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API Reference🔗

This section provides detailed API documentation for the main classes and functions.

Core Classes🔗

NEB🔗

Main class for Nudged Elastic Band calculations.

from neb_dynamics.neb import NEB

::: neb_dynamics.neb.NEB

MSMEP🔗

Multi-Step Minimum Energy Path calculator for handling complex reactions.

from neb_dynamics import MSMEP

::: neb_dynamics.msmep.MSMEP

Chain🔗

Container for a pathway consisting of multiple images.

from neb_dynamics import Chain

::: neb_dynamics.chain.Chain

StructureNode🔗

A node containing a molecular structure.

from neb_dynamics import StructureNode

::: neb_dynamics.nodes.node.StructureNode

Input Classes🔗

NEBInputs🔗

Configuration for NEB optimization.

from neb_dynamics.inputs import NEBInputs

::: neb_dynamics.inputs.NEBInputs

ChainInputs🔗

Configuration for chain behavior.

from neb_dynamics.inputs import ChainInputs

::: neb_dynamics.inputs.ChainInputs

GIInputs🔗

Configuration for geodesic interpolation.

from neb_dynamics.inputs import GIInputs

::: neb_dynamics.inputs.GIInputs

RunInputs🔗

Complete configuration for MSMEP calculations.

from neb_dynamics.inputs import RunInputs

::: neb_dynamics.inputs.RunInputs

Engines🔗

Engine (Abstract Base)🔗

Base class for all engines.

from neb_dynamics.engines import Engine

::: neb_dynamics.engines.engine.Engine

QCOPEngine🔗

Engine using QCOP for electronic structure calculations.

from neb_dynamics.engines import QCOPEngine

::: neb_dynamics.engines.qcop.QCOPEngine

ASEEngine🔗

Engine using ASE calculators.

from neb_dynamics.engines import ASEEngine

::: neb_dynamics.engines.ase.ASEEngine

Optimizers🔗

Optimizer (Abstract Base)🔗

Base class for optimizers.

from neb_dynamics.optimizers import Optimizer

VelocityProjectedOptimizer🔗

VPO optimizer with velocity projection.

from neb_dynamics.optimizers.vpo import VelocityProjectedOptimizer

ConjugateGradient🔗

Conjugate gradient optimizer.

from neb_dynamics.optimizers.cg import ConjugateGradient

LBFGS🔗

Limited-memory BFGS optimizer.

from neb_dynamics.optimizers.lbfgs import LBFGS

## Helper Functions

### chainhelpers

Utility functions for chain manipulation and visualization.

```python
import neb_dynamics.chainhelpers as ch

Common functions:

  • ch.run_geodesic() - Create chain using geodesic interpolation
  • ch.visualize_chain() - Visualize chain in 3D
  • ch.compute_NEB_gradient() - Calculate NEB gradient
  • ch.get_g_perps() - Get perpendicular gradients
  • ch._get_ind_minima() - Find indices of minima in chain