class VoronoiAnalysisTest(PymatgenTest): def setUp(self): self.ss = Xdatcar(os.path.join(test_dir, 'XDATCAR.MD')).structures self.s = self.ss[19] self.va = VoronoiAnalysis(cutoff=4.0) def test_voronoi_analysis(self): # Check for the Voronoi index of site i in Structure single_structure = self.va.voronoi_analysis(self.s, n=5) self.assertIn(single_structure.view(), np.array([5,4,2,5,3,1,0,2]).view(), "Cannot find the right polyhedron.") # Check for the presence of a Voronoi index and its frequency in # a ensemble (list) of Structures ensemble = self.va.from_structures(self.ss,step_freq=2,most_frequent_polyhedra=10) self.assertIn(('[2 3 3 3 1 1 0 0]', 6), ensemble, "Cannot find the right polyhedron in ensemble.")
def setUp(self): self.ss = Xdatcar(os.path.join(test_dir, 'XDATCAR.MD')).structures self.s = self.ss[19] self.va = VoronoiAnalysis(cutoff=4.0)