horton_part.adapters.gpaw module

Convert a legacy GPAW restart into a HORTON-Part periodic density archive.

This module is adapted from denspart.adapters.gpaw on DensPart’s lisa branch at commit ce0d986. GPAW is imported lazily so that it remains an optional interoperability dependency.

class GridPart(data, *densnames)

Bases: object

Helper class for collecting density grid data.

__init__(data, *densnames)
assemble_density_arrays(uniform_data, atoms)

Combine uniform and augmentation grids into HORTON-Part arrays.

Parameters:

  • uniform_data – Dictionary with detailed data from the uniform grid of a GPAW calculation.

  • atoms – List of dictionaries with atomic-grid data.

Returns:

Dictionary containing the data needed for periodic partitioning.

Return type:

density

compute_augmentation_spheres(uniform_data, setups, atoms, atnums, atcoords)

Compute the density density corrections within the muffin tin spheres on grids.

Parametes

uniform_data, setups, atoms

Data generated by get_uniform_grid_data and get_atomic_grid_data.

atnums

Atomic numbers

atcoords

Atomic (nuclear) coordinates.

All results are stored in the atoms argument.

compute_uniform_points(uniform_data)

Compute the trivial positions and weights of the uniform grid points.

dump_spline(data, key, y, setup, ell)

Convert a spline from a GPAW atom setup.

Parameters:

  • data – Dictionary in which the spline is stored.

  • key – Used for making dictionary keys.

  • y – Function values at the spline grid points.

  • setup – The GPAW setup to which this spline belongs.

  • ell – Angular momentum.

eval_correction(atom_data, setup_data)

Compute the pseudo to all-electron corrections for one muffin-tin sphere.

Parameters:

  • atom_data – Dictionary with the density matrices.

  • setup_data – Atomic (basis) functions stored on radial grids.

Returns:

The atomic grid for integrations in the muffin tin sphere.

Return type:

grid

Notes

Conventions used in variable names, following GPAW conventions: - with t = pseudo - without t = all-electron - c = core - v = valence

get_atomic_grid_data(calc)

Load atomic setups and atomic wavefunctions from GPAW calculation.

Parameters:

calc – GPAW calculator instance.

Returns:

  • setups – A dictionary with atomic setups used. Keys are atomic numbers and values are dictionaries with relevant data for later evaluation of the density corrections within the augmentation spheres.

  • atoms – A list with atomic wavefunction data. Contains dm and optional spindm.

get_horton2_order(ells)

Return a permutation of the basis functions to obtain HORTON 2 conventions.

Parameters:

ells – Array with angular momenta of the basis functions.

Returns:

Reordering of the basis functions.

Return type:

permutation

get_uniform_grid_data(calc, cellvecs, atnums, bohr)

Take the (pseudo) density on the the uniform grid. This is the easy part.

Parameters:

  • calc – GPAW calculator instance.

  • cellvecs – 3 x 3 array whose rows are cell vectors.

  • atnums – Array with atomic numbers.

  • bohr – The ASE conversion factor from bohr to angstrom.

Returns:

Dictionary with several items extracted from the GPAW calculator.

Return type:

uniform_data

main(args=None)

Command-line interface.

parse_args(args)

Parse command-line arguments.

prepare_input(atoms, calc)

Prepare HORTON-Part input from a GPAW run.

Parameters:

  • atoms – A list of ASE atoms from a GPAW calculation.

  • calc – The GPAW calculator instance

Returns:

A dictionary with all input data for a partitioning.

Return type:

input_data