Ellipsoids

[kevinstratford]

To do:

• [x] update colloid read/write to allow for extra ellipsoid state
• [x] Update file format to be interpreted correctly
• [x] ... and update documentation
• [x] File input to check a >= b >= c
• [x] Add information on ellipsoid initialistion
• [x] Disallow both euler angles and vectors in input (potentially confusing).
• [x] Impose b == c for squirmers?
• [x] Impose b == c for nemetics?
• [x] Anchoring must have orientation available
• [x] Check surface energy computation for anchoring in fe_lc_stats.c.
• [x] Add switch for rotational update algorithm
• [x] Add tests

Will not address at this time:

• No oblate squirmers or oblate objects with anchoring
• General ellipsoid normal/tangent algorithm
• Two dimensional ellipses

[kevinstratford]

We also need to be able to translate the type in older file inputs to the new regime,

enum colloid_type_enum {COLLOID_TYPE_DEFAULT = 0,
                        COLLOID_TYPE_ACTIVE,
                        COLLOID_TYPE_SUBGRID,
                        COLLOID_TYPE_JANUS};

These values would be translated to defaults, i.e.,

DEFAULT => bbl, sphere
ACTIVE  => bbl, sphere, active
SUBGRID => subgrid, sphere
JANUS   => use new attribute as required

So, the potential problem is that in reading an old input file, the code from v0.21.0 would ignore the type entry, but also find the new shape entry to be COLLOID_SHAPE_INVALID. An answer to make the assumption that we will fall back to inspect the type entry, and set the new shape etc parameters as suggested above. An appropriate warning should be issued if possible.

[kevinstratford]

The surface energy computation (specifically colloids_q_boundary_normal() has been updated to handle the ellipsoid normal. The (discrete) surface area computation should also remain valid.

There is not a large difference (few parts in 1000) in the tests observed in the surface energy.

[kevinstratford]

I've put this out in 0.21.0. It is not impossible that some errors persist, so more testing is required. Oblate objects also need attention.