def __init__(self, geometry, period, **kwargs):
"""Construct Periodic1DPrism instance.
Keyword args:
shift_vector: Origin of the body.
planes_normal: Plane definitions with normal vectors and distances.
planes_miller: Plane definitions with miller indices and distances.
"""
# Check for plane normals not orthogonal to axis (plane cuts axis)
self.periodicity = period
axis = self.periodicity.get_axis("cartesian")
planes_normal = self.pop_planes(geometry, kwargs)
projections = abs(np.dot(planes_normal[:,:3], axis.transpose()))
if np.any(projections > EPSILON):
error("Some plane(s) are not parallel to axis")
# Determine basal planes. Shift them with a small amount to make sure
# atoms do not stay outside due to arithmetic errors.
axisnorm = np.linalg.norm(axis[0])
axis0 = axis[0] / axisnorm
basal_planes = np.array(
[[ axis0[0], axis0[1], axis0[2], -PERIODIC_TOLERANCE ],
[ axis0[0], axis0[1], axis0[2], axisnorm + PERIODIC_TOLERANCE ]])
# Extend planes by basal planes and call base class
planes_normal = np.vstack(( basal_planes, planes_normal ))
kwargs["planes_normal"] = planes_normal
kwargs["planes_normal_coordsys"] = "cartesian"
Polyhedron.__init__(self, geometry, period, **kwargs)
def __init__(self, geometry, period, **kwargs):
"""Construct Periodic1DPrism instance.
Keyword args:
shift_vector: Origin of the body.
planes_normal: Plane definitions with normal vectors and distances.
planes_miller: Plane definitions with miller indices and distances.
"""
# Check for plane normals not orthogonal to axis (plane cuts axis)
self.periodicity = period
axis = self.periodicity.get_axis("cartesian")
planes_normal = self.pop_planes(geometry, kwargs)
projections = abs(np.dot(planes_normal[:, :3], axis.transpose()))
if np.any(projections > EPSILON):
error("Some plane(s) are not parallel to axis")
# Determine basal planes. Shift them with a small amount to make sure
# atoms do not stay outside due to arithmetic errors.
axisnorm = np.linalg.norm(axis[0])
axis0 = axis[0] / axisnorm
basal_planes = np.array(
[[axis0[0], axis0[1], axis0[2], -PERIODIC_TOLERANCE],
[axis0[0], axis0[1], axis0[2], axisnorm + PERIODIC_TOLERANCE]])
# Extend planes by basal planes and call base class
planes_normal = np.vstack((basal_planes, planes_normal))
kwargs["planes_normal"] = planes_normal
kwargs["planes_normal_coordsys"] = "cartesian"
Polyhedron.__init__(self, geometry, period, **kwargs)
def __init__(self, geometry, period, **kwargs):
"""Construct Periodic2DPlane instance.
Keyword args:
shift_vector: Origin of the body.
thickness: Distance between the upper and lower plane.
"""
self.periodicity = period
self.thickness = kwargs.get("thickness")
axis1, axis2 = self.periodicity.get_axis("cartesian")
# Surface normal vector
surfnorm = np.cross(axis1, axis2).astype(float)
surfnorm = surfnorm / np.linalg.norm(surfnorm)
# Normal vector of the side planes of the polyhedron, pointing inwards
n1 = np.cross(surfnorm, axis1)
n1 /= np.linalg.norm(n1)
n2 = np.cross(axis2, surfnorm)
n2 /= np.linalg.norm(n2)
# Distances of the side planes from the origin
d1 = np.dot(n1, axis2)
d2 = np.dot(n2, axis1)
# Sign of the positive distance
s1 = np.sign(d1)
s2 = np.sign(d2)
# Assemble polyhedron
kwargs["planes_normal"] = np.array(
[[ n1[0], n1[1], n1[2], 0.0 -s1 * PERIODIC_TOLERANCE ],
[ n1[0], n1[1], n1[2], d1 + s1 * PERIODIC_TOLERANCE ],
[ n2[0], n2[1], n2[2], 0.0 - s2 * PERIODIC_TOLERANCE ],
[ n2[0], n2[1], n2[2], d2 + s2 * PERIODIC_TOLERANCE ],
[ surfnorm[0], surfnorm[1], surfnorm[2], -self.thickness / 2.0 ],
[ surfnorm[0], surfnorm[1], surfnorm[2], self.thickness / 2.0 ]
])
kwargs["planes_normal_coordsys"] = "cartesian"
Polyhedron.__init__(self, geometry, period, **kwargs)
def atoms_inside(self, atoms):
"""Decides which atoms are inside the body (see Body class)."""
