vasp-pymatgen

name	vasp-pymatgen
version	1.0.0
description	Generate VASP inputs (INCAR/POSCAR/POTCAR/KPOINTS) via pymatgen.io.vasp.sets for DFT calculations: MPRelaxSet (geometry relaxation), MPStaticSet (SCF), MPNonSCFSet (band structure), MatPESStaticSet (MLFF energy/force labeling). INCAR is driven by pymatgen defaults; the agent only supplies user_incar_settings overrides. Use when the user asks to prepare VASP calculations, run DFT, or generate MLFF training data from structures. Do NOT use for VASP result post-processing / analysis, non-VASP DFT codes, or molecular dynamics — this skill only generates input files and submits jobs.
metadata	{"tools":["run_python","run_bash","load_skill_resource"],"dependent_skills":["bohrium"],"tags":["vasp","dft","relaxation","scf","band-structure","pymatgen","label","mlff"]}

VASP DFT Skill (pymatgen sets)

This skill generates VASP input files for common DFT calculation types: relaxation, SCF, band structure, and MLFF energy/force labeling. Workflow: obtain a structure → prepare inputs → submit to Bohrium → read results.

All input generation uses pymatgen.io.vasp.sets (MPRelaxSet, MPStaticSet, MPNonSCFSet, MatPESStaticSet). These classes own the INCAR defaults — the agent only passes user_incar_settings to override individual keys. Never write a full INCAR dict from scratch.

Load the reference file for the specific command you are about to run (see per-command pointers below).

Prerequisites

1. PMG_VASP_PSP_DIR — path to the VASP pseudopotential library (required for POTCAR generation):

   echo $PMG_VASP_PSP_DIR    # verify: should print a directory path
   

2. Python packages: pymatgen, ase, numpy :

   python -c "from pymatgen.io.vasp.sets import MatPESStaticSet; print('OK')"
   python -c "from ase.io import read; print('OK')"
   

3. Structure file readable by ASE — extxyz, POSCAR, CIF, or any ASE-supported format.

• The bohrium skill loaded (for job submission).

Stop and tell the user if PMG_VASP_PSP_DIR is not set or dependencies are missing.

user_incar_settings

All commands accept a Python dict of INCAR overrides. pymatgen merges these with its own defaults — the agent never writes a raw INCAR.

Format: { "TAG": value, ... } — keys are VASP INCAR tag names (case-sensitive).

Constraints:

• Use Python types: bool for logical flags (LCHARG, LWAVE), int for integers (NSW, NBANDS), float for reals (ENCUT, SIGMA).
• List types for per-atom tags: MAGMOM expects [float, ...], one per atom.
• None removes the tag from INCAR entirely (pymatgen-specific).

Common overrides:

Tag	Type	Purpose	Example
NCORE	int	Band-level parallelism	4
ENCUT	float	Plane-wave cutoff (eV)	600
ISPIN	int	Spin: 1=off, 2=on	2
LSORBIT	bool	Spin-orbit coupling	True
MAGMOM	list[float]	Initial magnetic moments	[5.0, 0.6]
NEDOS	int	DOS grid points	2000

Notes:

• NCORE controls band-level parallelism in VASP. Set it so that total_CPU_cores / NCORE is an integer (even workload distribution). A good starting point is NCORE ≈ √(cores):

  CPU cores	NCORE	cores / NCORE
  8	4	2
  16	4	4
  32	8	4
  64	8	8

• Add NCORE to user_incar_settings for each calculation type.

---

Mandatory workflow sequence

1. Obtain a structure — generate or load from file.
2. Prepare inputs — run the appropriate snippet via run_python.
3. Submit jobs — pass calc_dir_list to the bohrium skill.
4. Read results — after the job finishes, run read_results or collect_results.

Run exactly one property step at a time. Do not chain relaxation + SCF in a single step.

For MLFF energy/force labeling, use prepare_label as a standalone step — it replaces the relaxation → SCF chain with a single static calculation optimized for dataset generation (no charge density, no relaxation, KSPACING-based k-points).

---

Commands

prepare_relaxation

Structural relaxation with MPRelaxSet. Key params: STRUCTURE_FILE, FRAMES, USER_INCAR.

load_skill_resource(skill_name="vasp-pymatgen", path="references/relaxation.md")

prepare_scf

Static SCF with MPStaticSet. Prefer from_prev_calc(relax_dir) when a relaxation dir is available; falls back to direct structure input. Add SOC keys to USER_INCAR when needed. Always outputs CHGCAR.

load_skill_resource(skill_name="vasp-pymatgen", path="references/scf.md")

prepare_label

MLFF dataset static calculation with MatPESStaticSet. Optimised for energy/force labeling: no charge density output, KSPACING-based k-points, ENCUT=600, magnetism off by default. Use --spin for magnetic systems, --frames for multi-frame trajectories. Generates and validates INCAR/POSCAR/POTCAR in one step.

load_skill_resource(skill_name="vasp-pymatgen", path="references/label.md")

prepare_nscf_kpath

Band-structure NSCF with MPNonSCFSet(mode="line"). Uses from_prev_calc(scf_dir) — auto-copies CHGCAR and sets ICHARG=11. Key params: SCF_DIRS, SOC, USER_INCAR.

load_skill_resource(skill_name="vasp-pymatgen", path="references/nscf-kpath.md")

read_results

Parse vasprun.xml via Vasprun. Returns energy, forces, band gap, efermi, and (for nscf) band structure summary, etc.

load_skill_resource(skill_name="vasp-pymatgen", path="references/read-results.md")

---

Safety

Job submission confirmation: Before submitting, state the number of jobs, machine type, and estimated core-hours. Never batch-submit more than 50 jobs without explicit user approval.

Input validation: Reject structure files with unreasonable atom counts (< 1 or > 1000 atoms) or paths that traverse outside the working directory.

---

Submission

bohrium skill (Recommended for Bohrium users)

Submit jobs to Bohrium using the bohrium skill, which wraps the bohr CLI. This is the recommended submission method for users running on the Bohrium platform.

The INCAR/POSCAR/POTCAR generation is platform-agnostic. The submission layer is pluggable — replace bohrium with a Slurm or local queue system as needed.

For the full submission template and environment variables for VASP job on bohrium, see:

load_skill_resource(skill_name="vasp-pymatgen", path="references/bohr.md")

E2B sandbox execution

Run VASP inside a Bohrium E2B cloud sandbox: environment setup (oneAPI), mpirun, completion verification, file I/O, streaming download of large outputs, and the API key format caveat.

load_skill_resource(skill_name="vasp-pymatgen", path="references/e2b-sandbox-execution.md")