Cosmochlore

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SHAPE 2.1

SHAPE 2.1 is software published by the Electronic Structure Group (ESG) to calculate Continuous Shape Measures. autoSHAPE is the collection of Python scripts included in Timeo to run and parse SHAPE input and output files. It does the following:

  • Generates the necessary .dat input files for SHAPE automatically.
  • Runs SHAPE and parses the resulting .tab output.
  • Outputs a summary table from the .out and .tab files.

Setup

Make sure SHAPE 2.1 is installed and either on your system PATH, or set timeo.shape.exe_path in Options > Settings. See requirements for known platform issues.

Usage

  1. autoSHAPE uses the same selection criteria as Cosmochlore. Select a single atom for a centered measurement or several for a non-centered one. See selecting atoms.
  2. Run spy.Timeo.autoSHAPE() from the Olex2 command line, or from the Tools > Timeo > SHAPE 2.1 panel.

Output

autoSHAPE does not overwrite previous runs. Each run is stored in its own folder:

<FilePath>\autoSHAPE\<FileName>_<part>_<atoms>\<run>

Octahedral Distortion

Timeo includes its own Python reimplementation of the OctaDist1 algorithm. It is separate from the one in Cosmochlore (spy.Timeo.autoODIS(), see odis and the theory page).

Unlike the original implementation, this version identifies opposite faces and vertices of an octahedron using topological criteria. It constructs a convex hull that is topologically equivalent to an octahedron and uses face-vertex relationships to identify the oposite pairs of faces.

Limitations

The algorithm may fail when more than three vertices are coplanar, because the convex hull then degenerates into a different polyhedral shape. Calculated values are generally consistent with OctaDist, but discrepancies may occur for highly distorted octahedra or for structures approaching an ideal trigonal prism.

Several features of the original OctaDist program were omitted to simplify the integration with Olex2 and to remove redundant functionality.

Usage

  1. Open a structure in Olex2.
  2. Select the central atom of a six-coordinate complex.
  3. Run spy.Timeo.autoOCTADIST() from the Olex2 console or from the Tools > Timeo panel.
  4. Results are printed in the console. A graph showing the extracted octahedron is saved in <FilePath>/OH_distortion.
1.
Ketkaew, R. et al. OctaDist: a tool for calculating distortion parameters in spin crossover and coordination complexes. Dalton Transactions 50, 1086–1096 (2021).

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