pyiron.atomistics.job.sqs module¶
-
class
pyiron.atomistics.job.sqs.SQSJob(project, job_name)[source]¶ Bases:
pyiron.atomistics.job.atomistic.AtomisticGenericJobProduces special quasirandom structures designed to duplicate truly random chemical distributions as well as possible while using finite periodic cells.
A pyiron wrapper for the [SQS code of Dominik Gehringer](https://github.com/dgehringer/sqsgenerator).
‘Structural models used in calculations of properties of substitutionally random $A_{1-x}B_x$ alloys are usually constructed by randomly occupying each of the N sites of a periodic cell by A or B. We show that it is possible to design ‘‘special quasirandom structures’’ (SQS’s) that mimic for small N (even N=8) the first few, physically most relevant radial correlation functions of a perfectly random structure far better than the standard technique does. We demonstrate the usefulness of these SQS’s by calculating optical and thermodynamic properties of a number of semiconductor alloys in the local-density formalism.’ From the abstract of Zunger, Wei, Ferreira, and Bernard, Phys. Rev. Lett. 65 (1990) 353, DOI:https://doi.org/10.1103/PhysRevLett.65.353
- Input:
- mole_fractions (dict): Approximate chemical composition for the output structure(s), using chemical symbols
as the keys and floats as the values. Values should sum to 1, but within reason will be automatically adjusted to accommodate the number of atoms in the provided structure (adjustments printed to standard out). Vacancies can also be included using the key ‘0’.
- weights (list/numpy.ndarray): Specifies the weights of the individual shells. (Default is None, which uses the
inverse of the shell number for the weight, i.e. [1, 0.5, 0.3333333333, 0.25, 0.2, 0.166666667, 0.1428571429].)
- objective (float): Specifies the value the objective functions. The program tries to reach the specified
objective function. (Default is 0.)
- iterations (int): How many iterations to make searching for the most special quasirandom structure using a
random shuffling procedure. (Default is 1e6)
- n_output_structures (int): How many different SQS structures to return (in decreasing special
quasirandomness). (Default is 1.)
Example
Case I: Get SQS for a given mole fraction:
>>> job = SQSJob(job_name='sqs') >>> job.structure = structure >>> job.input.mole_fractions = {'Al': 0.8, 'Ni':0.2} >>> job.run()
Case II: Get SQS for a given structure already containing at least 2 elements:
>>> job = SQSJob(job_name='sqs') >>> job.structure = structure >>> job.run()
In Case II, if the mole fractions will be overwritten if you specify the values (like in Case I)
-
from_hdf(hdf=None, group_name=None)[source]¶ Recreates instance from the hdf5 file :param hdf: Path to the hdf5 file :type hdf: str :param group_name: Name of the group which contains the object :type group_name: str
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get_structure(iteration_step=- 1, wrap_atoms=True)[source]¶ Gets the structure from a given iteration step of the simulation (MD/ionic relaxation). For static calculations there is only one ionic iteration step :param iteration_step: Step for which the structure is requested :type iteration_step: int :param wrap_atoms: True if the atoms are to be wrapped back into the unit cell :type wrap_atoms: bool
- Returns
The required structure
- Return type
-
property
list_of_structures¶
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publication= {'sqs': {'method': {'author': ['Zunger, A.', 'Wei, S.-H.', 'Ferreira, L.G.', 'Bernard, J.E.'], 'doi': '10.1103/PhysRevLett.65.353', 'issue': '3', 'journal': 'Phys. Rev. Lett.', 'month': 'July', 'numpages': '0', 'pages': '353', 'publisher': 'American Physical Society', 'title': 'Special quasirandom structures', 'url': 'https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.65.353', 'volume': '65'}}}¶