Fix: make box smaller for no pbc structure (#84)

* fix: make box smaller for no pbc structure * Update src/mattersim/datasets/utils/convertor.py Co-authored-by: Han Yang <[email protected]> * chore: remove redundant --------- Co-authored-by: Han Yang <[email protected]>
microsoft · Feb 5, 2025 · f1028e5 · f1028e5
1 parent 4a07e10
commit f1028e5
Showing 1 changed file with 19 additions and 9 deletions.
diff --git a/src/mattersim/datasets/utils/convertor.py b/src/mattersim/datasets/utils/convertor.py
@@ -193,16 +193,26 @@ def convert(
                 min_z = np.min(atoms.positions[:, 2])
                 max_x = np.max(atoms.positions[:, 0])
                 max_y = np.max(atoms.positions[:, 1])
-                max_z = np.max(atoms.positions[:, 2])
-                x_len = max((max_x - min_x) * 10, 1000)
-                y_len = max((max_y - min_y) * 10, 1000)
-                z_len = max((max_z - min_z) * 10, 1000)
-                lattice_matrix = np.array(
-                    [[x_len, 0.0, 0.0], [0.0, y_len, 0.0], [0.0, 0.0, z_len]],
-                    dtype=float,
-                )
+                max_z = np.max(atoms.positions[:, 2])      
+                x_len = (max_x - min_x) + max(
+                    self.twobody_cutoff, self.threebody_cutoff
+                ) * 5
+                y_len = (max_y - min_y) + max(
+                    self.twobody_cutoff, self.threebody_cutoff
+                ) * 5
+                z_len = (max_z - min_z) + max(
+                    self.twobody_cutoff, self.threebody_cutoff
+                ) * 5
+                max_len = max(x_len, y_len, z_len)
+                x_len = y_len = z_len = max_len
+                lattice_matrix = np.eye(3) * max_len
                 pbc_ = np.array([1, 1, 1], dtype=int)
-                warnings.warn("No PBC detected, using a large supercell", UserWarning)
+                warnings.warn(
+                    "No PBC detected, using a large supercell with "
+                    f"size {x_len}x{y_len}x{z_len} Angstrom**3",
+                    UserWarning,
+                )
+
                 atoms.set_cell(lattice_matrix)
                 atoms.set_pbc(pbc_)
             else: