q734738781/vasp-input-preparation

vasp-input-preparation

Overview

Use this skill to produce execution-ready VASP input trees without fighting tool-enforced defaults.

Quick Start

1. Use vasp_prepare with the right preset: relax, static, freq, dos, or md.
2. Set regime correctly: bulk, slab, or gas.
3. Put one preparation campaign under one clean output_root.
4. Use patch_policy="safe" by default.
5. For dos and md, treat the preset as a starter template and do job-specific tuning through user_incar_patch in the same call.
6. If a later DOS/band branch should reuse CHGCAR, make that an explicit upstream requirement and preserve the file in the self-consistent stage.
7. If comparison-sensitive toggles matter (use_d3, use_dft_plus_u, enable_dipole, spin/MAGMOM, smearing, or reference-state choices), set them explicitly in the first preparation call and report them.
8. Use vasp_band_prepare instead of vasp_prepare when the job is a line-mode band-structure calculation with an explicit band KPOINTS.

Allowed tools

• fix_atoms_by_indices
• vasp_prepare
• vasp_band_prepare
• generate_kpath

Workflow

INCAR patching

• Use user_incar_patch for targeted job-specific INCAR controls.
• For DOS jobs, dos_charge_density_path copies a CHGCAR into the output root, enables ICHARG=11, and applies the recommended LMAXMIX baseline when absent.
• For DOS or MD presets, user_incar_patch is the main hook for controls such as NEDOS, ISMEAR, TEBEG, TEEND, POTIM, NSW, SMASS, or MDALGO.
• MAGMOM, LDAUU, and LDAUJ must be element-value maps such as {"Fe": 2.2}.
• Use null in user_incar_patch to request removal of a key from the final INCAR.
• Keep patch_policy="safe" by default; use force only when intentionally overriding canonical defaults.

1. Pick the right canonical preset

• Confirm the input path exists before preparing a VASP tree.
• vasp_prepare(preset="relax", ...) is for ionic relaxation jobs.
• vasp_prepare(preset="static", ...) is for static jobs and enforces NSW=1, IBRION=-1.
• vasp_prepare(preset="freq", ...) is for finite-difference vibrational jobs and enforces the frequency-specific overrides.
• vasp_prepare(preset="dos", ...) is for DOS/PDOS-style jobs. The tool starts from a bulk-leaning tetrahedron-style template with ISMEAR=-5, NEDOS=2001, LORBIT=11, and if dos_charge_density_path is provided it copies CHGCAR, sets ICHARG=11, and auto-fills a recommended LMAXMIX baseline when absent.
• vasp_prepare(preset="md", ...) is for molecular dynamics. The tool starts from a Nose-Hoover NVT-style template with IBRION=0, MDALGO=2, NSW=1000, POTIM=1.0, TEBEG=300, TEEND=300, and SMASS=0.

2. Choose the correct regime

• bulk: periodic bulk models; relax_cell=True is allowed only with preset="relax" and switches ISIF=3.
• slab: surface slabs; ISIF=2, KPOINTS z forced to 1, relax_cell=True is invalid.
• gas: molecules or gas references; forced 1x1x1 KPOINTS and relax_cell=True is invalid.

3. Respect built-in defaults

• The tool already owns the main preset, including pseudopotential family, ENCUT, EDIFF, smearing defaults, and relax-vs-SP mode settings.
• compute_dos, use_d3, use_dft_plus_u, and enable_dipole are the toggles worth surfacing when they matter.
• Project house default for k_product is 35 for production slab work unless the task explicitly provides a convergence-backed value.
• For DOS jobs, the preset is a recommended starting point, not a claim that one DOS INCAR works for every material class.
• For MD jobs, the preset is a recommended thermostat/template start, not a full replacement for system-specific choices of timestep, temperature schedule, thermostat mass, or ensemble controls.

4. Add a system-aware starting point

• The tool's canonical defaults are safe starters, but VASP Wiki guidance is more system-aware than a single global default. If the material class is known, surface the system-specific occupancy choice explicitly through user_incar_patch.
• Good start for unknown / high-throughput / gap-uncertain systems: ISMEAR=0, SIGMA=0.05-0.1; for clearly gapped or unknown-gap cases, consider EFERMI=MIDGAP.
• Good start for metallic relaxations or metallic force-sensitive work: ISMEAR=1, SIGMA=0.2; check that the entropy term is acceptably small before treating the setup as converged.
• Good start for adsorbate slab calculations: ISMEAR=0, SIGMA=0.1.
• Good start for semiconductors or insulators in bulk static or DOS-like post-processing: ISMEAR=-5 on a sufficiently dense Gamma-centered mesh.
• Good start for slab/gas/low-dimensional or tetrahedron-ineligible DOS work: do not assume tetrahedron is safe; fall back to ISMEAR=0 with small SIGMA, typically 0.03-0.1.
• Good start for gas references: keep ISYM=0, ISMEAR=0, SIGMA=0.01, and 1x1x1 KPOINTS.
• Treat these as explicit starting recipes, not convergence proofs. Once the system class is known, the starting recipe should be stated in the task packet instead of left implicit.

5. Override carefully

• user_incar_patch is for targeted overrides. For dos and md, it is also the preferred path for one-call tuning of method knobs.
• For DOS tuning, the common explicit overrides are ISMEAR, SIGMA, EFERMI, NEDOS, EMIN, EMAX, and occasionally LMAXMIX.
• MAGMOM, LDAUU, and LDAUJ must be element maps.
• patch_policy="safe" rejects overrides only for the small protected set of preset/regime-bound keys. For dos and md, safe intentionally leaves most method controls overrideable so the model can change NEDOS, ISMEAR, NSW, POTIM, TEBEG, TEEND, SMASS, MDALGO, and similar knobs without switching to force.
• patch_policy="force" applies the patch after canonical defaults, including explicit removal with null.
• Only use force when you are intentionally breaking the preset identity itself, for example replacing IBRION with a non-matching job type or tearing down other protected invariants.

