horton_part.core.proatomdb module

Pro-atom databases

class ProAtomDB(records)

Bases: object

__init__(records)

Parameters:

records (sequence of ProAtomRecord instances) –

A sequence of ProAtomRecord instances. If two or more records have

the same number and charge, only the lowest in energy is retained.

Based on the records present it is determined which records are safe to use, i.e. apparently not bound by the basis set.

compact(nel_lost)

Make the pro-atoms more compact

Argument:

nel_lost

This parameter controls the part of the tail that gets neglected. This is the (maximym) number of electrons in the part that gets discarded.

Note that only ‘safe’ atoms are considered to determine the cutoff radius.

get_charges(number, safe=False)

get_numbers()

Return the element numbers present in the database

get_record(number, charge)

get_rgrid(number)

get_rho(number, parameters=0, combine='linear', do_deriv=False)

Construct a proatom density on a grid.

Arguments:

number

The element

Optional arguments:

parameters

This argument may take two forms:

• Integer: the charge of the pro-atom

• Dictionary: a linear or geometric combination of different charged pro-atoms. The keys are the charges and the values are the coefficients.

combine

In case parameters is an array, this determines the type of combination: ‘linear’ or ‘geometric’.

do_deriv

When set to True, the derivative of rho is also returned. In case the derivative is not available, the second return value is None.

get_spline(number, parameters=0, combine='linear')

Construct a proatom spline.

Arguments: See get_rho method.

normalize()

property size

Number of proatoms in the database.

class ProAtomRecord(number, charge, energy, rgrid, rho, deriv=None, pseudo_number=None, ipot_energy=None)

Bases: object

A single proatomic density record

__init__(number, charge, energy, rgrid, rho, deriv=None, pseudo_number=None, ipot_energy=None)

Parameters:

• number (int) – The atomic number of the proatom.

• charge (int) – The net charge of the proatom.

• energy (float) – The total energy of the proatom.

• rgrid (instance RadialGrid) – The radial grid on which the density (and optional radial density derivatives) are tabulated.

• rho (np.ndarray) – The electron density on the grid.

• deriv (np.ndarray) – The radial derivative of the electron density.

• pseudo_number (int, default=None) – The effective core charge. If None, it is set to number.

• ipot_energy (float, default=None) – The ionization potential.

property charge

The atomic charge.

chop(npoint)

Reduce the proatom to the given number of radial grid points.

compute_radii(populations)

Compute approximate radii and grid points at which the atom contains the given populations

Arguments:

populations

A list of populations for which the corresponding radii have to be computed.

property deriv

The radial derivative of the density on a radial grid.

property energy

The total electronic energy.

get_moment(order)

Return the integral of rho*r**order

property ipot_energy

The ionization potential.

property number

The atomic number.

property population

The total number of electrons.

property pseudo_number

The pseudo atomic number (effective core charge)

property pseudo_population

The total effective number of electrons.

property rgrid

The radial grid.

property rho

The density on a radial grid.

property safe

When safe is True, this pro atom is safe to use, i.e. not know to be basis-set bound

update_safe(other)

Update the safe attribute based on a comparison with other records.

Arguments:

other

Another instance of ProAtomRecord