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Natorbs

Natorbs — Python utility to compute natural/natural-spin orbitals and NOCVs

Description

Natorbs computes natural/natural spin-density orbitals based on canonical unrestricted (UHF-type) orbitals resulting from HF or DFT calculations. It can also compute natural orbitals for chemical valence (NOCVs), given the orbitals of a molecule and its constituing fragments.

The program was created in response to the demand in the course of our own studies on the electronic structure of open-shell systems, especially transition-metal complexes. By generating natural/spin orbitals one can immediately identify the orbitals carrying unpaired electrons among, possibly, hundreds of orbitals, most of which are empty or describe closed shells. Such a diagnosis tool is particularly valuable for complicated electronic structure (broken-symmetry solutions / antiferromagnetic coupling / biradicals and multiradicals). It could be useful, however, to facilitate interpretation of any open-shell UHF-type calculations.

Natorbs works with a number of quantum-chemical programs and was created with the aim of being independent software. It reads the input data (geometry and MOs) using either either through cclib or via Molden format. It saves the output data (the desired flavour of natural orbitals) in Molden format, so that like Molden or Gabedit can read these orbitals for visualization. Note that Natorbs reconstructs the overlap integrals of the atomic basis functions from the provided molecular orbitals (exactly if all the virtuals are provided or approximately otherwise).

Hints

To use Natorbs with Gaussian, you can use either the cclib interface (i.e., directly read the Gaussian output file) or Molden format (i.e., first read the Gaussian output file into Molden and then export it to Molden format). In both cases make sure that the basis set and LCAO coeficients of orbitals are available in the output file (e.g., put in your route section: "gfinput iop(6/7=3) pop=regular"). Remember – if Molden cannot read your orbitals, Natorbs will not be able either! In some cases when using the cclib interface, option "-1" may be helpful. See the manual.

License

[scroll below for the English version]

Program Natorbs został niniejszym udostępniony nieodpłatnie na zasadach tzw. trzyklauzulowej licencji BSD. Copyright 2021 Uniwersytet Jagielloński, Dr hab. Mariusz Radoń

  1. Redystrybucje kodu źródłowego muszą zawierać powyższą informację o prawach autorskich, niniejszą listę warunków i poniższe zastrzeżenie.
  2. Redystrybucje kodu w formie binarnej muszą zawierać powyższą informację o prawach autorskich, tę listę warunków i poniższe wyłączenie odpowiedzialności w dokumentacji i/lub innych materiałach dostarczonych wraz z dystrybucją.
  3. Ani nazwisko (nazwa) właściciela praw autorskich, ani nazwiska jego współautorów nie mogą być używane do popierania lub promowania produktów wywodzących się z tego oprogramowania bez uprzedniej pisemnej zgody.

Natorbs software is hereby made available free of charge under the terms of the 3-clause BSD license.
Copyright 2021 Jagiellonian University, Dr hab. Mariusz Radoń

  1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
  2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
  3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

For further details, see LICENSE.txt file distrubuted with Natorbs.

The Natorbs program is also highlighted on the website of Centre for Technology Transfer CITTRU, Jagiellonion University.

Citation

M.Radoń, Natorbs v1.0, Jagiellonian University, Krakow, Poland, 2021; available from https://tungsten.ch.uj.edu.pl/~mradon/natorbs.

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