Module dynamics 

Structs

MdFrame

One trajectory frame for molecular-dynamics sampling.

MdTrajectory

Full trajectory output for exploratory molecular dynamics.

NebImage

One image (node) on a simplified NEB path.

NebPathResult

Simplified NEB output for low-cost pathway exploration.

ReactionDynamicsConfig

Configuration for a full reaction dynamics computation.

ReactionDynamicsFrame

A single frame along the reaction coordinate.

ReactionDynamicsResult

Full result of a reaction dynamics computation.

Enums

MdBackend

Force backend for molecular dynamics.

NebBackend

Energy backend for NEB path calculations.

Functions

atomic_mass_amu

centre_at_origin

Translate coords so COM is at origin.

com_flat

Centre-of-mass of a flat coordinate array.

compute_backend_energy_and_gradients

Compute energy and gradients using the specified backend.

compute_reaction_dynamics

Compute a full reaction dynamics path: embed reactants + products, build oriented complexes, run NEB for the reactive region, and generate approach/departure frames — all energies computed in Rust with the chosen quantum-chemistry method.

compute_simplified_neb_path

Build a simplified NEB-like path using linear interpolation and spring-coupled relaxation.

compute_simplified_neb_path_configurable

Build a simplified NEB path with a configurable energy backend.

map_atoms_greedy

Greedy atom mapping between two complexes by element and distance.

neb_backend_energy_and_gradient

Compute energy and return both energy (kcal/mol) and flat gradient (kcal/mol/Å).

neb_backend_energy_kcal

Compute energy-only for any NEB backend (used for single-point comparisons).

neb_energy_and_gradient

Compute energy (kcal/mol) and gradients (kcal/mol/Å) for a NEB image using the specified backend.

reorder_coords

Reorder product coords into reactant atom order using mapping.

simulate_nose_hoover

Nosé-Hoover chain thermostat for rigorous NVT sampling.

simulate_velocity_verlet

Run molecular dynamics using Velocity Verlet with a configurable force backend.

simulate_velocity_verlet_uff

Run short exploratory molecular dynamics using Velocity Verlet and optional Berendsen NVT.

slide_molecules

Rigid-body slide: move each molecule’s atoms toward/away from the global COM.

trajectory_to_xyz

Export an MD trajectory to XYZ format string.