# Copyright (C) 2010-2022 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ESPResSo is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import collections.abc
from .script_interface import ScriptInterfaceHelper, script_interface_register, ScriptObjectList
[docs]class Shape:
_so_bind_methods = ("calc_distance", "is_inside")
[docs]@script_interface_register
class Cylinder(Shape, ScriptInterfaceHelper):
"""
A cylinder shape.
Attributes
----------
center : (3,) array_like of :obj:`float`
Coordinates of the center of the cylinder.
axis : (3,) array_like of :obj:`float`
Axis of the cylinder.
radius : :obj:`float`
Radius of the cylinder.
length : :obj:`float`
Length of the cylinder.
direction : :obj:`int`
Surface orientation, for +1 the normal points
out of the mantel, for -1 it points inward.
open : :obj:`bool`
cylinder is open or has caps.
"""
_so_name = "Shapes::Cylinder"
[docs]@script_interface_register
class Ellipsoid(Shape, ScriptInterfaceHelper):
"""
An ellipsoid.
For now only ellipsoids of revolution are supported.
The symmetry axis is aligned parallel to the x-direction.
Attributes
----------
center : (3,) array_like of :obj:`float`
Coordinates of the center of the ellipsoid.
a : :obj:`float`
Semiaxis along the axis of rotational symmetry.
b : :obj:`float`
Equatorial semiaxes.
direction : :obj:`int`
Surface orientation, for +1 the normal points
out of the mantel, for -1 it points inward.
"""
_so_name = "Shapes::Ellipsoid"
[docs]@script_interface_register
class Rhomboid(Shape, ScriptInterfaceHelper):
"""
A parallelepiped.
Attributes
----------
a : (3,) array_like of :obj:`float`
First base vector.
b : (3,) array_like of :obj:`float`
Second base vector.
c : (3,) array_like of :obj:`float`
Third base vector.
corner : (3,) array_like of :obj:`float`
Lower left corner of the rhomboid.
direction : :obj:`int`
Surface orientation, for +1 the normal points
out of the mantel, for -1 it points inward.
"""
_so_name = "Shapes::Rhomboid"
[docs]@script_interface_register
class Slitpore(Shape, ScriptInterfaceHelper):
"""
.. figure:: figures/slitpore.png
:alt: Schematic for the Slitpore shape with labeled geometrical parameters.
:align: center
:height: 8.00000cm
Attributes
----------
channel_width : :obj:`float`
lower_smoothing_radius : :obj:`float`
pore_length : :obj:`float`
pore_mouth : :obj:`float`
pore_width : :obj:`float`
upper_smoothing_radius : :obj:`float`
dividing_plane : :obj:`float`
"""
_so_name = "Shapes::Slitpore"
[docs]@script_interface_register
class Sphere(Shape, ScriptInterfaceHelper):
"""
A sphere.
Attributes
----------
center : (3,) array_like of :obj:`float`
Center of the sphere
radius : :obj:`float`
Radius of the sphere.
direction : :obj:`int`
Surface orientation, for +1 the normal points
out of the mantel, for -1 it points inward.
"""
_so_name = "Shapes::Sphere"
[docs]@script_interface_register
class SpheroCylinder(Shape, ScriptInterfaceHelper):
"""
A cylinder with hemispheres as caps.
Attributes
----------
center : (3,) array_like of :obj:`float`
Coordinates of the center of the cylinder.
axis : (3,) array_like of :obj:`float`
Axis of the cylinder.
radius : :obj:`float`
Radius of the cylinder.
direction : :obj:`int`
Surface orientation, for +1 the normal points
out of the mantel, for -1 it points inward.
length : :obj:`float`
Length of the cylinder (not including the caps).
"""
_so_name = "Shapes::SpheroCylinder"
[docs]@script_interface_register
class Torus(Shape, ScriptInterfaceHelper):
"""
A torus shape.