6. Keep output layout clean

• Single structure input writes to output_root/<stem>/.
• Directory input preserves relative layout and appends <stem>/ per structure.
• Do not mix unrelated relax and SP campaigns in the same ambiguous tree.

7. Add explicit band-path or phonon handoffs

• Use generate_kpath only after a relaxed bulk baseline is accepted; it emits the band-path KPOINTS, not a full calc directory.
• Use vasp_band_prepare when that line-mode KPOINTS should become a dedicated band-structure job root.
• For phonon workflows, keep displacement generation outside vasp_prepare; the prepare tool should only own the force-job input deck after the displacement set already exists.

8. Prepare frequency jobs explicitly if requested

• Do not treat vibrational thermochemistry jobs as ordinary relax or SP jobs. Prepare them as a separate stage after the relevant relaxed structure is finalized.
• For finite-difference frequency runs, use IBRION=5, POTIM=0.015, NFREE=2, and ISYM=0.
• For slab adsorbate frequency jobs, do not blindly preserve the relax-stage selective-dynamics mask. A relaxed adsorbate-slab structure may still have mobile surface atoms, which is not acceptable for adsorbate-only vibrational thermochemistry. If the target is adsorbate-only slab thermochemistry and ads_indices are available, explicitly run fix_atoms_by_indices(indices=ads_indices, reverse=true) on the relaxed adsorbate-slab structure before writing the frequency input.
• Treat this explicit refixing step as mandatory unless the task explicitly requests a broader vibrational model.
• Keep the frequency job on the same scientifically relevant electronic-structure footing as the corresponding energy campaign: same ENCUT, EDIFF, smearing policy, spin treatment, DFT+U, D3, dipole correction, and other reference-sensitive toggles.

Method-critical defaults

• Do not silently rely on defaults for use_d3, use_dft_plus_u, enable_dipole, spin treatment, or reference-state-sensitive INCAR toggles when they affect comparison.
• Keep clean slab, gas-phase reference, adsorbed structures, and downstream static calculations scientifically comparable.
• When the system class is known, prefer a VASP-Wiki-style explicit smearing recipe over silent inheritance of the tool baseline.
• For unknown systems, ISMEAR=0 with small SIGMA is the safer generic starting point than jumping directly to Methfessel-Paxton.
• For metallic relaxations, a practical first explicit recipe is ISMEAR=1, SIGMA=0.2, then check the entropy term before treating it as production-worthy.
• For adsorbate slab calculations, ISMEAR=0, SIGMA=0.1 is the project-default explicit starting recipe.
• For slab adsorption studies, do not set relax_cell=true unless the task explicitly requires a variable-cell study and the system is not in slab mode.
• For slab work, use k*a ~= 35 Å as the initial project default unless convergence evidence justifies something else.
• Do not force bulk references to obey the slab default. Bulk k_product should be chosen from the bulk convergence requirement, not copied mechanically from slab policy.
• For DOS / projected-DOS / finer electronic-structure jobs, it is acceptable to increase k_product to around 50 when the extra sampling is part of the stated objective.
• For DOS, keep in mind the VASP-recommended pattern: relax first, then do a DOS-oriented static stage; do not rely on relax-stage DOSCAR as the final result.
• The default DOS preset is VASP-Wiki-aligned for bulk tetrahedron DOS, not a universal recommendation for slab/gas/low-dimensional meshes. If the mesh cannot support tetrahedra or the system class is uncertain, override to ISMEAR=0 with small SIGMA (0.03-0.1).
• For semiconducting or insulating bulk post-processing, ISMEAR=-5 is a good explicit start only when the mesh is dense enough and Gamma-centered.
• For clearly gapped or unknown-gap systems using Gaussian fallback, consider surfacing EFERMI=MIDGAP.
• For tetrahedron DOS, keep the mesh Gamma-centered and dense enough to justify interpolation.
• If reusing a converged CHGCAR, surface that explicitly with dos_charge_density_path, and make sure the upstream self-consistent stage actually kept CHGCAR (for example by setting LCHARG=True there).
• For fixed-density DOS/band reuse (ICHARG=11), VASP Wiki recommends LMAXMIX=2/4/6 for s,p / d / f dominated systems; the tool now auto-fills a baseline when absent, but deliberate overrides should still be reported.
• Tune NEDOS together with EMIN/EMAX when narrow peaks or edge resolution matter; VASP Wiki recommends checking the integrated DOS to confirm the grid is fine enough.
• For MD, explicitly state whether you are keeping the default Nose-Hoover template or overriding thermostat/integration controls through user_incar_patch.
• Always report any non-default toggles that materially affect interpretation.
• When frequency-derived thermochemistry is the target, do not silently reuse generic relax or SP INCARs; surface the frequency-specific overrides explicitly.

Output Contract

Return:

• output_root_rel
• representative prepared directory
• selected preset and regime
• generated k_grid
• any non-default method toggles or overrides that materially affect execution

References

• Inspect the tool schema/source when edge cases around k_product, DFT+U, or INCAR normalization matter.
• Use band-and-dos-analysis or phonon-displacement-workflow when the task goes beyond pure input preparation.
• Hand off band/DOS follow-up to band-and-dos-analysis, strain grids to elastic-property-workup, displacement sets to phonon-displacement-workflow, and MD trajectories to md-diffusion-analysis.