phonopy 4.2.2__tar.gz → 4.3.1__tar.gz

{phonopy-4.2.2 → phonopy-4.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phonopy
-Version: 4.2.2
+Version: 4.3.1
 Summary: This is the phonopy module.
 Author-Email: Atsushi Togo <atz.togo@gmail.com>
 License-Expression: BSD-3-Clause
@@ -14,7 +14,7 @@ Requires-Dist: matplotlib>=2.2.2
 Requires-Dist: h5py>=3.0
 Requires-Dist: spglib>=2.5
 Requires-Dist: symfc>=1.7
-Requires-Dist: phonors>=0.2.0
+Requires-Dist: phonors>=0.3.0
 Provides-Extra: cp2k
 Requires-Dist: cp2k-input-tools; extra == "cp2k"
 Provides-Extra: seekpath

phonopy-4.3.1/example/NaCl-wien2k/README.md

@@ -0,0 +1,26 @@
+# NaCl phonon calculation with Wien2k
+
+NaCl phonon calculation with Wien2k output files. The supercell structures are
+made by
+
+```bash
+% phonopy-init --wien2k -c NaCl.struct -d --dim="2 2 2" --pa auto
+```
+
+This is also done for restoring `phonopy_disp.yaml` that is used in the next step.
+`FORCE_SETS` is obtained by
+
+```bash
+% phonopy-init --wien2k -f NaCl-001.scf NaCl-002.scf
+```
+
+Phonon analysis is done such as
+
+```bash
+% phonopy-load --band "0.0 0.0 0.0  0.5 0.0 0.0  0.5 0.5 0.0  0.0 0.0 0.0  0.5 0.5 0.5" -p
+```
+or
+```bash
+% phonopy-load --band "0.0 0.0 0.0  0.5 0.0 0.0  0.5 0.5 0.0  0.0 0.0 0.0  0.5 0.5 0.5" -p -s
+```
+to save a "band.pdf" file

phonopy-4.3.1/example/NaCl-wien2k-P1/README.md

@@ -0,0 +1,26 @@
+# NaCl phonon calculation with Wien2k
+NaCl phonon calculation with Wien2k output files. The supercell structures are
+made by
+
+```bash
+% phonopy-init --wien2k -c NaCl.struct -d --dim="2 2 2" --pa auto
+```
+
+This is also done for restoring `phonopy_disp.yaml` that is used in the next step.
+`FORCE_SETS` is obtained by
+
+```bash
+% phonopy-init --wien2k -f NaCl-001.scf NaCl-002.scf
+```
+
+Phonon analysis is done such as
+
+```bash
+% phonopy-load --band "0.0 0.0 0.0  0.5 0.0 0.0  0.5 0.5 0.0  0.0 0.0 0.0  0.5 0.5 0.5" -p
+```
+or
+
+```bash
+% phonopy-load --band "0.0 0.0 0.0  0.5 0.0 0.0  0.5 0.5 0.0  0.0 0.0 0.0  0.5 0.5 0.5" -p -s
+```
+to save a "band.pdf" file

{phonopy-4.2.2 → phonopy-4.3.1}/example/Si-lammps/README.md

@@ -39,28 +39,32 @@ LAMMPS interface.
 3. Make `FORCE_SETS`
 
    ```
-   % phonopy -f lammps_forces_Si.0
+   % phonopy-init -f lammps_forces_Si.0
            _
      _ __ | |__   ___  _ __   ___   _ __  _   _
     | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
     | |_) | | | | (_) | | | | (_) || |_) | |_| |
     | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
     |_|                            |_|    |___/
-                                         2.18.0
+                                     4.3.1.dev1
 
-   Compiled with OpenMP support (max 10 threads).
-   Python version 3.11.0
-   Spglib version 2.0.2
+   -------------------------[time 2026-06-29 15:16:12]-------------------------
+   Rust backend (phonors) using rayon (10 threads).
+   Python version 3.13.11
+   Spglib version 2.7.0
 
