Merge branch 'rc'

.pre-commit-config.yaml

@@ -11,15 +11,15 @@ repos:
   - id: check-added-large-files
 
 - repo: https://github.com/pycqa/flake8
-  rev: 6.1.0
+  rev: 7.0.0
   hooks:
   - id: flake8
     args:
     - "--max-line-length=88"
     - "--ignore=E203,W503"
 
 - repo: https://github.com/psf/black
-  rev: 23.12.0
+  rev: 24.1.1
   hooks:
   - id: black
     args:

doc/changelog.md

@@ -2,6 +2,10 @@
 
 # Change Log
 
+## Feb-2-2024: Version 2.9.2
+
+- `boundary_mfp` value is stored in `kappa-*.hdf5` file when it is specified.
+
 ## Dec-26-2023: Version 2.9.1
 
 - Release to build conda-forge package.

doc/command-options.md

@@ -561,6 +561,8 @@ Then running with isotope calculation:
 In the result hdf5 file, currently isotope scattering strength is not written
 out, i.e., `gamma` is still imaginary part of self energy of ph-ph scattering.
 
+(boundary_mfp_option)=
+
 ### `--boundary-mfp`, `--bmfp` (`BOUNDARY_MFP`)
 
 A most simple phonon boundary scattering treatment is included. $v_g/L$ is just

doc/conf.py

@@ -1,4 +1,5 @@
 """Sphinx phono3py configuration file."""
+
 #
 # phono3py documentation build configuration file, created by
 # sphinx-quickstart on Wed Jun 26 13:13:14 2013.
@@ -59,7 +60,7 @@
 # The short X.Y version.
 version = "2.9"
 # The full version, including alpha/beta/rc tags.
-release = "2.9.1"
+release = "2.9.2"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/hdf5_howto.md

@@ -123,8 +123,9 @@ The array shape is (irreducible q-point, phonon band).
 (kappa_hdf5_file_gamma)=
 ### gamma
 
-Imaginary part of self energy. The physical unit is THz, where THz
-is in the ordinal frequency not the angular frequency.
+Imaginary part of self energy of phonon bubble diagram (phonon-phonon
+scattering). The physical unit is THz, where THz is in the ordinal frequency not
+the angular frequency.
 
 The array shape for all grid-points (irreducible q-points) is
 (temperature, irreducible q-point, phonon band).
@@ -262,9 +263,16 @@ P_{\mathbf{q}j} = \frac{1}{(3n_\mathrm{a})^2} \sum_{\lambda'\lambda''}
 $$
 
 This is not going to be calculated in the RTA thermal coductivity
-calculation mode by default. To calculate this, `--full_pp` option
+calculation mode by default. To calculate this, `--full-pp` option
 has to be specified (see {ref}`full_pp_option`).
 
+### boundary_mfp
+
+A value specified by {ref}`boundary_mfp_option`. The physical unit is
+micrometre.
+
+When `--boundary-mfp` option is explicitly specified, its value is stored here.
+
 ### kappa_unit_conversion
 
 This is used to convert the physical unit of lattice thermal

example/Si-PBEsol/Si.py

@@ -1,4 +1,5 @@
 """Example to run thermal conductivity of Si."""
+
 import numpy as np
 from phonopy.interface.vasp import read_vasp
 

example/zb-ZnTe-PBEsol/launch_phono3py_ZnTe_PBEsol_222.py

@@ -1,4 +1,5 @@
 """Launch script of ZnTe AiiDA calculation using aiida-phononpy."""
+
 from aiida.engine import submit
 from aiida.manage.configuration import load_profile
 from aiida.orm import Bool, Float, Str

phono3py/__init__.py

@@ -1,4 +1,5 @@
 """Shortcuts to important classes, methods, and variables."""
+
 # Copyright (C) 2019 Atsushi Togo
 # All rights reserved.
 #

phono3py/api_isotope.py

@@ -1,4 +1,5 @@
 """API for isotope scattering."""
+
 # Copyright (C) 2019 Atsushi Togo
 # All rights reserved.
 #

phono3py/api_jointdos.py

@@ -1,4 +1,5 @@
 """API for joint-density-of-states calculation."""
+
 # Copyright (C) 2019 Atsushi Togo
 # All rights reserved.
 #

phono3py/api_phono3py.py

@@ -1,4 +1,5 @@
 """Phono3py main class."""
+
 # Copyright (C) 2016 Atsushi Togo
 # All rights reserved.
 #

phono3py/conductivity/base.py

@@ -1,4 +1,5 @@
 """Thermal conductivity base class."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #
@@ -375,6 +376,8 @@ def __init__(
         volume = self._pp.primitive.volume
         self._conversion_factor = unit_to_WmK / volume
 
