Remove v1 compatibility

phono3py/api_isotope.py

@@ -33,8 +33,6 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
-import warnings
-
 import numpy as np
 from phonopy.units import VaspToTHz
 
@@ -53,7 +51,6 @@ def __init__(
         sigmas=None,
         frequency_factor_to_THz=VaspToTHz,
         use_grg=False,
-        store_dense_gp_map=True,
         symprec=1e-5,
         cutoff_frequency=None,
         lapack_zheev_uplo="L",
@@ -66,21 +63,13 @@ def __init__(
         else:
             self._sigmas = sigmas
 
-        if not store_dense_gp_map:
-            warnings.warn(
-                "Phono3pyIsotope init parameter of store_dense_gp_map is deprecated. "
-                "This will be always set True.",
-                DeprecationWarning,
-            )
-
         self._iso = Isotope(
             mesh,
             primitive,
             mass_variances=mass_variances,
             band_indices=band_indices,
             frequency_factor_to_THz=frequency_factor_to_THz,
             use_grg=use_grg,
-            store_dense_gp_map=store_dense_gp_map,
             symprec=symprec,
             cutoff_frequency=cutoff_frequency,
             lapack_zheev_uplo=lapack_zheev_uplo,

phono3py/api_jointdos.py

@@ -33,8 +33,6 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
-import warnings
-
 import numpy as np
 from phonopy.structure.cells import Primitive, Supercell
 from phonopy.structure.symmetry import Symmetry
@@ -72,7 +70,6 @@ def __init__(
         SNF_coordinates="reciprocal",
         is_mesh_symmetry=True,
         is_symmetry=True,
-        store_dense_gp_map=True,
         symprec=1e-5,
         output_filename=None,
         log_level=0,
@@ -94,14 +91,6 @@ def __init__(
         self._is_mesh_symmetry = is_mesh_symmetry
         self._is_symmetry = is_symmetry
 
-        if not store_dense_gp_map:
-            warnings.warn(
-                "Phono3pyJointDos init parameter of store_dense_gp_map is deprecated. "
-                "This will be set always True.",
-                DeprecationWarning,
-            )
-        self._store_dense_gp_map = store_dense_gp_map
-
         self._use_grg = use_grg
         self._SNF_coordinates = SNF_coordinates
         self._symprec = symprec
@@ -165,7 +154,7 @@ def mesh_numbers(self, mesh_numbers):
             use_grg=self._use_grg,
             force_SNF=False,
             SNF_coordinates=self._SNF_coordinates,
-            store_dense_gp_map=self._store_dense_gp_map,
+            store_dense_gp_map=True,
         )
 
     def initialize(self, mesh_numbers):
@@ -180,7 +169,6 @@ def initialize(self, mesh_numbers):
             frequency_factor_to_THz=self._frequency_factor_to_THz,
             frequency_scale_factor=self._frequency_scale_factor,
             is_mesh_symmetry=self._is_mesh_symmetry,
-            store_dense_gp_map=self._store_dense_gp_map,
             symprec=self._symprec,
             filename=self._filename,
             log_level=self._log_level,

phono3py/api_phono3py.py

@@ -153,13 +153,10 @@ def __init__(
         is_mesh_symmetry=True,
         use_grg=False,
         SNF_coordinates="reciprocal",
-        symmetrize_fc3q=None,
-        store_dense_gp_map=True,
-        store_dense_svecs=True,
+        make_r0_average: bool = False,
         symprec=1e-5,
         calculator: Optional[str] = None,
         log_level=0,
-        lapack_zheev_uplo=None,
     ):
         """Init method.
 
@@ -213,23 +210,18 @@ def __init__(
             `reciprocal` or `direct`. Space of coordinates to generate grid
             generating matrix either in direct or reciprocal space. The default
             is `reciprocal`.
-        symmetrize_fc3q : Deprecated.
-            See Phono3py.init_phph_interaction().
-        store_dense_gp_map : bool, optional, Deprecated.
-            Use dense format of BZ grid system. Default is True.
-        store_dense_svecs : bool, optional, Deprecated.
-            Shortest vectors are stored in the dense array format. This is
-            expected to be always True. Setting False is for rough compatibility
-            with v1.x. Default is True.
+        make_r0_average : bool, optional
+            fc3 transformation from real to reciprocal space is done
+            around three atoms and averaged when True. Default is False, i.e.,
+            only around the first atom. Setting False is for rough compatibility
+            with v2.x. Default is True.
         symprec : float, optional
             Tolerance used to find crystal symmetry. Default is 1e-5.
         calculator : str, optional.
             Calculator used for computing forces. This is used to switch the set
             of physical units. Default is None, which is equivalent to "vasp".
         log_level : int, optional
             Verbosity control. Default is 0. This can be 0, 1, or 2.
-        lapack_zheev_uplo : Deprecated.
-            See Phono3py.init_phph_interaction().
 
