nebwalk 0.8.0

Calculator-agnostic nudged elastic band library with MLIP-assisted barrier pre-screening and DFT validation workflows

nebwalk

nebwalk is a lightweight, transparent, ASE-compatible Nudged Elastic Band (NEB/CI-NEB) library for minimum-energy paths, transition-state barriers, and diffusion mechanisms in atomistic simulations.

It is designed for fast prototyping with classical and machine-learned calculators, while remaining compatible with DFT backends through ASE.

pip install nebwalk

Current source version: v0.8.0.

---

Why nebwalk?

nebwalk focuses on one task: making NEB workflows simple, inspectable, and calculator-agnostic.

It is useful when you want to:

• build and optimize minimum-energy paths;
• run standard NEB or climbing-image NEB;
• switch between EMT, MACE-MP-0, Egret-1t, Quantum ESPRESSO, VASP, or any ASE-compatible calculator;
• prototype surface diffusion, vacancy migration, adsorbate hopping, and molecular conformational changes;
• export profiles as plots, CSV files, and ASE trajectories;
• keep the NEB implementation transparent enough to inspect, test, and modify.

This is not a black-box workflow manager. It is a compact research-code layer around ASE calculators and atomic structures.

---

Features

• Standard NEB and climbing-image NEB (CI-NEB).
• Improved tangent estimate following Henkelman and Jónsson.
• Perpendicular potential-force projection and spring-force projection.
• FIRE optimizer, suitable for the non-conservative NEB force field.
• Linear, IDPP, and regularized geodesic-style interpolation.
• Minimum-image-convention-aware interpolation and NEB forces for periodic systems.
• Variable spring constants to concentrate images near high-energy regions.
• High-level run_neb_calculation() API with calculator factories.
• Thread-based parallel image evaluation for CPU calculators.
• GPU note: thread-parallel image evaluation (n_workers > 1) is only safe with CPU calculators. With CUDA-backed calculators (MACE-MP-0 or Egret-1t on GPU), use n_workers=1. GPU parallelism across images requires per-image CUDA streams or process isolation, which is out of scope for nebwalk.
• Restart from ASE .traj files with fresh calculator instances.
• Energy-profile plotting, CSV export, and .traj output.
• Quantum ESPRESSO helper layer through ASE calculator construction.

MLIP-assisted workflow (v0.7.0+)

In addition to the v0.6.x NEB/CI-NEB engine, v0.7.0 adds:

• MLIP-assisted NEB workflow through run_mlip_assisted_neb().
• Active-learning-ready image selection.
• peak_plus_neighbors selection of the barrier-sensitive image and neighboring images.
• Selected-image export as .xyz, .traj, and .json.
• Clean handoff from MLIP/MACE NEB to DFT/QE refinement.

---

Installation

Stable installation from PyPI

pip install nebwalk

Optional MACE support:

pip install "nebwalk[mace]"

Check the installed version:

python -c "import nebwalk; print(nebwalk.__version__ if hasattr(nebwalk, '__version__') else 'installed')"

Latest source from GitHub

pip install git+https://github.com/Rifat19R/nebwalk.git

Development installation

git clone https://github.com/Rifat19R/nebwalk.git
cd nebwalk
pip install -e ".[dev]"
pytest tests/ -v

---

Quick start

from ase.calculators.emt import EMT
from nebwalk import NEBRunConfig, run_neb_calculation

initial = ...  # relaxed ase.Atoms endpoint
final = ...    # relaxed ase.Atoms endpoint

config = NEBRunConfig(
    n_images=7,
    interpolation="idpp",
    k=0.1,
    k_min=0.033,
    climb=True,
    climb_delay=50,
    fmax=0.05,
    max_steps=500,
)

result = run_neb_calculation(
    initial=initial,
    final=final,
    calculator_factory=lambda: EMT(),
    config=config,
)

print(f"Converged       : {result.converged}")
print(f"Barrier         : {result.barrier:.3f} eV")
print(f"Reverse barrier : {result.reverse_barrier:.3f} eV")
print(f"Reaction energy : {result.reaction_energy:.3f} eV")

result.neb.plot("profile.png")
result.neb.save_csv("profile.csv")
result.neb.save_trajectory("path.traj")

The calculator factory must return a fresh calculator instance. Do not share one ASE calculator object across all images.

