Polycrystal generation breaks molecular integrity for H₂O systems

[lnnbig]

I am attempting to construct polycrystalline ice using the --polycrystal command. In this system, H₂O is treated as a molecular unit with fixed geometry and a strict 2:1 H:O stoichiometry. Therefore, the molecular integrity of each water molecule must be preserved during structure generation.

However, during polycrystal construction, mdapy performs Voronoi tessellation and cuts grains accordingly while treating atoms as independent particles. As a consequence, grain-boundary formation can slice through molecules, leaving isolated oxygen or hydrogen atoms at grain boundaries.

Is there a recommended workflow in mdapy to construct polycrystalline systems composed of molecules (such as H₂O) while preserving molecular integrity?

[mushroomfire]

Hi, @lnnbig

Mdapy is not designed for constructing molecular crystals, and I am not sure whether this is a general limitation. However, for your case, a possible workflow is as follows:

• First construct the polycrystal without removing overlapping atoms (set overlap_distance to zero).

• Use the cal_chemical_species method in mdapy to identify water molecules and remove the non-water atoms.

• Build the neighbor list using build_neighbor, then check for overlapping atoms and remove closely spaced water molecules accordingly.

This workflow may require writing a small script. If you still have questions, feel free to add my QQ for further discussion.