+        self._averaged_pp_interaction = None
+
         # `self._velocity_obj` is the instance of an inherited class of
         # `GroupVelocity`. `self._init_velocity()` is the method setup the instance,
         # which must be implmented in the inherited class of `ConductivityBase`.
@@ -632,6 +635,11 @@ def get_averaged_pp_interaction(self):
         )
         return self.averaged_pp_interaction
 
+    @property
+    def boundary_mfp(self) -> float:
+        """Return boundary MFP."""
+        return self._boundary_mfp
+
     def get_number_of_sampling_grid_points(self):
         """Return number of grid points.
 

phono3py/conductivity/direct_solution.py

@@ -1,4 +1,5 @@
 """Calculate lattice thermal conductivity by direct solution."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #
@@ -108,7 +109,6 @@ def __init__(
         self._init_velocity(gv_delta_q)
 
         self._lang = lang
-        self._averaged_pp_interaction = None
         self._collision_eigenvalues = None
         self._is_reducible_collision_matrix = is_reducible_collision_matrix
         self._solve_collective_phonon = solve_collective_phonon
@@ -517,9 +517,9 @@ def _set_collision_matrix_at_sigmas(self, i_gp):
                 else:
                     i_data = 0
                 self._gamma[j, k, i_data] = self._collision.imag_self_energy
-                self._collision_matrix[
-                    j, k, i_data
-                ] = self._collision.get_collision_matrix()
+                self._collision_matrix[j, k, i_data] = (
+                    self._collision.get_collision_matrix()
+                )
 
     def _prepare_collision_matrix(self):
         """Collect pieces and construct collision matrix."""

phono3py/conductivity/kubo.py

@@ -1,4 +1,5 @@
 """Kubo thermal conductivity base class."""
+
 # Copyright (C) 2022 Atsushi Togo
 # All rights reserved.
 #

phono3py/conductivity/rta.py

@@ -1,4 +1,5 @@
 """Lattice thermal conductivity calculation with RTA."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #
@@ -97,7 +98,6 @@ def __init__(
         self._gamma_detail_at_q = None
         self._use_ave_pp = use_ave_pp
         self._use_const_ave_pp = None
-        self._averaged_pp_interaction = None
         self._num_ignored_phonon_modes = None
 
         super().__init__(
@@ -298,9 +298,9 @@ def _set_gamma_at_sigmas(self, i):
                     self._gamma_N[j, k, i] = g_N
                     self._gamma_U[j, k, i] = g_U
                 if self._is_gamma_detail:
-                    self._gamma_detail_at_q[
-                        k
-                    ] = self._collision.get_detailed_imag_self_energy()
+                    self._gamma_detail_at_q[k] = (
+                        self._collision.get_detailed_imag_self_energy()
+                    )
 
     def _set_gamma_at_sigmas_lowmem(self, i):
         """Calculate gamma without storing ph-ph interaction strength.

phono3py/conductivity/utils.py

@@ -1,4 +1,5 @@
 """Utilities for lattice thermal conductivity calculation."""
+
 # Copyright (C) 2022 Atsushi Togo
 # All rights reserved.
 #
@@ -268,6 +269,7 @@ def write_kappa(
         qpoints = br.qpoints
         grid_points = br.grid_points
         weights = br.grid_weights
+        boundary_mfp = br.boundary_mfp
 
         for i, sigma in enumerate(sigmas):
             if kappa is None:
@@ -314,6 +316,7 @@ def write_kappa(
             write_kappa_to_hdf5(
                 temperatures,
                 mesh,
+                boundary_mfp=boundary_mfp,
                 bz_grid=bz_grid,
                 frequency=frequencies,
                 group_velocity=gv,
@@ -487,13 +490,13 @@ def write_collision(
     @staticmethod
     def write_kappa(
         lbte: "cond_LBTE_type",
-        volume,
-        is_reducible_collision_matrix=False,
-        write_LBTE_solution=False,
-        pinv_solver=None,
-        compression="gzip",
-        filename=None,
-        log_level=0,
+        volume: float,
+        is_reducible_collision_matrix: bool = False,
+        write_LBTE_solution: bool = False,
+        pinv_solver: Optional[int] = None,
+        compression: str = "gzip",
+        filename: Optional[str] = None,
+        log_level: int = 0,
     ):
         """Write kappa related properties into a hdf5 file."""
         from phono3py.conductivity.direct_solution import (
@@ -546,6 +549,7 @@ def write_kappa(
         f_vector = lbte.get_f_vectors()
         mode_cv = lbte.mode_heat_capacities
         mfp = lbte.get_mean_free_path()
+        boundary_mfp = lbte.boundary_mfp
 
