Merge branch 'develop' into rc

phonopy · Dec 5, 2024 · ddb7b32 · ddb7b32
2 parents 56de0fe + 354cd97
commit ddb7b32
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -11,7 +11,7 @@ repos:
     exclude: ^example/AlN-LDA/
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.7.4
+  rev: v0.8.1
   hooks:
   - id: ruff
     args: [ "--fix", "--show-fixes" ]

diff --git a/doc/changelog.md b/doc/changelog.md
@@ -2,6 +2,10 @@
 
 # Change Log
 
+## Dec-6-2024: Version 3.9.0
+
+- Update to follow the change of phonopy's internal functions
+
 ## Nov-25-2024: Version 3.8.0
 
 - Follow the change due to phonopy's refactoring of MLP interface.

diff --git a/doc/command-options.md b/doc/command-options.md
@@ -406,6 +406,10 @@ These are shortcuts of `--fc-calc symfc` and `--fc-calc alm`, respectively.
 Please be careful that `--symfc` and `--sym-fc` (deprecated) are similar, but
 different.
 
+Refer to the [symfc](https://phonopy.github.io/phonopy/setting-tags.html#symfc)
+and [alm](https://phonopy.github.io/phonopy/setting-tags.html#alm) sections in
+the Phonopy documentation for additional details.
+
 ## Force constants
 
 (compact_fc_option)=

diff --git a/doc/conf.py b/doc/conf.py
@@ -58,9 +58,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = "3.8"
+version = "3.9"
 # The full version, including alpha/beta/rc tags.
-release = "3.8.0"
+release = "3.9.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/doc/install.md b/doc/install.md
@@ -61,6 +61,7 @@ See an example at {ref}`install_an_example`. In the standard output, flags and
 libraries found by cmake are shown. Please carefully check if those
 configurations are expected ones or not.
 
+(install_without_lapacke)=
 ### Building without linking LAPACKE
 
 **Experimental**
@@ -118,7 +119,14 @@ wrong python libraries can be imported.
    For x86-64 system:
 
    ```bash
-   % conda install numpy scipy h5py pyyaml matplotlib-base c-compiler cxx-compiler "libblas=*=*mkl" spglib mkl-include cmake
+   % conda install numpy scipy h5py pyyaml matplotlib-base c-compiler cxx-compiler cmake spglib
+   ```
+
+   Unless {ref}`install_without_lapacke`, the following packages will be
+   necessary to compile phono3py:
+
+   ```bash
+   % conda install "libblas=*=*mkl" mkl-include
    ```
 
    A libblas library can be chosen among `[openblas, mkl, blis, netlib]`. If
@@ -128,20 +136,21 @@ wrong python libraries can be imported.
    % conda install "libblas=*=*openblas"
    ```
 
-   For macOS ARM64 system, currently only openblas can be chosen:
+   For macOS ARM64 system:
 
    ```bash
-   % conda install numpy scipy h5py pyyaml matplotlib-base c-compiler cxx-compiler spglib cmake openblas
+   % conda install numpy scipy h5py pyyaml matplotlib-base c-compiler cxx-compiler spglib cmake
    ```
 
-   Note that using hdf5 files on NFS mounted file system, you may have to disable
-   file locking by setting
+   Unless {ref}`install_without_lapacke`, the following package will be
+   necessary to compile phono3py:
 
    ```bash
-   export HDF5_USE_FILE_LOCKING=FALSE
+   % conda install openblas
    ```
 
-   Install the latest phonopy and phono3py from github sources:
+   The latest phonopy and phono3py are obtained from github, and they are
+   compiled and installed by:
 
    ```bash
    % mkdir dev
@@ -154,28 +163,37 @@ wrong python libraries can be imported.
    % pip install . -vvv
    ```
 
-   The editable install (`pip install -e`) may not work depending on the
-   computer environment. The conda packages dependency can often change and this
-   recipe may not work properly. So if you find this instruction doesn't work,
-   it is very appreciated if letting us know it in the phonopy mailing list.
+## Dependent libraries
+
+### OpenMP
+
+#### GCC on Ubuntu
+
+With system provided gcc, `libgomp1` may be necessary to enable OpenMP
+multithreading support. This library is probably installed already in your
+system. If you don't have it and you use Ubuntu linux, it is installed by:
+
+```bash
+% sudo apt-get install libgomp1
+```
 
 (install_lapacke)=
-## Installation of LAPACKE
+### LAPACKE
 
 LAPACK library is used in a few parts of the code to diagonalize matrices.
 LAPACK*E* is the C-wrapper of LAPACK and LAPACK relies on BLAS. Both
 single-thread or multithread BLAS can be used in phono3py. In the following,
 multiple different ways of installation of LAPACKE are explained.
 
