assyst.plot

Helper plotting functions.

assyst.plot.aspect_ratio_histogram(structures: list[Atoms], **kwargs)[source]

Plot histogram of cell aspect ratios (max / min lattice parameter).

Parameters:
Returns:

Return value of matplotlib.pyplot.hist()

assyst.plot.concentration_histogram(structures: list[Atoms], elements: Iterable[str] | None = None, **kwargs)[source]

Plot histogram of concentrations.

Parameters:

  • structures (list of ase.Atoms) – structures to plot

  • elements (iterable of str) – which element concentrations to plot, by default all present

  • **kwargs – passed through to seaborn.histplot()

assyst.plot.distance_histogram(structures: list[Atoms], rmax: float = 6.0, reduce: Literal['min', 'mean'] | Callable[[Iterable[float]], float] | None = 'min', **kwargs)[source]

Plot histogram of per-atom volumes.

Parameters:

  • structures (list of ase.Atoms) – structures to plot

  • rmax (float) – maximum cutoff to consider neighborhood

  • reduce (callable from array of floats to float) – applied to the neighbor distances per structure, and should reduce a single scalar that is binned; if None plot all atomic distances concatenated

  • **kwargs – passed through to matplotlib.pyplot.hist()

Returns:

Return value of matplotlib.pyplot.hist()

assyst.plot.energy_distance(structures: list[Atoms], rmax: float = 6.0, reduce: Literal['min', 'mean'] | Callable[[Iterable[float]], float] = 'min', **kwargs)[source]

Plot energy per atom versus neighbor distance.

Requires that ase.calculators.singlepoint.SinglePointCalculator are attached to the atoms, either from a relaxation for final training set calculation.

Parameters:

  • structures (list of ase.Atoms) – structures to plot

  • rmax (float) – maximum cutoff to consider neighborhood

  • reduce (callable from array of floats to float) – applied to the neighbor distances per structure to reduce them to a single scalar; "min" and "mean" are recognized as shortcuts; structures with no neighbors within rmax are silently skipped

  • **kwargs – passed through to matplotlib.pyplot.scatter() or matplotlib.pyplot.hexbin()

assyst.plot.energy_histogram(structures: list[Atoms], **kwargs)[source]

Plot energy per atom histogram.

Requires that ase.calculators.singlepoint.SinglePointCalculator are attached to the atoms, either from a relaxation for final training set calculation.

Parameters:
Returns:

Return value of matplotlib.pyplot.hist()

assyst.plot.energy_volume(structures: list[Atoms], **kwargs)[source]

Plot energy per atom versus volume per atom.

Requires that ase.calculators.singlepoint.SinglePointCalculator are attached to the atoms, either from a relaxation for final training set calculation.

Parameters:
assyst.plot.lattice_angle_histogram(structures: list[Atoms], **kwargs)[source]

Plot histogram of lattice angles alpha, beta, and gamma.

Parameters:

  • structures (list of ase.Atoms) – structures to plot

  • **kwargs – passed through to seaborn.histplot()

assyst.plot.lattice_parameter_histogram(structures: list[Atoms], **kwargs)[source]

Plot histogram of lattice parameters a, b, and c.

Parameters:

  • structures (list of ase.Atoms) – structures to plot

  • **kwargs – passed through to seaborn.histplot()

assyst.plot.radial_distribution(structures: list[Atoms], rmax: float = 6.0, **kwargs)[source]

Plot radial distribution of neighbors in training set.

Calculates all neighbors in all structures and histograms them together. Bins are weighted by 1/(4 pi r^2), but because the density in each structure can be different, the plot does not yield something that can be directly compared to a Radial Distribution Function. It can be used to locate prefered bonding distances or sampling of the radial neighborhood in a training set given suitable data.

Parameters:
Returns:

Return value of matplotlib.pyplot.hist()

assyst.plot.size_histogram(structures: list[Atoms], **kwargs)[source]

Plot histogram of number of atoms.

Parameters:
Returns:

Return value of matplotlib.pyplot.hist()

assyst.plot.volume_histogram(structures: list[Atoms], **kwargs)[source]

Plot histogram of per-atom volumes.

Parameters:
Returns:

Return value of matplotlib.pyplot.hist()