refactor: replace Logger with RunLogger and streamline logging setup

tests/environment/test_atom.py

@@ -0,0 +1,19 @@
+from diceplayer.environment import Atom
+
+import unittest
+
+
+class TestAtom(unittest.TestCase):
+    def test_class_instantiation(self):
+        atom = Atom(
+            lbl=1,
+            na=1,
+            rx=1.0,
+            ry=1.0,
+            rz=1.0,
+            chg=1.0,
+            eps=1.0,
+            sig=1.0,
+        )
+
+        self.assertIsInstance(atom, Atom)