NEB Pre-processing

This page explains the VQkit pre-processing workflow for generating Nudged Elastic Band (NEB) images and preparing NEB calculations.

The NEB tools are available from:

[1] Pre-processing
[12] NEB Intermediate Images

VQkit supports NEB preparation for:

  • VASP;

  • Quantum ESPRESSO.

The pre-processing workflow focuses on creating a consistent sequence of intermediate structures between an initial and a final state.

For detailed NEB post-processing, energy-profile analysis, barrier extraction, and practical examples, see:

Tutorials -> NEB

NEB concept

The Nudged Elastic Band method is used to estimate a minimum-energy reaction path between two known endpoint structures.

The two required endpoint states are:

  • initial state;

  • final state.

VQkit interpolates between these structures to generate intermediate images.

Conceptually:

\[\mathbf{R}_i = (1-\lambda_i)\mathbf{R}_{\mathrm{initial}} + \lambda_i\mathbf{R}_{\mathrm{final}}\]

where:

  • \(\mathbf{R}_i\) is the geometry of image i;

  • \(\lambda_i\) is the interpolation fraction;

  • the first image corresponds to the initial state;

  • the last image corresponds to the final state.

The generated images are starting guesses for the NEB optimization.

They should not be interpreted as transition states before the NEB calculation converges.

Open the NEB image generator

Choose:

[12] NEB Intermediate Images

VQkit displays:

NEB / TRANSITION-STATE IMAGE GENERATION

[1] VASP
[2] Quantum ESPRESSO
[0] Back

Choose the electronic-structure code used for the NEB calculation.

VASP NEB preparation

Choose:

[1] VASP

VQkit asks for the initial structure.

The default is:

Initial structure file in current directory [POSCAR]:

If the initial structure is named POSCAR, press Enter.

Final structure

VQkit then asks:

Final structure file in current directory [CONTCAR]:

If CONTCAR is present, it is used as the default final state.

You may enter another valid VASP structure filename if needed.

Number of intermediate images

VQkit asks:

Number of intermediate images [5]:

This number refers only to the structures between the two endpoints.

For example:

5 intermediate images

correspond to:

initial
image 1
image 2
image 3
image 4
image 5
final

giving seven structures in total.

Output folder

VQkit asks:

Output folder [VQkit_NEB_images]:

The generated interpolation set is written inside this directory.

A typical VASP NEB structure is organized as numbered image folders.

For example:

VQkit_NEB_images/
├── 00/
├── 01/
├── 02/
├── 03/
├── 04/
├── 05/
└── 06/

where:

  • 00 is the initial state;

  • the middle directories contain interpolated images;

  • the last directory is the final state.

VASP endpoint requirements

Before generating the path, ensure that the initial and final structures have:

  • the same number of atoms;

  • the same species;

  • the same atomic ordering;

  • compatible lattice definitions;

  • physically corresponding atoms.

Atom correspondence is critical.

For example, atom 5 in the initial state must correspond to atom 5 in the final state.

If atom ordering differs, simple interpolation can produce an unphysical path.

VASP interpolation cautions

A direct linear interpolation can fail when:

  • an atom crosses a periodic boundary;

  • two atoms pass through each other;

  • the endpoint structures differ by a large reconstruction;

  • molecular rotation dominates the pathway;

  • the initial and final cells are inconsistent.

Always inspect every generated image before running NEB.

Quantum ESPRESSO NEB preparation

Choose:

[2] Quantum ESPRESSO

VQkit prepares a native neb.x input workflow.

Endpoint inputs

VQkit searches for QE endpoint input files.

Typical names are:

initial.in
final.in

If these are unavailable, other *.in files in the directory may be selected.

Both endpoint files must represent valid QE pw.x structures.

Endpoint consistency

The initial and final QE states must have:

  • the same number of atoms;

  • the same species ordering;

  • compatible lattice vectors;

  • matching atomic correspondence.

If the structures are incompatible, VQkit stops rather than generating an invalid path.

Intermediate-image count

VQkit asks:

Number of intermediate images [5]:

In the current QE workflow, the total image count must be greater than three.

Therefore, use at least:

2 intermediate images

between the initial and final endpoints.

For example:

initial
image 1
image 2
final

gives four total images.

QE NEB output file

VQkit asks:

QE neb.x input file [VQkit_QE_neb.in]:

The generated file follows the native QE neb.x structure.

A simplified layout is:

BEGIN
BEGIN_PATH_INPUT

&PATH
   string_method = 'neb',
   restart_mode = 'from_scratch',
   nstep_path = 100,
   num_of_images = ...
   opt_scheme = 'broyden',
   CI_scheme = 'no-CI',
   path_thr = 0.05,
/

END_PATH_INPUT

BEGIN_ENGINE_INPUT

... pw.x settings ...

BEGIN_POSITIONS

FIRST_IMAGE
ATOMIC_POSITIONS angstrom
...

INTERMEDIATE_IMAGE
ATOMIC_POSITIONS angstrom
...

LAST_IMAGE
ATOMIC_POSITIONS angstrom
...

END_POSITIONS

...

END_ENGINE_INPUT
END

The generated file is intended as a starting point and should be reviewed before submission.

QE CIF inspection images

VQkit also asks:

CIF image-check folder [VQkit_NEB_CIF_images]:

It writes the interpolated images as CIF files for visual inspection.

Typical filenames are:

00_initial.cif
01_image.cif
02_image.cif
...
06_final.cif

These CIF structures represent the same interpolated path written into the QE NEB input.

Visual validation

VQkit asks:

Have you checked/approved the intermediate CIF images? [y/N]:

If you answer:

N

VQkit warns that the calculation should not be submitted until the images have been inspected.

This check is intentional.

NEB interpolation can produce mathematically valid but chemically unreasonable structures.

What to inspect in every image

Before submission, inspect:

  • interatomic distances;

  • bond-breaking sequence;

  • bond-forming sequence;

  • atomic overlaps;

  • periodic-boundary crossings;

  • molecular orientation;

  • substrate distortion;

  • migrating atom trajectory.

For adsorption or diffusion systems, confirm that the interpolated path follows a physically plausible migration channel.

QE execution

A typical command is:

neb.x -in VQkit_QE_neb.in > neb.out

The exact execution command depends on your QE installation and HPC environment.

Review before running QE NEB

Check the generated input carefully.

In particular, verify:

  • prefix;

  • outdir;

  • pseudopotential filenames;

  • pseudo_dir;

  • ecutwfc;

  • ecutrho;

  • k-point mesh;

  • spin settings;

  • Hubbard corrections;

  • smearing;

  • atomic constraints;

  • &PATH settings.

The generated defaults are not universal for every reaction pathway.

Climbing-image NEB

The generated QE template currently uses:

CI_scheme = 'no-CI'

This corresponds to a standard NEB starting configuration.

If a climbing-image calculation is required, modify the QE &PATH settings according to the desired workflow after the standard path has been reasonably optimized.

Similarly for VASP, climbing-image settings should be enabled only when appropriate for the NEB stage.

Number of images

Too few images

Using too few images can:

  • miss important pathway curvature;

  • poorly resolve the transition-state region;

  • produce inaccurate barriers.

Too many images

Using many images:

  • increases computational cost;

  • can make convergence slower;

  • may be unnecessary for simple pathways.

The appropriate number depends on:

  • reaction complexity;

  • atomic displacement;

  • pathway length;

  • desired barrier resolution.

For many simple surface or diffusion reactions, approximately 5-7 intermediate images are a reasonable starting point, but the number should be validated for the specific system.

Cell consistency

For a conventional solid-state NEB pathway, the endpoint cells should normally be identical unless a variable-cell transition-path method is specifically intended.

Large differences between endpoint cells can make interpolation physically meaningless.

Periodic boundary conditions

A common NEB error occurs when a moving atom is represented on opposite sides of the periodic cell in the two endpoints.

For example:

initial x = 0.95
final   x = 0.05

A direct interpolation may move the atom across almost the entire cell instead of across the short periodic distance.

Inspect periodic wrapping before generating the path.

Atom ordering

NEB interpolation assumes consistent atomic identity.

Example initial ordering:

Pt Pt Pt O H

The final structure must preserve the same corresponding order.

A final file ordered as:

O Pt Pt Pt H

is not equivalent for interpolation even though the chemical composition is the same.

Endpoint optimization

The initial and final states should normally be independently relaxed before constructing the NEB path.

Poorly optimized endpoints can lead to:

  • artificial barrier contributions;

  • unstable endpoint forces;

  • difficult NEB convergence.

The endpoint energy minima should be well defined.

VASP preparation after interpolation

After the image folders are generated, the user still needs to prepare the remaining VASP NEB inputs.

Typically this includes:

INCAR
KPOINTS
POTCAR

and the HPC job script.

The NEB-specific INCAR may include settings such as the intended number of images and optimizer controls.

These should be chosen according to the VASP NEB workflow used by the researcher.

Do not distribute POTCAR files publicly.

Quantum ESPRESSO preparation after interpolation

For QE, VQkit writes the native neb.x input directly, but the user should still review all engine and path parameters.

Ensure that the required QE saved-data and pseudopotential paths are valid on the system where neb.x will run.

NEB convergence

A generated path is only the initial guess.

The final path must be optimized until the NEB forces satisfy the chosen convergence criteria.

A visually smooth starting path does not imply that the final NEB barrier is converged.

Transition-state interpretation

The highest-energy image of a standard NEB path is only an approximation to the transition-state region.

A more accurate saddle-point estimate may require:

  • climbing-image NEB;

  • further transition-state refinement;

  • vibrational confirmation of the saddle point where appropriate.

Connection to NEB post-processing

After the NEB calculation finishes, VQkit can analyze a completed image directory containing numeric image folders.

The post-processing workflow extracts:

  • image energies;

  • relative energies;

  • transition-state candidate;

  • forward barrier;

  • reverse barrier;

  • reaction energy.

It generates:

VQkit_NEB_PROFILE.dat
VQkit_NEB_ANALYSIS_summary.txt
VQkit_NEB_PROFILE.png
VQkit_NEB_PROFILE.pdf

For the full analysis workflow, see:

Tutorials -> NEB

Scientific cautions

VQkit automates image generation, but it cannot determine whether the reaction pathway is chemically meaningful.

The user must verify:

  • endpoint stability;

  • atom correspondence;

  • periodic wrapping;

  • intermediate geometry quality;

  • image count;

  • NEB convergence;

  • transition-state interpretation.

A numerically converged NEB calculation can still represent the wrong physical path if the initial interpolation was inappropriate.