hipart — Fuzzy atom partitioning

All HiPart scripts use the modules described below to perform their analysis. The internals of HiPart can also be used to write your own population analysis code.

hipart.context — Contexts instead of global variables

exception hipart.context.ContextError

class hipart.context.Context(filename, options)

This class is an extension to the concept of global variables.

It ensures that an entire context of data structures, files and directories is present and sane. One can pass around a context variable instead of the individual global variables.

check_tag(extra)

Make sure our context is compatible with the data in the workdir.

num_lebedev

version = 2

class hipart.context.Options(lebedev=110, do_clean=False, do_work=True, do_output=True, verbose=True, threshold=0.0001, max_iter=500, fix_total_charge=True, do_random=True, save_mem=False)

hipart.schemes — Partitioning schemes and derived quantities

exception hipart.schemes.ParseError

hipart.wavefn — Electronic structure representation

hipart.wavefn.load_wavefunction(filename)

class hipart.wavefn.FCHKWaveFunction(filename, options)

compute_atomic_overlap(grid, weights)

compute_density(grid)

compute_orbitals(grid)

compute_potential(grid)

compute_spin_density(grid)

init_naturals(work)

log()

hipart.wavefn.get_num_filled(occupations)

hipart.wavefn.compute_naturals(dmat, num_dof)

hipart.atoms and hipart.atomdb — Atomic databases

class hipart.atoms.AtomProfile(number, rgrid, records)

get_atom_fn(population=None)

class hipart.atoms.AtomTable(filename)

class hipart.atomdb.Options(lebedev=110, rlow=2e-05, rhigh=20.0, num_steps=100, max_ion=2, qc=False, do_work=True, verbose=True, do_random=True)

hipart.atomdb.run_atomdb(executable, lot, atom_numbers, options, directory='.')

hipart.atomdb.main(args=None)

hipart.fit — ESP cost functions

class hipart.fit.ChargeDipoleCostFunction(N, design_matrix, expected_values, weights, total_charge)

correlation(charges, dipoles=None)

full_vector(charges, dipoles=None)

model_rms(charges, dipoles=None)

rmsd(charges, dipoles=None)

write_to_file(filename)

class hipart.fit.ESPCostFunction(coordinates, grid_points, grid_weights, densities, potentials, total_charge)

hipart.grids — Numerical integration grids

class hipart.grids.Grid(prefix, work, points, dump=True)

dump(suffix, array, ignore=False)

classmethod from_prefix(prefix, work)

load(suffix, shape=None)

size

class hipart.grids.AtomicGrid(prefix, work, points, dump=True)

classmethod from_parameters(prefix, work, center, rgrid, agrid)

class hipart.grids.RBaseIntGrid(rs)

get_description()

get_weights(size=None)

integrate(integrand)

integrate_cumul(integrand)

class hipart.grids.RLogIntGrid(r_low, r_high, steps)

get_description()

class hipart.grids.REquiIntGrid(r_low, r_high, steps)

get_description()

hipart.grids.get_rgrid_from_description(s)

class hipart.grids.ABaseIntGrid

generate_points(center, rs)

get_description()

integrate(integrand)

minimum(function)

class hipart.grids.ALebedevIntGrid(num_lebedev, do_random=True)

generate_points(center, rs)

get_description()

integrate(integrand)

maximum(function)

minimum(function)

hipart.lebedev_laikov — Lebedev Laikov angular grid data

hipart.lebedev_laikov.get_grid(number)

hipart.spline — Cubic spline interpolation

class hipart.spline.LinearSpline(x, y)

__call__(x)

class hipart.spline.CubicSpline(x, y)

__call__(x)

hipart.io — IO for Hipart file formats

class hipart.io.Output(directory=None, numbers=None)

active

dump_atom_fields(filename, table, labels, name)

dump_atom_matrix(filename, matrix, name)

dump_atom_scalars(filename, scalars, name)

dump_atom_vectors(filename, vectors, name)

dump_esp_cost(filename, esp_cost)

dump_esp_test(filename, dipole_q, dipole_p, dipole_qp, dipole_qm, mol_esp_cost, charges, dipoles)

dump_overlap_matrices(filename, overlap_matrices)

hipart.io.dump_atom_scalars(filename, scalars, name, numbers=None)

Dump an array of scalar atomic quantities into a text file.

Arguments:

filename – The file to dump in.

scalars – An array of scalars, e.g. atomic charges.

Optional arguments:

numbers – An array with atomic numbers to decorate the file

name – the name of the quantity to decorate the file

hipart.io.load_atom_scalars(filename)

Load atomic scalars written with dump_atom_scalars().

Argument:

filename – The file to load from.

Returns the array with scalars.

hipart.io.dump_atom_vectors(filename, vectors, name, numbers=None)

Dump an array of atomic 3D-vector quantities into a text file.

Arguments:

filename – The file to dump in.

vectors – An array of 3D-vectors, e.g. atomic dipoles.

Optional arguments:

numbers – An array with atomic numbers to decorate the file

name – the name of the quantity to decorate the file

hipart.io.load_atom_vectors(filename)

Load atomic vectors written with dump_atom_vectors().

Argument:

filename – The file to load from.

Returns the array with vectors.

hipart.io.dump_atom_matrix(filename, matrix, name, numbers=None)

Dump a 2D-array of atomic pair quantities into a text file.

Arguments:

filename – The file to dump in.

matrix – A 2D-array of atomic pair quantities, e.g. bond orders.

Optional arguments:

numbers – An array with atomic numbers to decorate the file

name – the name of the quantity to decorate the file

hipart.io.load_atom_matrix(filename)

Load atomic pair quantities written with dump_atom_matrix().

Argument:

filename – The file to load from.

Returns the square array with pair quantities.

hipart.io.dump_atom_fields(filename, table, labels, name, numbers=None)

Dump a table with multiple scalar atomic quantities into a text file.

Arguments:

filename – The file to dump in.

table – A 2D-array of atomic scalar quantities, e.g. the atomic multipole expansions. Each column corresponds to a quantity and each row corresponds to an atom.

labels – The labels of the atomic quantities. The number of labels and the number of columns in the table must be the same.

Optional arguments:

numbers – An array with atomic numbers to decorate the file

name – the name of the quantity to decorate the file

hipart.io.load_atom_fields(filename)

Load multiple atomic quantities written with dump_atom_fields().

Argument:

filename – The file to load from.

Returns a tuple with two results: (i) the table with atomic scalar quantities and (ii) the labels from the table header.

hipart.io.dump_overlap_matrices(filename, overlap_matrices, numbers=None)

Dump a the atomic overlap matrices into a text file.

Arguments:

filename – The file to dump in.

overlap_matrices – A list with (square) atomic overlap matrices.

Optional arguments:

numbers – An array with atomic numbers to decorate the file

hipart.opts — Command line parsion for hi-*.py scripts

hipart.opts.parse_command_line(script_usage)

hipart.log — Screen output

class hipart.log.ProgressBar(label, n, indent=0, width=80, verbose=True)

__call__(inc=1)

dump(s)

class hipart.log.Log

__call__(s)

begin(s)

end()

level

pb(s, num)

set_verbose(verbose)

hipart.work — Control temporary work files

class hipart.work.Work(directory=None, do_clean=False)

active

clean()

create()

dump(name, array, ignore=False)

load(name, shape=None)