---

MLIP-assisted NEB workflow

nebwalk can now run a fast calculator/MLIP NEB first, identify the barrier-sensitive images, and export those images for higher-level DFT/QE refinement.

This is an active-learning-ready workflow layer. It does not yet retrain the MLIP or perform uncertainty-guided selection automatically.

from ase.calculators.emt import EMT
from nebwalk import NEBRunConfig
from nebwalk.active import MLIPActiveNEBConfig, run_mlip_assisted_neb

result = run_mlip_assisted_neb(
    initial=initial,
    final=final,
    mlip_calculator_factory=lambda: EMT(),  # replace with MACE/Egret/custom MLIP
    neb_config=NEBRunConfig(n_images=7, interpolation="idpp", climb=True),
    active_config=MLIPActiveNEBConfig(
        selection_strategy="peak_plus_neighbors",
        n_select=3,
        output_dir="selected_for_qe",
    ),
)

print(result.mlip_barrier)
print(result.selected_indices)

The selected images are intended for DFT/QE refinement, single-point validation, or later active-learning labeling.

---

Example with MACE-MP-0

from mace.calculators import mace_mp
from nebwalk import NEBRunConfig, run_neb_calculation

def make_calc():
    return mace_mp(
        model="medium",
        dispersion=False,
        default_dtype="float64",
        device="cpu",  # use "cuda" if available
    )

config = NEBRunConfig(
    n_images=5,
    interpolation="idpp",
    k=0.5,
    climb=True,
    climb_delay=50,
    fmax=0.03,
    max_steps=1000,
)

result = run_neb_calculation(initial, final, make_calc, config)

MACE-MP-0 is a PBE-level foundation model. It can be excellent for rapid prototyping, but absolute barriers should be validated against DFT or experiment for the specific chemistry.

---

What materials can nebwalk handle?

nebwalk operates on ASE Atoms objects, so the practical materials space is defined by the calculator you attach.

Currently demonstrated or directly supported workflow classes include:

Class	Examples
Molecular paths	H3 Morse benchmark, ethane torsion
Surface diffusion	Al/Cu/Ni/Pd/Ru slab adsorbate hopping, H on Cu(111)
Bulk vacancy migration	fcc metals, hcp Mg, simple oxides
Ionic migration	MgO, Li2O-style vacancy/interstitial paths
2D/slab systems	MXenes, MAX phases, graphene-derived slabs, catalytic surfaces
DFT-backed systems	Quantum ESPRESSO via ASE calculator helpers

The code is calculator-agnostic. The scientific reliability of any result still depends on the chosen calculator, pseudopotentials, k-points, slab thickness, coverage, spin state, and convergence settings.

---

Benchmark spotlight: H diffusion on Cu(111)

A reproducible benchmark is included in:

benchmarks/h_cu111_mace_mp/

The measured result uses MACE-MP-0 with a 4×4×4 Cu(111) slab, one H adatom (1/16 ML), 15 Å vacuum, bottom two Cu layers fixed, IDPP interpolation, and CI-NEB.

Elementary fcc → hcp hop

Quantity	Result
Calculator	MACE-MP-0 small
Path	fcc hollow → bridge-like TS → hcp hollow
Internal images	5
Converged	True
Wall time	2.67 min
Forward barrier	125.92 meV
Reverse barrier	136.67 meV
Reaction energy	−10.75 meV
TS image	3

The profile is a clean single-saddle elementary hop:

image 00:   +0.000 meV   fcc initial
image 01:  +44.614 meV
image 02: +111.234 meV
image 03: +125.917 meV   transition state
image 04: +104.770 meV
image 05:  +33.294 meV
image 06:  -10.749 meV   hcp final

fcc → fcc full hop

A longer fcc-to-fcc hop also converged. It shows the expected two-saddle sequence:

fcc → bridge TS → hcp hollow → bridge TS → fcc

Quantity	Result
Calculator	MACE-MP-0 small
Internal images	7
Converged	True
Wall time	6.42 min
Forward barrier	125.56 meV
Reverse barrier	125.41 meV
Reaction energy	+0.146 meV

This confirms endpoint equivalence and path symmetry.

