fix: DistanceConfFilter is optimized and the bug in BoxSkewnessConfFilter is fixed. (#292)

The DistanceConfFilter is optimized and the bug in BoxSkewnessConfFilter
is fixed.

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

- **Bug Fixes**
- Improved accuracy of hydrogen distance checks by updating the safe
distance value.
- Enhanced structure validation by refining lattice length and skewness
checks for better symmetry handling.

- **Refactor**
- Streamlined distance and lattice checks to operate directly on the
original structure, improving efficiency and reliability.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: Carrotkingdom

dpgen2/exploration/selector/distance_conf_filter.py

@@ -21,7 +21,7 @@
 )
 
 safe_dist_dict = {
-    "H": 1.2255,
+    "H": 0.612,
     "He": 0.936,
     "Li": 1.8,
     "Be": 1.56,
@@ -169,16 +169,48 @@ def check(
             pbc=(not frame.nopbc),
         )
 
-        P = [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
-        extended_structure = make_supercell(structure, P)
-
-        coords = extended_structure.positions
-        symbols = extended_structure.get_chemical_symbols()
+        coords = structure.positions
+        symbols = structure.get_chemical_symbols()
+        cell, _ = structure.get_cell().standard_form()
+        cell = cell.array
+
+        a1 = cell[0]
+        a2 = cell[1]
+        a3 = cell[2]
+
+        all_combinations = {
+            "a1": np.linalg.norm(a1),
+            "a2": np.linalg.norm(a2),
+            "a3": np.linalg.norm(a3),
+            "a1+a2": np.linalg.norm(a1 + a2),
+            "a1+a3": np.linalg.norm(a1 + a3),
+            "a2+a3": np.linalg.norm(a2 + a3),
+            "a1-a2": np.linalg.norm(a1 - a2),
+            "a1-a3": np.linalg.norm(a1 - a3),
+            "a2-a3": np.linalg.norm(a2 - a3),
+            "a1+a2+a3": np.linalg.norm(a1 + a2 + a3),
+            "a1+a2-a3": np.linalg.norm(a1 + a2 - a3),
+            "a1-a2+a3": np.linalg.norm(a1 - a2 + a3),
+            "a1-a2-a3": np.linalg.norm(a1 - a2 - a3),
+            "-a1+a2+a3": np.linalg.norm(-a1 + a2 + a3),
+            "-a1+a2-a3": np.linalg.norm(-a1 + a2 - a3),
+            "-a1-a2+a3": np.linalg.norm(-a1 - a2 + a3),
+            "-a1-a2-a3": np.linalg.norm(-a1 - a2 - a3),
+        }
+
+        A = list(all_combinations.values())
+        B = [safe_dist[type_i] * 2 for type_i in symbols]
+
+        for a in A:
+            for b in B:
+                if a < b:
+                    print(f"Lattice length {a:.3f} is less than safe distance {b:.3f} ")
+                    return False
 
         num_atoms = len(coords)
         for i in range(num_atoms):
             for j in range(i + 1, num_atoms):
-                dist = extended_structure.get_distance(i, j, mic=True)
+                dist = structure.get_distance(i, j, mic=True)
                 type_i = symbols[i]
                 type_j = symbols[j]
                 dr = safe_dist[type_i] + safe_dist[type_j]
@@ -269,9 +301,9 @@ def check(
         cell, _ = structure.get_cell().standard_form()
 
         if (
-            cell[1][0] > np.tan(self.theta / 180.0 * np.pi) * cell[1][1]  # type: ignore
-            or cell[2][0] > np.tan(self.theta / 180.0 * np.pi) * cell[2][2]  # type: ignore
-            or cell[2][1] > np.tan(self.theta / 180.0 * np.pi) * cell[2][2]  # type: ignore
+            np.abs(cell[1][0]) > np.tan(self.theta / 180.0 * np.pi) * cell[1][1]  # type: ignore
+            or np.abs(cell[2][0]) > np.tan(self.theta / 180.0 * np.pi) * cell[2][2]  # type: ignore
+            or np.abs(cell[2][1]) > np.tan(self.theta / 180.0 * np.pi) * cell[2][2]  # type: ignore
         ):
             logging.warning("Inclined box")
             return False