def value_for_coords_and_displacements(self, pairs, internal_coord, cart_coords):
cart_coords = tuple(cart_coords)
disps = [0] * (len(internal_coord.atoms) * 3)
for coord, ndeltas in pairs:
idx = internal_coord.internal_indices_for_coordinates(coord)[0]
disps[idx] = ndeltas
coord_idxs = internal_coord.internal_indices_for_coordinates(*cart_coords)
dispcoord = self.coordinate_with_cartesian_displacements(internal_coord, disps)
if len(cart_coords) == 0:
# For some reason, BondAngle thinks it's a subclass of PeriodicCoordinate (!?)
if hasattr(dispcoord, 'possible_values_for_xyz'):
baseval = internal_coord.value_for_xyz(
Matrix([a.pos for a in internal_coord.atoms])
)
pos_vals = dispcoord.possible_values_for_xyz(
Matrix([a.pos for a in dispcoord.atoms])
)
# Including the half-periods makes this work...
# TODO fix and/or justify this
val = min(*(pos_vals + tuple(p+math.pi for p in pos_vals)), key=lambda p: abs(p - baseval))
# No need to convert angular units, since value_for_xyz always returns Radians
return val
else:
val = dispcoord.value
if hasunits(internal_coord) and internal_coord.units.genre is AngularUnit:
val *= dispcoord.units.to(Radians)
return val
else:
B = dispcoord.get_b_tensor(max_order=len(cart_coords))
return B[tuple(coord_idxs)]
def __init__(self, symbol, position, **kwargs):
self._init_common(**kwargs)
self.symbol = symbol
if hasunits(position):
if 'units' not in kwargs:
self._cartesian_units = position.units
elif self._cartesian_units != kwargs['units']:
position = position.in_units(self._cartesian_units)
self.position = Vector(position, copy=True, units=self.cartesian_units)
def __init__(self, symbol, position, **kwargs):
self._init_common(**kwargs)
self.symbol = symbol
if hasunits(position):
if 'units' not in kwargs:
self._cartesian_units = position.units
elif self._cartesian_units != kwargs['units']:
position = position.in_units(self._cartesian_units)
self.position = Vector(position, copy=True, units=self.cartesian_units)
def __init__(self, molecule, coords=None, units=None):
self._b_tensor_for_cart_rep = {}
self.molecule = molecule
self._init_units(units)
self.coords = []
for i, coord in enumerate(coords or []):
cunits=self.units[coord.default_delta.units.genre] if hasunits(coord.default_delta) else None
new_coord = coord.copy_for_representation(self, index=i, units=cunits)
self.coords.append(new_coord)
self.molecule.internal_representations.append(self)
def __init__(self, molecule, coords=None, units=None):
self._b_tensor_for_cart_rep = {}
self.molecule = molecule
self._init_units(units)
self.coords = []
for i, coord in enumerate(coords or []):
cunits = self.units[coord.default_delta.units.genre] if hasunits(
coord.default_delta) else None
new_coord = coord.copy_for_representation(self,
index=i,
units=cunits)
self.coords.append(new_coord)
self.molecule.internal_representations.append(self)
def __str__(self):
namestrs = []
valstrs = []
it = np.nditer(self, flags=['multi_index'])
for x in it:
namestrs.append(", ".join(shortstr(self.representation[i]) for i in it.multi_index))
valstrs.append("{: .8f}{}".format(float(x), (" " + str(self.units) if hasunits(self) else '')))
width=max(len(s) for s in namestrs) + 4
ret_val = self.__class__.__name__ + ":\n"
for name, val in zip(namestrs, valstrs):
ret_val += ("{:>"+str(width)+"}: {}\n").format(name, val)
ret_val += " for representation:\n{}".format(indent(str(self.representation)))
return ret_val
def __str__(self):
namestrs = []
valstrs = []
it = np.nditer(self, flags=['multi_index'])
for x in it:
namestrs.append(", ".join(
shortstr(self.representation[i]) for i in it.multi_index))
valstrs.append("{: .8f}{}".format(
float(x), (" " + str(self.units) if hasunits(self) else '')))
width = max(len(s) for s in namestrs) + 4
ret_val = self.__class__.__name__ + ":\n"
for name, val in zip(namestrs, valstrs):
ret_val += ("{:>" + str(width) + "}: {}\n").format(name, val)
ret_val += " for representation:\n{}".format(
indent(str(self.representation)))
return ret_val
def value(self, new_val):
if hasunits(new_val):
self._value = new_val.in_units(self.units).value
else:
self._value = new_val
def value(self, new_val):
if hasunits(new_val):
self._value = new_val.in_units(self.units).value
else:
self._value = new_val
