Fix for missing lattice matches in ZSLGenerator (#3127)

* Fixed the missing upper bound in self.max_area / (film/substrate)_area due to the range() function in generate_sl_transformation_sets(). This was resulting in some film/substrate matches to be within the tolerances being ignored. See the related PR for details.

* Updated the assertion conditions in the unittests to reflect the changes made in ZSLGenerator.

Author: fyalcin

pymatgen/analysis/interfaces/tests/test_substrate_analyzer.py

@@ -30,7 +30,7 @@ def test_init(self):
         s = SubstrateAnalyzer()
 
         matches = list(s.calculate(film, substrate, film_elac))
-        assert len(matches) == 192
+        assert len(matches) == 296
         for match in matches:
             assert match is not None
             assert isinstance(match.match_area, float)

pymatgen/analysis/interfaces/tests/test_zsl.py

@@ -54,14 +54,14 @@ def test_bidirectional(self):
         z = ZSLGenerator(max_area_ratio_tol=0.05, max_angle_tol=0.05, max_length_tol=0.05)
 
         matches = list(z(self.film.lattice.matrix[:2], self.substrate.lattice.matrix[:2]))
-        assert len(matches) == 48
+        assert len(matches) == 60
 
         matches = list(z(self.substrate.lattice.matrix[:2], self.film.lattice.matrix[:2]))
-        assert len(matches) == 40
+        assert len(matches) == 52
 
         z.bidirectional = True
         matches = list(z(self.substrate.lattice.matrix[:2], self.film.lattice.matrix[:2]))
-        assert len(matches) == 48
+        assert len(matches) == 60
 
         for match in matches:
             assert match is not None

pymatgen/analysis/interfaces/zsl.py

@@ -122,13 +122,13 @@ def generate_sl_transformation_sets(self, film_area, substrate_area):
         """
         transformation_indices = [
             (ii, jj)
-            for ii in range(1, int(self.max_area / film_area))
-            for jj in range(1, int(self.max_area / substrate_area))
+            for ii in range(1, int(np.ceil(self.max_area / film_area)))
+            for jj in range(1, int(np.ceil(self.max_area / substrate_area)))
             if np.absolute(film_area / substrate_area - float(jj) / ii) < self.max_area_ratio_tol
         ] + [
             (ii, jj)
-            for ii in range(1, int(self.max_area / film_area))
-            for jj in range(1, int(self.max_area / substrate_area))
+            for ii in range(1, int(np.ceil(self.max_area / film_area)))
+            for jj in range(1, int(np.ceil(self.max_area / substrate_area)))
             if np.absolute(substrate_area / film_area - float(ii) / jj) < self.max_area_ratio_tol
         ]
         transformation_indices = list(set(transformation_indices))