I am attempting to construct polycrystalline ice using the atomsk --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, Atomsk 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 Atomsk to construct polycrystalline systems composed of molecules (such as H₂O) while preserving molecular integrity?
I am attempting to construct polycrystalline ice using the atomsk --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, Atomsk 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 Atomsk to construct polycrystalline systems composed of molecules (such as H₂O) while preserving molecular integrity?