abaucs/stru: add UT for the case of chaotic atomic species (#854)

Add UT for PR #852 

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## Summary by CodeRabbit

* **Bug Fixes**
* Corrected the handling of per-atom properties to ensure they are
accurately matched to the correct atom indices when exporting structure
files.

* **Tests**
* Added a new test to verify proper output formatting and grouping of
atomic species, even when atomic species indices are unordered.

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---------

Signed-off-by: SuperBing <[email protected]>
Co-authored-by: SuperBing <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: root <pxlxingliang>

Author: 3 people

tests/test_abacus_stru_dump.py

@@ -206,6 +206,61 @@ def test_dump_move_from_vasp(self):
 """
         self.assertTrue(stru_ref in c)
 
+    def test_dump_chaotic_atomic_species(self):
+        import copy
+
+        import numpy as np
+
+        temp_system = copy.deepcopy(self.system_ch4)
+        temp_system.data["atom_types"] = np.array([1, 0, 1, 1, 1])
+        temp_system.data["coords"] = np.array(
+            [[[1, 1, 1], [0, 0, 0], [2, 2, 2], [3, 3, 3], [4, 4, 4]]]
+        )
+        temp_system.data["move"] = np.array(
+            [[[1, 0, 0], [0, 1, 1], [1, 1, 1], [1, 1, 1], [1, 1, 1]]]
+        )
+        velocity = np.array([[1, 1, 1], [2, 2, 2], [3, 3, 3], [4, 4, 4], [5, 5, 5]])
+        mag = np.array(
+            [[11, 11, 11], [22, 22, 22], [33, 33, 33], [44, 44, 44], [55, 55, 55]]
+        )
+        constrain = np.array([1, 0, 1, 0, 1])
+        sc = np.array([[0, 1, 1], [0, 0, 1], [1, 1, 1], [1, 1, 1], [1, 1, 1]])
+        lambda_ = np.array(
+            [
+                [0.1, 0.2, 0.3],
+                [0.4, 0.5, 0.6],
+                [0.7, 0.8, 0.9],
+                [1.0, 1.1, 1.2],
+                [1.3, 1.4, 1.5],
+            ]
+        )
+        temp_system.to(
+            "stru",
+            "STRU_tmp",
+            velocity=velocity,
+            mag=mag,
+            constrain=constrain,
+            sc=sc,
+            lambda_=lambda_,
+        )
+
+        assert os.path.isfile("STRU_tmp")
+        with open("STRU_tmp") as f:
+            lines = f.read()
+        ref_c = """C
+0.0
+1
+0.000000000000 0.000000000000 0.000000000000 0 1 1 v 2.000000000000 2.000000000000 2.000000000000 mag 22.000000000000 22.000000000000 22.000000000000 sc 0 0 1 lambda 0.400000000000 0.500000000000 0.600000000000
+H
+0.0
+4
+1.000000000000 1.000000000000 1.000000000000 1 0 0 v 1.000000000000 1.000000000000 1.000000000000 mag 11.000000000000 11.000000000000 11.000000000000 sc 0 1 1 lambda 0.100000000000 0.200000000000 0.300000000000
+2.000000000000 2.000000000000 2.000000000000 1 1 1 v 3.000000000000 3.000000000000 3.000000000000 mag 33.000000000000 33.000000000000 33.000000000000 sc 1 1 1 lambda 0.700000000000 0.800000000000 0.900000000000
+3.000000000000 3.000000000000 3.000000000000 1 1 1 v 4.000000000000 4.000000000000 4.000000000000 mag 44.000000000000 44.000000000000 44.000000000000 sc 1 1 1 lambda 1.000000000000 1.100000000000 1.200000000000
+4.000000000000 4.000000000000 4.000000000000 1 1 1 v 5.000000000000 5.000000000000 5.000000000000 mag 55.000000000000 55.000000000000 55.000000000000 sc 1 1 1 lambda 1.300000000000 1.400000000000 1.500000000000"""
+
+        self.assertTrue(ref_c in lines)
+
 
 class TestABACUSParseStru(unittest.TestCase):
     def test_parse_pos_oneline(self):