    Calculator interface: lammps
    Displacements were read from "phonopy_disp.yaml".
+     Number of supercell files: 1
+     Number of displacements in "phonopy_disp.yaml": 1
    1. Drift force of "lammps_forces_Si.0" to be subtracted
     -0.00000000  -0.00000000  -0.00000000
    Forces parsed from LAMMPS output were rotated by F=R.F(lammps) with R:
-     0.00000 0.57735 0.57735
-     0.70711 0.57735 0.57735
-     0.70711 -0.57735 -0.57735
+     0.00000 0.81650 0.57735
+     0.70711 -0.40825 0.57735
+     0.70711 0.40825 -0.57735
    "FORCE_SETS" has been created.
+   -------------------------[time 2026-06-29 15:16:12]-------------------------
                     _
       ___ _ __   __| |
      / _ \ '_ \ / _` |

{phonopy-4.2.2 → phonopy-4.3.1}/example/Si-lammps/generate_displacements.py

@@ -7,7 +7,6 @@ from phonopy.interface.phonopy_yaml import read_cell_yaml
 cell = read_cell_yaml("phonopy_unitcell.yaml")
 ph = phonopy.load(
     unitcell=cell,
-    primitive_matrix="auto",
     supercell_matrix=[2, 2, 2],
     calculator="lammps",
 )

phonopy-4.3.1/example/Si-lammps-ace/README.md

@@ -0,0 +1,81 @@
+# Si example using LAMMPS interface (ACE potential)
+
+This example computes the phonon band structure of diamond silicon using the
+LAMMPS `pair_style pace` (atomic cluster expansion, ACE). It is a self-running
+alternative to the `polymlp`-based `Si-lammps` example: any LAMMPS build that
+includes the `ML-PACE` package can run it (for instance the conda-forge `lammps`
+package).
+
+## Potential file and license
+
+The silicon ACE potential file `Si_npj_CompMat2021.ace` is taken from the
+dataset accompanying
+
+> Y. Lysogorskiy, C. van der Oord, A. Bochkarev, S. Menon, M. Rinaldi, T.
+> Hammerschmidt, M. Mrovec, A. Thompson, G. Csanyi, C. Ortner, and R. Drautz,
+> "Performant implementation of the atomic cluster expansion (PACE) and
+> application to copper and silicon", npj Comput. Mater. 7, 97 (2021).
+
+It is distributed on Zenodo under the **CC-BY-4.0** license:
+
+> DOI: 10.5281/zenodo.4734036 (https://doi.org/10.5281/zenodo.4734036)
+
+Download `Si_npj_CompMat2021.ace` from that record into this directory before
+running LAMMPS. The file is not redistributed with phonopy; please observe the
+CC-BY-4.0 attribution terms (cite the reference above).
+
+## Lattice constant
+
+`lammps_structure_Si` uses the experimental room-temperature (~300 K) lattice
+constant of silicon, a = 5.431 A (a / 2 = 2.71550 A). The ACE equilibrium
+lattice constant differs slightly from this value, so a small residual stress
+may show up as near-zero or slightly imaginary acoustic frequencies around
+Gamma. To remove it, relax the cell with the potential first (see the
+structure-optimization appendix in the phonopy LAMMPS documentation) and use the
+relaxed constant instead.
+
+## Steps
+
+1. Generate supercells with displacements. Two equivalent routes are provided.
+
+   (a) From the LAMMPS structure file `lammps_structure_Si`:
+
+   ```
+   % phonopy-init --lammps -c lammps_structure_Si -d --dim 2 2 2
+   ```
+
+   (b) From the unit cell defined in `phonopy_unitcell.yaml`:
+
+   ```
+   % python generate_displacements.py
+   ```
+
+   Route (b) keeps the cell in its original (unrotated) orientation in
+   `phonopy_disp.yaml`, whereas route (a) reads the cell in the rotated LAMMPS
+   triclinic convention. Either way, `supercell-001` follows the LAMMPS structure
+   input format with rotated basis vectors, and the forces obtained from LAMMPS
+   are rotated back to the original coordinate system automatically in step 3.
+
+2. Run LAMMPS
+
+   ```bash
+   % lmp -in in.force
+   ```
+
+   Rename the LAMMPS output file `force.0` to `lammps_forces_Si.0`.
+
+3. Make `FORCE_SETS`
+
+   ```
+   % phonopy-init -f lammps_forces_Si.0
+   ```
+
+   The drift force (the net force on the whole supercell) is subtracted and the
+   forces are rotated back to the original orientation; the rotation matrix is
+   printed in the output.
+
+4. Plot the phonon band structure
+
+   ```
+   % phonopy --band auto -p
+   ```

