Initial Work on Reading Crystal and Creation Gaussian Input

tests/shared/system/test_atom.py

@@ -0,0 +1,19 @@
+from crystalpol.shared.system.atom import Atom
+
+import unittest
+
+
+class TestAtom(unittest.TestCase):
+    def test_atom_instantiation(self):
+        atom = Atom(
+            na=1,
+            rx=0,
+            ry=0,
+            rz=0,
+        )
+
+        self.assertIsInstance(atom, Atom)
+
+
+if __name__ == '__main__':
+    unittest.main()

tests/shared/system/test_crystal.py

@@ -0,0 +1,102 @@
+import unittest
+
+from crystalpol.shared.system.atom import Atom
+from crystalpol.shared.system.crystal import Crystal
+from crystalpol.shared.system.molecule import Molecule
+
+
+class TestCrystal(unittest.TestCase):
+    def test_class_instantiation(self):
+        # Note that this is not a valid crystal
+        crystal_structure = [
+            ['H']
+        ]
+
+        crystal = Crystal(crystal_structure)
+
+        self.assertIsInstance(crystal, Crystal)
+
+    def test_is_valid_cell(self):
+        crystal_structure = [
+            ['H ']
+        ]
+
+        crystal = Crystal(crystal_structure)
+
+        molecule = Molecule("TESTE")
+        molecule.add_atom(
+            Atom(
+                na=1,
+                rx=0,
+                ry=0,
+                rz=0,
+            )
+        )
+
+        self.assertTrue(crystal._is_valid_cell([molecule]))
+
+        molecule.add_atom(
+            Atom(
+                na=1,
+                rx=0,
+                ry=0,
+                rz=0,
+            )
+        )
+
+        self.assertFalse(crystal._is_valid_cell([molecule]))
+
+    def test_add_cell(self):
+        # Note that this is not a valid crystal
+        crystal_structure = [
+            ['H ']
+        ]
+
+        crystal = Crystal(crystal_structure)
+
+        molecule = Molecule("TESTE")
+        molecule.add_atom(
+            Atom(
+                na=1,
+                rx=0,
+                ry=0,
+                rz=0,
+            )
+        )
+
+        crystal.add_cell([molecule])
+
+        self.assertIsInstance(crystal, Crystal)
+
+    def test_add_cell_raises_exception(self):
+        # Note that this is not a valid crystal
+        crystal_structure = [
+            ['H ']
+        ]
+
+        crystal = Crystal(crystal_structure)
+
+        molecule = Molecule("TESTE")
+        molecule.add_atom(
+            Atom(
+                na=1,
+                rx=0,
+                ry=0,
+                rz=0,
+            )
+        )
+        molecule.add_atom(
+            Atom(
+                na=1,
+                rx=0,
+                ry=0,
+                rz=0,
+            )
+        )
+
+        with self.assertRaises(ValueError):
+            crystal.add_cell([molecule])
+
+
+if __name__ == '__main__':
+    unittest.main()

tests/shared/system/test_molecule.py

@@ -0,0 +1,87 @@
+from crystalpol.shared.system.molecule import Molecule
+from crystalpol.shared.system.atom import Atom
+
+import io
+
+import unittest
+
+
+class TestMolecule(unittest.TestCase):
+    def test_class_instantiation(self):
+        molecule = Molecule("TEST")
+
+        self.assertEqual(molecule.mol_name, "TEST")
+        self.assertIsInstance(molecule, Molecule)
+
+    def test_add_atom(self):
+        molecule = Molecule("TEST")
+
+        atom = Atom(
+            na=1,
+            rx=0,
+            ry=0,
+            rz=0,
+        )
+
+        molecule.add_atom(atom)
+
+        self.assertEqual(len(molecule.atoms), 1)
+        self.assertEqual(molecule.atoms[0], atom)
+
+    def test_update_charges(self):
+        molecule = Molecule("TEST")
+
+        atom = Atom(
+            na=1,
+            rx=0,
+            ry=0,
+            rz=0,
+        )
+
+        molecule.add_atom(atom)
+
+        molecule.update_charges([1])
+
+        self.assertEqual(molecule.atoms[-1].chg, 1)
+
+    def test_update_charges_raises_exception(self):
+        molecule = Molecule("TEST")
+
+        atom = Atom(
+            na=1,
+            rx=0,
+            ry=0,
+            rz=0,
+        )
+
+        molecule.add_atom(atom)
+
+        with self.assertRaises(ValueError):
+            molecule.update_charges([1, 1])
+
+    def test_print_mol_info(self):
+        molecule = Molecule("TEST")
+
+        atom = Atom(
+            na=1,
+            rx=0,
+            ry=0,
+            rz=0,
+        )
+
+        molecule.add_atom(atom)
+
+        with io.StringIO() as file:
+            molecule.print_mol_info(file)
+
+            file.seek(0)
+            info_string = file.read()
+
+        self.assertIsNotNone(info_string)
+        self.assertTrue(len(info_string) > 0)
+        self.assertTrue("Molecule Name: TEST" in info_string)
+        self.assertTrue("H    r: [0, 0, 0]    charge: None" in info_string)
+
+
+if __name__ == '__main__':
+    unittest.main()