chemtools.toolbox.conceptual.CondensedConceptualDFT

class chemtools.toolbox.conceptual.CondensedConceptualDFT(dict_population, model='quadratic', coordinates=None, numbers=None)[source]

Condensed conceptual density functional theory (DFT) analysis of quantum chemistry output files.

Condensed conceptual DFT reactivity descriptors \(\{p_A\}_{A=1}^{N_A}\), partition the local descriptors between atoms in molecules, and integrate it to obtain condense property.

Note: If only one molecule is provided, the frontier molecular orbital (FMO) approach is
invoked, otherwise finite difference (FD) approach is taken. If FD approach is taken, the geometries and atomic numbers of all molecules can be different only for fragment of molecular response (approach=’RMF’).

Initialize class.

Parameters:
  • dict_population (dict) – Dictionary of number of electrons \(N\) (key) and corresponding atomic population array (value).
  • model (str, optional) – Energy model used to calculate condensed reactivity descriptors. The available models include: “linear”, “quadratic”, and “general”. Please see “” for more information.
  • coordinates (ndarray, optional) – Atomic coordinates of atomic centers.
  • numbers (ndarray, optional) – Atomic number of atomic centers.
classmethod from_file(fname, model, approach='FMR', scheme='h', **kwargs)[source]

Initialize class from calculation output file(s).

Parameters:
  • fname (str, sequence of str) – String specifying the path to a molecule’s file, or sequence of strings specifying path to molecule files.
  • model (str) – Energy model used to calculate condensed reactivity descriptors. Available models are “linear” and “quadratic”.
  • approach (str, optional) – Choose between “FMR” (fragment of molecular response) or “RMF” (response of molecular fragment).
  • scheme (str, optional) – Partitioning scheme. Options: “h”, “hi”, “mbis”.
  • kwargs (dict, optional) – Extra keyword arguments required for partitioning, like ‘grid’ and ‘proatomdb’.
classmethod from_molecule(molecule, model, approach='FMR', scheme='h', **kwargs)[source]

Initialize class from Molecule object(s).

Parameters:
  • molecule (Molecule or Sequence of Molecule) – Instance of Molecule class, or sequence of Molecule class instances.
  • model (str) – Energy model used to calculate condensed reactivity descriptors. Available models are “linear” and “quadratic”.
  • approach (str, optional) – Choose between “FMR” (fragment of molecular response) or “RMF” (response of molecular fragment).
  • scheme (str, optional) – Partitioning scheme. Options: “h”, “hi”, “mbis”.
  • kwargs (dict, optional) – Extra keyword arguments required for partitioning, like ‘grid’ and ‘proatomdb’.
coordinates

Cartesian coordinates of atoms.

static load_file(fnames)

Return Molecule instances corresponding to fnames.

Parameters:fnames (str or Sequence of str) – Strings specifying the path to molecule’s file, or sequence of strings specifying path to molecule files.
model

Energy model.

numbers

Atomic numbers of atoms.