structuretoolkit.analyse.pyscal.find_solids

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structuretoolkit.analyse.pyscal.find_solids#

structuretoolkit.analyse.pyscal.find_solids(structure: Atoms, neighbor_method: str = 'cutoff', cutoff: float = 0.0, bonds: float = 0.5, threshold: float = 0.5, avgthreshold: float = 0.6, cluster: bool = False, q: int = 6, right: bool = True, return_sys: bool = False) → int | Any[source]#

Get the number of solids or the corresponding pyscal system. Calls necessary pyscal methods as described in https://pyscal.org/en/latest/methods/03_solidliquid.html.

Parameters:

  • structure (Atoms) – The structure to analyze.

  • neighbor_method (str, optional) – Method used to get neighborlist. See pyscal documentation. Defaults to “cutoff”.

  • cutoff (float, optional) – Adaptive if 0. Defaults to 0.

  • bonds (float, optional) – Number or fraction of bonds to consider atom as solid. Defaults to 0.5.

  • threshold (float, optional) – See pyscal documentation. Defaults to 0.5.

  • avgthreshold (float, optional) – See pyscal documentation. Defaults to 0.6.

  • cluster (bool, optional) – See pyscal documentation. Defaults to False.

  • q (int, optional) – Steinhard parameter to calculate. Defaults to 6.

  • right (bool, optional) – See pyscal documentation. Defaults to True.

  • return_sys (bool, optional) – Whether to return number of solid atoms or pyscal system. Defaults to False.

Returns:

Number of solids or pyscal system when return_sys=True.

Return type:

Union[int, pyscal.system.System]

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