pymatgen.command_line.mcsqs_caller module¶
Module to call mcsqs, distributed with AT-AT https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/
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class
Sqs
(bestsqs: pymatgen.core.structure.Structure, objective_function: Union[float, str], allsqs: List, clusters: List, directory: str)[source]¶ Bases:
tuple
Return type for run_mcsqs.
Create new instance of Sqs(bestsqs, objective_function, allsqs, clusters, directory)
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bestsqs
: pymatgen.core.structure.Structure[source]¶ Alias for field number 0
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run_mcsqs
(*args, **kwargs) → 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
- Parameters
scaling (int or list) –
- Scaling factor to determine supercell. Two options are possible:
(preferred) Scales number of atoms, e.g., for a structure with 8 atoms, scaling=4 would lead to a 32 atom supercell
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