User-defined shapes

Pass your own reference polyhedra to cshm with -r/--ref, pointing to one or more YAML files. Each shape must have the same number of vertices as the structure you are analyzing.

Format

reference.yaml

symbol:
  name:
  symmetry:
  vertices:
    - [x, y, z]
    - ...
  centre:
    - [x, y, z]
 
symbol2:
  ...

A single reference.yaml file can contain several reference polyhedra. Comments are also supported by the YAML parser: every line that starts with # is ignored.

Cosmochlore’s YAML parser is somewhat flexible when specifying the key names. It accepts the following synonyms:

Key	Synonyms	Value type
symbol		name
name		name
symmetry	symm	name
vertices	ligands	[x, y, z]
centre	center, metal	[x, y, z]

Examples

File containing one shape

ebcT-6.yaml

ebcT-6:
 name: Edge-bicapped tetrahedron
 symm: D2d
 vertices:
   - [0.5000, 0.5000, -0.6495]
   - [1.0000, 1.0000, 0.0000]
   - [1.0000, 0.0000, 1.0000]
   - [0.0000, 1.0000, 1.0000]
   - [0.5000, 0.5000, 1.6495]
   - [0.0000, 0.0000, 0.0000]
 centre:
   - [0.5000, 0.5000, 0.5000]

A file with more than one shape, using key synonyms and commented-out vertices:

reference.yaml

ebcT-6:
 name: Edge-bicapped tetrahedron
 symm: D2d
 vertices:
   - [0.5000, 0.5000, -0.6495]
   - [1.0000, 1.0000, 0.0000]
   - [1.0000, 0.0000, 1.0000]
   - [0.0000, 1.0000, 1.0000]
   - [0.5000, 0.5000, 1.6495]
   - [0.0000, 0.0000, 0.0000]
 centre:
   - [0.5000, 0.5000, 0.5000]
 
fvCU-6:
 name: Face-divacant cube
 symm: C2v
 vertices:
   #    - [ 1.000000000000,  0.000000000000, -0.707106780000]
   - [0.000000000000, 1.000000000000, -0.707106780000]
   #    - [-1.000000000000,  0.000000000000, -0.707106780000]
   - [-0.000000000000, -1.000000000000, -0.707106780000]
   - [1.000000000000, 0.000000000000, 0.707106780000]
   - [0.000000000000, 1.000000000000, 0.707106780000]
   - [-1.000000000000, 0.000000000000, 0.707106780000]
   - [-0.000000000000, -1.000000000000, 0.707106780000]
 center:
   - [0.000000000000, 0.000000000000, 0.000000000000]