`ccu.fancyplots.data`¶

Classes for the storage of FancyPlots relevant data.

The class ccu.fancyplots.data.FancyCache describes how data is imported to and exported from FancyPlots.

The class ccu.fancyplots.data.FEDData defines how free energy diagram is stored.

The class ccu.fancyplots.data.FormattingParameters defines how plot formatting parameters are stored.

The class ccu.fancyplots.data.Annotation defines how plot annotations are stored.

Examples

The internal data from FancyPlots can be accessed via the attribute ccu.fancyplots._gui.root.FancyPlotsGUI.cache and dumped into a human-readable form via the following idiom:

>>> import json
>>> from pathlib import Path
>>> from ccu.fancyplots.data import DEFAULT_PARAMETERS
>>> from ccu.fancyplots.data import FancyCache
>>> data = {
...     "energy_data": [
...         [0, 0.2, 0.33, -0.5],
...         [0, -0.1, 0.25, 0],
...     "mechanism": ["*", "*CHOO", "*CO", "CO"],
...     "legend_labels: ["Cu(111)", "Cu-NP"],
>>> annotations = []
>>> formatting_parameters = DEFAULT_PARAMETERS
>>> cache = FancyCache(
...     formatting_parameters,
...     diagram_data=data,
...     annotations=annotations,
...)
>>> with Path("fancy.cache").open(
...     mode="w", encoding="utf-8"
... ) as file:  
...     _ = json.dump(cache, file, indent=2)

The same file (fancy.cache) can be loaded into a convenient format for FancyPlots via the following idiom:

>>> import json
>>> from pathlib import Path
>>> from ccu.fancyplots.data import FancyCache
>>> with Path("fancy.cache").open(  
...     mode="r", encoding="utf-8"
... ) as file:
...     cache = FancyCache(**json.load(file))

class ccu.fancyplots.data.Annotation(color: str = 'k', fontsize: float = 11.2, text: str = '', x: float = 0.0, y: float = 0.0)[source]¶

Bases: NamedTuple

A free energy diagram annotation.

Variables:

color (str) – The color to use for the annotation.
fontsize (float) – The fontsize to use for the annotation.
text (str) – The annotation text.
x (float) – The x-coordinate of the annotation.
y (float) – The y-coordinate of the annotation.

Create new instance of Annotation(color, fontsize, text, x, y)

_asdict()¶: Return a new dict which maps field names to their values.

_field_defaults = {'color': 'k', 'fontsize': 11.2, 'text': '', 'x': 0.0, 'y': 0.0}¶

_fields = ('color', 'fontsize', 'text', 'x', 'y')¶

classmethod _make(iterable)¶: Make a new Annotation object from a sequence or iterable

_replace(**kwds)¶: Return a new Annotation object replacing specified fields with new values

color: str¶: Alias for field number 0

fontsize: float¶: Alias for field number 1

text: str¶: Alias for field number 2

x: float¶: Alias for field number 3

y: float¶: Alias for field number 4

ccu.fancyplots.data.DEFAULT_PARAMETERS = {'boxsize': (6, 4.5), 'colors': ('black', 'blue', 'red', 'lime', 'fuchsia'), 'dpi': 1200, 'font': 'Sans Serif', 'fontsize': 14, 'legend_loc': 'best', 'linewidth': 2.25, 'markeredgewidth': 0.3, 'markersize': 7, 'savename': 'fed.svg', 'tick_dec': 2, 'tick_double': False, 'tick_loc': 'out', 'tick_min': 0, 'title': '', 'xlabel': 'Reaction Coordinate', 'xlim': None, 'xscale': None, 'ylabel': '$\\Delta$G / eV', 'ylim': None, 'yscale': 'linear'}¶: The default formatting parameters for FancyPlots

class ccu.fancyplots.data.FEDData[source]¶

Bases: TypedDict

Energies and metadata for a free energy diagram.

Variables:

energy_data (list[list[float | None]]) – A list of lists. Each list defines energies for each step in the mechanism.
mechanism (list[str]) – The labels for each mechanism step.
legend_labels (list[str | None]) – The legend labels for each pathway.

Valid ccu.fancyplots.data.FEDData instances should satisfy the following condition for seamless use with FancyPlots:

The lengths of each element in ccu.fancyplots.data.FEDData.energy_data should be equal to the lengths of ccu.fancyplots.data.FEDData.mechanism and ccu.fancyplots.data.FEDData.legend_labels. This translates to the condition that the number of energies defined for each step should equal the number of steps in the mechanism.

energy_data: list[list[float | None]]¶

legend_labels: list[str | None]¶

mechanism: list[str]¶

class ccu.fancyplots.data.FancyCache(style_parameters: FormattingParameters, diagram_data: FEDData, annotations: list[Annotation])[source]¶

Bases: object

The data model for caching/loading data into FancyPlots.

Variables:

style_parameters (ccu.fancyplots.data.FormattingParameters) – The formatting parameters to use to plot the free energy diagram.
diagram_data (ccu.fancyplots.data.FEDData) – The energy data and metadata for plotting the free energy diagram.
annotations (list[ccu.fancyplots.data.Annotation]) – The annotations associated with the free energy diagram.