coarse_grain module

Full Documentation for hippynn.molecular_dynamics.coarse_grain module. Click here for a summary page.

cg_one_average(bead_values)

Unweighted average

cg_one_center_of_geometry_pbc(bead_values, frame_cell, wrap_into_cell=True)

Position center of geometry using PBC

cg_one_center_of_mass_pbc(bead_values, bead_masses, frame_cell, wrap_into_cell=True)

Position center of mass using PBC

cg_one_mass_weighted_average(bead_values, bead_masses)

General mass-weighted average (eg. for velocities when using COM position mapping)

cg_one_sum(bead_values)

Sum of values

coarse_grain_all(values, atom_to_bead, coarse_grain_one, masses=None, cells=None, atom_species=None, bead_species=None, single_frame=False)

Apply a user-defined coarse_grain_one function to all beads across all frames.

The user-supplied function, coarse_grain_one, should take bead_values as an argument, which will correspond the the values of values for one bead in one frame. It can optionally take bead_masses, frame_cell, bead_atom_species, and bead_type as additional arguments. It should return the coarse_grained version of values for the bead given the data provided.

This function loops over each frame (if single_frame=False) and over each bead (as defined by atom_to_bead) and applies coarse_grain_one to each bead. Returns the resulting values in an array of shape (n_frames, n_beads, …) or (n_beads, …) where the trailing dimensions match the output of coarse_grain_one.

See examples of pre-defined coarse_grain_one options in hippynn.molecular_dynamics.coarse_grain.

Parameters:

• values – Array of data to coarse-grain. Shape (n_frames, n_atoms, d) if single_frame=False or (n_atoms, d) if single_frame=True.

• atom_to_bead – Integer array of shape (n_frames, n_atoms,) or (n_atoms,) mapping each atom to a bead.

• coarse_grain_one – Function to coarse-grain one bead’s data.

• masses – (Optional) Array of shape (n_frames, n_atoms,) or (n_atoms,) of masses. Values for the current frame/bead passed to coarse_grain_one if provided.

• cells – (Optional) Array of shape (n_frames, 3, 3) or (3, 3) of cell matrices. The cell for the current frame is passed to coarse_grain_one if provided.

• atom_species – (Optional) Array of shape (n_frames, n_atoms,) or (n_atoms,) of atom species, defined in any manner you choose. Values for the current frame passed to coarse_grain_one if provided.

• bead_species – (Optional) Array of shape (n_frames, max_bead_idx+1,) or (max_bead_idx+1,) where max_bead_idx is the maximum value in atom_to_bead. Values for the current frame/bead passed to coarse_grain_one if provided.

• single_frame – (Optional) Use to specify if data arrays contain a frame axis. Defaults to False.

Returns:

Array of coarse-grained values. Shape (n_frames, n_beads, …) if single_frame=False or (n_beads, …) if single_frame=True.

compute_bead_indices(atom_to_bead)

Compute bead indices from an atom-to-bead mapping.

Parameters:

atom_to_bead – Array of shape (n_atoms,) mapping each atom to a bead.

Returns:

Tuple (beads, bead_indices) where: - beads is a sorted array of unique bead labels. - bead_indices is a dict mapping each bead label to its atom indices.

padded_ndarray_from_list(list_of_lists)

validate_bead_species(bead_species, atom_to_bead, n_frames)

validate_cells(cells, n_frames)

validate_nframes_natoms(value, value_name, n_frames, n_atoms)