Attributes
----------
center : (3,) array_like of :obj:`float`
Coordinates of the center of the torus.
normal : (3,) array_like of :obj:`float`
Normal axis of the torus.
radius : :obj:`float`
Radius of the torus.
tube_radius : :obj:`float`
Radius of the tube.
direction : :obj:`int`
Surface orientation, for +1 the normal points
out of the mantel, for -1 it points inward.
"""
_so_name = "Shapes::Torus"
[docs]@script_interface_register
class Wall(Shape, ScriptInterfaceHelper):
"""
An infinite plane.
Attributes
----------
dist : :obj:`float`
Distance from the origin.
normal : (3,) array_like of :obj:`int`
Normal vector of the plane (needs not to be length 1).
"""
_so_name = "Shapes::Wall"
[docs]@script_interface_register
class SimplePore(Shape, ScriptInterfaceHelper):
"""
Two parallel infinite planes, and a cylindrical channel connecting them.
The cylinder and the planes are connected by torus segments with an
adjustable radius.
Attributes
----------
radius: :obj:`float`
The radius of the pore.
length: :obj:`float`
The distance between the planes.
smoothing_radius: :obj:`float`
Radius of the torus segments
axis: (3,) array_like of :obj:`float`
Axis of the cylinder and normal of the planes
center: (3,) array_like of :obj:`float`
Position of the center of the cylinder.
"""
_so_name = "Shapes::SimplePore"
[docs]@script_interface_register
class HollowConicalFrustum(Shape, ScriptInterfaceHelper):
"""
Hollow conical frustum shape.
Attributes
----------
cyl_transform_params : :class:`espressomd.math.CylindricalTransformationParameters`,
Parameters of the spacial orientation of the frustum. Contained must be parameters for ``center`` and ``axis``. ``orientation`` has no effect, unless ``central_angle != 0``
r1: :obj:`float`
Radius r1.
r2: :obj:`float`
Radius r2.
length: :obj:`float`
Length of the conical frustum along ``axis``.
thickness: float
The thickness of the frustum. Also determines the rounding radius of the edges
direction: :obj:`int`, optional
Surface orientation, for +1 the normal points
out of the mantel, for -1 it points inside of the shape. Defaults to 1
central_angle: :obj:`float`, optional
A ``central_angle`` creates an opening in the frustum along the side, centered symmetrically around the ``direction`` of ``cyl_transform_params``. Must be between ``0`` and ``2 pi``. Defaults to 0.
.. image:: figures/conical_frustum.png
"""
_so_name = "Shapes::HollowConicalFrustum"
[docs]@script_interface_register
class Union(Shape, ScriptObjectList):
"""A union of shapes.
This shape represents a union of shapes where the distance to the union
is defined by the smallest distance to any shape contained in the union.
Methods
-------
size()
Number of shapes contained in the union.
clear()
Remove all shapes from the union.
"""
_so_name = "Shapes::Union"
_so_bind_methods = Shape._so_bind_methods + ("size", "empty", "clear")
[docs] def add(self, shape):
"""
Add a shape to the union.
Parameters
----------
shape : array_like / instance of :class:`espressomd.shapes.Shape`
Shape instance(s) to be added to the union.
"""
def _add(self, shape):
if isinstance(shape, Shape):
self.call_method("add", object=shape)
else:
raise ValueError("Only shapes can be added.")
if isinstance(shape, collections.abc.Iterable):
for s in shape:
_add(self, s)
else:
_add(self, shape)
[docs] def remove(self, shape):
"""
Remove a shape from the union.
Parameters
----------
shape : array_like / instance of :class:`espressomd.shapes.Shape`
Shape instance(s) to be removed from the union.
"""
def _remove(self, shape):
if isinstance(shape, Shape):
self.call_method("remove", object=shape)
else:
raise ValueError("Only shapes can be removed.")
if isinstance(shape, collections.abc.Iterable):
for s in shape:
_remove(self, s)
else:
_remove(self, shape)