phonopy-4.3.1/example/Si-lammps-ace/band.conf

@@ -0,0 +1,4 @@
+ATOM_NAME = Si
+BAND = 1/2 1/2 1/2  0 0 0  1/2 0 1/2  3/8 3/8 3/4  0 0 0
+BAND_LABELS = L \Gamma X K \Gamma
+BAND_POINTS = 101

phonopy-4.3.1/example/Si-lammps-ace/generate_displacements.py

@@ -0,0 +1,26 @@
+"""A script to generate supercells with displacements for LAMMPS.
+
+Generating the supercells from a yaml unit cell keeps the cell in its original
+(unrotated) Cartesian orientation in ``phonopy_disp.yaml``, in contrast to
+reading a LAMMPS structure file, which is given in the rotated triclinic
+convention. The generated ``supercell-001`` follows the LAMMPS structure input
+format; the forces obtained from LAMMPS are rotated back automatically when
+FORCE_SETS is created.
+
+"""
+
+import phonopy
+from phonopy.interface.calculator import write_supercells_with_displacements
+from phonopy.interface.phonopy_yaml import read_cell_yaml
+
+cell = read_cell_yaml("phonopy_unitcell.yaml")
+ph = phonopy.load(
+    unitcell=cell,
+    supercell_matrix=[2, 2, 2],  # use a larger size (e.g. [4, 4, 4]) for convergence
+    calculator="lammps",
+)
+ph.generate_displacements()
+ph.save("phonopy_disp.yaml")
+write_supercells_with_displacements(
+    "lammps", ph.supercell, ph.supercells_with_displacements
+)

phonopy-4.3.1/example/Si-lammps-ace/in.force

@@ -0,0 +1,10 @@
+units metal
+
+read_data supercell-001
+
+pair_style pace
+pair_coeff * * Si_npj_CompMat2021.ace Si
+
+dump phonopy all custom 1 force.* id type x y z fx fy fz
+dump_modify phonopy format line "%d %d %15.8f %15.8f %15.8f %15.8f %15.8f %15.8f"
+run 0

phonopy-4.3.1/example/Si-lammps-ace/lammps_structure_Si

@@ -0,0 +1,21 @@
+#
+
+2 atoms
+1 atom types
+
+0.0 3.8402969286241397 xlo xhi
+0.0 3.32579469826386 ylo yhi
+0.0 3.1355893119688574 zlo zhi
+
+1.9201484643120703 1.9201484643120703 1.1085982327546207 xy xz yz
+
+
+Atom Type Labels
+
+1 Si
+
+
+Atoms
+
+1 Si 0.0 0.0 0.0
+2 Si 1.9201484643120703 1.1085982327546202 0.7838973279922143

phonopy-4.3.1/example/Si-lammps-ace/phonopy_unitcell.yaml

@@ -0,0 +1,12 @@
+unit_cell:
+  # Experimental room-temperature (~300 K) lattice constant of silicon,
+  # a = 5.431 A, so the FCC basis vector component is a / 2 = 2.71550 A.
+  lattice:
+    - [0.000000000000000, 2.715500000000000, 2.715500000000000] # a
+    - [2.715500000000000, 0.000000000000000, 2.715500000000000] # b
+    - [2.715500000000000, 2.715500000000000, 0.000000000000000] # c
+  points:
+    - symbol: Si # 1
+      coordinates: [0.000000000000000, 0.000000000000000, 0.000000000000000]
+    - symbol: Si # 2
+      coordinates: [0.250000000000000, 0.250000000000000, 0.250000000000000]

{phonopy-4.2.2 → phonopy-4.3.1}/example/Ti-lammps/README.md

@@ -11,31 +11,40 @@ University](http://cms.mtl.kyoto-u.ac.jp/seko/mlp-repository/index.html).
 1. Read a lammps input structure file and create supercells with
 
    ```
-   % phonopy --lammps -c lammps_structure_Ti -d --dim 4 4 3
+   % phonopy-init --lammps -c lammps_structure_Ti -d --dim 4 4 3
            _
      _ __ | |__   ___  _ __   ___   _ __  _   _
-    | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
-    | |_) | | | | (_) | | | | (_) || |_) | |_| |
-    | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
-    |_|                            |_|    |___/
-                                         2.18.0
+   | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
+   | |_) | | | | (_) | | | | (_) || |_) | |_| |
+   | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
+   |_|                            |_|    |___/
+                                         4.3.1
 
