atom types
// loop variable
Size i;
AtomTypes& atom_types = parameters.getAtomTypes();
number_of_atom_types_ = atom_types.getNumberOfTypes();
// allocate two onedimensional fields for the two parameters
// and a two dimensional field of boolean variables.
// we might have to delete old stuff lying around
if (k_)
delete [] k_;
if (r0_)
delete [] r0_;
if (is_defined_)
delete [] is_defined_;
k_ = new float[number_of_atom_types_ * number_of_atom_types_];
r0_ = new float[number_of_atom_types_ * number_of_atom_types_];
is_defined_ = new bool[number_of_atom_types_ * number_of_atom_types_];
for (i = 0; i < number_of_atom_types_ * number_of_atom_types_; i++)
{
is_defined_[i] = false;
}
StringHashMap<Index>::Iterator it;
// determine the factor to convert the parameters to the standard units used
// as a default, energies are assumend to be in kJ/mol and distances in Angstrom
double factor_k = 1.0;
double factor_r0 = 1.0;
if (options.has("unit_k"))
{
if (options["unit_k"] == "kcal/mol")
{
factor_k = Constants::JOULE_PER_CAL;
}
if (options["unit_k"] == "cal/mol")
{
factor_k = Constants::JOULE_PER_CAL * 0.001;
}
if (options["unit_k"] == "J/mol")
{
factor_k = 0.001;
}
}
if (options.has("unit_r0"))
{
if (options["unit_r0"] == "pm")
{
factor_k = 0.1;
}
}
Atom::Type type_I;
Atom::Type type_J;
String type_name_I;
String type_name_J;
String key;
Index index = 0;
for (it = section_entries_.begin(); !(it == section_entries_.end()); ++it)
{
key = (*it).first;
if ((key.size() > 0) && (key.find_first_of(" ", 0) > 0))
{
type_name_I = key.before(" ", 0);
type_name_J = key.after(" ", 0);
if ((atom_types.hasType(type_name_I)) && (atom_types.hasType(type_name_J)))
{
type_I = atom_types.getType(type_name_I);
type_J = atom_types.getType(type_name_J);
index = (Index)(type_I * number_of_atom_types_ + type_J);
is_defined_[index] = true;
k_ [index] = getValue(key, "k").toFloat() * factor_k;
r0_ [index] = getValue(key, "r0").toFloat() * factor_r0;
index = (Index)(type_I + number_of_atom_types_ * type_J);
is_defined_[index] = true;
k_ [index] = getValue(key, "k").toFloat() * factor_k;
r0_ [index] = getValue(key, "r0").toFloat() * factor_r0;
}
}
}
return true;
}
bool QuadraticBondStretch::hasParameters(Atom::Type I, Atom::Type J) const
{
if ((I < 0) || ((Size)I >= number_of_atom_types_))
{
return false;
}
if ((J < 0) || ((Size)J >= number_of_atom_types_))
{
return false;
}
return is_defined_[I * number_of_atom_types_ + J];
}
QuadraticBondStretch::Values QuadraticBondStretch::getParameters
(Atom::Type I, Atom::Type J) const
{
QuadraticBondStretch::Values parameters;
assignParameters(parameters, I, J);
return parameters;
}
bool QuadraticBondStretch::assignParameters
(QuadraticBondStretch::Values& parameters,
Atom::Type I, Atom::Type J) const
{
if (hasParameters(I, J))
{
parameters.k = k_[I * number_of_atom_types_ + J];
parameters.r0 = r0_[I * number_of_atom_types_ + J];
return true;
}
return false;
}
} // namespace BALL
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