qstack.compound

Molecular structure parsing and manipulation.

qstack.compound.basis_flatten(mol, return_both=True, return_shells=False)[source]

Flatten a basis set definition for AOs.

Parameters:

  • mol (pyscf.gto.Mole) – pyscf Mole object.

  • return_both (bool) – Whether to return both AO info and primitive Gaussian info. Defaults to True.

  • return_shells (bool) – Whether to return angular momenta and starting indices per shell (2l+1-sized group of orbitals that share a radial function and l value). Defaults to False.

Returns:

3×mol.nao int array where each column corresponds to an AO and rows are:

  • 0: atom index,

  • 1: angular momentum quantum number l,

  • 2: magnetic quantum number m.

If return_both is True, also returns: - numpy.ndarray: 2×mol.nao×max_n float array where index (i,j,k) means:

  • i: 0 for exponent, 1 for contraction coefficient of a primitive Gaussian,

  • j: AO index,

  • k: radial function index (padded with zeros if necessary).

If return_shells is True, also returns: - numpy.ndarray: starting AO indices for each shell.

Return type:

  • numpy.ndarray

qstack.compound.fragment_partitioning(fragments, prop_atom_inp, normalize=True)[source]

Compute the contribution of each fragment.

Parameters:

  • fragments (list) – Fragment definition as list of numpy arrays.

  • prop_atom_inp (numpy.ndarray or list of numpy.ndarray) – Atomic contributions to property(ies).

  • normalize (bool) – Whether to normalize fragment partitioning. Defaults to True.

Returns:

Contribution of each fragment. Returns list if input was list, array otherwise.

Return type:

list or numpy.ndarray

qstack.compound.fragments_read(frag_file)[source]

Load fragment definition from a file.

Parameters:

frag_file (str) – Path to the fragment file containing space-separated atom indices (1-based).

Returns:

List of numpy arrays containing the fragment indices.

Return type:

list

qstack.compound.make_atom(q, basis, ecp=None)[source]

Create a single-atom molecule at the origin.

Parameters:

  • q (str) – Element symbol.

  • basis (str or dict) – Basis set.

  • ecp (str) – ECP to use. Defaults to None.

Returns:

Single-atom pyscf Mole object.

Return type:

pyscf.gto.Mole

qstack.compound.make_auxmol(mol, basis, copy_ecp=False)[source]

Build an auxiliary Mole object given a basis set and a pyscf Mole object.

Parameters:

  • mol (pyscf.gto.Mole) – Original pyscf Mole object.

  • basis (str or dict) – Basis set.

  • copy_ecp (bool) – Whether to copy ECP from original molecule. Defaults to False.

Returns:

Auxiliary pyscf Mole object.

Return type:

pyscf.gto.Mole

qstack.compound.mol_to_xyz(mol, fout, fmt='xyz')[source]

Convert a pyscf Mole object into a molecular file in xyz format.

Parameters:

  • mol (pyscf.gto.Mole) – pyscf Mole object.

  • fout (str) – Name (including path) of the xyz file to write.

  • fmt (str) – Output format. Defaults to “xyz”.

Returns:

String containing the xyz formatted data.

Return type:

str

Raises:

NotImplementedError – If fmt is not “xyz”.

qstack.compound.numbers(mol)[source]

Get atom numbers of a molecule.

Use this function to get atomic NUMBERS to index elements. Use mol.atom_charges() to get CHARGES (it returns effective charges when ECP are used).

Parameters:

mol (pyscf.gto.Mole) – pyscf Mole object.

Returns:

Array of atomic numbers.

Return type:

numpy.ndarray

qstack.compound.rotate_molecule(mol, a, b, g, rad=False)[source]

Rotate a molecule: transform nuclear coordinates given a set of Cardan angles.

Parameters:

  • mol (pyscf.gto.Mole) – Original pyscf Mole object.

  • a (float) – Alpha Euler angle.

  • b (float) – Beta Euler angle.

  • g (float) – Gamma Euler angle.

  • rad (bool) – Whether the angles are in radians. Defaults to False (degrees).

Returns:

pyscf Mole object with transformed coordinates.

Return type:

pyscf.gto.Mole

qstack.compound.xyz_comment_line_parser(line)[source]

Read the ‘comment’ line of a XYZ file and tries to infer its meaning.

Parameters:

line (str) – Comment line from XYZ file.

Returns:

Dictionary containing parsed properties (charge, spin, etc.).

Return type:

dict

qstack.compound.xyz_to_mol(inp, basis='def2-svp', charge=None, spin=None, ignore=False, unit=None, ecp=None, parse_comment=False)[source]

Read a molecular file in xyz format and returns a pyscf Mole object.

Parameters:

  • inp (str) – Path of the xyz file to read, or xyz file contents.

  • basis (str or dict) – Basis set. Defaults to “def2-svp”.

  • charge (int) – Provide/override charge of the molecule. Defaults to None.

  • spin (int) – Provide/override spin of the molecule (alpha electrons - beta electrons). Defaults to None.

  • ignore (bool) – If True, assume molecule is closed-shell and assign charge either 0 or -1. Defaults to False.

  • unit (str) – Provide/override units (Ang or Bohr). Defaults to None.

  • ecp (str) – ECP to use. Defaults to None.

  • parse_comment (bool) – Whether to parse the comment line for properties. Defaults to False.

Returns:

pyscf Mole object containing the molecule information.

Return type:

pyscf.gto.Mole

Raises:

RuntimeError – If units are not recognized or if minao basis requires ECP for heavy atoms.