Interpretation

The Cu(111) benchmark validates the NEB workflow: endpoint handling, minimum-image interpolation, CI-NEB optimization, image-energy reporting, and profile export. The absolute MACE barrier should not be overinterpreted as an experimental activation energy. Experiments on H/Cu(111) report macroscopic diffusion behavior affected by thermal activation, quantum effects, coverage, and surface morphology. MACE-MP-0 is trained to reproduce PBE-level energetics, so a lower static flat-terrace barrier is expected.

---

Validated results

EMT is included for fast local testing only — no GPU, no download required. For quantitative results use MACE-MP-0 or DFT (QE). Errors attributed to the calculator are documented explicitly; convergence of the NEB path itself is verified in every case by checking endpoint ΔE ≈ 0 for symmetric hops.

20 systems validated across 4 calculators.

System	Calculator	Purpose	Barrier	Reference	Error
Morse H3 collinear	Morse (analytical)	algorithm test	0.200 eV	0.193 eV (exact)	4%
Al adatom / Al(100)	EMT	speed test	0.237 eV	~0.40 eV (DFT-PBE)	finite-size slab
Cu adatom / Cu(100)	EMT	speed test	0.418 eV	~0.44 eV (DFT-PBE)	4.6%
Ni adatom / Ni(100)	EMT	speed test	0.555 eV	~0.63 eV (DFT-GGA)	12%§
Ethane C–C torsion	Egret-1t	ML organic	0.113 eV	0.126 eV (exp.)	10%
Al vacancy / FCC Al	MACE-MP-0	benchmark	0.508 eV	0.61 eV (DFT-PBE)	17%†
Mg vacancy / HCP Mg	MACE-MP-0	benchmark	0.508 eV	~0.52 eV (DFT-PBE)	2%
Li vacancy / Li₂O	MACE-MP-0	benchmark	0.284 eV	~0.28 eV (DFT-GGA)	1.4%
Mg vacancy / MgO	MACE-MP-0	benchmark	2.254 eV	~2.20 eV (DFT-PBE)	2.5%
H diffusion / Cu(111)	MACE-MP-0	benchmark	0.126 eV	~0.15 eV (DFT-PBE)	~16%¶
Cu vacancy / FCC Cu	EMT	speed test	0.755 eV	~0.70 eV (DFT-PBE)	7.9%
Ni vacancy / FCC Ni	EMT	speed test	1.095 eV	~1.04 eV (DFT-PBE)	5.3%
Pd vacancy / FCC Pd	EMT	speed test	0.839 eV	~0.91 eV (DFT-PBE)	7.8%
Ag vacancy / FCC Ag	EMT	speed test	0.682 eV	~0.66 eV (DFT-PBE)	3.3%
Pt vacancy / FCC Pt	EMT	speed test	0.971 eV	~1.49 eV (DFT-PBE)	34.8%‡
Au vacancy / FCC Au	EMT	speed test	0.590 eV	~0.68 eV (DFT-PBE)	13.3%
Au vacancy / FCC Au	MACE-MP-0	benchmark	0.725 eV	~0.68 eV (DFT-PBE)	6.7%
Al vacancy / FCC Al	QE/PBE	benchmark	0.564 eV	~0.61 eV (DFT-PBE)	7.6%
W vacancy / BCC W	QE/PBE	benchmark	1.561 eV	~1.66 eV (DFT-PBE)	5.9%
Mo vacancy / BCC Mo	QE/PBE	benchmark	1.281 eV	~1.35 eV (DFT-PBE)	5.1%

† MACE-MP-0 systematically underestimates vacancy migration barriers by 10–20%. Known model limitation, not a nebwalk bug.

‡ EMT does not capture relativistic effects in Pt. NEB converged cleanly in 60 steps — error is from the calculator.

§ Ni adatom on Ni(100): EMT underestimates barriers due to d-band character at the Ni(100) saddle-point geometry. Profile shape and convergence correct.

¶ H/Cu(111): surface diffusion benchmark. Error reflects MACE-MP-0 surface accuracy limitations, not a library bug.

---

Other examples

python examples/morse_h3.py
python examples/mlip_assisted_neb_emt.py
python examples/al_diffusion_emt.py
python examples/ethane_egret.py
python examples/al_vacancy_macemp.py
python examples/mg_vacancy_macemp.py
python examples/li2o_vacancy_macemp.py
python examples/cu_adatom_cu100_emt.py
python examples/ni_adatom_ni100_emt.py
python examples/mg_vacancy_mgo_macemp.py
python examples/al_diffusion_qe.py
python examples/al_vacancy_qe.py

A larger benchmark suite (38 systems, EMT/MACE/Egret) is available in examples/v8/.

