slab-construction-and-surface-modeling

name	slab-construction-and-surface-modeling
description	Use this skill for slab construction, vacuum and layer choices, surface supercell setup, and atom-fixing strategy in heterogeneous catalysis workflows.

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. Decide whether the slab is for adsorption, surface-energy ranking, or another surface model before calling build_slab.
2. For adsorption-ready slabs, prefer orthogonal=true unless the user explicitly needs the native non-orthogonal surface cell.
3. Build and review the termination family, including a surface-coordination audit, before choosing a slab; do not silently use the first emitted termination.
4. Apply layer-based, height-based, or explicit-index fixing deliberately.
5. Use supercell only when coverage or lateral separation requires it.

Allowed tools

• build_slab
• fix_atoms_by_layers
• fix_atoms_by_height
• fix_atoms_by_indices
• 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.
• For adsorption calculations, pass orthogonal=true by default so adsorbate placement, lateral separation, and downstream cell interpretation use a c-oriented orthogonal slab. Use orthogonal=false only when preserving the native surface cell is intentional, and report that exception.
• Keep slab_thickness, vacuum_thickness, supercell, orthogonal, and lll_reduce fixed across compared slabs unless there is a reason to change them.
• Treat termination_index=0 as a label, not a scientific default. Compare the emitted terminations by stoichiometry, exposed species/layers, polarity, symmetry, and visual sanity before selecting one for fixing or adsorption.
• Numerically inspect both exposed surfaces after cutting. Unless a specific reactive or defective termination is requested, prefer relatively higher surface-atom coordination within the comparable termination family. A large number of CN=1 surface atoms is a dangling-atom warning and normally grounds rejection or deprioritization because it suggests an empirically high-energy surface; first rule out a bad neighbor cutoff, thin slab, wrong cut/orientation, polarity, or malformed geometry. Do not present this heuristic as a calculated surface energy.

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.
• fix_atoms_by_indices uses explicit 0-based atom indices and is the safest choice when downstream metadata such as ads_indices already identifies the target atoms.
• All three fixing tools support reverse=true, which inverts the usual meaning and keeps the selected atoms free while freezing everything else.
• 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.
• supercell preserves selective_dynamics in POSCAR/VASP outputs, so fixed/free masks can survive lateral expansion when the input already carries them.

Method-critical defaults

• Keep slab thickness, vacuum thickness, termination choice, and freezing policy fixed across a comparison set.
• Keep the surface-layer definition and neighbor algorithm/cutoff fixed when comparing coordination distributions across terminations; report per-element low-coordination counts and the indices of any CN=1 surface atoms.
• For adsorption-ready slab construction, the project preference is orthogonal=true; any non-orthogonal adsorption slab must be intentional and stated.
• Termination provenance review is mandatory before adsorption or surface ranking. This is not a proof from one POSCAR; record which terminations were generated or supplied, the visible exposed-layer/stoichiometry/polarity evidence used, and any uncertainty. If the task provides only one slab with no provenance, state that the termination has not been reviewed and either inspect it or regenerate the termination family.
• Do not compare surface calculations if the mask or cell expansion strategy changed silently.

Output Contract

Return:

• slab structure path(s)
• chosen termination or termination set
• termination provenance evidence or the reason a single provided termination was accepted despite limited certainty
• surface-coordination evidence and any CN=1 warning, including the atom indices and criterion used
• orthogonal setting and any exception to the adsorption default
• fixing strategy and key parameters
• whether inherited selective_dynamics was preserved through any supercell expansion

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.
• If you are screening terminations as a workflow, hand off to surface-and-termination-screening once the slab family is ready.