-   Compiled with OpenMP support (max 10 threads).
-   Python version 3.10.8
-   Spglib version 2.0.2
+   -------------------------[time 2026-06-29 15:11:48]-------------------------
+   Rust backend (phonors) using rayon (10 threads).
+   Python version 3.13.11
+   Spglib version 2.7.0
 
    Calculator interface: lammps
    Crystal structure was read from "lammps_structure_Ti".
    Unit of length: angstrom
    Displacements creation mode
+     Systematic displacements
    Settings:
      Supercell: [4 4 3]
+     Primitive matrix:
+       [ 1.00000000e+00 -1.30752844e-17  0.00000000e+00]
+       [0. 1. 0.]
+       [0. 0. 1.]
    Spacegroup: P6_3/mmc (194)
+   Number of symmetry operations in supercell: 1152
    Use -v option to watch primitive cell, unit cell, and supercell structures.
 
+   Generated number of supercells: 1
    "phonopy_disp.yaml" and supercells have been created.
 
    Summary of calculation was written in "phonopy_disp.yaml".
+   -------------------------[time 2026-06-29 15:11:48]-------------------------
                     _
       ___ _ __   __| |
      / _ \ '_ \ / _` |
@@ -55,28 +64,32 @@ University](http://cms.mtl.kyoto-u.ac.jp/seko/mlp-repository/index.html).
 3. Make `FORCE_SETS`
 
    ```
-   % phonopy -f lammps_forces_Ti.0
+   % phonopy-init -f lammps_forces_Ti.0
            _
      _ __ | |__   ___  _ __   ___   _ __  _   _
     | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
     | |_) | | | | (_) | | | | (_) || |_) | |_| |
     | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
     |_|                            |_|    |___/
-                                         2.18.0
+                                          4.3.1
 
-   Compiled with OpenMP support (max 10 threads).
-   Python version 3.10.8
-   Spglib version 2.0.2
+   -------------------------[time 2026-06-29 15:14:24]-------------------------
+   Rust backend (phonors) using rayon (10 threads).
+   Python version 3.13.11
+   Spglib version 2.7.0
 
    Calculator interface: lammps
    Displacements were read from "phonopy_disp.yaml".
+     Number of supercell files: 1
+     Number of displacements in "phonopy_disp.yaml": 1
    1. Drift force of "lammps_forces_Ti.0" to be subtracted
     -0.00000000  -0.00000000   0.00000000
    Forces parsed from LAMMPS output were rotated by F=R.F(lammps) with R:
      1.00000 0.00000 0.00000
-     0.00000 0.00000 0.00000
-     0.00000 1.00000 1.00000
+     0.00000 1.00000 0.00000
+     0.00000 0.00000 1.00000
    "FORCE_SETS" has been created.
+   -------------------------[time 2026-06-29 15:14:24]-------------------------
                     _
       ___ _ __   __| |
      / _ \ '_ \ / _` |

{phonopy-4.2.2 → phonopy-4.3.1}/phonopy/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '4.2.2'
-__version_tuple__ = version_tuple = (4, 2, 2)
+__version__ = version = '4.3.1'
+__version_tuple__ = version_tuple = (4, 3, 1)
 
-__commit_id__ = commit_id = 'ge3a4edae1'
+__commit_id__ = commit_id = 'gbaf530aed'

{phonopy-4.2.2 → phonopy-4.3.1}/phonopy/api_phonopy.py

@@ -2514,13 +2514,17 @@ class Phonopy:
         'free_energy', 'entropy', and 'heat_capacity'.
         Each value of corresponding key is as follows:
 
-        temperatures: ndarray
+        temperatures : ndarray
+            Temperatures in K.
             shape=(temperatures, ), dtype='double'
         free_energy : ndarray
+            Helmholtz free energies in kJ/mol.
             shape=(temperatures, ), dtype='double'
         entropy : ndarray
+            Entropies in J/K/mol.
             shape=(temperatures, ), dtype='double'
         heat_capacity : ndarray
+            Heat capacities in J/K/mol.
             shape=(temperatures, ), dtype='double'
 
         .. deprecated::