         """
         self._symprec = symprec
@@ -239,21 +231,13 @@ def __init__(
         self._use_grg = use_grg
         self._SNF_coordinates = SNF_coordinates
 
-        if not store_dense_gp_map:
-            warnings.warn(
-                "Phono3py init parameter of store_dense_gp_map is deprecated. "
-                "This will be set always True.",
-                DeprecationWarning,
-            )
-        self._store_dense_gp_map = store_dense_gp_map
-
-        if not store_dense_svecs:
+        if not make_r0_average:
             warnings.warn(
-                "Phono3py init parameter of store_dense_svecs is deprecated. "
-                "This will be set always True.",
+                "Phono3py init parameter of make_r0_average is deprecated. "
+                "This is always True but exists for backward compatibility.",
                 DeprecationWarning,
             )
-        self._store_dense_svecs = store_dense_svecs
+        self._make_r0_average = make_r0_average
 
         self._cutoff_frequency = cutoff_frequency
         self._calculator: Optional[str] = calculator
@@ -361,26 +345,6 @@ def __init__(
             )
             self.sigma_cutoff = sigma_cutoff
 
-        if symmetrize_fc3q is not None:
-            warnings.warn(
-                "Phono3py init parameter of symmetrize_fc3q is deprecated. "
-                "Set this at Phono3py.init_phph_interaction().",
-                DeprecationWarning,
-            )
-            self._symmetrize_fc3q = symmetrize_fc3q
-        else:
-            self._symmetrize_fc3q = None
-
-        if lapack_zheev_uplo is not None:
-            warnings.warn(
-                "Phono3py init parameter of lapack_zheev_uplo is deprecated. "
-                "Set this at Phono3py.init_phph_interaction().",
-                DeprecationWarning,
-            )
-            self._lapack_zheev_uplo = lapack_zheev_uplo
-        else:
-            self._lapack_zheev_uplo = None
-
     @property
     def version(self):
         """Return phono3py release version number.
@@ -1331,8 +1295,7 @@ def init_phph_interaction(
         nac_q_direction=None,
         constant_averaged_interaction=None,
         frequency_scale_factor=None,
-        symmetrize_fc3q=False,
-        make_r0_average=False,
+        symmetrize_fc3q: bool = False,
         lapack_zheev_uplo="L",
         openmp_per_triplets=None,
     ):
@@ -1367,10 +1330,6 @@ def init_phph_interaction(
         symmetrize_fc3q : bool, optional
             fc3 in phonon space is symmetrized by permutation symmetry.
             Default is False.
-        make_r0_average : bool, optional
-            fc3 transformation from real to reciprocal space is done
-            around three atoms and averaged when True. Default is False, i.e.,
-            only around the first atom.
         lapack_zheev_uplo : str, optional
             'L' or 'U'. Default is 'L'. This is passed to LAPACK zheev
             used for phonon solver.
@@ -1389,16 +1348,6 @@ def init_phph_interaction(
             msg = "Phono3py.fc2 of instance is not found."
             raise RuntimeError(msg)
 
-        if self._symmetrize_fc3q is None:
-            _symmetrize_fc3q = symmetrize_fc3q
-        else:
-            _symmetrize_fc3q = self._symmetrize_fc3q
-
-        if self._lapack_zheev_uplo is None:
-            _lapack_zheev_uplo = lapack_zheev_uplo
-        else:
-            _lapack_zheev_uplo = self._lapack_zheev_uplo
-
         self._interaction = Interaction(
             self._primitive,
             self._bz_grid,
@@ -1410,9 +1359,9 @@ def init_phph_interaction(
             frequency_scale_factor=frequency_scale_factor,
             cutoff_frequency=self._cutoff_frequency,
             is_mesh_symmetry=self._is_mesh_symmetry,
-            symmetrize_fc3q=_symmetrize_fc3q,
-            make_r0_average=make_r0_average,
-            lapack_zheev_uplo=_lapack_zheev_uplo,
+            symmetrize_fc3q=symmetrize_fc3q,
+            make_r0_average=self._make_r0_average,
+            lapack_zheev_uplo=lapack_zheev_uplo,
             openmp_per_triplets=openmp_per_triplets,
         )
         self._interaction.nac_q_direction = nac_q_direction
@@ -2545,9 +2494,7 @@ def _get_primitive_cell(self, supercell, supercell_matrix, primitive_matrix):
         else:
             t_mat = np.dot(inv_supercell_matrix, primitive_matrix)
 