atoms_inside_body = Polyhedron.atoms_inside(self, atoms)
atoms_inside_body *= self.periodicity.mask_unique(
atoms - self.shift_vector, atoms_inside_body)
return atoms_inside_body
def atoms_inside(self, atoms):
"""Decides which atoms are inside the body (see Body class)."""
atoms_inside_body = Polyhedron.atoms_inside(self, atoms)
atoms_inside_body *= self.periodicity.mask_unique(
atoms - self.shift_vector, atoms_inside_body)
return atoms_inside_body
def __init__(self, geometry, period, **kwargs):
"""Construct Periodic3DSupercell instance.
Keyword args:
shift_vector: Origin of the body.
thickness: Distance between the upper and lower plane.
"""
self.periodicity = period
axis1, axis2, axis3 = self.periodicity.get_axis("cartesian")
# Normal vector of the side planes of the polyhedron
n12 = np.cross(axis1, axis2)
n23 = np.cross(axis2, axis3)
n31 = np.cross(axis3, axis1)
n12 /= np.linalg.norm(n12)
n23 /= np.linalg.norm(n23)
n31 /= np.linalg.norm(n31)
# Distances of the side planes from the origin
d12 = np.dot(n12, axis3)
d23 = np.dot(n23, axis1)
d31 = np.dot(n31, axis2)
# Sign of positive distance
s12 = np.sign(d12)
s23 = np.sign(d23)
s31 = np.sign(d31)
# Assemble polyhedron
kwargs["planes_normal"] = np.array([
[n12[0], n12[1], n12[2], -s12 * PERIODIC_TOLERANCE],
[n23[0], n23[1], n23[2], -s23 * PERIODIC_TOLERANCE],
[n31[0], n31[1], n31[2], -s31 * PERIODIC_TOLERANCE],
[n12[0], n12[1], n12[2], d12 + s12 * PERIODIC_TOLERANCE],
[n23[0], n23[1], n23[2], d23 + s23 * PERIODIC_TOLERANCE],
[n31[0], n31[1], n31[2], d31 + s31 * PERIODIC_TOLERANCE],
])
kwargs["planes_normal_coordsys"] = "cartesian"
Polyhedron.__init__(self, geometry, period, **kwargs)
def __init__(self, geometry, period, **kwargs):
"""Construct Periodic3DSupercell instance.
Keyword args:
shift_vector: Origin of the body.
thickness: Distance between the upper and lower plane.
"""
self.periodicity = period
axis1, axis2, axis3 = self.periodicity.get_axis("cartesian")
# Normal vector of the side planes of the polyhedron
n12 = np.cross(axis1, axis2)
n23 = np.cross(axis2, axis3)
n31 = np.cross(axis3, axis1)
n12 /= np.linalg.norm(n12)
n23 /= np.linalg.norm(n23)
n31 /= np.linalg.norm(n31)
# Distances of the side planes from the origin
d12 = np.dot(n12, axis3)
d23 = np.dot(n23, axis1)
d31 = np.dot(n31, axis2)
# Sign of positive distance
s12 = np.sign(d12)
s23 = np.sign(d23)
s31 = np.sign(d31)
# Assemble polyhedron
kwargs["planes_normal"] = np.array(
[[ n12[0], n12[1], n12[2], -s12 * PERIODIC_TOLERANCE ],
[ n23[0], n23[1], n23[2], -s23 * PERIODIC_TOLERANCE ],
[ n31[0], n31[1], n31[2], -s31 * PERIODIC_TOLERANCE ],
[ n12[0], n12[1], n12[2], d12 + s12 * PERIODIC_TOLERANCE ],
[ n23[0], n23[1], n23[2], d23 + s23 * PERIODIC_TOLERANCE ],
[ n31[0], n31[1], n31[2], d31 + s31 * PERIODIC_TOLERANCE ],
])
kwargs["planes_normal_coordsys"] = "cartesian"
Polyhedron.__init__(self, geometry, period, **kwargs)