def __init__(self,
atom,
direction,
parent=None,
parent_internal_coordinate=None,
index=None,
value=None,
freeze_value=False,
units=DistanceUnit.default,
**kwargs):
""" Constructor
:Parameters:
atom : `Atom`
The atom represented by the coordinate
index : `int`
The index of the coordinate in the parent representation
direction : `int`
The direction (x, y, or z) that the coordinate describes. (0 for x, 1 for y, 2 for z, which are also class constants)
parent : `CartesianRepresentation`
The representation containing the coordinate `self`
"""
self._atom = atom
self._direction = direction
if freeze_value:
# TODO think through the implications of this when I'm a little more cogent
if value is not None:
self._value = strip_units(value, units)
elif not self.is_orphaned():
self._value = strip_units(
atom.position[direction] if value is None else value,
units)
else:
raise ValueError(
"don't know how to get value for orphaned CartesianCoordinate"
)
elif value is not None:
raise NotImplementedError(
"value given for CartesianCoordinate, but"
" 'freeze_value' was not set to True; this sort"
" of functionality is not yet implemented.")
if parent_internal_coordinate is not None:
self.parent_internal_coordinate = parent_internal_coordinate
self._index = index
super(CartesianCoordinate, self)._init(units=units,
parent=parent,
freeze_value=freeze_value,
**kwargs)
if not self.is_orphaned():
self._index = self.molecule.index(atom) * 3 + self.direction
def __init__(self,
atom,
direction,
parent=None,
parent_internal_coordinate=None,
index=None,
value=None,
freeze_value=False,
units=DistanceUnit.default,
**kwargs):
""" Constructor
:Parameters:
atom : `Atom`
The atom represented by the coordinate
index : `int`
The index of the coordinate in the parent representation
direction : `int`
The direction (x, y, or z) that the coordinate describes. (0 for x, 1 for y, 2 for z, which are also class constants)
parent : `CartesianRepresentation`
The representation containing the coordinate `self`
"""
self._atom = atom
self._direction = direction
if freeze_value:
# TODO think through the implications of this when I'm a little more cogent
if value is not None:
self._value = strip_units(value, units)
elif not self.is_orphaned():
self._value = strip_units(atom.position[direction] if value is None else value, units)
else:
raise ValueError("don't know how to get value for orphaned CartesianCoordinate")
elif value is not None:
raise NotImplementedError("value given for CartesianCoordinate, but"
" 'freeze_value' was not set to True; this sort"
" of functionality is not yet implemented.")
if parent_internal_coordinate is not None:
self.parent_internal_coordinate = parent_internal_coordinate
self._index = index
super(CartesianCoordinate, self)._init(
units=units,
parent=parent,
freeze_value=freeze_value,
**kwargs
)
if not self.is_orphaned():
self._index = self.molecule.index(atom) * 3 + self.direction
def __init__(self,
robustness=InternalCoordinate.b_tensor_finite_difference_rigor,
delta=InternalCoordinate.b_tensor_finite_difference_delta,
units=None,
forward=False):
self.robustness = robustness
self.delta = delta
if self.cartesian_representation is not None:
self.delta = strip_units(self.delta, units)
self.forward = forward
self.displaced_molecules = {}
self.displaced_coordinates = {}
self.fdiff_instances = {}
def is_zero(self, cutoff=None):
""" Returns True if all elements of `self` have absolute values less than `cutoff`, which defaults
to `Tensor.zero_cutoff`
.. note::
`Tensor.zero_cutoff` is treated as a pseudo-class attribute for Tensor instances, meaning individual
instances can also set a `zero_cutoff` attribute which will take precidence over the class-level
default.
"""
if cutoff:
cutoff = strip_units(cutoff, self.units)
else:
cutoff = self.zero_cutoff
return super(Tensor, self).is_zero(cutoff)
def is_zero(self, cutoff=None):
""" Returns True if all elements of `self` have absolute values less than `cutoff`, which defaults
to `Tensor.zero_cutoff`
.. note::
`Tensor.zero_cutoff` is treated as a pseudo-class attribute for Tensor instances, meaning individual
instances can also set a `zero_cutoff` attribute which will take precidence over the class-level
default.
"""
if cutoff:
cutoff = strip_units(cutoff, self.units)
else:
cutoff = self.zero_cutoff
return super(Tensor, self).is_zero(cutoff)
