slab-construction-and-surface-modeling

Overview

Use this skill to build slab models, choose a freezing strategy, and resize the surface cell without corrupting later adsorption workflows.

Quick Start

1. Build slabs from a bulk reference before applying any fixing policy.
2. Treat termination choice, vacuum, and slab thickness as part of the comparison contract.
3. Apply either layer-based or height-based fixing deliberately.
4. Use supercell only when coverage or lateral separation requires it.

Suggested tools

• build_slab
• fix_atoms_by_layers
• fix_atoms_by_height
• supercell

Workflow

1. Build slabs with explicit termination policy

• build_slab can run on one bulk structure or a whole bulk_dir.
• It emits every termination for the chosen Miller index, not just one surface.
• Keep slab_thickness, vacuum_thickness, supercell, orthogonal, and lll_reduce fixed across compared slabs unless there is a reason to change them.

2. Freeze atoms with one clear rule

• fix_atoms_by_layers bins atoms by z using layer_tol; freeze_layers must not exceed the detected layer count.
• fix_atoms_by_height freezes atoms inside explicit z_ranges and rejects invalid ranges.
• centralize=true is a real geometry transform; use it intentionally, not by habit.

3. Expand cells only after fixing policy is understood

• supercell supports single-file and batch directory mode.
• It drops all selective-dynamics information, so do not call it after you have already finalized atom constraints unless you plan to rebuild them.

Output Contract

Return:

• slab structure path(s)
• chosen termination or termination set
• fixing strategy and key parameters
• whether supercell invalidated previous selective-dynamics flags

References

• If the task needs adsorption-ready slabs, hand off the post-fix structures to adsorption-site-screening instead of mixing slab generation and adsorption placement in one step.