NATORBS(1)

NAME
Natorbs - program for computing natural/spin orbitals

SYNOPSIS
natorbs [options] filename

DESCRIPTION
Natorbs is a utility for post-processing the results of quantum-chemical calculations. It computes natural/natural spin orbitals based on canonical unrestricted (UHF-type) orbitals resulting from HF or DFT calculations. It can also compute natural orbitals for chemical valence (NOCVs) based on the orbitals of a molecule and its constituing fragments. The input data are read using cclib or from Molden format file, the resulting orbitals are saved in Molden format.

ARGUMENTS

Single mandatory argument (filename) is the name of the file containg molecule specification (i.e. geometry, basis set and molecular orbitals) in Molden Format or any format that cclib can parse. In case of NOCV (--nocv) it must be followed by a list of analogous (Molden Format or cclib) files for all the fragments. The ordering of fragments and ordering of atoms in the fragments is important and must agree with their ordering in the molecule: 1 2 3 4 5 <--- 1 2 | 3 4 5 (molecule) (fragm 1) (fragm 2)

RESULTS
Natorbs compute natural/spin or NOCV orbitals and writes them in Molden Format. The output file name is specified with the -o option, the default name is derived from the filename by adding `.natorbs.out' suffix. The default behavior is to compute natural orbitals based on UHF-type orbitals.

OPTIONS

Natorbs accepts the following options:

-h, --help
    Display the lists of all commandline options.

--version
    Display the version info and exit

-v, --verbose
    Display verbose messages on stdout.

-g, --debug
    Display very detailed debug messages on stdout.

-s, --spin
    Calculate natural spin orbitals (spin density orbitals) instead of (default) natural orbitals.

--nocv
    Calculate NOCV for a given molecule with respect to the corresponding promolecule(fragment[, fragment2, ...]). The order of the input files on the command line: molecule, fragment1 [, fragment2, ...]

-o outfile, --output=outfile
    Write the result to `outfile'. By default they are written to inputfile.natorbs.out.

-t <value>, --treshold=<value>
    Set treshold for saving output orbitals: orbitals whose occupation number do not differ more than <value> from ``closed shell'' values 0 (zero) or 2 (two) will not saved Default for <value> is 0.1. Setting <value> to 0.0 (zero) will pring all orbitals. A reasonable treshold which can greatly reduce the number of printed orbitals is 0.1-0.01.

-1, --ignore_symmetry, --ignore-symmetry
    By default natorbs recognizes symmetry labels of input orbitals and computes resulting natural/spin orbitals per each irrep separately. This option makes it to ignore the symmetry labels of the input orbitals, which is useful if these labels are wrong and should be ignored for some other reason.

EXAMPLE
natorbs -t 0.05 --spin --output=spinorbs uhfmo Input molecular orbitals are taken from uhfmo, spin orbitals will be computed and written to spinorbs. A non standard treshold (0.05) for saving the generated spin orbitals will be used.

SEE ALSO
Some (experimental) options of the program may not be listed above. They can be, however, seen with the --help option. Files README.md and LICENSE.txt are provided with the distribution. The latest version of natorbs is available from the project website: https://tungsten.ch.uj.edu.pl/~mradon/natorbs . For detailed description of the Molden Format see http://www.cmbi.ru.nl/molden . Definitions of natural/natural-spin orbitals can be found in quantum-chemistry literature. Basically, they are defined as eigenvectors of one-particle density or spin-density matrix, respectively. The connection between spin-unrestricted orbitals and natural orbitals is explained in the seminal paper: A. Amos and G. Hall, Proc. Roy. Soc. A, 1961, 263, 483, doi: 10.1098/rspa.1961.0175. For description of the NOCV method see the following paper: M. Mitoraj and A. Michalak, J. Mol. Model. 2007, 13, 347, doi: 10.1007/s00894-006-0149-4. The pairing property of NOCVs: M. Radon Theor. Chem. Acc. 2008, 120, 337, doi: 10.1007/s00214-008-0428-5. Some applications of programs Natorbs, mainly its NOCV stuff, can be found in the following papers: M. Radon, E. Broclawik, J. Chem. Theory Comput., 2007, 3, 728-734, doi 10.1021/ct600363a; M. Radon, P. Kozyra, A. Stepniewski, J. Datka, E. Broclawik, Can. J. Chem., 2013, 91, 538-543, doi: 10.1139/cjc-2012-0536; P. Kozyra, M. Radon, J. Datka E. Broclawik Struct. Chem., 2012, 23, 1349-1356, doi: 10.1007/s11224-012-0050-y; K. Gora-Marek, A. Stepniewski, M. Radon, E. Broclawik, Phys. Chem. Chem. Phys., 2014, 16, 24089-24098, doi: 10.1039/C4CP03350G; E. Broclawik, A. Stepniewski, M. Radon, J. Inorg. Biochem., 2014, 136, 147-153, doi 10.1016/j.jinorgbio.2014.01.010.

AUTHORS
Dr hab. Mariusz Radon <mradon@chemia.uj.edu.pl>

THANKS
To Mariusz Mitoraj and Artur Michalak for valuable discussions about the NOCV method.