fix PBC bug

tests/test_datasets.py

@@ -75,6 +75,10 @@ def test_datasets_h5py(tmp_path, dataset, request):
         assert "observables/atoms/mlip_energy_2/value" in f
         assert "observables/atoms/mlip_stress/value" in f
 
+        npt.assert_array_equal(
+            f["particles/atoms/box"].attrs["boundary"], ["none", "none", "none"]
+        )
+
 
 def test_two_datasets(tmp_path, s22_all_properties, s22_mixed_pbc_cell):
     io_a = znh5md.IO(tmp_path / "test.h5", particle_group="a")
@@ -110,3 +114,23 @@ def test_two_datasets_external(tmp_path, s22_all_properties, s22_mixed_pbc_cell)
 
         assert len(io_a) == len(s22_all_properties)
         assert len(io_b) == len(s22_mixed_pbc_cell)
+
+
+def test_pbc(tmp_path, s22_mixed_pbc_cell):
+    io = znh5md.IO(tmp_path / "test.h5")
+    io.extend(s22_mixed_pbc_cell)
+
+    pbc = ["periodic" if x else "none" for x in io[0].pbc]
+
+    with h5py.File(tmp_path / "test.h5", "r") as f:
+        assert "/particles/atoms/position/value" in f
+        assert "/particles/atoms/box" in f
+
+        npt.assert_array_equal(f["particles/atoms/box"].attrs["boundary"], pbc)
+        for idx, atom in enumerate(s22_mixed_pbc_cell):
+            npt.assert_array_equal(
+                f["particles/atoms/box/edges/value"][idx], atom.get_cell()
+            )
+            # Do we want to rename "pbc" to "boundary" and make if "none" or "periodic" as well?
+            # This should only exist if requested
+            npt.assert_array_equal(f["particles/atoms/box/pbc/value"][idx], atom.pbc)

tests/test_read_write.py

@@ -1,3 +1,5 @@
+import ase
+import numpy as np
 import numpy.testing as npt
 import pytest
 
@@ -33,3 +35,15 @@ def test_append_false(tmp_path, s22_all_properties):
     znh5md.write(file, s22_all_properties)
     with pytest.raises(FileExistsError):
         znh5md.write(file, s22_all_properties, append=False)
+
+
+def test_write_H(tmp_path):
+    n_atoms = 10
+    images = [
+        ase.Atoms("H" * n_atoms, positions=np.random.rand(n_atoms, 3))
+        for _ in range(10000)
+    ]
+    file = tmp_path / "test.h5"
+    znh5md.write(file, images)
+    atoms = znh5md.read(file)
+    assert atoms == images[-1]

znh5md/io.py

@@ -204,8 +204,9 @@ def _create_particle_group(self, f, data):
         self._create_group(g_particle_grp, "position", data.positions, "Angstrom")
         self._create_group(g_particle_grp, "box/edges", data.cell)
         g_particle_grp["box"].attrs["dimension"] = 3
-        boundary = [["periodic" if y else "none" for y in x] for x in data.pbc]
-        g_particle_grp["box"].attrs["boundary"] = boundary
+        g_particle_grp["box"].attrs["boundary"] = [
+            "periodic" if y else "none" for y in data.pbc[0]
+        ]
 
         if self.pbc_group and data.pbc is not None:
             self._create_group(g_particle_grp, "box/pbc", data.pbc)