odis

Computes the octahedral distortion parameters of a six-coordinate centre.

cosmochlore odis <NAME> [OPTIONS]

Important

odis needs a centred structure with exactly one central atom and six ligands (7 atoms in the .xyz file).

Options

Flag	Value	Description
-c, --center	<POSITION>	1-based position of the atom in the .xyz table that is the centre of the structure. Defaults to the first atom (position 1) when omitted.
-f, --full		Full analysis of the octahedron, including CShM (against OC-6/TPR-6) and CSoM (against the common octahedral distortion point groups) values.
-t, --table		Write the output table to a .csv file.

Examples

Distorted octahedral iron(II) complex, full analysis

Using the FeHS.xyz structure from the `cshm` example:

cosmochlore odis FeHS.xyz -t --full

Will output:

Input file: FeHS.xyz
==================================
Octahedral distortion parameters
----------------------------------
Mean d(M-X)          2.1623  Ang
Zeta                 0.3622  Ang
Delta              0.001007
Sigma                 82.29  deg
Theta                306.81  deg
Volume              12.9644  Ang^3
----------------------------------
Tau                   54.42  deg
Mu                     0.17  Ang
==================================
Writing output table to FeHS_odis_table.csv...
 
Input file: FeHS.xyz
============================================
Symbol  Shape            Symmetry   CShM
--------------------------------------------
OC-6    Octahedron       Oh         2.089
TPR-6   Trigonal prism   D3h        11.079
--------------------------------------------
Writing output table to FeHS_cshm_table.csv...
 
Input file: FeHS.xyz
========================
Point group  Deviation
------------------------
Oh           5.380
D4h          5.611
D3h          17.716
D3d          5.691
D2h          5.948
C4v          4.947
C3v          5.198
C2v          2.420
------------------------
Writing output table to FeHS_csom_table.csv...
Program finished in 922.3647ms

Passing the -t/--table flag writes the distortion parameters to a <NAME>_odis_table.csv. Passing the -f/--full flag additionally computes the CShM against the ideal octahedron and trigonal prism (OC-6, TPR-6) and the CSoM against the eight point groups most commonly seen in octahedral distortions (Oh, D4h, D3h, D3d, D2h, C4v, C3v, C2v).

Regular octahedron

An ideal FeCl6 octahedron gives zero for every distortion parameter:

FeCl6.xyz

7
XYZ file generated by Avogadro.
Fe     1.2889910070    0.2026346242   -1.6127757085
Cl1     1.1209697778    1.0253810914    0.5087540521
Cl2     2.6810029387    1.9226151063   -2.1695533400
Cl3     1.4570122351   -0.6201118472   -3.7343054675
Cl4    -0.5110376178    1.4559449613   -2.2413785693
Cl5    -0.1030209260   -1.5173458570   -1.0559980774
Cl6     3.0890196344   -1.0506757097   -0.9841728488

cosmochlore odis FeCl6.xyz

Will output:

Input file: FeCl6.xyz
==================================
Octahedral distortion parameters
----------------------------------
Mean d(M-X)          2.2817  Ang
Zeta                 0.0000  Ang
Delta              0.000000
Sigma                  0.00  deg
Theta                  0.00  deg
Volume              15.8379  Ang^3
----------------------------------
Tau                    0.00  deg
Mu                     0.00  Ang
==================================
Program finished in 356.8µs

Only the mean bond length and the volume, which describe the size of the octahedron rather than its distortion, are non-zero.