Add tests for periodic module

Author: marco-2023

atomdb/__init__.py

@@ -24,6 +24,8 @@
 
 from atomdb.promolecule import *
 
+from atomdb.periodic import *
+
 
 __version__ = version
 r"""AtomDB version string."""

atomdb/test/test_periodic.py

@@ -0,0 +1,121 @@
+import pytest
+import numpy as np
+from atomdb.periodic import num2sym, sym2num, name2num, num2name, Atom
+
+
+def test_num2sym():
+    assert num2sym[1] == "H"
+    assert num2sym[6] == "C"
+    assert num2sym[26] == "Fe"
+
+
+def test_sym2num():
+    assert sym2num["H"] == 1
+    assert sym2num["C"] == 6
+    assert sym2num["Fe"] == 26
+
+
+def name2num():
+    assert sym2num["hydrogen"] == 1
+    assert sym2num["carbon"] == 6
+    assert sym2num["iron"] == 26
+
+    assert sym2num["Hydrogen"] == 1
+    assert sym2num["Carbon"] == 6
+    assert sym2num["Iron"] == 26
+
+
+def num2name():
+    assert sym2num[1] == "Hydrogen"
+    assert sym2num[6] == "Carbon"
+    assert sym2num[26] == "Iron"
+
+
+def test_atom_invalid_element():
+    with pytest.raises(Exception):
+        Atom("InvalidElement")
+
+
+def test_atom_invalid_symbol():
+    with pytest.raises(Exception):
+        Atom("AA")
+
+
+def test_atom_invalid_atnum():
+    with pytest.raises(Exception):
+        Atom(-2)
+
+
+def test_atom_invalid_charge():
+    with pytest.raises(Exception):
+        Atom(1, charge=2)
+    with pytest.raises(Exception):
+        Atom(1, charge=1.5)
+    with pytest.raises(Exception):
+        Atom(112, charge=-10)
+
+
+def test_get_attributes():
+    # will test getting the attributes of the atom for Hydrogen and Carbon
+
+    atom = Atom(1)
+    assert atom.atnum == 1
+    assert atom.atsym == "H"
+    assert atom.atname == "Hydrogen"
+    assert atom.charge == 0
+
+    h_data = {
+        "atnum": 1,
+        "atsym": "H",
+        "atname": "Hydrogen",
+        "charge": 0,
+        "group": 1,
+        "period": 1,
+        "multiplicity": 2,
+        "cov_radius": {"cordero": 0.31, "bragg": np.nan, "slater": 0.25},
+        "vdw_radius": {
+            "bondi": 1.2,
+            "truhlar": np.nan,
+            "rt": 1.1,
+            "batsanov": np.nan,
+            "dreiding": 3.195,
+            "uff": 2.886,
+            "mm3": 1.62,
+        },
+        "at_radius": {"wc": 0.529192875, "cr": 0.53},
+        "eneg": {"pauling": 2.2},
+        "pold": {"crc": 0.666793, "chu": 4.5},
+        "c6": {"chu": 6.499026705},
+        "mass": {"stb": 1.007975},
+    }
+    for i in h_data:
+        assert getattr(atom, i) == h_data[i]
+
+    atom = Atom(6)
+    c_data = {
+        "atnum": 6,
+        "atsym": "C",
+        "atname": "Carbon",
+        "charge": 0,
+        "group": 14,
+        "period": 2,
+        "multiplicity": 3,
+        "cov_radius": {"cordero": 0.7445337366, "bragg": 0.77, "slater": 0.7},
+        "vdw_radius": {
+            "bondi": 1.7,
+            "truhlar": np.nan,
+            "rt": 1.77,
+            "batsanov": 1.7,
+            "dreiding": 3.8983,
+            "uff": 3.851,
+            "mm3": 2.04,
+        },
+        "at_radius": {"wc": 0.62, "cr": 0.67},
+        "eneg": {"pauling": 2.55},
+        "pold": {"crc": 1.76, "chu": 12.0},
+        "c6": {"chu": 46.6},
+        "mass": {"stb": 12.0106},
+    }
+
+    for i in c_data:
+        assert getattr(atom, i) == c_data[i]