Initial Work on Reading Crystal and Creation Gaussian Input

tests/test_polarization.py

@@ -0,0 +1,101 @@
+from crystalpol.polarization import Polarization
+from crystalpol.shared.config import Config
+from crystalpol.shared.system.atom import Atom
+from crystalpol.shared.system.molecule import Molecule
+
+from unittest import TestCase, mock
+import unittest
+
+
+GEOM_DATA = """\
+    Cl      0.529511   -1.626652    1.247344
+    N       3.703161    2.470259    1.679277
+    Cl      0.362927   -1.511555    4.375374
+    N       3.582138    2.531106    3.906529
+"""
+
+
+class TestPolarization(TestCase):
+
+    def setUp(self):
+        self.config = Config(
+            mem=42,
+            n_atoms=2,
+            level="b3lyp/aug-cc-pVDZ"
+        )
+
+    def test_class_instantiation(self):
+        pol = Polarization("geom_file", "outfile", self.config)
+
+        self.assertIsInstance(pol, Polarization)
+
+    def test_get_molecules_from_lines(self):
+        pol = Polarization("geom_file", "outfile", self.config)
+
+        lines = [
+            "Cl      0.529511   -1.626652    1.247344",
+            "N       3.703161    2.470259    1.679277",
+            "Cl      0.362927   -1.511555    4.375374",
+            "N       3.582138    2.531106    3.906529",
+        ]
+
+        molecules = pol._get_molecules_from_lines(lines)
+
+        self.assertIsNotNone(molecules)
+        self.assertTrue(any(atom.symbol == "Cl" for atom in molecules[0]))
+        self.assertTrue(any(atom.symbol == "N " for atom in molecules[1]))
+
+    def test_get_molecules_from_lines_raises_exception(self):
+        pol = Polarization("geom_file", "outfile", self.config)
+
+        lines = [
+            "Cl      0.529511   -1.626652    1.247344",
+            "N       3.703161    2.470259    1.679277",
+            "Cl      0.362927   -1.511555    4.375374",
+            "N       3.582138    2.531106    3.906529",
+            "N       3.582138    2.531106    3.906529",
+        ]
+
+        with self.assertRaises(RuntimeError):
+            pol._get_molecules_from_lines(lines)
+
+    def test_get_crystal_structure(self):
+        pol = Polarization("geom_file", "outfile", self.config)
+
+        molecule = Molecule("TEST")
+        molecule.add_atom(
+            Atom(
+                na=1,
+                rx=0,
+                ry=0,
+                rz=0,
+            )
+        )
+
+        structure = pol._get_crystal_structure(molecule)
+        self.assertEqual(structure, ['H '])
+
+    @mock.patch('builtins.open', mock.mock_open(read_data=GEOM_DATA))
+    def test_read_crystal(self):
+        pol = Polarization("geom_file", "outfile", self.config)
+
+        pol.read_crystal()
+
+        self.assertIsNotNone(pol.crystal)
+        self.assertEqual(len(pol.crystal), 2)
+        self.assertEqual(len(pol.crystal[0]), 1)
+
+
+    @mock.patch('builtins.open', mock.mock_open(read_data=GEOM_DATA))
+    def test_run(self):
+        pol = Polarization("geom_file", "outfile", self.config)
+
+        pol.run()
+
+        self.assertIsNotNone(pol.crystal)
+        self.assertEqual(len(pol.crystal), 2)
+        self.assertEqual(len(pol.crystal[0]), 1)
+
+
+if __name__ == '__main__':
+    unittest.main()