Merge pull request #200 from pyiron/base_test

Add two more tests for LAMMPS base

Author: jan-janssen

tests/test_ase_interface.py

@@ -12,6 +12,7 @@
     get_structure_indices,
     get_lammps_indicies_from_ase_structure,
     set_selective_dynamics,
+    UnfoldingPrism,
 )
 
 
@@ -127,6 +128,22 @@ def test_get_lammps_indicies_from_ase_structure(self):
         self.assertEqual(len(set(indicies)), 1)
         self.assertEqual(set(indicies), {1})
 
+    def test_unfolding_prism_cubic(self):
+        prism = UnfoldingPrism(self.structure_cubic.cell.array)
+        self.assertEqual(
+            prism.get_lammps_prism_str(),
+            ('8.1000000000', '8.1000000000', '8.1000000000', '0E-10', '0E-10', '0E-10')
+        )
+        self.assertTrue(np.all(np.isclose(prism.pos_to_lammps(position=[[1.0, 1.0, 1.0]]), np.array([1.0, 1.0, 1.0]))))
+
+    def test_unfolding_prism_skewed(self):
+        prism = UnfoldingPrism(self.structure_skewed.cell.array)
+        self.assertTrue(np.all(np.isclose(
+            [np.abs(float(s)) for s in prism.get_lammps_prism_str()],
+            [5.7275649276, 4.9602167291, 4.6765371804, 2.8637824638, 2.8637824638, 1.6534055764]
+        )))
+        self.assertTrue(np.all(np.isclose(prism.pos_to_lammps(position=[[1.0, 1.0, 1.0]]), np.array([1.41421356, 0.81649658, 0.57735027]))))
+
 
 class TestConstraints(unittest.TestCase):
     @classmethod
@@ -189,4 +206,4 @@ def test_selective_dynamics_wrong_plane(self):
             [2, 1, 0],
         ))
         with self.assertRaises(ValueError):
-            set_selective_dynamics(structure=atoms, calc_md=False)
+            set_selective_dynamics(structure=atoms, calc_md=False)

tests/test_base.py

@@ -26,6 +26,16 @@ def setUpClass(cls):
     def tearDownClass(cls):
         cls.lmp.close()
 
+    def test_file_not_found(self):
+        lmp = LammpsBase(
+            cores=1,
+            oversubscribe=False,
+            working_directory=".",
+            cmdargs=["-cite", self.citation_file]
+        )
+        with self.assertRaises(FileNotFoundError):
+            lmp.file("file_does_not_exist.txt")
+
     def test_extract_atom(self):
         f = self.lmp.extract_atom("f")
         self.assertEqual(len(f), 256)
@@ -52,6 +62,7 @@ def test_gather_atoms(self):
         ids = self.lmp.extract_atom("id")
         self.assertEqual(len(ids), 256)
         self.assertEqual(self.lmp.get_natoms(), 256)
+        self.assertEqual(self.lmp.natoms, 256)
 
     def test_extract_fix(self):
         x = self.lmp.extract_fix("2", 0, 1, 1)