molecular_system

class molecular_system.MolecularSystem

Defines a molecular system, containing different kinds of quantum ‘species’ i.e. atoms, muon, positrons, etc. (dict)

add_atom(symbol, origin, units='ANGSTROMS', quantum=False, basis_name=None, basis_file=None)

Adds an atom to the molecular system.

Parameters

  • symbol (str) – Symbol of the atom.

  • origin (ndarray) – Origin of the atom (Cartesian coordinates)

  • units (str, optional) – Units of the origin, valid values are ‘ANGSTROMS’ or ‘BOHR’

add_elementary_particle(symbol, origin, units='ANGSTROMS', size=1, basis_name=None, basis_file=None, basis_set=None, particle=None)

Adds an elementary particle into the molecular system.

Parameters

  • symbol (str) – Symbol of the elementary particle.

  • origin (ndarray) – Origin of the elementary particle (Cartesian coordinates)

  • units (str, optional) – Units of the origin, valid values are ‘ANGSTROMS’ or ‘Bohr’

  • size (int) – Number of elementary particle to be added.

add_nucleus(symbol, origin, units='ANGSTROMS', size=1, basis_name=None, basis_file=None)

Adds a nucleus to the molecular system.

Parameters

  • symbol (str) – Symbol of the nucleus ie. H_2 (Deuterium).

  • origin (ndarray) – Origin of the nucleus (Cartesian coordinates)

  • units (str, optional) – Units of the origin, valid values are ‘ANGSTROMS’ or ‘BOHR’

  • size (int) – Number of particles to be added.

get_basis(symbol)

Returns the basis set of the system of a given symbol particle.

Returns

basis set

Return type

napmo.BasisSet

get_species(sid)

Return a list with the species symbol or sid

Parameters

  • symbol (str) – symbol of the species. ie. e-, e+, etc. Default None

  • sid (int) – the species if. sid > 0. Default None

property point_charges

List with the point charges in the molecule

set_charges(data, open_shell=False)

Adds new particles to the existent species in the system. If electrons, split the species e- into e-alpha and e-beta electrons accordingly to the given charge and multiplicity.

Parameters

  • data (dict) – information with charge and multiplicity for each species

  • open_shell (bool) – whether the electrons should be split or not.

size_particles(symbol)

Returns the number of particles of a given species symbol in the object.

Returns

Number of particles of the species symbol

Return type

int

property size_species

Returns the number of quantum species in the system.