3.12.1. horton.part.base – Base classes for (atoms-in-molecules) partitioning algorithms

class horton.part.base.Part(coordinates, numbers, pseudo_numbers, grid, moldens, spindens, local, lmax)

Bases: horton.cache.JustOnceClass

Arguments:

coordinates

An array (N, 3) with centers for the atom-centered grids.

numbers

An array (N,) with atomic numbers.

pseudo_numbers

An array (N,) with effective charges. When set to None, this defaults to“numbers.astype(float)“.

grid

The integration grid

moldens

The spin-summed electron density on the grid.

spindens

The spin difference density on the grid. (Can be None)

local

Whether or not to use local (non-periodic) subgrids for atomic integrals.

lmax

The maximum angular momentum in multipole expansions.

__getitem__(key)

__init__(coordinates, numbers, pseudo_numbers, grid, moldens, spindens, local, lmax)

Arguments:

coordinates

An array (N, 3) with centers for the atom-centered grids.

numbers

An array (N,) with atomic numbers.

pseudo_numbers

An array (N,) with effective charges. When set to None, this defaults to“numbers.astype(float)“.

grid

The integration grid

moldens

The spin-summed electron density on the grid.

spindens

The spin difference density on the grid. (Can be None)

local

Whether or not to use local (non-periodic) subgrids for atomic integrals.

lmax

The maximum angular momentum in multipole expansions.

clear()

Discard all cached results, e.g. because wfn changed

compute_pseudo_population(index)

do_all()

Computes all properties and return a list of their keys.

do_charges(instance)

do_moments(instance)

do_partitioning(instance)

do_populations(instance)

do_spin_charges(instance)

get_grid(index=None)

Return an integration grid

Optional arguments:

index

The index of the atom. If not given, a grid for the entire system is returned. If self.local is False, a full system grid is always returned.

get_memory_estimates()

get_moldens(index=None, output=None)

get_spindens(index=None, output=None)

get_wcor(index)

Return the weight corrections on a grid

See get_grid for the meaning of the optional arguments

to_atomic_grid(index, data)

update_at_weights()

Updates the at_weights arrays in the case (and all related arrays)

cache

coordinates

grid

linear = False

lmax

local

name = None

natom

numbers

pseudo_numbers

class horton.part.base.WPart(coordinates, numbers, pseudo_numbers, grid, moldens, spindens=None, local=True, lmax=3)

Bases: horton.part.base.Part

Arguments:

coordinates

An array (N, 3) with centers for the atom-centered grids.

numbers

An array (N,) with atomic numbers.

pseudo_numbers

An array (N,) with effective charges. When set to None, this defaults to“numbers.astype(float)“.

grid

A Molecular integration grid. This must be a BeckeMolGrid instance with mode==’keep’ or mode==’only’.

moldens

The spin-summed electron density on the grid.

Optional arguments:

spindens

The spin difference density on the grid.

local

If True: use the proper atomic grid for each AIM integral. If False: use the entire molecular grid for each AIM integral.

lmax

The maximum angular momentum in multipole expansions.

__getitem__(key)

__init__(coordinates, numbers, pseudo_numbers, grid, moldens, spindens=None, local=True, lmax=3)

Arguments:

coordinates

An array (N, 3) with centers for the atom-centered grids.

numbers

An array (N,) with atomic numbers.

pseudo_numbers

An array (N,) with effective charges. When set to None, this defaults to“numbers.astype(float)“.

grid

A Molecular integration grid. This must be a BeckeMolGrid instance with mode==’keep’ or mode==’only’.

moldens

The spin-summed electron density on the grid.

Optional arguments:

spindens

The spin difference density on the grid.

local

If True: use the proper atomic grid for each AIM integral. If False: use the entire molecular grid for each AIM integral.

lmax

The maximum angular momentum in multipole expansions.

clear()

Discard all cached results, e.g. because wfn changed

compute_pseudo_population(index)

do_all()

Computes all properties and return a list of their keys.

do_charges(instance)

do_density_decomposition(instance)

do_hartree_decomposition(instance)

do_moments(instance)

do_partitioning(instance)

do_populations(instance)

do_spin_charges(instance)

get_grid(index=None)

Return an integration grid

Optional arguments:

index

The index of the atom. If not given, a grid for the entire system is returned. If self.local is False, a full system grid is always returned.

get_memory_estimates()

get_moldens(index=None, output=None)

get_spindens(index=None, output=None)

get_wcor(index)

to_atomic_grid(index, data)

update_at_weights()

Updates the at_weights arrays in the case (and all related arrays)

cache

coordinates

grid

linear = False

lmax

local

name = None

natom

numbers

pseudo_numbers

class horton.part.base.CPart(coordinates, numbers, pseudo_numbers, grid, moldens, spindens=None, local=True, lmax=3, wcor_numbers=None, wcor_rcut_max=2.0, wcor_rcond=0.1)

Bases: horton.part.base.Part

Arguments:

grid

The uniform integration grid based on the cube file.

moldens

The spin-summed electron density on the grid.

Optional arguments:

spindens

The spin difference density on the grid.

local

Whether or not to use local (non-periodic) sub grids for atomic integrations.

lmax

The maximum angular momentum in multipole expansions.

wcor_numbers

The list of element numbers for which weight corrections are needed.

wcor_rcut_max

The maximum cutoff sphere used for the weight corrections.

wcor_rcond

The regularization strength for the weight correction equations.

__getitem__(key)

__init__(coordinates, numbers, pseudo_numbers, grid, moldens, spindens=None, local=True, lmax=3, wcor_numbers=None, wcor_rcut_max=2.0, wcor_rcond=0.1)

Arguments:

grid

The uniform integration grid based on the cube file.

moldens

The spin-summed electron density on the grid.

Optional arguments:

spindens

The spin difference density on the grid.

local

Whether or not to use local (non-periodic) sub grids for atomic integrations.

lmax

The maximum angular momentum in multipole expansions.

wcor_numbers

The list of element numbers for which weight corrections are needed.

wcor_rcut_max

The maximum cutoff sphere used for the weight corrections.

wcor_rcond

The regularization strength for the weight correction equations.

clear()

Discard all cached results, e.g. because wfn changed

compute_pseudo_population(index)

do_all()

Computes all properties and return a list of their keys.

do_charges(instance)

do_moments(instance)

do_partitioning(instance)

do_populations(instance)

do_spin_charges(instance)

get_cutoff_radius(index)

get_grid(index=None)

Return an integration grid

Optional arguments:

index

The index of the atom. If not given, a grid for the entire system is returned. If self.local is False, a full system grid is always returned.

get_memory_estimates()

get_moldens(index=None, output=None)

get_spindens(index=None, output=None)

get_wcor(index=None)

get_wcor_funcs(index)

to_atomic_grid(index, data)

update_at_weights()

Updates the at_weights arrays in the case (and all related arrays)

cache

coordinates

grid

linear = False

lmax

local

name = None

natom

numbers

pseudo_numbers

wcor_numbers