Merge branch 'rc'

.pre-commit-config.yaml

@@ -37,7 +37,7 @@ repos:
       name: isort (python)
 
 - repo: https://github.com/Takishima/cmake-pre-commit-hooks
-  rev: v1.9.5
+  rev: v1.9.6
   hooks:
     - id: clang-format
       args:

doc/changelog.md

@@ -2,6 +2,10 @@
 
 # Change Log
 
+## Jun-7-2024: Version 3.0.4
+
+- Bug fix when handling different supercell size of fc2 than that of fc3.
+
 ## May-4-2024: Version 3.0.3
 
 - Release to follow the update of phonopy.

doc/conf.py

@@ -60,7 +60,7 @@
 # The short X.Y version.
 version = "3.0"
 # The full version, including alpha/beta/rc tags.
-release = "3.0.3"
+release = "3.0.4"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/index.md

@@ -23,7 +23,13 @@ Papers that may introduce phono3py:
   <http://dx.doi.org/10.1103/PhysRevB.91.094306> (arxiv
   <http://arxiv.org/abs/1501.00691>).
 - Introduction to phono3py application:
-  <https://doi.org/10.1103/PhysRevB.97.224306> (open access).
+  <https://journals.jps.jp/doi/10.7566/JPSJ.92.012001> (open access),
+  and phono3py inputs for 103 compounds found in Fig.17
+  <https://github.com/atztogo/phonondb/blob/main/mdr/phono3py_103compounds_fd/README.md>
+- Implementation of phono3py:
+  <https://iopscience.iop.org/article/10.1088/1361-648X/acd831> (open access)
+
+A set of pre-calculated data for phono3py in
 
 ```{image} Si-kaccum.png
 :width: 20%

phono3py/cui/load.py

@@ -36,6 +36,7 @@
 from __future__ import annotations
 
 import os
+import pathlib
 from collections.abc import Sequence
 from typing import Optional, Union
 
@@ -390,14 +391,13 @@ def set_dataset_and_force_constants(
         cutoff_pair_distance=cutoff_pair_distance,
         log_level=log_level,
     )
-    if ph3py.phonon_supercell_matrix is not None:
-        read_fc["fc2"] = _set_dataset_phonon_dataset_or_fc2(
-            ph3py,
-            ph3py_yaml=ph3py_yaml,
-            fc2_filename=fc2_filename,
-            forces_fc2_filename=forces_fc2_filename,
-            log_level=log_level,
-        )
+    read_fc["fc2"] = _set_dataset_phonon_dataset_or_fc2(
+        ph3py,
+        ph3py_yaml=ph3py_yaml,
+        fc2_filename=fc2_filename,
+        forces_fc2_filename=forces_fc2_filename,
+        log_level=log_level,
+    )
 
     # Cases that dataset is in phono3py.yaml but not forces.
     if ph3py.dataset is None:
@@ -487,14 +487,14 @@ def _set_dataset_or_fc3(
             cutoff_pair_distance,
             log_level,
         )
-    elif os.path.isfile("fc3.hdf5"):
+    elif pathlib.Path("fc3.hdf5").exists():
         fc3 = read_fc3_from_hdf5(filename="fc3.hdf5", p2s_map=p2s_map)
         _check_fc3_shape(ph3py, fc3)
         ph3py.fc3 = fc3
         read_fc3 = True
         if log_level:
             print('fc3 was read from "fc3.hdf5".')
-    elif os.path.isfile("FORCES_FC3"):
+    elif pathlib.Path("FORCES_FC3").exists():
         _set_dataset_for_fc3(
             ph3py,
             ph3py_yaml,
@@ -544,14 +544,17 @@ def _set_dataset_phonon_dataset_or_fc2(
             "phonon_fc2",
             log_level,
         )
-    elif os.path.isfile("fc2.hdf5"):
+    elif pathlib.Path("fc2.hdf5").exists():
         fc2 = read_fc2_from_hdf5(filename="fc2.hdf5", p2s_map=phonon_p2s_map)
         _check_fc2_shape(ph3py, fc2)
         ph3py.fc2 = fc2
         read_fc2 = True
         if log_level:
             print('fc2 was read from "fc2.hdf5".')
-    elif os.path.isfile("FORCES_FC2"):
+    elif (
+        pathlib.Path("FORCES_FC2").exists()
+        and ph3py.phonon_supercell_matrix is not None
+    ):
         _set_dataset_for_fc2(
             ph3py,
             ph3py_yaml,
@@ -583,7 +586,10 @@ def _set_dataset_phonon_dataset_or_fc2(
             "fc2",
             log_level,
         )
-    elif os.path.isfile("FORCES_FC3"):
+    elif (
+        pathlib.Path("FORCES_FC3").exists()
+        and ph3py.phonon_supercell_matrix is not None
