add test for NEBAnalysis.get_plot() (#3570)

Author: janosh

pymatgen/analysis/transition_state.py

@@ -166,32 +166,25 @@ def get_plot(self, normalize_rxn_coordinate: bool = True, label_barrier: bool =
             plt.Axes: matplotlib axes object.
         """
         ax = pretty_plot(12, 8)
-        scale = 1 if not normalize_rxn_coordinate else 1 / self.r[-1]
-        x = np.arange(0, np.max(self.r), 0.01)
-        y = self.spline(x) * 1000
+        scale = 1 / self.r[-1] if normalize_rxn_coordinate else 1
+        xs = np.arange(0, np.max(self.r), 0.01)
+        ys = self.spline(xs) * 1000
         relative_energies = self.energies - self.energies[0]
-        ax.plot(
-            self.r * scale,
-            relative_energies * 1000,
-            "ro",
-            x * scale,
-            y,
-            "k-",
-            linewidth=2,
-            markersize=10,
-        )
-        ax.set_xlabel("Reaction coordinate")
+        ax.plot(self.r * scale, relative_energies * 1000, "ro", xs * scale, ys, "k-", linewidth=2, markersize=10)
+
+        ax.set_xlabel("Reaction Coordinate")
         ax.set_ylabel("Energy (meV)")
-        ax.set_ylim((np.min(y) - 10, np.max(y) * 1.02 + 20))
+        ax.set_ylim((np.min(ys) - 10, np.max(ys) * 1.02 + 20))
         if label_barrier:
-            data = zip(x * scale, y)
+            data = zip(xs * scale, ys)
             barrier = max(data, key=lambda d: d[1])
-            ax.plot([0, barrier[0]], [barrier[1], barrier[1]], "k--")
+            ax.plot([0, barrier[0]], [barrier[1], barrier[1]], "k--", linewidth=0.5)
             ax.annotate(
-                f"{np.max(y) - np.min(y):.0f} meV",
+                f"{np.max(ys) - np.min(ys):.0f} meV",
                 xy=(barrier[0] / 2, barrier[1] * 1.02),
                 xytext=(barrier[0] / 2, barrier[1] * 1.02),
                 horizontalalignment="center",
+                fontsize=18,
             )
         plt.tight_layout()
         return ax

tests/analysis/test_transition_state.py

@@ -2,6 +2,7 @@
 
 import json
 
+from matplotlib import pyplot as plt
 from numpy.testing import assert_allclose
 
 from pymatgen.analysis.transition_state import NEBAnalysis, combine_neb_plots
@@ -19,12 +20,12 @@
 __date__ = "2/5/16"
 
 
-test_dir = f"{TEST_FILES_DIR}/neb_analysis"
+TEST_DIR = f"{TEST_FILES_DIR}/neb_analysis"
 
 
 class TestNEBAnalysis(PymatgenTest):
     def test_run(self):
-        neb_analysis1 = NEBAnalysis.from_dir(f"{test_dir}/neb1/neb")
+        neb_analysis1 = NEBAnalysis.from_dir(f"{TEST_DIR}/neb1/neb")
         neb_analysis1_from_dict = NEBAnalysis.from_dict(neb_analysis1.as_dict())
         json_data = json.dumps(neb_analysis1.as_dict())
 
@@ -47,7 +48,7 @@ def test_run(self):
 
         neb_analysis1.setup_spline(spline_options={"saddle_point": "zero_slope"})
         assert_allclose(neb_analysis1.get_extrema()[1][0], (0.50023335723480078, 325.20003984140203))
-        with open(f"{test_dir}/neb2/neb_analysis2.json") as f:
+        with open(f"{TEST_DIR}/neb2/neb_analysis2.json") as f:
             neb_analysis2_dict = json.load(f)
         neb_analysis2 = NEBAnalysis.from_dict(neb_analysis2_dict)
         assert_allclose(neb_analysis2.get_extrema()[1][0], (0.37255257367467326, 562.40825334519991))
@@ -56,6 +57,15 @@ def test_run(self):
         assert_allclose(neb_analysis2.get_extrema()[1][0], (0.30371133723478794, 528.46229631648691))
 
     def test_combine_neb_plots(self):
-        neb_dir = f"{test_dir}/neb1/neb"
+        neb_dir = f"{TEST_DIR}/neb1/neb"
         neb_analysis = NEBAnalysis.from_dir(neb_dir)
         combine_neb_plots([neb_analysis, neb_analysis])
+
+    def test_get_plot(self):
+        neb_dir = f"{TEST_DIR}/neb1/neb"
+        neb_analysis = NEBAnalysis.from_dir(neb_dir)
+        ax = neb_analysis.get_plot()
+        assert isinstance(ax, plt.Axes)
+        assert ax.texts[0].get_text() == "326 meV", "Unexpected annotation text"
+        assert ax.get_xlabel() == "Reaction Coordinate"
+        assert ax.get_ylabel() == "Energy (meV)"