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Shapes maintenance #3728

Merged
merged 11 commits into from
May 25, 2020
18 changes: 14 additions & 4 deletions doc/sphinx/constraints.rst
Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,7 @@ Available shapes are listed below.
- :class:`espressomd.shapes.Sphere`
- :class:`espressomd.shapes.SpheroCylinder`
- :class:`espressomd.shapes.Stomatocyte`
- :class:`espressomd.shapes.Torus`
- :class:`espressomd.shapes.HollowConicalFrustum`
- :class:`espressomd.shapes.Union`

Expand Down Expand Up @@ -400,13 +401,12 @@ The region is described as a pore (lower vertical part of the "T"-shape) and a c
.. figure:: figures/slitpore.png
:alt: Schematic for the Slitpore shape with labeled geometrical parameters.
:align: center
:height: 6.00000cm
:height: 10.00000cm

The parameter ``channel_width`` specifies the distance between the top and the plateau edge.
The parameter ``pore_length`` specifies the distance between the bottom and the plateau edge.
The parameter ``pore_width`` specifies the distance between the two plateau edges, it is the space between the left and right walls of the pore region.
The parameter ``pore_mouth`` specifies the location (z-coordinate) of the pore opening (center). It is always centered in the x-direction.
The parameter ``dividing_plane`` specifies the location (z-coordinate) of the middle between the two walls.
The parameters ``pore_mouth`` and ``dividing_plane`` specify the location in the z-coordinate resp. x-coordinate of the pore opening.

All the edges are smoothed via the parameters ``upper_smoothing_radius`` (for the concave corner at the edge of the plateau region) and ``lower_smoothing_radius`` (for the convex corner at the bottom of the pore region).
The meaning of the geometrical parameters can be inferred from the schematic in Fig. :ref:`slitpore <figure-slitpore>`.
Expand All @@ -427,7 +427,7 @@ Pictured is an example constraint with a ``Slitpore`` shape created with ::
pore_length=20,
pore_mouth=30,
pore_width=5,
dividing_plane=40)
dividing_plane=25)

system.constraints.add(shape=slitpore, particle_type=0, penetrable=True)

Expand Down Expand Up @@ -459,6 +459,16 @@ Pictured is an example constraint with a ``SpheroCylinder`` shape created with :
system.constraints.add(shape=spherocylinder, particle_type=0)


Torus
"""""

:class:`espressomd.shapes.Torus`

It is positioned at ``center`` and has a radius ``radius`` with tube radius ``tube_radius``.
The ``normal`` parameter is the torus rotation axis, which is normalized in the program.
The direction ``direction`` determines the force direction, ``-1`` for inward and ``+1`` for outward.


HollowConicalFrustum
""""""""""""""""""""

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