{phonopy-4.2.2 → phonopy-4.3.1}/phonopy/api_qha.py

@@ -154,7 +154,7 @@ class PhonopyQHA:
         Returns
         -------
         list
-            Thermal expansion coefficients at temperatues.
+            Thermal expansion coefficients at temperatues in K^-1.
             shape=(temperatures, )
 
         """
@@ -167,7 +167,7 @@ class PhonopyQHA:
         Returns
         -------
         ndarray
-            Helmholtz free energies calculated at temperatures and volumes.
+            Helmholtz free energies calculated at temperatures and volumes in eV.
             shape=(temperatures, volumes)
 
         """
@@ -180,7 +180,7 @@ class PhonopyQHA:
         Returns
         -------
         ndarray
-            Equilibrium volumes at temperatures
+            Equilibrium volumes at temperatures in Angstrom^3.
             shape=(temperatures,), dtype=float
 
         """
@@ -193,7 +193,7 @@ class PhonopyQHA:
         Returns
         -------
         ndarray
-            Gibbs free energies at temperatures.
+            Gibbs free energies at temperatures in eV.
             shape=(temperatures, ), dtype=float
 
         """
@@ -206,7 +206,7 @@ class PhonopyQHA:
         Returns
         -------
         ndarray
-            Bulk modulus at constant pressure and temperatures
+            Bulk modulus at constant pressure and temperatures in GPa.
             shape=(temperatures, ), dtype=float
 
         """
@@ -378,7 +378,7 @@ class PhonopyQHA:
     def plot_gibbs_temperature(
         self,
         xlabel: str = "Temperature (K)",
-        ylabel: str = "Gibbs free energy",
+        ylabel: str = "Gibbs free energy (eV)",
     ) -> Any:
         """Return pyplot of Gibbs free energy vs temperature."""
         return self._qha.plot_gibbs_temperature(xlabel=xlabel, ylabel=ylabel)
@@ -392,7 +392,7 @@ class PhonopyQHA:
     def plot_bulk_modulus_temperature(
         self,
         xlabel: str = "Temperature (K)",
-        ylabel: str = "Bulk modulus",
+        ylabel: str = "Bulk modulus (GPa)",
     ) -> Any:
         """Return pyplot of bulk modulus vs temperature."""
         return self._qha.plot_bulk_modulus_temperature(xlabel=xlabel, ylabel=ylabel)

{phonopy-4.2.2 → phonopy-4.3.1}/phonopy/cui/collect_cell_info.py

@@ -151,7 +151,7 @@ def get_cell_info(
         # site-mixture (merged mixtures or weighted species), so re-applying
         # the --site-mixture weights would fail. Skip in that case; the
         # persisted cell already has the information.
-        if cell_info.unitcell.has_mixtures or cell_info.unitcell.has_weighted_species:
+        if cell_info.unitcell.is_site_mixture:
             if log_level:
                 print(
                     "Site mixture is already defined in the input cell; "

{phonopy-4.2.2 → phonopy-4.3.1}/phonopy/cui/phonopy_vasp_efe_script.py

@@ -59,9 +59,11 @@ from phonopy.qha.electron import get_free_energy_at_T
 class PhonopyVaspEfeMockArgs:
     """Mock args of ArgumentParser."""
 
+    scale_factor: float = 1.0
     tmax: float = 1000.0
     tmin: float = 0.0
     tstep: float = 10.0
+    quiet: bool = False
     filenames: Sequence[os.PathLike | str] | None = None
 
 
@@ -69,6 +71,13 @@ def get_options() -> argparse.Namespace:
     """Parse command-line options."""
     parser = argparse.ArgumentParser(description="Phonopy vasp-efe command-line-tool")
     default_vals = PhonopyVaspEfeMockArgs()
+    parser.add_argument(
+        "--scale-factor",
+        dest="scale_factor",
+        type=float,
+        default=default_vals.scale_factor,
+        help="Scaling factor for volume, energy, and free energy (default: 1.0)",
+    )
     parser.add_argument(
         "--tmax",
         dest="tmax",
@@ -90,6 +99,13 @@ def get_options() -> argparse.Namespace:
         default=default_vals.tstep,
         help="Calculated temperature step",
     )
+    parser.add_argument(
+        "--quiet",
+        dest="quiet",
+        action="store_true",
+        default=default_vals.quiet,
+        help="Suppress progress messages printed while reading vasprun.xml files",
+    )
     parser.add_argument(
         "filenames",
         nargs="*",
@@ -110,20 +126,55 @@ def get_free_energy_lines(temperatures: NDArray, free_energies: NDArray) -> list
 
