Timeo options are phil parameters. Edit them in Options > Settings or from the panels. All names below are relative to timeo.
General
Parameter
Default
Description
gui.location
'tools'
The tab item where the Timeo GUI appears.
gui.before
'images'
The tool before which the Timeo GUI appears.
merge_ligands
False
Merge π-bonded ligands into their centroid before measuring.
exclude_h
False
Leave hydrogen and deuterium atoms out of the coordination polyhedron.
part_codes
''
Space-separated disorder part codes, each measured as one structure. Every digit of a code is a part: 01 02 measures parts 0+1 and 0+2, 34 parts 3+4, 0 part 0 only. Leave empty to measure part 0 with each other part. See disorder.
External programs
Parameter
Default
Description
shape.exe_path
''
Explicit path to the SHAPE executable. Leave empty to search PATH.
cosmochlore.exe_path
''
Explicit path to the Cosmochlore executable. Leave empty to search PATH.
Cosmochlore: cshm
Parameter
Default
Description
cosmochlore.cshm.table
False
Write a _cshm_table.csv file next to the .xyz.
cosmochlore.cshm.ideal
False
Write a _ideal.xyz file with the reconstructed reference shapes.
Cosmochlore: csom
Parameter
Default
Description
cosmochlore.csom.point_groups
''
Default space-separated point groups for autoCSOM(), e.g. Oh D4h D3d.
cosmochlore.csom.mode
'auto'
Default centering mode: auto, first, centroid or manual.
cosmochlore.csom.vector
''
Manual centering vector x y z, used only when mode = manual.
cosmochlore.csom.full
False
Write a per-operation _details.csv file for each point group.
cosmochlore.csom.table
False
Write a _csom_table.csv summary file.
cosmochlore.csom.operated
False
Write operated .xyz/.mol2 files showing each symmetry operation applied.
cosmochlore.csom.ignore_labels
False
Ignore atom labels when matching atoms between structures.
cosmochlore.csom.seeds
20
Number of candidate symmetry-axis directions (Fibonacci hemisphere) that seed the axis search. Range 1–1000.
cosmochlore.csom.iterations
200
Maximum number of Nelder-Mead iterations spent refining each seed. Range 1–10000.
cosmochlore.csom.tolerance_exponent
6
Convergence tolerance of the Nelder-Mead refinement as a power of ten, N meaning 1e-N. Range 1–15.
Cosmochlore: odis
Parameter
Default
Description
cosmochlore.odis.full
False
Also compute CShM (OC-6/TPR-6) and CSoM against common octahedral distortions.