def __call__(self, x, do_gradient=False):
"""Compute the energy (and gradient) for a set of Cartesian coordinates
Argument:
| ``x`` -- the Cartesian coordinates
| ``do_gradient`` -- when set to True, the gradient is also
computed and returned. [default=False]
"""
x = x.reshape((-1, 3))
result = 0.0
gradient = np.zeros(x.shape, float)
if self.dm_quad > 0.0:
result += ff_dm_quad(x, self.dm0, self.dmk, self.dm_quad, gradient,
self.matrix, self.reciprocal)
if self.dm_reci:
result += ff_dm_reci(x, self.vdw_radii, self.dm, self.dm_reci,
gradient, self.matrix, self.reciprocal)
if self.bond_quad:
result += ff_bond_quad(x, self.bond_edges, self.bond_lengths,
self.bond_quad, gradient, self.matrix,
self.reciprocal)
if self.span_quad:
result += ff_bond_quad(x, self.span_edges, self.span_lengths,
self.span_quad, gradient, self.matrix,
self.reciprocal)
if self.bond_hyper:
result += ff_bond_hyper(x, self.bond_edges, self.bond_lengths,
self.bond_hyper_scale, self.bond_hyper,
gradient, self.matrix, self.reciprocal)
if do_gradient:
return result, gradient.ravel()
else:
return result
def __call__(self, x, do_gradient=False):
"""Compute the energy (and gradient) for a set of Cartesian coordinates
Argument:
| ``x`` -- the Cartesian coordinates
| ``do_gradient`` -- when set to True, the gradient is also
computed and returned. [default=False]
"""
x = x.reshape((-1, 3))
result = 0.0
gradient = numpy.zeros(x.shape, float)
if self.dm_quad > 0.0:
result += ff_dm_quad(x, self.dm0, self.dmk, self.dm_quad,
gradient, self.matrix, self.reciprocal)
if self.dm_reci:
result += ff_dm_reci(x, self.vdw_radii, self.dm, self.dm_reci,
gradient, self.matrix, self.reciprocal)
if self.bond_quad:
result += ff_bond_quad(x, self.bond_edges, self.bond_lengths,
self.bond_quad, gradient, self.matrix,
self.reciprocal)
if self.span_quad:
result += ff_bond_quad(x, self.span_edges, self.span_lengths,
self.span_quad, gradient, self.matrix,
self.reciprocal)
if self.bond_hyper:
result += ff_bond_hyper(x, self.bond_edges, self.bond_lengths,
self.bond_hyper_scale, self.bond_hyper,
gradient, self.matrix, self.reciprocal)
if do_gradient:
return result, gradient.ravel()
else:
return result
def __call__(self, x, do_gradient=False):
x = x.reshape((-1,3))
result = 0.0
gradient = numpy.zeros(x.shape, float)
if self.dm_quad > 0.0:
result += ff_dm_quad(x, self.dm0, self.dmk, self.dm_quad, self.unitcell, self.unitcell_reciproke, self.unitcell_active, gradient)
if self.dm_reci:
result += ff_dm_reci(1.0*self.vdw_radii, x, self.dm, self.dm_reci, self.unitcell, self.unitcell_reciproke, self.unitcell_active, gradient)
if self.bond_quad:
result += ff_bond_quad(x, self.bond_pairs, self.bond_lengths, self.bond_quad, self.unitcell, self.unitcell_reciproke, self.unitcell_active, gradient)
if self.span_quad:
result += ff_bond_quad(x, self.span_pairs, self.span_lengths, self.span_quad, self.unitcell, self.unitcell_reciproke, self.unitcell_active, gradient)
if self.bond_hyper:
result += ff_bond_hyper(x, self.bond_pairs, self.bond_lengths, 5.0, self.bond_hyper, self.unitcell, self.unitcell_reciproke, self.unitcell_active, gradient)
if do_gradient:
return result, gradient.ravel()
else:
return result