-        return get_primitive(
-            supercell, t_mat, self._symprec, store_dense_svecs=self._store_dense_svecs
-        )
+        return get_primitive(supercell, t_mat, self._symprec, store_dense_svecs=True)
 
     def _determine_primitive_matrix(self, primitive_matrix):
         pmat = get_primitive_matrix(primitive_matrix, symprec=self._symprec)
@@ -2571,7 +2518,7 @@ def _set_mesh_numbers(
             use_grg=self._use_grg,
             force_SNF=False,
             SNF_coordinates=self._SNF_coordinates,
-            store_dense_gp_map=self._store_dense_gp_map,
+            store_dense_gp_map=True,
         )
 
     def _init_dynamical_matrix(self):

phono3py/cui/load.py

@@ -77,8 +77,6 @@ def load(
     is_mesh_symmetry=True,
     is_compact_fc=False,
     use_grg=False,
-    store_dense_gp_map=True,
-    store_dense_svecs=True,
     symprec=1e-5,
     log_level=0,
 ) -> Phono3py:
@@ -229,12 +227,6 @@ def load(
         cells. Default is False.
     use_grg : bool, optional
         Use generalized regular grid when True. Default is False.
-    store_dense_gp_map : bool, optional, Deprecated
-        Use new format of BZ grid system. Default is True.
-    store_dense_svecs : bool, optional, Deprecated
-        Shortest vectors are stored in the dense array format. This is expected
-        to be always True. Setting False is for rough compatibility with v1.x.
-        Default is True.
     symprec : float, optional
         Tolerance used to find crystal symmetry. Default is 1e-5.
     log_level : int, optional
@@ -305,8 +297,6 @@ def load(
         is_symmetry=is_symmetry,
         is_mesh_symmetry=is_mesh_symmetry,
         use_grg=use_grg,
-        store_dense_gp_map=store_dense_gp_map,
-        store_dense_svecs=store_dense_svecs,
         calculator=calculator,
         log_level=log_level,
     )

phono3py/cui/phono3py_script.py

@@ -741,6 +741,7 @@ def init_phono3py(
         is_symmetry=settings.is_symmetry,
         is_mesh_symmetry=settings.is_mesh_symmetry,
         use_grg=settings.use_grg,
+        make_r0_average=settings.is_fc3_r0_average,
         symprec=symprec,
         calculator=interface_mode,
         log_level=log_level,
@@ -1036,7 +1037,6 @@ def init_phph_interaction(
         constant_averaged_interaction=ave_pp,
         frequency_scale_factor=updated_settings["frequency_scale_factor"],
         symmetrize_fc3q=settings.is_symmetrize_fc3_q,
-        make_r0_average=settings.is_fc3_r0_average,
         lapack_zheev_uplo=settings.lapack_zheev_uplo,
     )
 

phono3py/other/isotope.py

@@ -100,7 +100,6 @@ def __init__(
         bz_grid=None,
         frequency_factor_to_THz=VaspToTHz,
         use_grg=False,
-        store_dense_gp_map=True,
         symprec=1e-5,
         cutoff_frequency=None,
         lapack_zheev_uplo="L",
@@ -146,7 +145,7 @@ def __init__(
                 lattice=self._primitive.cell,
                 symmetry_dataset=primitive_symmetry.dataset,
                 use_grg=use_grg,
-                store_dense_gp_map=store_dense_gp_map,
+                store_dense_gp_map=True,
             )
 
     def set_grid_point(self, grid_point):

phono3py/other/tetrahedron_method.py

@@ -36,8 +36,10 @@
 import numpy as np
 from phonopy.structure.tetrahedron_method import TetrahedronMethod
 
+from phono3py.phonon.grid import BZGrid
 
-def get_unique_grid_points(grid_points, bz_grid):
+
+def get_unique_grid_points(grid_points, bz_grid: BZGrid):
     """Collect grid points on tetrahedron vertices around input grid points.
 
     Find grid points of 24 tetrahedra around each grid point and
@@ -88,7 +90,7 @@ def get_unique_grid_points(grid_points, bz_grid):
 def get_integration_weights(
     sampling_points,
     grid_values,
-    bz_grid,
+    bz_grid: BZGrid,
     grid_points=None,
     bzgp2irgp_map=None,
     function="I",

phono3py/phonon3/gruneisen.py

@@ -37,7 +37,8 @@
 
 import numpy as np
 from phonopy.harmonic.dynamical_matrix import get_dynamical_matrix
-from phonopy.structure.cells import sparse_to_dense_svecs
+from phonopy.structure.atoms import PhonopyAtoms
+from phonopy.structure.cells import Primitive
 from phonopy.structure.grid_points import get_qpoints
 from phonopy.units import VaspToTHz
 
@@ -126,8 +127,8 @@
         self,
         fc2,
         fc3,
-        supercell,
-        primitive,
+        supercell: PhonopyAtoms,
+        primitive: Primitive,
         nac_params=None,
         nac_q_direction=None,
         ion_clamped=False,
@@ -151,12 +152,7 @@
         )
         self._nac_q_direction = nac_q_direction
 
-        svecs, multi = self._pcell.get_smallest_vectors()
-        if self._pcell.store_dense_svecs:
-            self._svecs = svecs
-            self._multi = multi
-        else:
-            self._svecs, self._multi = sparse_to_dense_svecs(svecs, multi)
+        self._svecs, self._multi = self._pcell.get_smallest_vectors()
 
         if self._ion_clamped:
             num_atom_prim = len(self._pcell)