fix(gromacs): preserve first-seen element order

dpdata/formats/gromacs/gro.py

@@ -77,7 +77,12 @@ def file_to_system_data(fname: FileType, format_atom_name=True, **kwargs):
                 posis = np.array(posis)
                 if frame == 1:
                     system["orig"] = np.zeros(3)
-                    system["atom_names"] = list(set(names))
+                    # A .gro file does not carry a separate atom-type table.  When
+                    # callers do not provide ``type_map``, infer that table from
+                    # the first occurrence of each atom name.  ``dict`` preserves
+                    # insertion order, unlike ``set`` whose hash-dependent order
+                    # could silently change the type IDs used by later exporters.
+                    system["atom_names"] = list(dict.fromkeys(names))
                     system["atom_numbs"] = [
                         names.count(ii) for ii in system["atom_names"]
                     ]

tests/gromacs/type_order.gro

@@ -0,0 +1,7 @@
+Generated with MDTraj, t= 0.0
+ 4
+    1MOL     LI    1   0.254   0.254   0.024
+    2MOL     CL    2   0.507   0.000   0.000
+    3MOL      P    3   0.507   0.507   0.507
+    4MOL     S1    4   0.896   0.389   0.118
+   1.01400   1.01400   1.01400   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000

tests/test_gromacs_gro.py

@@ -7,6 +7,16 @@
 
 
 class TestGromacsGro(unittest.TestCase):
+    def test_infer_atom_types_in_first_seen_order(self):
+        # Without an explicit type_map, atom names define the type IDs in the
+        # order in which they first occur in the .gro file. Checking membership
+        # alone would miss the order regression reported for this conversion.
+        system = dpdata.System("gromacs/type_order.gro")
+
+        self.assertEqual(system["atom_names"], ["Li", "Cl", "P", "S"])
+        self.assertEqual(system["atom_numbs"], [1, 1, 1, 1])
+        self.assertEqual(system["atom_types"].tolist(), [0, 1, 2, 3])
+
     def test_read_file(self):
         system = dpdata.System("gromacs/1h.gro", type_map=["H", "O"])
         self.assertTrue("H" in system["atom_names"])