 def get_fe_ev_lines(
     args: argparse.Namespace | PhonopyVaspEfeMockArgs,
+    verbose: bool = False,
 ) -> tuple[list[str], list[str]]:
-    """Return Free energy vs volume lines."""
+    """Return Free energy vs volume lines.
+
+    When ``verbose`` is True, progress is printed to stdout: which file is
+    being read and what is found in it (volume, NELECT, the k-point mesh
+    used for the electronic free energy).
+
+    """
     volumes = []
     energy_sigma0 = []
     free_energies = []
     temperatures = None
     assert args.filenames is not None
-    for filename in args.filenames:
+    filenames = list(args.filenames)
+    if verbose:
+        print(
+            "Reading %d vasprun.xml file(s), T = %g..%g K step %g K"
+            % (len(filenames), args.tmin, args.tmax, args.tstep)
+        )
+        sys.stdout.flush()
+    for i, filename in enumerate(filenames):
+        if verbose:
+            print("  [%d/%d] reading %s" % (i + 1, len(filenames), filename))
+            sys.stdout.flush()
         vxml = parse_vasprunxml(filename)
-        weights = vxml.k_weights
-        eigenvalues = vxml.eigenvalues[:, :, :, 0]
+        # With KPOINTS_OPT the electronic DOS (hence the free energy) is
+        # evaluated on the denser kpoints_opt mesh, so prefer it when present.
+        if vxml.has_kpoints_opt:
+            weights = vxml.k_weights_kpoints_opt
+            eigenvalues = vxml.eigenvalues_kpoints_opt[:, :, :, 0]
+            k_mesh = vxml.k_mesh_kpoints_opt
+            kpoints_label = "KPOINTS_OPT mesh"
+        else:
+            weights = vxml.k_weights
+            eigenvalues = vxml.eigenvalues[:, :, :, 0]
+            k_mesh = vxml.k_mesh
+            kpoints_label = "SCF mesh"
         n_electrons = vxml.NELECT
         assert n_electrons is not None
         energy = vxml.energies[-1, 1]
+        if verbose:
+            k_mesh_str = "x".join("%d" % m for m in k_mesh)
+            print(
+                "        volume = %.4f A^3, NELECT = %g, "
+                "free energy on %s (%s)"
+                % (vxml.volume[-1], n_electrons, kpoints_label, k_mesh_str)
+            )
+            sys.stdout.flush()
         temps, fe = get_free_energy_at_T(
             args.tmin, args.tmax, args.tstep, eigenvalues, weights, n_electrons
         )
@@ -135,11 +186,19 @@ def get_fe_ev_lines(
         else:
             assert (np.abs(temperatures - temps) < 1e-5).all()
     assert temperatures is not None
+    if verbose:
+        print("Done. %d volume(s) processed." % len(filenames))
+        sys.stdout.flush()
+
+    scale_factor = args.scale_factor
+    volumes = np.array(volumes) * scale_factor
+    energy_sigma0 = np.array(energy_sigma0) * scale_factor
+    free_energies = np.array(free_energies) * scale_factor
 
     lines_fe = []
     lines_fe.append(("# volume:  " + " %15.8f" * len(volumes)) % tuple(volumes))
     lines_fe.append("#    T(K)     Free energies")
-    lines_fe += get_free_energy_lines(temperatures, np.transpose(free_energies))
+    lines_fe += get_free_energy_lines(temperatures, free_energies.T)
 
     lines_ev = ["#   cell volume        energy of cell other than phonon"]
     lines_ev += [
@@ -157,7 +216,8 @@ def main(**argparse_control: PhonopyVaspEfeMockArgs) -> None:
     else:
         args = get_options()
 
-    lines_fe, lines_ev = get_fe_ev_lines(args)
+    verbose = not getattr(args, "quiet", False)
+    lines_fe, lines_ev = get_fe_ev_lines(args, verbose=verbose)
 
     with open("fe-v.dat", "w") as w:
         w.write("\n".join(lines_fe))