pymatgen.command_line.mcsqs_caller module

Module to call mcsqs, distributed with AT-AT

class Sqs(bestsqs, objective_function, allsqs, clusters, directory)[source]

Bases: tuple

Return type for run_mcsqs. bestsqs: Structure objective_function: Union[float, str] allsqs: List clusters: List directory: str


Alias for field number 2


Alias for field number 0


Alias for field number 3


Alias for field number 4


Alias for field number 1

run_mcsqs(structure: pymatgen.core.structure.Structure, clusters: Dict[int, float], scaling: Union[int, List[int]] = 1, search_time: float = 60, directory: Optional[str] = None, instances: Optional[int] = None, temperature: Union[int, float] = 1, wr: float = 1, wn: float = 1, wd: float = 0.5, tol: float = 0.001)pymatgen.command_line.mcsqs_caller.Sqs[source]

Helper function for calling mcsqs with different arguments :param structure: Disordered pymatgen Structure object :type structure: Structure :param clusters: Dictionary of cluster interactions with entries in the form

number of atoms: cutoff in angstroms

  • scaling (int or list) –

    Scaling factor to determine supercell. Two options are possible:
    1. (preferred) Scales number of atoms, e.g., for a structure with 8 atoms, scaling=4 would lead to a 32 atom supercell

    2. A sequence of three scaling factors, e.g., [2, 1, 1], which specifies that the supercell should have dimensions 2a x b x c

    Defaults to 1.

  • search_time (float) – Time spent looking for the ideal SQS in minutes (default: 60)

  • directory (str) – Directory to run mcsqs calculation and store files (default: None runs calculations in a temp directory)

  • instances (int) – Specifies the number of parallel instances of mcsqs to run (default: number of cpu cores detected by Python)

  • temperature (int or float) – Monte Carlo temperature (default: 1), “T” in atat code

  • wr (int or float) – Weight assigned to range of perfect correlation match in objective function (default = 1)

  • wn (int or float) – Multiplicative decrease in weight per additional point in cluster (default: 1)

  • wd (int or float) – Exponent of decay in weight as function of cluster diameter (default: 0.5)

  • tol (int or float) – Tolerance for matching correlations (default: 1e-3)


Tuple of Pymatgen structure SQS of the input structure, the mcsqs objective function,

list of all SQS structures, and the directory where calculations are run