         coleigs = lbte.get_collision_eigenvalues()
         # After kappa calculation, the variable is overwritten by unitary matrix
@@ -612,6 +616,7 @@ def write_kappa(
             write_kappa_to_hdf5(
                 temperatures,
                 mesh,
+                boundary_mfp=boundary_mfp,
                 bz_grid=bz_grid,
                 frequency=frequencies,
                 group_velocity=gv,

phono3py/conductivity/wigner.py

@@ -1,4 +1,5 @@
 """Wigner thermal conductivity base class."""
+
 # Copyright (C) 2022 Michele Simoncelli
 # All rights reserved.
 #

phono3py/cui/create_force_constants.py

@@ -1,4 +1,5 @@
 """Force constants calculation utilities for command line user interface."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/cui/create_supercells.py

@@ -1,4 +1,5 @@
 """Utilities of main CUI script."""
+
 # Copyright (C) 2015 Atsushi Togo
 # All rights reserved.
 #

phono3py/cui/kaccum_script.py

@@ -1,4 +1,5 @@
 """Phono3py kaccum command line script."""
+
 import argparse
 import sys
 

phono3py/cui/load.py

@@ -1,4 +1,5 @@
 """Phono3py loader."""
+
 # Copyright (C) 2019 Atsushi Togo
 # All rights reserved.
 #

phono3py/cui/phono3py_argparse.py

@@ -1,4 +1,5 @@
 """Phono3py command option argument parser."""
+
 # Copyright (C) 2015 Atsushi Togo
 # All rights reserved.
 #

phono3py/cui/phono3py_script.py

@@ -1,4 +1,5 @@
 """Phono3py main command line script."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/cui/settings.py

@@ -1,4 +1,5 @@
 """Phono3py command option and conf file parser."""
+
 # Copyright (C) 2015 Atsushi Togo
 # All rights reserved.
 #

phono3py/cui/show_log.py

@@ -1,4 +1,5 @@
 """Utilities to show various logs for main CUI script."""
+
 # Copyright (C) 2015 Atsushi Togo
 # All rights reserved.
 #

phono3py/cui/triplets_info.py

@@ -1,4 +1,5 @@
 """Show and write triplets information."""
+
 # Copyright (C) 2015 Atsushi Togo
 # All rights reserved.
 #

phono3py/file_IO.py

@@ -1,4 +1,5 @@
 """File I/O methods."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #
@@ -32,9 +33,12 @@
 # LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
+from __future__ import annotations
 
 import os
 import warnings
+from collections.abc import Sequence
+from typing import Optional, Union
 
 import h5py
 import numpy as np
@@ -918,6 +922,7 @@ def write_collision_eigenvalues_to_hdf5(
 def write_kappa_to_hdf5(
     temperature,
     mesh,
+    boundary_mfp: float = None,
     bz_grid=None,
     frequency=None,
     group_velocity=None,
@@ -1058,6 +1063,8 @@ def write_kappa_to_hdf5(
             w.create_dataset("sigma_cutoff_width", data=sigma_cutoff)
         if kappa_unit_conversion is not None:
             w.create_dataset("kappa_unit_conversion", data=kappa_unit_conversion)
+        if boundary_mfp is not None:
+            w.create_dataset("boundary_mfp", data=boundary_mfp)
 
         if verbose:
             text = "Thermal conductivity related properties "
@@ -1720,12 +1727,12 @@ def get_length_of_first_line(f):
 
 def _get_filename_suffix(
     mesh,
-    grid_point=None,
-    band_indices=None,
-    sigma=None,
-    sigma_cutoff=None,
-    temperature=None,
-    filename=None,
+    grid_point: Optional[int] = None,
+    band_indices: Optional[Union[np.ndarray, Sequence]] = None,
+    sigma: Optional[float] = None,
+    sigma_cutoff: Optional[float] = None,
+    temperature: Optional[float] = None,
+    filename: Optional[str] = None,
 ):
     """Return filename suffix corresponding to parameters."""
     suffix = "-m%d%d%d" % tuple(mesh)

phono3py/interface/alm.py

@@ -1,4 +1,5 @@
 """ALM interface for force constants calculation."""
+
 # Copyright (C) 2016 Atsushi Togo
 # All rights reserved.
 #

phono3py/interface/calculator.py

@@ -1,4 +1,5 @@
 """Utilities of calculator interfaces."""
+
 # Copyright (C) 2020 Atsushi Togo
 # All rights reserved.
 #

phono3py/interface/fc_calculator.py

@@ -1,4 +1,5 @@
 """Interfaces for force constants calculators."""
+
 # Copyright (C) 2019 Atsushi Togo
 # All rights reserved.
 #