Vector<double> BoundingLayer::calculate_second_derivative(const Vector<double>& inputs) const
{
std::ostringstream buffer;
const size_t bounding_neurons_number = get_bounding_neurons_number();
const Vector<double> outputs = calculate_outputs(inputs);
for(size_t i = 0; i < bounding_neurons_number; i++)
{
if(outputs[i] == lower_bounds[i])
{
buffer << "OpenNN Exception: BoundingLayer class.\n"
<< "Vector<double> calculate_outputs(const Vector<double>&) const method.\n"
<< "Output is equal to lower bound. The bounding function is not differentiable at this point.\n";
throw std::logic_error(buffer.str());
}
else if(outputs[i] == upper_bounds[i])
{
buffer << "OpenNN Exception: BoundingLayer class.\n"
<< "Vector<double> calculate_outputs(const Vector<double>&) const method.\n"
<< "Output is equal to upper bound. The bounding function is not differentiable at this point.\n";
throw std::logic_error(buffer.str());
}
}
Vector<double> second_derivative(bounding_neurons_number, 0.0);
return(second_derivative);
}
/*!
* Off-site contribution to the force constant matrix, i.e. the
* 3*n_atoms x 3*n_atoms matrix D_ij for i != j.
*/
void FCLJCut::offsite(const CrystalSurface *surf,
const CrystalSurface::lattice_neighbor_t *pair,
int ab, double *_D, Error *error)
{
int itype = surf->get_type(pair->indexi);
int jtype = surf->get_type(pair->indexj);
vec<double, 3> e(pair->r);
e /= e.nrm2();
mat<double> D(3, _D);
outer(e, e, D);
mat<double> perp = identity<double>(3) - D;
double k = second_derivative(itype, jtype, pair->rnorm);
double kappa = first_derivative(itype, jtype, pair->rnorm)/pair->rnorm;
D *= -k;
perp *= kappa;
D -= perp;
}
/*!
* Dump generic text info to file
*/
void FCLJCut::dump_info(FILE *f, CrystalSurface *surf, Error *error)
{
ForceConstants::dump_info(f, surf, error);
int nat = surf->get_number_of_atoms();
fprintf(f, "Force constants for each neighbor shell:\n");
for (int i = 0; i < nat; i++) {
int itype = surf->get_type(i);
fprintf(f, "Atom %i, k (kappa) = ", i);
for (int j = 0; j < 10; j++) {
const CrystalSurface::lattice_neighbor_t *neigh =
surf->get_neighbors(i);
int nneigh = surf->get_number_of_neighbors(i);
int n = 0;
while (n < nneigh && neigh->neighbor_shell != j) {
n++;
neigh++;
}
if (n < nneigh) {
int jtype = surf->get_type(neigh->indexj);
fprintf(f, "%f (%f) ",
second_derivative(itype, jtype, neigh->rnorm),
first_derivative(itype, jtype, neigh->rnorm)/
neigh->rnorm);
}
}
fprintf(f, "\n");
}
double linf[nat];
linear(surf, linf, error);
fprintf(f, "Linear forces on each atom = ");
for (int i = 0; i < nat; i++) fprintf(f, "%f ", linf[i]);
fprintf(f, "\n");
}
