pymatgen.command_line.mcsqs_caller module

Module to call mcsqs, distributed with AT-AT https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/

class Sqs(bestsqs, objective_function, allsqs, clusters, directory)

Bases: tuple

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

allsqs

Alias for field number 2

bestsqs

Alias for field number 0

clusters

Alias for field number 3

directory

Alias for field number 4

objective_function

Alias for field number 1

run_mcsqs(structure: Structure, clusters: dict[int, float], scaling: int | list[int] = 1, search_time: float = 60, directory: str | None = None, instances: int | None = None, temperature: int | float = 1, wr: float = 1, wn: float = 1, wd: float = 0.5, tol: float = 0.001) → Sqs

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

Parameters

• 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)

Returns

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