diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 49bbb3a..d018172 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -10,7 +10,7 @@ repos:
   - id: check-added-large-files
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.6.2
+  rev: v0.6.3
   hooks:
   - id: ruff
     args: [ "--fix", "--show-fixes" ]
diff --git a/src/phelel/base/Dij_qij.py b/src/phelel/base/Dij_qij.py
index 5ec4a84..a808b8b 100644
--- a/src/phelel/base/Dij_qij.py
+++ b/src/phelel/base/Dij_qij.py
@@ -633,7 +633,7 @@ def run(self, Dij_per, Dij_disps, qij_per, qij_disps, displacements, lm_channels
 
     def _allocate_arrays(self, ncdij, lmdim):
         dtype = "c%d" % (np.dtype("double").itemsize * 2)
-        natom = self._supercell.get_number_of_atoms()
+        natom = len(self._supercell)
         shape = (ncdij, len(self.atom_indices), 3, natom, lmdim, lmdim)
         self._dDijdu = np.zeros(shape, dtype=dtype, order="C")
         self._dqijdu = np.zeros(shape, dtype=dtype, order="C")
diff --git a/src/phelel/file_IO.py b/src/phelel/file_IO.py
index 2f9a8e8..89060b9 100644
--- a/src/phelel/file_IO.py
+++ b/src/phelel/file_IO.py
@@ -112,7 +112,7 @@ def read_phelel_params_hdf5(
                 cell=f["supercell_lattice"][:].T,
                 scaled_positions=f["supercell_positions"][:],
                 symbols=[atom_data[n][1] for n in f["supercell_numbers"][:]],
-                masses=f["supercell_masses"],
+                masses=f["supercell_masses"][:],
             )
             symmetry = Symmetry(supercell)
             if "atom_indices_in_derivatives" in f:
@@ -131,7 +131,7 @@ def read_phelel_params_hdf5(
 
         if log_level:
             print(f'dV/du was read from "{filename}".')
-            print('dDij/du was read from "{filename}".')
+            print(f'dDij/du was read from "{filename}".')
     else:
         raise FileNotFoundError(f'"{filename}" was not found.')
 
diff --git a/src/phelel/velph/cli/phono3py/init.py b/src/phelel/velph/cli/phono3py/init.py
index 0b832d1..5a91393 100644
--- a/src/phelel/velph/cli/phono3py/init.py
+++ b/src/phelel/velph/cli/phono3py/init.py
@@ -27,7 +27,10 @@ def run_init(
     """
     convcell = parse_cell_dict(toml_dict["unitcell"])
     supercell_matrix = toml_dict["phelel"].get("supercell_dimension", None)
-    phonon_supercell_matrix = toml_dict["phonopy"].get("supercell_dimension", None)
+    if "phonopy" in toml_dict:
+        phonon_supercell_matrix = toml_dict["phonopy"].get("supercell_dimension", None)
+    else:
+        phonon_supercell_matrix = None
     if "primitive_cell" in toml_dict:
         primitive = parse_cell_dict(toml_dict["primitive_cell"])
         primitive_matrix = np.dot(np.linalg.inv(convcell.cell.T), primitive.cell.T)
diff --git a/test/velph/cli/phono3py/init/test_phono3py_init.py b/test/velph/cli/phono3py/init/test_phono3py_init.py
index 0f1586c..cb97d7e 100644
--- a/test/velph/cli/phono3py/init/test_phono3py_init.py
+++ b/test/velph/cli/phono3py/init/test_phono3py_init.py
@@ -16,7 +16,8 @@ def test_phono3py_init_random_displacements(distance: float):
 supercell_dimension = [4, 4, 2]
 amplitude = {distance}
 fft_mesh = [18, 18, 28]
-[vasp.supercell.incar]
+
+[vasp.phonopy.incar]
 lwap = true
 isym = 0
 kpar = 2
@@ -31,7 +32,7 @@ def test_phono3py_init_random_displacements(distance: float):
 lcharg = false
 addgrid = true
 lsorbit = true
-[vasp.supercell.kpoints]
+[vasp.phonopy.kpoints]
 mesh = [6, 6, 7]
 
 [unitcell]