Structure Comparison

Structure Comparison#

Configuration#

[Structure Comparison]

Changed in version 2.1_TBA: In TOML, this will be [Structure_Comparison]

pydantic model eon.schema.StructureComparisonConfig[source]#

Show JSON schema
{
   "title": "StructureComparisonConfig",
   "type": "object",
   "properties": {
      "energy_difference": {
         "default": 0.01,
         "description": "How different in energy two configurations must be to be considered different structures.",
         "title": "Energy Difference",
         "type": "number"
      },
      "distance_difference": {
         "default": 0.1,
         "description": "The maximum distance two mapped atoms may be for two configurations to be considered equivalent.",
         "title": "Distance Difference",
         "type": "number"
      },
      "indistinguishable_atoms": {
         "default": true,
         "description": "Use an algorithm to compare structures that does not distinguish between atoms of the same element. The numbering of the atoms does not affect the structural comparison.",
         "title": "Indistinguishable Atoms",
         "type": "boolean"
      },
      "check_rotation": {
         "default": false,
         "description": "Finds optimal overlap of structures via rotation before comparing them. Use this option in systems where structures can become rotated, such as nanoparticles.",
         "title": "Check Rotation",
         "type": "boolean"
      },
      "brute_neighbors": {
         "default": false,
         "description": "Determine neighbors by brute force (use this with nonorthogonal boxes).",
         "title": "Brute Neighbors",
         "type": "boolean"
      },
      "neighbor_cutoff": {
         "default": 3.3,
         "description": "Atoms within this distance of each other are considered neighbors.",
         "title": "Neighbor Cutoff",
         "type": "number"
      },
      "use_covalent": {
         "default": false,
         "description": "Use the covalent radii of atoms to determine neighbors.",
         "title": "Use Covalent",
         "type": "boolean"
      },
      "covalent_scale": {
         "default": 1.3,
         "description": "Scale factor for covalent radii when determining neighbors.",
         "title": "Covalent Scale",
         "type": "number"
      },
      "remove_translation": {
         "default": true,
         "description": "Remove translational components when comparing structures.",
         "title": "Remove Translation",
         "type": "boolean"
      }
   }
}

Config:

  • use_attribute_docstrings: bool = True

Fields:
field brute_neighbors: bool = False#

Determine neighbors by brute force (use this with nonorthogonal boxes).

field check_rotation: bool = False#

Finds optimal overlap of structures via rotation before comparing them. Use this option in systems where structures can become rotated, such as nanoparticles.

field covalent_scale: float = 1.3#

Scale factor for covalent radii when determining neighbors.

field distance_difference: float = 0.1#

The maximum distance two mapped atoms may be for two configurations to be considered equivalent.

field energy_difference: float = 0.01#

How different in energy two configurations must be to be considered different structures.

field indistinguishable_atoms: bool = True#

Use an algorithm to compare structures that does not distinguish between atoms of the same element. The numbering of the atoms does not affect the structural comparison.

field neighbor_cutoff: float = 3.3#

Atoms within this distance of each other are considered neighbors.

field remove_translation: bool = True#

Remove translational components when comparing structures.

field use_covalent: bool = False#

Use the covalent radii of atoms to determine neighbors.

References#

Contents