fix: infer optional CALYPSO inputs

dpgen2/exploration/task/caly_task_group.py

@@ -144,12 +144,19 @@ def set_params(
             self.atomic_number = [atomic_symbols.index(i) for i in self.name_of_atoms]
         else:
             self.name_of_atoms = name_of_atoms
-            self.atomic_number = atomic_number
-
-        if isinstance(distance_of_ions, dict):
+            self.atomic_number = (
+                [atomic_number_map[name] for name in self.name_of_atoms]
+                if atomic_number is None
+                else atomic_number
+            )
+
+        if distance_of_ions is None or isinstance(distance_of_ions, dict):
+            # Generate a complete distance matrix from the maintained
+            # covalent-radius table when the optional matrix is omitted.
             updated_table = copy.deepcopy(covalent_radii)
-            for key, value in distance_of_ions.items():
-                updated_table[atomic_number_map[key]] = value
+            if isinstance(distance_of_ions, dict):
+                for key, value in distance_of_ions.items():
+                    updated_table[atomic_number_map[key]] = value
 
             temp_distance_mtx = np.zeros((numb_of_species, numb_of_species))
             for i in range(numb_of_species):

tests/exploration/test_make_task_group_from_config.py

@@ -126,3 +126,18 @@ def test_make_caly_input(self):
     def test_caly_task_group(self):
         tgroup = make_calypso_task_group_from_config(self.config)
         self.assertTrue(isinstance(tgroup, CalyTaskGroup))
+
+    def test_infers_optional_atomic_numbers_and_distances(self):
+        """Generate CALYPSO-required values when optional fields are absent."""
+        config = {
+            "name_of_atoms": ["Li", "La"],
+            "numb_of_atoms": [10, 10],
+            "numb_of_species": 2,
+        }
+
+        task_group = make_calypso_task_group_from_config(config)
+
+        self.assertEqual(task_group.atomic_number, [3, 57])
+        self.assertEqual(task_group.distance_of_ions.shape, (2, 2))
+        self.assertTrue(np.all(task_group.distance_of_ions > 0))
+        self.assertEqual(len(task_group.make_task()), 1)