Plotly Support (#195)

* plot fed * plot fef * plot fed * plot fed * plot fed * plot fed * remove uid * remove uid * moved phase plot * moved phase plot * moved phase plot * moved phase plot * moved phase plot * plot tests plot tests plot tests plot tests plot tests * plot tests * plot tests
materialsproject · May 21, 2024 · 8a44d47 · 8a44d47
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diff --git a/pymatgen/analysis/defects/plotting/phases.py b/pymatgen/analysis/defects/plotting/phases.py
@@ -1,142 +1,6 @@
 """Plotting functions for competing phases."""
 
-from __future__ import annotations
+# Contents moved to pymatgen.analysis.defects.plotting.thermo
+from .thermo import plot_chempot_2d
 
-import logging
-from typing import TYPE_CHECKING
-
-from matplotlib import pyplot as plt
-from matplotlib.patches import Polygon
-from pymatgen.util.string import latexify
-from scipy.spatial import ConvexHull
-
-if TYPE_CHECKING:
-    from matplotlib.axes import Axes
-    from pymatgen.analysis.defects.thermo import FormationEnergyDiagram
-    from pymatgen.core import Element
-
-# check if labellines is installed
-try:
-    from labellines import labelLines
-except ImportError:
-
-    def labelLines(*args, **kwargs) -> None:  # noqa: ARG001, ANN002
-        """Dummy function if labellines is not installed."""
-
-
-__author__ = "Jimmy Shen"
-__copyright__ = "Copyright 2022, The Materials Project"
-__maintainer__ = "Jimmy Shen @jmmshn"
-__date__ = "July 2023"
-
-logger = logging.getLogger(__name__)
-
-
-def plot_chempot_2d(
-    fed: FormationEnergyDiagram,
-    x_element: Element,
-    y_element: Element,
-    ax: Axes | None = None,
-    min_mu: float = -5.0,
-    label_lines: bool = False,
-    x_vals: list[float] | None = None,
-    label_fontsize: int = 12,
-) -> None:
-    """Plot the chemical potential diagram for two elements.
-
-    Args:
-        fed:
-            The formation energy diagram.
-        x_element:
-            The element to use for the x-axis.
-        y_element:
-            The element to use for the y-axis.
-        ax:
-            The matplotlib axes to plot on. If None, a new figure will be created.
-        min_mu:
-            The minimum chemical potential to plot.
-        label_lines:
-            Whether to label the lines with the competing phases. Requires Labellines to be installed.
-        x_vals:
-            The x position of the line labels. If None, defaults will be used.
-        label_fontsize:
-            The fontsize for the line labels.
-    """
-    PLOT_PADDING = 0.1
-    ax = ax or plt.gca()
-    hull2d = _convex_hull_2d(
-        fed.chempot_limits,
-        x_element=x_element,
-        y_element=y_element,
-        competing_phases=fed.competing_phases,
-    )
-    x_min = float("inf")
-    y_min = float("inf")
-    clip_path = []
-    for p1, p2, phase in hull2d:
-        p_txt = ", ".join(map(latexify, phase.keys()))
-        ax.axline(p1, p2, label=p_txt, color="k")
-        ax.scatter(p1[0], p1[1], color="k")
-        x_m_ = p1[0] if p1[0] > min_mu else float("inf")
-        y_m_ = p1[1] if p1[1] > min_mu else float("inf")
-        x_min = min(x_min, x_m_)
-        y_min = min(y_min, y_m_)
-        clip_path.append(p1)
-
-    patch = Polygon(
-        clip_path,
-        closed=True,
-    )
-    ax.add_patch(patch)
-
-    ax.set_xlabel(rf"$\Delta\mu_{{{x_element}}}$ (eV)")
-    ax.set_ylabel(rf"$\Delta\mu_{{{y_element}}}$ (eV)")
-    ax.set_xlim(x_min - PLOT_PADDING, 0 + PLOT_PADDING)
-    ax.set_ylim(y_min - PLOT_PADDING, 0 + PLOT_PADDING)
-    if label_lines:
-        labelLines(ax.get_lines(), align=False, xvals=x_vals, fontsize=label_fontsize)
-
-
-def _convex_hull_2d(
-    points: list[dict],
-    x_element: Element,
-    y_element: Element,
-    competing_phases: list | None = None,
-) -> list:
-    """Compute the convex hull of a set of points in 2D.
-
-    Args:
-        points:
-            A list of dictionaries with keys "x" and "y" and values as floats.
-        x_element:
-            The element to use for the x-axis.
-        y_element:
-            The element to use for the y-axis.
-        tol:
-            The tolerance for determining if two points are the same in the 2D plane.
-        competing_phases:
-            A list of competing phases for each point.
-
-    Returns:
-        A list of dictionaries with keys "x" and "y" that form the vertices of the
-        convex hull.
-    """
-    if competing_phases is None:
-        competing_phases = [None] * len(points)
-    xy_points = [(pt[x_element], pt[y_element]) for pt in points]
-    hull = ConvexHull(xy_points)
-    xy_hull = [xy_points[i] for i in hull.vertices]
-
-    def _get_line_data(i1: int, i2: int) -> tuple:
-        cp1 = competing_phases[hull.vertices[i1]]
-        cp2 = competing_phases[hull.vertices[i2]]
-        shared_keys = cp1.keys() & cp2.keys()
-        shared_phase = {k: cp1[k] for k in shared_keys}
-        return xy_hull[i1], xy_hull[i2], shared_phase
-
-    # return all pairs of points:
-    pt_and_phase = [
-        _get_line_data(itr - 1, itr) for itr in range(1, len(hull.vertices))
-    ]
-    pt_and_phase.append(_get_line_data(len(hull.vertices) - 1, 0))
-    return pt_and_phase
+__all__ = ["plot_chempot_2d"]