For a clean Al vacancy QE rerun, remove stale partial QE outputs through the script's explicit clean flag:

export ESPRESSO_PSEUDO=$HOME/pseudo
export AL_PSEUDO=Al.pbe-n-kjpaw_psl.1.0.0.UPF
export ESPRESSO_COMMAND="/absolute/path/to/pw.x"
export NEBWALK_QE_CLEAN=1
python examples/al_vacancy_qe.py
tail -f al_vacancy_qe.log

Some calculators are intentionally optional. Egret-1t model files and MACE model weights are not distributed with this repository.

---

Quantum ESPRESSO Interface

nebwalk includes a built-in interface to Quantum ESPRESSO via nebwalk.qe. Use this for production NEB calculations where universal MLIPs are out of distribution — surface reactions, MXene catalysis, MAX phase defects.

from nebwalk import run_neb_calculation, NEBRunConfig
from nebwalk.qe import QEParams, make_qe_factory, validate_qe_setup

params = QEParams(
    ecutwfc                = 60.0,       # plane-wave cutoff (Ry)
    ecutrho                = 480.0,      # 8× ecutwfc for PAW
    kpts                   = (4, 4, 1), # k-point grid for metal slab
    occupations            = "smearing",
    smearing               = "marzari-vanderbilt",
    degauss                = 0.02,
    nspin                  = 2,          # required for Fe, Co, Ni, Mn
    starting_magnetization = {1: 0.5},   # species 1 = 50% spin-up
)

# Validates pw.x binary and all UPF files exist before starting
validate_qe_setup(
    pseudo_dir       = "/path/to/pseudo",
    pseudopotentials = {"Fe": "Fe.pbe-spn-kjpaw_psl.1.0.0.UPF",
                        "N":  "N.pbe-n-radius_5.UPF"},
    command          = "/absolute/path/to/pw.x",
)

# Each image gets an independent subdirectory — prevents wavefunction conflicts
factory = make_qe_factory(
    params           = params,
    pseudo_dir       = "/path/to/pseudo",
    pseudopotentials = {"Fe": "Fe.pbe-spn-kjpaw_psl.1.0.0.UPF",
                        "N":  "N.pbe-n-radius_5.UPF"},
    base_dir         = "neb_qe_workdir",
    command          = "/absolute/path/to/pw.x",   # or "mpirun -np 4 /absolute/path/to/pw.x"
)

result = run_neb_calculation(
    initial            = initial,
    final              = final,
    calculator_factory = factory,
    config             = NEBRunConfig(n_images=7, climb=True, fmax=0.05),
)
print(f"Barrier: {result.barrier:.3f} eV")

QEParams key parameters:

Parameter	Default	Notes
ecutwfc	40.0	Plane-wave cutoff (Ry). Check your pseudopotential's recommended value.
ecutrho	320.0	Charge density cutoff (Ry). Use 8× ecutwfc for USPP/PAW, 4× for NC.
kpts	(1,1,1)	k-point grid. (1,1,1) for molecules; (4,4,1) for metal slabs.
nspin	1	Set to 2 for magnetic systems (Fe, Co, Ni, Mn). Required — not optional.
starting_magnetization	None	Dict of {species_index: value}. Required when nspin=2.
conv_thr	1e-8	SCF convergence threshold (Ry). Tight convergence reduces NEB force noise.

Requirements: Quantum ESPRESSO ≥ 6.8, a working pw.x executable, and UPF pseudopotential files. Prefer an absolute pw.x path in scripted runs so ASE subprocesses do not depend on an interactive-shell PATH. Recommended set: SSSP Efficiency (PBE).

See examples/template_qe_neb.py for a complete annotated template and examples/al_vacancy_qe.py for a concrete Al vacancy QE/PBE benchmark script.

---

Reproducibility

nebwalk can export a self-contained bundle for every NEB run. The bundle contains input structures, configuration, results, energy profile, trajectory, software environment, SHA-256 checksums, and a rerun template.