-### OpenBLAS provided by conda
+#### OpenBLAS provided by conda
 
 The installation of LAPACKE is easy by conda. It is:
 
 ```bash
 % conda install -c conda-forge openblas
 ```
 
-### Netlib LAPACKE provided by Ubuntu package manager (with single-thread BLAS)
+#### Netlib LAPACKE provided by Ubuntu package manager (with single-thread BLAS)
 
 LAPACKE (http://www.netlib.org/lapack/lapacke.html) can be installed from the
 Ubuntu package manager (`liblapacke` and `liblapacke-dev`):
@@ -184,7 +202,17 @@ Ubuntu package manager (`liblapacke` and `liblapacke-dev`):
 % sudo apt-get install liblapack-dev liblapacke-dev
 ```
 
-(install_openmp)=
+## Using HDF5 files on NFS mounted file system
+
+If you are using HDF5 files on an NFS-mounted file system, you might need to
+disable file locking. This can be done by setting the following environment
+variable:
+
+```bash
+export HDF5_USE_FILE_LOCKING=FALSE
+```
+
+<!-- (install_openmp)=
 ## Multithreading and its controlling by C macro
 
 Phono3py uses multithreading concurrency in two ways. One is that written in the
@@ -201,17 +229,7 @@ be deactivated at the compilation time. This is achieved by setting the C macro
 `MULTITHREADED_BLAS`, which can be written in `CMakeLists.txt`. Deactivating the
 multithreading of BLAS using the environment variables is not recommended
 because it is also used in the non-nested parts of the code and these
-multithreadings are unnecessary to be deactivated.
-
-### OpenMP library of gcc
-
-With system provided gcc, `libgomp1` may be necessary to enable OpenMP
-multithreading support. This library is probably installed already in your
-system. If you don't have it and you use Ubuntu linux, it is installed by:
-
-```bash
-% sudo apt-get install libgomp1
-```
+multithreadings are unnecessary to be deactivated. -->
 
 ## Trouble shooting
 

diff --git a/phono3py/api_phono3py.py b/phono3py/api_phono3py.py
@@ -1231,8 +1231,7 @@ def generate_displacements(
         is_diagonal: bool = True,
         number_of_snapshots: Optional[int] = None,
         random_seed: Optional[int] = None,
-        is_random_distance: bool = False,
-        min_distance: Optional[float] = None,
+        max_distance: Optional[float] = None,
     ):
         """Generate displacement dataset in supercell for fc3.
 
@@ -1270,7 +1269,10 @@ def generate_displacements(
         Parameters
         ----------
         distance : float, optional
-            Constant displacement Euclidean distance. Default is 0.03.
+            Constant displacement Euclidean distance. Default is 0.03. For
+            random direction and random distance displacements generation, this
+            value is also used as `min_distance`, is used to replace generated
+            random distances smaller than this value by this value.
         cutoff_pair_distance : float, optional
             This is used as a cutoff Euclidean distance to determine if each
             pair of displacements is considered to calculate fc3 or not. Default
@@ -1295,14 +1297,10 @@ def generate_displacements(
             None.
         random_seed : int or None, optional
             Random seed for random displacements generation. Default is None.
-        is_random_distance : bool, optional
-            Random direction displacements are generated also with random
-            amplitudes. The maximum value is defined by `distance` and minimum
-            value is given by `min_distance`. Default is False.
-        min_distance : float or None, optional
-            In random direction displacements generation with random distance
-            (`is_random_distance=True`), the minimum distance is given by this
-            value.
+        max_distance : float or None, optional
+            In random direction and distance displacements generation, this
+            value is specified. In random direction and random distance
+            displacements generation, this value is used as `max_distance`.
 
         """
         if number_of_snapshots is not None and number_of_snapshots > 0:
@@ -1312,8 +1310,7 @@ def generate_displacements(
                 distance=distance,
                 is_plusminus=is_plusminus is True,
                 random_seed=random_seed,
-                is_random_distance=is_random_distance,
-                min_distance=min_distance,
+                max_distance=max_distance,
             )
         else:
             direction_dataset = get_third_order_displacements(
@@ -1342,37 +1339,39 @@ def generate_fc2_displacements(
         is_diagonal: bool = False,
         number_of_snapshots: Optional[int] = None,
         random_seed: Optional[int] = None,
-        is_random_distance: bool = False,
-        min_distance: Optional[float] = None,
+        max_distance: Optional[float] = None,
     ):
         """Generate displacement dataset in phonon supercell for fc2.
 
-        This systematically generates single atomic displacements
-        in supercells to calculate phonon_fc2 considering crystal symmetry.
-        When this method is called, existing cache of supercells with
-        displacements for fc2 are removed.
+        This systematically generates single atomic displacements in supercells
+        to calculate phonon_fc2 considering crystal symmetry. When this method
+        is called, existing cache of supercells with displacements for fc2 are
+        removed.
 
         Note
         ----
-        is_diagonal=False is chosen as the default setting intentionally
-        to be consistent to the first displacements of the fc3 pair
-        displacemets in supercell.
+        is_diagonal=False is chosen as the default setting intentionally to be
+        consistent to the first displacements of the fc3 pair displacemets in
+        supercell.
 
         Parameters
         ----------
         distance : float, optional
-            Constant displacement Euclidean distance. Default is 0.03.
