porereax.bond_length

Module for sampling bond lengths and bond orders.

The module provides BondLengthSampler to sample bond length histograms (in Angstroms) or ReaxFF bond order histograms for specified bonds.

Classes

BondLengthSampler

Sampler class for bond lengths and bond orders between bonded atom pairs.

Module Contents

class porereax.bond_length.BondLengthSampler(name_out: str, bonds: list, dimension: str, region, process_id: int, atom_lib: dict, masses: dict, num_frames: int, box: numpy.ndarray, system_properties: dict, num_bins: int, range: tuple)

Bases: porereax.meta_sampler.BondSampler

Sampler class for bond lengths and bond orders between bonded atom pairs.

sample(frame_id: int, mol_index: dict, mol_bonds: dict, bond_mask: dict, frame: object, bond_enum: object, positions_transformed: numpy.ndarray)

Sample data for the current frame. Must be implemented by subclasses.

join_samplers(num_cores)

Join sampler data from multiple processes.

Parameters:

num_cores (int) – Number of parallel processes used for sampling.