fix: relax atol and rtol value of padding atoms UT (#4892)

The UT of padding atoms(pytorch backend) sometimes fails like:
```
Mismatched elements: 1 / 2 (50%)
Max absolute difference among violations: 1.97471693e-08
Max relative difference among violations: 6.45619919e-07
 ACTUAL: array([[-0.236542],
       [ 0.030586]])
 DESIRED: array([[-0.236542],
       [ 0.030586]])
= 1 failed, 15442 passed, 4135 skipped, 97877 deselected, 224 warnings in 2825.25s (0:47:05) =
```

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **Tests**
- Adjusted numerical comparison assertions to use both absolute and
relative tolerances in padding-related tests.
- Aligns checks between computed results and references, improving
resilience to minor floating-point variation.
- Reduces intermittent test failures across environments and dependency
versions.
  - No impact on features, performance, or user workflows.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Author: Chengqian-Zhang

source/tests/pt/test_padding_atoms.py

@@ -49,7 +49,8 @@ def setUp(self) -> None:
         self.sel = [16, 8]
         self.rcut = 2.2
         self.rcut_smth = 0.4
-        self.atol = 1e-8
+        self.atol = 1e-6
+        self.rtol = 1e-5
 
 
 class TestPaddingAtoms(unittest.TestCase, TestCaseSingleFrameWithoutNlist):
@@ -79,6 +80,7 @@ def test_padding_atoms_consistency(self):
             to_numpy_array(result[var_name].cpu().detach()),
             np.mean(to_numpy_array(result[f"atom_{var_name}"].cpu().detach()), axis=1),
             atol=self.atol,
+            rtol=self.rtol,
         )
         # test padding atoms
         padding_atoms_list = [1, 5, 10]
@@ -105,6 +107,7 @@ def test_padding_atoms_consistency(self):
                 to_numpy_array(result[var_name].cpu().detach()),
                 to_numpy_array(result_padding[var_name].cpu().detach()),
                 atol=self.atol,
+                rtol=self.rtol,
             )