BigDFT.Spillage module

A module which contains the routines needed for computing the spillage values.

class MatrixMetadata(filename)[source]

This class contains the information stored in the sparse matrix metadata file.

Parameters:: filename (str) – the name of the metadata file to initialize from.

atoms

a list of atoms with their positions and associated basis functions.

matdim

the dimension of the matrix.

get_frag_indices(system)[source]

Retrieve the indices of the matrix associated with each fragment of a system.

Parameters:: system (Systems.System) – the set of fragments to get the indices of.
Returns:: a mapping from fragment to indices.
Return type:: (dict)

get_at_indices(id_at)[source]

Retrieve the indices of the matrix associated with given atoms

serial_compute_puritybase(sfile, dfile)[source]

This routine computes the matrix K*S using python.

You will need this for computing the purity values.

Parameters:

sfile (str) – the file name of the overlap matrix. Must be in ccs of mtx format.
dfile (str) – the file name of the density kernel. Must be in ccs of mtx format.

Returns:

K*S

Return type:

(scipy.sparse.csc, scipy.sparse.csc)

serial_compute_spillagebase(sfile, hfile)[source]

This routine computes the matrix S^{-1}*H using python.

You will need this for computing the spillage values.

Parameters:

sfile (str) – the file name of the overlap matrix. Must be in ccs of mtx format.
hfile (str) – the file name of the hamiltonian. Must be in ccs of mtx format.

Returns:

Sinverse * H

Return type:

(scipy.sparse.csc, scipy.sparse.csc)

invert_ccs(mat)[source]

Invert a CSC matrix and restore a sparsity pattern such as it can be written without the need for large files.

read_ccs(fname)[source]

Read a CCS matrix from file into a scipy csc matrix.

This routine uses the CCS matrix files that CheSS generates. :param fname: name of the file. :type fname: str