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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: gradient.C,v 1.8 2005/12/23 17:02:43 amoll Exp $
// Atom gradient class: this class represents the gradient (i.e. the negative forces)
// for a given system as a vector<Vector3>. THe gradient is stored in units of kJ/(mol A)
#include <BALL/MOLMEC/COMMON/gradient.h>
#include <BALL/MOLMEC/COMMON/atomVector.h>
#include <BALL/KERNEL/atom.h>
using namespace std;
namespace BALL
{
Gradient::Gradient()
: norm(0.0),
inv_norm(0.0),
rms(0.0),
valid_(false)
{
}
Gradient::Gradient(const AtomVector& atoms)
{
set(atoms);
}
Gradient::Gradient(const Gradient& gradient, bool /* deep */)
: vector<Vector3>()
{
set(gradient);
}
Gradient::~Gradient()
{
valid_ = false;
}
void Gradient::set(const AtomVector& atoms)
{
// change the size to hold all vectors
Size max_index = (Size)atoms.size();
resize(max_index);
// copy all forces.
// the gradient is the negative force and is
// stored in units of kJ/(mol A). The forces
// are in units of Newton, so we have to use
// a conversion factor of -1.0 / 1e3 (J->kJ) / 1e10 (m->A) * NA (1->mol)
norm = 0.0;
Iterator it(begin());
for (Size i = 0; i < max_index; ++i, ++it)
{
*it = atoms[i]->getForce() * Constants::NA / -1.0e13;
norm += (*it) * (*it);
}
// calculate the norm and its inverse
norm = sqrt(norm);
inv_norm = 1.0 / norm;
if (max_index > 0)
{
rms = norm / sqrt(3.0 * (double)max_index);
}
else
{
rms = 0.0;
}
// the gradient is now valid
valid_ = true;
}
void Gradient::set(const Gradient& gradient)
{
// copy the gradient
resize(gradient.size());
copy(gradient.begin(), gradient.end(), begin());
//copy the norm and the valid_ flag
norm = gradient.norm;
inv_norm = gradient.inv_norm;
rms = gradient.rms;
valid_ = gradient.valid_;
}
Gradient& Gradient::operator = (const Gradient& rhs)
{
set(rhs);
return *this;
}
Gradient& Gradient::operator = (const AtomVector& rhs)
{
set(rhs);
return *this;
}
// dot product of two gradients
double Gradient::operator * (const Gradient& gradient) const
{
Size max_index = (Size)size();
if (gradient.size() != max_index)
{
throw Exception::InvalidRange(__FILE__, __LINE__, gradient.size());
}
double result = 0.0;
for (Size i = 0; i < max_index; i++)
{
result += operator[](i) * gradient[i];
}
return result;
}
void Gradient::negate()
{
// iterate over all vectors and flip the sign
for (Iterator it = begin(); it != end(); ++it)
{
*it *= -1.0;
}
}
void Gradient::normalize()
{
// iterate over all vectors and flip the sign
// (TVector3::negate)
for (Iterator it = begin(); it != end(); ++it)
{
*it *= inv_norm;
}
// reset the norm and its inverse
// and calculate hte root mean square
norm = 1.0;
inv_norm = 1.0;
if (size() > 0)
{
rms = 1.0 / sqrt(3.0 * (double)size());
}
else
{
rms = 0.0;
}
}
bool Gradient::isValid() const
{
return valid_;
}
void Gradient::invalidate()
{
valid_ = false;
}
} // namespace BALL
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