waterEntropy.utils package

Submodules

waterEntropy.utils.dask_clusters module

Helpers for setting up dask clusters on HPC.

waterEntropy.utils.dask_clusters.check_slurm_env()

Check if SLURM_CPU_BIND is set in env and delete if so to satisfy cpu bind request on some machines.

waterEntropy.utils.dask_clusters.slurm_configure_cluster(args)

Configure a SLURM HPC cluster to run bigger jobs on.

waterEntropy.utils.dask_clusters.slurm_directives(args)

Process extra directives and directives to be skipped.

waterEntropy.utils.dask_clusters.slurm_prologues(args)

Process any extra environment variables to be used.

waterEntropy.utils.dask_clusters.slurm_submit_master(args)

Submit a master worker process for coordinating dask cluster setup, orchestration and shutdown.

waterEntropy.utils.dask_clusters.system_network_interface()

Get best candidate for HPC network interface from commonly known ones.

waterEntropy.utils.helpers module

These functions are generally here to help with saving stats of simulation data

waterEntropy.utils.helpers.nested_dict()

Create a nested dictionary, usually used to save statistics from a simulation

waterEntropy.utils.selections module

Functions for common MDAnalysis selections

waterEntropy.utils.selections.find_bonded_atoms(atom_idx: int, system)

for a given atom, find its bonded heavy and H atoms

Parameters:

• atom_idx – atom index to find bonded heavy atom for

• system – mdanalysis instance of all atoms in current frame

waterEntropy.utils.selections.find_bonded_heavy_atom(atom_idx: int, system)

for a given atom, if it is a hydrogen, find what heavy atom it is bonded to

Parameters:

• atom_idx – atom index to find bonded heavy atom for

• system – mdanalysis instance of all atoms in current frame

waterEntropy.utils.selections.find_molecule_UAs(molecule)

For a given molecule, return the heavy atoms it constitutes

Parameters:

molecule – mdanalysis instance of atoms in a frame

waterEntropy.utils.selections.find_solute_molecules(system)

For a given system, find molecules containing more than one UA or is not a single UA molecule that contains an oxygen atom and return the resids for these molecules. Filter out MDAnalysis definition of water molecules by default.

Parameters:

system – mdanalysis instance of atoms in a frame

waterEntropy.utils.selections.get_selection(system, selection_type: str, indices: list[int])

For a list of indices, turn this list into a string and use it to select by a particular MDAnalysis selection type e.g. resid or index

Parameters:

• system – mdanalysis instance of atoms in a frame

• selection_type – string for what selection to make in mdanalysis, e.g index, resid

• indices – list of numbers corresponding to the atoms or resids to select

waterEntropy.utils.selections.guess_length_scale(molecule)

Guess what the length scale of the molecule is

Parameters:

molecule – MDAnalysis instance of molecule

Module contents

waterEntropy: calculate water entropy near heterogeneous interfaces