porereax.meta_sampler

Module providing parent Sampler classes

The module provides Sampler, AtomSampler, and BondSampler as base classes for sampling various properties of MD simulations.

Classes

Sampler	Base class for samplers.
AtomSampler	Base class for samplers that sample atoms with optional bonded atoms.
BondSampler	Sampler class for bonds.

Module Contents

class porereax.meta_sampler.Sampler(name_out, dimension, region, process_id, atom_lib, masses, num_frames, box, system_properties, **parameters)

Bases: abc.ABC

Base class for samplers.

save_object()

abstractmethod 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.

get_mols()

Retrieve the defined molecules for sampling.

Returns:

molecules – Dictionary of molecules defined for sampling.

Return type:

dict

class porereax.meta_sampler.AtomSampler(name_out, atoms, dimension, region, process_id, atom_lib, masses, num_frames, box, system_properties, **parameters)

Bases: Sampler

Base class for samplers that sample atoms with optional bonded atoms.

class porereax.meta_sampler.BondSampler(name_out, bonds, dimension, region, process_id, atom_lib, masses, num_frames, box, system_properties, **parameters)

Bases: Sampler

Sampler class for bonds.

get_bonds()

Retrieve the defined bonds for sampling.

Returns:

bonds – Dictionary of bonds defined for sampling.

Return type:

dict