+            Constant displacement Euclidean distance. Default is 0.03. For
+            random direction and random distance displacements generation, this
+            value is also used as `min_distance`, is used to replace generated
+            random distances smaller than this value by this value.
         is_plusminus : True, False, or 'auto', optional
             With True, atomis are displaced in both positive and negative
-            directions. With False, only one direction. With 'auto',
-            mostly equivalent to is_plusminus=True, but only one direction
-            is chosen when the displacements in both directions are
-            symmetrically equivalent. Default is 'auto'.
+            directions. With False, only one direction. With 'auto', mostly
+            equivalent to is_plusminus=True, but only one direction is chosen
+            when the displacements in both directions are symmetrically
+            equivalent. Default is 'auto'.
         is_diagonal : Bool, optional
-            With False, the displacements are made along the basis
-            vectors of the supercell. With True, direction not along the basis
-            vectors can be chosen when the number of the displacements
-            may be reduced. Default is False.
+            With False, the displacements are made along the basis vectors of
+            the supercell. With True, direction not along the basis vectors can
+            be chosen when the number of the displacements may be reduced.
+            Default is False.
         number_of_snapshots : int or None, optional
             Number of snapshots of supercells with random displacements. Random
             displacements are generated displacing all atoms in random
@@ -1382,14 +1381,10 @@ def generate_fc2_displacements(
             None.
         random_seed : int or None, optional
             Random seed for random displacements generation. Default is None.
-        is_random_distance : bool, optional
-            Random direction displacements are generated also with random
-            amplitudes. The maximum value is defined by `distance` and minimum
-            value is given by `min_distance`. Default is False.
-        min_distance : float or None, optional
-            In random direction displacements generation with random distance
-            (`is_random_distance=True`), the minimum distance is given by this
-            value.
+        max_distance : float or None, optional
+            In random direction and distance displacements generation, this
+            value is specified. In random direction and random distance
+            displacements generation, this value is used as `max_distance`.
 
         """
         if number_of_snapshots is not None and number_of_snapshots > 0:
@@ -1399,8 +1394,7 @@ def generate_fc2_displacements(
                 distance=distance,
                 is_plusminus=is_plusminus is True,
                 random_seed=random_seed,
-                is_random_distance=is_random_distance,
-                min_distance=min_distance,
+                max_distance=max_distance,
             )
         else:
             phonon_displacement_directions = get_least_displacements(
@@ -2649,8 +2643,7 @@ def _generate_random_displacements(
         distance: float = 0.03,
         is_plusminus: bool = False,
         random_seed: Optional[int] = None,
-        is_random_distance: bool = False,
-        min_distance: Optional[float] = None,
+        max_distance: Optional[float] = None,
     ):
         if random_seed is not None and random_seed >= 0 and random_seed < 2**32:
             _random_seed = random_seed
@@ -2664,8 +2657,7 @@ def _generate_random_displacements(
             distance,
             random_seed=_random_seed,
             is_plusminus=is_plusminus,
-            is_random_distance=is_random_distance,
-            min_distance=min_distance,
+            max_distance=max_distance,
         )
         dataset["displacements"] = d
         return dataset

diff --git a/phono3py/cui/create_force_constants.py b/phono3py/cui/create_force_constants.py
@@ -529,20 +529,19 @@ def run_pypolymlp_to_compute_forces(
                 if v is not None:
                     print(f"  {k}: {v}")
 
-    if forces_in_dataset(ph3py.mlp_dataset):
+    if pathlib.Path(mlp_filename).exists():
+        if log_level:
+            print(f'Load MLPs from "{mlp_filename}".')
+        ph3py.load_mlp(mlp_filename)
+    elif forces_in_dataset(ph3py.mlp_dataset):
         if log_level:
             print("Developing MLPs by pypolymlp...", flush=True)
         ph3py.develop_mlp(params=mlp_params)
         ph3py.save_mlp(filename=mlp_filename)
         if log_level:
             print(f'MLPs were written into "{mlp_filename}"', flush=True)
     else:
-        if pathlib.Path(mlp_filename).exists():
-            if log_level:
-                print(f'Load MLPs from "{mlp_filename}".')
-            ph3py.load_mlp(mlp_filename)
-        else:
-            raise RuntimeError(f'"{mlp_filename}" is not found.')
+        raise RuntimeError(f'"{mlp_filename}" is not found.')
 
     if log_level:
         print("-" * 30 + " pypolymlp end " + "-" * 31, flush=True)

diff --git a/phono3py/cui/phono3py_script.py b/phono3py/cui/phono3py_script.py
@@ -37,7 +37,6 @@
 from __future__ import annotations
 
 import argparse
-import datetime
 import pathlib
 import sys
 from typing import Optional
@@ -50,6 +49,7 @@
     print_end,
     print_error,
     print_error_message,
+    print_time,
     print_version,
     set_magnetic_moments,
     store_nac_params,
@@ -124,15 +124,6 @@ def print_end_phono3py():
     print_end()
 
 
-def print_time():
-    """Print current time."""
-    print(
-        "-------------------------"
-        f'[time {datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")}]'
-        "-------------------------"
-    )
-
-
 def finalize_phono3py(
     phono3py: Phono3py,
     confs_dict,