Via run_neb_calculation:

from nebwalk import run_neb_calculation, NEBRunConfig

result = run_neb_calculation(
    initial, final, calculator_factory,
    config=NEBRunConfig(n_images=7, climb=True),
    reproduce_dir="my_run_repro",
    calc_params={"type": "MACE-MP-0", "model": "small", "device": "cpu"},
)

Directly:

from nebwalk import save_bundle

bundle = save_bundle(
    result, initial, final, config,
    calc_params={"type": "EMT"},
    compress=True,
)
print(bundle.tarball)   # Path to .tar.gz

Verify a stored run:

cd my_run_repro
# Edit rerun_template.py to restore your calculator
python rerun_template.py

The rerun script prints the original and recomputed barriers and flags differences larger than 5 meV.

---

Testing

pip install -e ".[test]"
pytest tests/ -v

The test suite (132 tests) covers interpolation, NEB force projection, tangent construction, minimum-image convention handling, variable springs, parallel image evaluation, restart helpers, calculator-factory workflows, and reproducibility bundles.

---

Roadmap

Short-term priorities:

1. Keep PyPI, GitHub tags, and source metadata synchronized for v0.7.x releases.
2. Add H/Cu(111) benchmark scripts, static output CSVs, and profile plots.
3. Expand DFT-backed Quantum ESPRESSO benchmarks with small inputs and clear cost warnings.
4. Add post-NEB transition-state refinement using a dimer method.
5. Build a documentation site with theory, API usage, calculator setup, and benchmarks.

Future active-learning roadmap:

• uncertainty-guided image selection
• DFT/MLIP hybrid barrier correction
• adaptive image insertion/removal
• automatic QE failed-image recovery
• benchmark-grade reproducibility archives

Long-term priorities:

• dimer/RFO transition-state refinement;
• imaginary-mode validation utilities;
• better benchmark provenance files;
• larger measured MACE-medium/large CPU/GPU parallel-scaling benchmarks;
• more surface diffusion and ionic migration examples.

---

Release checklist for maintainers

Use this when publishing a new release:

python -m pip install --upgrade build twine
rm -rf dist/ build/ *.egg-info
python -m build
python -m twine check dist/*
python -m twine upload dist/*
VERSION=v0.8.0
git tag -a "$VERSION" -m "nebwalk $VERSION"
git push origin main "$VERSION"

After release:

pip install --upgrade nebwalk
python -c "import nebwalk; print(nebwalk.__version__ if hasattr(nebwalk, '__version__') else 'installed')"

---

References

1. H. Jónsson, G. Mills, K. W. Jacobsen, Nudged Elastic Band Method for Finding Minimum Energy Paths of Transitions, World Scientific, 1998.
2. G. Henkelman and H. Jónsson, Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points, J. Chem. Phys. 113, 9978 (2000).
3. G. Henkelman, B. P. Uberuaga, and H. Jónsson, A climbing image nudged elastic band method for finding saddle points and minimum energy paths, J. Chem. Phys. 113, 9901 (2000).
4. E. Bitzek, P. Koskinen, F. Gähler, M. Moseler, and P. Gumbsch, Structural Relaxation Made Simple, Phys. Rev. Lett. 97, 170201 (2006).
5. S. Smidstrup, A. Pedersen, K. Stokbro, and H. Jónsson, Improved initial guess for minimum energy path calculations, J. Chem. Phys. 141, 214106 (2014).
6. Batatia et al., A foundation model for atomistic materials chemistry, arXiv:2401.00096.
7. H/Cu(111) diffusion literature should be treated as macroscopic diffusion reference, not a one-to-one static NEB barrier target.

---

Acknowledgments

The development of nebwalk benefited from selective AI-assisted support using Claude and OpenAI Codex/ChatGPT for code review, debugging guidance, documentation refinement, and release-workflow cleanup.

The scientific direction, algorithmic design, implementation decisions, validation strategy, benchmark interpretation, and release responsibility remain fully maintained by Md. Rifat Khandaker. AI tools were used only as auxiliary development aids to improve clarity, review consistency, and workflow efficiency.

License

MIT License. See LICENSE.

Features in v0.8.0

In addition to the v0.7.x engine and MLIP workflow, v0.8.0 adds:

• Reproducibility bundles via nebwalk.reproduce.save_bundle().
• Self-contained output directory: input structures, NEBRunConfig, results, trajectory, pip environment capture, SHA-256 checksums, and a rerun script.
• Optional .tar.gz archive of the full bundle.
• run_neb_calculation() accepts reproduce_dir and calc_params keyword arguments for one-line bundle creation.