+    ):
         # suppose fc3.hdf5 is read but fc2.hdf5 doesn't exist.
         _set_dataset_for_fc2(
             ph3py,

phono3py/interface/phono3py_yaml.py

@@ -42,8 +42,8 @@
 import numpy as np
 from phonopy.interface.phonopy_yaml import (
     PhonopyYaml,
-    PhonopyYamlDumper,
-    PhonopyYamlLoader,
+    PhonopyYamlDumperBase,
+    PhonopyYamlLoaderBase,
     load_yaml,
     phonopy_yaml_property_factory,
 )
@@ -82,7 +82,7 @@ class Phono3pyYamlData:
     phonon_primitive: Optional[Primitive] = None
 
 
-class Phono3pyYamlLoader(PhonopyYamlLoader):
+class Phono3pyYamlLoader(PhonopyYamlLoaderBase):
     """Phono3pyYaml loader."""
 
     def __init__(
@@ -115,18 +115,18 @@ def _parse_all_cells(self):
 
         """
         super()._parse_all_cells()
-        if "phonon_primitive_cell" in self._yaml:
-            self._data.phonon_primitive = self._parse_cell(
-                self._yaml["phonon_primitive_cell"]
-            )
-        if "phonon_supercell" in self._yaml:
-            self._data.phonon_supercell = self._parse_cell(
-                self._yaml["phonon_supercell"]
-            )
         if "phonon_supercell_matrix" in self._yaml:
             self._data.phonon_supercell_matrix = np.array(
                 self._yaml["phonon_supercell_matrix"], dtype="intc", order="C"
             )
+            if "phonon_primitive_cell" in self._yaml:
+                self._data.phonon_primitive = self._parse_cell(
+                    self._yaml["phonon_primitive_cell"]
+                )
+            if "phonon_supercell" in self._yaml:
+                self._data.phonon_supercell = self._parse_cell(
+                    self._yaml["phonon_supercell"]
+                )
 
     def _parse_dataset(self):
         """Parse phonon_dataset.
@@ -137,8 +137,6 @@ def _parse_dataset(self):
         self._data.phonon_dataset = self._get_dataset(
             self._data.phonon_supercell, key_prefix="phonon_"
         )
-        if self._data.phonon_dataset is None:
-            self._data.phonon_dataset = self._get_dataset(self._data.phonon_supercell)
 
     def _parse_fc3_dataset(self):
         """Parse force dataset for fc3.
@@ -168,7 +166,7 @@ def _parse_fc3_dataset(self):
         self._data.dataset = dataset
 
         # This case should work only for v2.2 or later.
-        if self._data.dataset is None and "displacements" in self._yaml:
+        if self._data.dataset is None:
             self._data.dataset = self._get_dataset(self._data.supercell)
 
     def _parse_fc3_dataset_type1(self, natom):
@@ -263,7 +261,7 @@ def _parse_fc3_dataset_type1_without_forces(self, data1, d2, disp2_id):
         return disp2_id
 
 
-class Phono3pyYamlDumper(PhonopyYamlDumper):
+class Phono3pyYamlDumper(PhonopyYamlDumperBase):
     """Phono3pyYaml dumper."""
 
     _default_dumper_settings = {
@@ -286,13 +284,14 @@ def _cell_info_yaml_lines(self):
 
         """
         lines = super()._cell_info_yaml_lines()
-        lines += self._supercell_matrix_yaml_lines(
-            self._data.phonon_supercell_matrix, "phonon_supercell_matrix"
-        )
-        lines += self._primitive_yaml_lines(
-            self._data.phonon_primitive, "phonon_primitive_cell"
-        )
-        lines += self._phonon_supercell_yaml_lines()
+        if self._data.phonon_supercell_matrix is not None:
+            lines += self._supercell_matrix_yaml_lines(
+                self._data.phonon_supercell_matrix, "phonon_supercell_matrix"
+            )
+            lines += self._primitive_yaml_lines(
+                self._data.phonon_primitive, "phonon_primitive_cell"
+            )
+            lines += self._phonon_supercell_yaml_lines()
         return lines
 
     def _phonon_supercell_yaml_lines(self):

phono3py/version.py

@@ -34,4 +34,4 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
-__version__ = "3.0.3"
+__version__ = "3.0.4"