new mechanisms in fix_del and fix_nucl: "micro" coarse-grained rates

[emasoero]

This mechanism is to be developed as part of the biomineralization project.

The idea is that particles are microns-sized but still only appear or disappear (no radii reduction/increase as partial dissolution/growth). The underlying assumptions are that:

• dissolution/precipitation is governed by kink atoms on the particles' surface, producing layer-by-layer mechanisms
• coordination between particles dictates how many surfaces are exposed
• stress per particle are assumed uniformly distributed between all atoms in a particle

[aleenalex]

A new mechanism micro was created which takes additionally 3 input variables (fraction of kinks, excessive internal energy etc). Co-ordination number need to be calculated. A general strategy needs to be devised to take into account different sized particles. Binning particles of similar size into groups could be a way to determine coordination correctly.

[aleenalex]

How to implement energy penalty for heterogenous precipitation? A factor may be added to the rate equation to introduce an energy penalty if particle type A is trying to precipitate on particle type B. This ensures that growth is favoured more than coverage.

[aleenalex]

Atom properties are already extracted from lammps. For mech_micro we need to extract the pair properties. We used compute property/local to extract "patom1 ptom2 ptype1 and ptype2". The for the atoms and types extracted we compute pair/local "dist". All these are written into a dump file. Pair information such as pair id, type and distance that goes to each processor was determined.