Input generation

The theoinp utility allows quick generation of the input information needed by TheoDORE. You can invoke theoinp using

theodore theoinp

When running theoinp, the relevant options are suggested by default and only minimal input by the user is needed. It is however advised to take a look at the program specific information for the different interfaced quantum chemistry codes. After running theoinp a list of keywords is written to the file dens_ana.in.

  optional arguments:
  ---------------------------------------------------
    -h/--help                 show this help message and exit                             



usage: theodore ... theoinp [-h]  

Input generation for TheoDORE

Molecular fragment definition

A key input quantity for the charge transfer number analysis in TheoDORE is the molecular fragment definition. First, the user has to decide on how to separate the system under study into fragments. There is no unique way to do so, and it may be necessary to try out different fragmentation schemes to produce the most meaningful results.

There are six different ways of specifying the fragment information in theoinp.

Mode for specifying molecular fragments (at_lists):
    [ 1] Manual input
    [ 2] Automatic generation by fragment (using python-openbabel)
    [ 3] Automatic generation for transition metal complexes (using python-openbabel)
    [ 4] Mixed manual/automatic generation (using python-openbabel)
    [ 5] Automatic generation by element (using python-openbabel)
    [ 6] Leave empty and fill out later

  • In mode 1 you will be asked to enter the indices of the atoms that belong to the different fragments successively.

  • Mode 2 is a special utility for automatic fragment definition. If the system of interest is composed of different molecules, these are detected automatically. Further customization can be performed by exporting the molecule in .mol format and changing the bond definitions by using for example Avogadro.

  • Mode 3 is a shortcut version of mode 2 that specifically works for transition metal complexes, see Coord. Chem. Rev., 361, 74 (2018). You simply have to add the atom of the transition metal and the system is automatically separated into the transition metal and the different ligands.

  • Mode 4 allows you to specify one or more fragments manually and applies Mode 2 for the remaining atoms.

  • Mode 5 automatically separates the list according to the different chemical elements present.

  • For mode 6 the dens_ana.in file has to be edited manually. For example, the input

at_lists = [ [1,3,4], [2,5,6] ]

means that there are two molecular fragments. The first contains atoms 1, 3, and 4, the second 2, 5, and 6.

Note: For Modes 2-4, the molecule should be given in a file format containing information about bonds, for example .mol format.