Periodic Builder: layer builder (stacked layers with interlayer ions and water) for all periodic codes
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调研方向
Start by reading the Periodic Builder implementation and the related issues #241, #262, and #181; the payload does not name source files or tests. Work out how the shared builder can accept layers, spacing or hydration, lateral shifts, and interlayer contents across supported codes. Done means the listed clay, layered double hydroxide, graphite, and layered oxide examples can be built and wrapped in the new cell.
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描述
Agreed 2026-10-16 for 9.3.0. Build layered structures in the Builder's Periodic Builder, independent of the code, so they serve GROMACS, Quantum ESPRESSO and later CP2K.
Inputs:
- a layer: the current structure, e.g. a unit cell made with Generate and replicated;
- number of layers;
- basal spacing d001, or a hydration state for clays (1W to 5W);
- lateral shift between layers, e.g. a/3, b/3 for clays or AB stacking for graphite;
- what goes between the layers: nothing, ions (type and count, or count from the layer charge, with a minimum distance), water (molecules per interlayer).
- Everything is wrapped into the new cell.
Examples to cover: a 2-layer Na/Cu montmorillonite with 2-3 water layers (modelled on a MATLAB atom-toolbox buildsystem.m: layers at [a/3, b/3, d001], ions placed at random at least 3.5 Å apart, solvate each interlayer, wrap); a layered double hydroxide with interlayer anions; graphite (AB, no interlayer); LiCoO2-type layered oxides (Li between layers).
Force field is separate:
- GROMACS: MINFF via atomipy in GROMACS Prepare's MINFF source (atomipy and min.ff bundled), types and charges for clays, oxides and hydroxides. Graphite and similar need another parameter set.
- QE: no force field needed.
Related: #241 (MINFF), #262 (periodic molecules), #181 (battery electrodes).
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