Cosmochlore in Timeo

Cosmochlore is developed to function either as a standalone CLI tool or as a background process to Timeo. Timeo wraps three of its subcommands. Each one writes its output next to the structure and prints the results table to the Olex2 console.

Function	Cosmochlore command	Description
spy.Timeo.autoCSHM()	cshm	Continuous Shape Measures against the built-in and user-defined reference polyhedra.
spy.Timeo.autoCSOM()	csom	Continuous Symmetry Operation Measures against a list of point groups.
spy.Timeo.autoODIS()	odis	Octahedral distortion parameters. Select the central atom of a six-coordinate complex.

Every option has a phil parameter, editable in Options > Settings or from the panel itself. See settings. Most options of Cosmochlore are accessible through the GUI.

Note

The gidx command is not wrapped by Timeo.

Usage

1. Open a structure in Olex2.
2. Select the atoms to include. One atom gives a centered shape, several atoms give a non-centered shape. See selecting atoms.
3. Run a function from the console or from the Tools > Timeo > Cosmochlore panel.
4. Results are printed to the console and saved in <FilePath>/cosmochlore/.

autoCSHM

Runs cshm. Two options control the extra files:

• timeo.cosmochlore.cshm.table: write _cshm_table.csv next to the .xyz.
• timeo.cosmochlore.cshm.ideal: write _ideal.xyz with the reconstructed reference shapes.

User-defined shapes

Reference shapes beyond the built-in ones can be added as .yaml files in the user_shapes/ folder of the plugin. The CShM panel has an Open user defined shapes folder button. The file format is described in user-defined shapes. A mismatched vertex count is reported as an error by Cosmochlore itself.

autoCSOM

Runs csom. Point groups are given as a space-separated list, for example Oh D4h D3d.

Option	Description
point_groups	Default list of point groups to test.
mode	Centering mode: auto, first, centroid or manual.
vector	Manual centering vector x y z, used only when mode = manual.
full, table, operated	Write the per-operation details, the summary table and the operated structures.
ignore_labels	Ignore atom labels when matching atoms between structures.
seeds	Number of candidate symmetry-axis directions that seed the axis search (default 20).
iterations	Maximum Nelder-Mead iterations per seed (default 200).
tolerance_exponent	Convergence tolerance as a power of ten, N meaning 1e-N (default 6).

autoODIS

Runs odis on the selected central atom of a six-coordinate complex. With timeo.cosmochlore.odis.full it also computes CShM (OC-6/TPR-6) and CSoM against common octahedral distortions, and timeo.cosmochlore.odis.table writes _odis_table.csv.

This is independent of Timeo’s own octahedral distortion implementation.