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doc: shapes: document Stomatocyte pitfalls
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jngrad committed May 22, 2020
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Expand Up @@ -341,13 +341,19 @@ This command should be used with care.
The position can be any point in the simulation box and is set via the (3,) array_like parameter ``center``.
The orientation of the (cylindrically symmetric) stomatocyte is given by an ``axis`` (a (3,) array_like of :obj:`float`),
which points in the direction of the symmetry axis and does not need to be normalized.
The parameters: ``outer_radius``, ``inner_radius``, and ``layer_width``, specify the shape of the stomatocyte.
Here inappropriate choices of these parameters can yield undesired results.
Parameters ``outer_radius``, ``inner_radius``, and ``layer_width`` specify the
shape of the stomatocyte. Here inappropriate choices of parameters can yield
undesired results, such as discontinuous shapes or NaN values. Always use
values greater than 1 for ``inner_radius`` to avoid NaN values.
The width ``layer_width`` is used as a scaling parameter.
That is, a stomatocyte given by ``outer_radius:inner_radius:layer_width`` = 7:3:1
is half the size of the stomatocyte given by 7:3:2.
Not all choices of the parameters give reasonable values for the shape of the stomatocyte,

Not all choices of parameters give reasonable values for the shape of the stomatocyte,
but the combination 7:3:1 is a good point to start from when trying to modify the shape.
If you observe jumps in forces for particles inside the stomatocyte cavity,
your parameters are most likely wrong, in which case the OpenGL visualizer
will typically fail to draw dots inside the stomatocyte cavity.


.. figure:: figures/shape-stomatocyte1.png
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