phonopy 4.2.2__tar.gz → 4.3.0__tar.gz

{phonopy-4.2.2 → phonopy-4.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phonopy
-Version: 4.2.2
+Version: 4.3.0
 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-4.3.0/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-4.3.0/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-4.3.0}/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 = '4.3.0'
+__version_tuple__ = version_tuple = (4, 3, 0)
 
-__commit_id__ = commit_id = 'ge3a4edae1'
+__commit_id__ = commit_id = 'g2193d7f65'

{phonopy-4.2.2 → phonopy-4.3.0}/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-4.3.0}/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-4.3.0}/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-4.3.0}/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))

{phonopy-4.2.2 → phonopy-4.3.0}/phonopy/cui/show_symmetry.py

@@ -36,6 +36,7 @@
 
 import numpy as np
 import spglib
+from numpy.typing import NDArray
 
 try:
     spglib.error.OLD_ERROR_HANDLING = False
@@ -51,9 +52,10 @@ from phonopy.interface.calculator import (
 from phonopy.interface.phonopy_yaml import PhonopyYaml
 from phonopy.structure.atoms import PhonopyAtoms
 from phonopy.structure.cells import (
+    argsort_by_key,
     determinant,
     guess_primitive_matrix,
-    sort_positions_by_symbols,
+    raise_if_suffixed_symbols,
 )
 from phonopy.structure.symmetry import Symmetry
 
@@ -74,22 +76,12 @@ def check_symmetry(phonon: Phonopy, cell_info: PhonopyCellInfoResult):
     spglib_cell = spglib.refine_cell(phonon.primitive.totuple(), symprec)
     assert spglib_cell is not None
     bravais_lattice, bravais_pos, bravais_numbers = spglib_cell
-    _, _, _, perm = sort_positions_by_symbols(bravais_numbers)
-    if phonon.primitive.has_mixtures:
-        # spglib returns species_ids verbatim when the input has mixtures, so
-        # rebuild PhonopyAtoms via the species table instead of atomic numbers.
-        bravais = PhonopyAtoms(
-            species_table=phonon.primitive.species_table,
-            species_ids=bravais_numbers[perm],
-            scaled_positions=bravais_pos[perm],
-            cell=bravais_lattice,
-        )
-    else:
-        bravais = PhonopyAtoms(
-            numbers=bravais_numbers[perm],
-            scaled_positions=bravais_pos[perm],
-            cell=bravais_lattice,
-        )
+    bravais = _rebuild_bravais_cell(
+        phonon.primitive,
+        np.array(bravais_lattice, dtype="double"),
+        np.array(bravais_pos, dtype="double"),
+        np.array(bravais_numbers, dtype="int64"),
+    )
     trans_mat = guess_primitive_matrix(bravais, symprec=symprec)
     ph = Phonopy(
         bravais,
@@ -128,6 +120,37 @@ def check_symmetry(phonon: Phonopy, cell_info: PhonopyCellInfoResult):
         _show_symmetry_yaml(phonon, cell_info, base_fname, ph)
 
 
+def _rebuild_bravais_cell(
+    cell: PhonopyAtoms,
+    bravais_lattice: NDArray[np.double],
+    bravais_pos: NDArray[np.double],
+    bravais_numbers: NDArray[np.int64],
+) -> PhonopyAtoms:
+    """Rebuild the refined Bravais cell from a spglib ``refine_cell`` result.
+
+    For site-mixture cells ``totuple`` hands species ids (not atomic
+    numbers) to spglib, so ``bravais_numbers`` are species ids and the
+    species table of ``cell`` must be used to restore symbols, masses, and
+    mixture weights (both merged mixtures and weighted species). Ordinary
+    cells map the returned atomic numbers directly.
+
+    """
+    perm = argsort_by_key(bravais_numbers)
+    if cell.is_site_mixture:
+        return PhonopyAtoms(
+            species_table=cell.species_table,
+            species_ids=bravais_numbers[perm],
+            scaled_positions=bravais_pos[perm],
+            cell=bravais_lattice,
+        )
+    raise_if_suffixed_symbols(cell)
+    return PhonopyAtoms(
+        numbers=bravais_numbers[perm],
+        scaled_positions=bravais_pos[perm],
+        cell=bravais_lattice,
+    )
+
+
 def _show_symmetry_yaml(
     phonon: Phonopy, cell_info: PhonopyCellInfoResult, base_fname: str, ph: Phonopy
 ):

{phonopy-4.2.2 → phonopy-4.3.0}/phonopy/harmonic/derivative_dynmat.py

@@ -242,7 +242,7 @@ class DerivativeOfDynamicalMatrix:
                 reclat,
                 self._svecs,
                 self._multi,
-                self._dynmat.scaled_masses,
+                self._dynmat.normalization_masses,
                 self._s2p_map,
                 self._p2s_map,
                 nac_factor,
@@ -262,7 +262,7 @@ class DerivativeOfDynamicalMatrix:
                 np.array(np.linalg.inv(self._pcell.cell), dtype="double", order="C"),
                 self._svecs,
                 self._multi,
-                self._dynmat.scaled_masses,
+                self._dynmat.normalization_masses,
                 self._s2pp_map,
                 np.arange(len(self._p2s_map), dtype="int64"),
                 nac_factor,
@@ -354,7 +354,7 @@ class DerivativeOfDynamicalMatrix:
             reclat,
             self._svecs,
             self._multi,
-            self._dynmat.scaled_masses,
+            self._dynmat.normalization_masses,
             s2_for_inner,
             fc_row,
             born=born if kernel_is_nac else None,
@@ -411,7 +411,7 @@ class DerivativeOfDynamicalMatrix:
 
         # Mass weighting: the kernel returns without 1/sqrt(m_k m_k'),
         # matching the value-side `get_recip_dipole_dipole` convention.
-        inv_sqrt_m = 1.0 / np.sqrt(self._dynmat.scaled_masses)
+        inv_sqrt_m = 1.0 / np.sqrt(self._dynmat.normalization_masses)
         mass_pair = np.outer(inv_sqrt_m, inv_sqrt_m)
         dd *= mass_pair[None, :, None, :, None]
 
@@ -447,7 +447,8 @@ class DerivativeOfDynamicalMatrix:
             s_j = self._p2s_map[j]
             fc_row = s_i if is_full_fc else i
             mass = np.sqrt(
-                self._dynmat.scaled_masses[i] * self._dynmat.scaled_masses[j]
+                self._dynmat.normalization_masses[i]
+                * self._dynmat.normalization_masses[j]
             )
             ddm_local = np.zeros((num_elem, 3, 3), dtype=np.cdouble)
 
@@ -656,7 +657,7 @@ class DerivativeOfDynamicalMatrix:
             d_dd += ZTZ * C * phase_pair[None, :, None, :, None]
 
         # Mass weighting 1 / sqrt(m_k m_kp)
-        inv_sqrt_m = 1.0 / np.sqrt(self._dynmat.scaled_masses)
+        inv_sqrt_m = 1.0 / np.sqrt(self._dynmat.normalization_masses)
         mass_pair = np.outer(inv_sqrt_m, inv_sqrt_m)
         d_dd *= mass_pair[None, :, None, :, None]
         d_dd *= factor