pyiron.atomistics.structure.pyscal module

pyiron.atomistics.structure.pyscal.analyse_centro_symmetry(atoms, num_neighbors=12)

Analyse centrosymmetry parameter

Parameters

• atoms – Atoms object

• num_neighbors (int) – number of neighbors

Returns

list of centrosymmetry parameter

Return type

csm (list)

pyiron.atomistics.structure.pyscal.analyse_cna_adaptive(atoms, mode='total', ovito_compatibility=False)

Use common neighbor analysis

Parameters

• atoms (pyiron.structure.atoms.Atoms) – The structure to analyze.

• mode ("total"/"numeric"/"str") –

  Controls the style and level of detail of the output. - total : return number of atoms belonging to each structure - numeric : return a per atom list of numbers- 0 for unknown,

  1 fcc, 2 hcp, 3 bcc and 4 icosa

  • str : return a per atom string of sructures

• ovito_compatibility (bool) – use ovito compatiblity mode

Returns

(depends on mode)

pyiron.atomistics.structure.pyscal.analyse_diamond_structure(atoms, mode='total', ovito_compatibility=False)

Analyse diamond structure

Parameters

• atoms – Atoms object

• mode ("total"/"numeric"/"str") – Controls the style and level

• detail of the output. (of) –

  • total : return number of atoms belonging to each structure

  • numericreturn a per atom list of numbers- 0 for unknown,

    1 fcc, 2 hcp, 3 bcc and 4 icosa

  • str : return a per atom string of sructures

• ovito_compatibility (bool) – use ovito compatiblity mode

Returns

(depends on mode)

pyiron.atomistics.structure.pyscal.analyse_voronoi_volume(atoms)

Calculate the Voronoi volume of atoms

Parameters

atoms – (pyiron.structure.atoms.Atoms): The structure to analyze.

pyiron.atomistics.structure.pyscal.get_steinhardt_parameter_structure(atoms, neighbor_method='cutoff', cutoff=0, n_clusters=2, q=(4, 6), averaged=False, clustering=True)

Calculate Steinhardts parameters

Parameters

• atoms – Atoms object

• neighbor_method (str) – can be [‘cutoff’, ‘voronoi’]

• cutoff (float) – can be 0 for adaptive cutoff or any other value

• n_clusters (int) – number of clusters for K means clustering

• q (list) – can be from 2-12, the required q values to be calculated

• averaged (bool) – If True, calculates the averaged versions of the parameter

• clustering (bool) – If True, cluster based on the q values

Returns

calculated q parameters

Return type

q (list)

pyiron.atomistics.structure.pyscal.publication()