From 56b1d7885c15959e56bd36a6b7145ec50955ffe9 Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Sat, 24 Aug 2024 16:02:01 +0900
Subject: [PATCH 01/13] Update version in doc

---
 doc/conf.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/conf.py b/doc/conf.py
index 19a19a0b..d091ca08 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -58,9 +58,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = "3.3"
+version = "3.4"
 # The full version, including alpha/beta/rc tags.
-release = "3.3.4"
+release = "3.4.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

From feb22c22c1b77f8da34f07237504a8161282ef1a Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Sun, 25 Aug 2024 17:17:37 +0900
Subject: [PATCH 02/13] Prefer symbols to numbers when creating PhonopyAtoms

---
 test/interface/test_phono3py_yaml.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/interface/test_phono3py_yaml.py b/test/interface/test_phono3py_yaml.py
index 6702c50f..4972544c 100644
--- a/test/interface/test_phono3py_yaml.py
+++ b/test/interface/test_phono3py_yaml.py
@@ -31,7 +31,7 @@ def test_read_phono3py_yaml():
             [0.0, 0.5, 0.0],
             [0.0, 0.0, 0.5],
         ],
-        numbers=[11, 11, 11, 11, 17, 17, 17, 17],
+        symbols=["Na", "Na", "Na", "Na", "Cl", "Cl", "Cl", "Cl"],
     )
     assert isclose(cell, cell_ref)
 

From f34764604a4a2f96c6edc67d9f107be80337e835 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 26 Aug 2024 23:34:25 +0000
Subject: [PATCH 03/13] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.6.1 → v0.6.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.1...v0.6.2)
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 84862979..a5b78599 100644
--- 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: v0.6.1
+  rev: v0.6.2
   hooks:
   - id: ruff
     args: [ "--fix", "--show-fixes" ]

From 3eaa76fa2c7539a363bac250fd0e74630b30e323 Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Sat, 31 Aug 2024 21:58:57 +0900
Subject: [PATCH 04/13] Display interface mode in CLI

---
 doc/command-options.md                 | 76 ++++++++++++++++----------
 phono3py/cui/create_force_constants.py |  7 ++-
 phono3py/cui/create_force_sets.py      | 27 +++++++--
 phono3py/cui/phono3py_script.py        |  3 +-
 phono3py/cui/show_log.py               | 32 +++++++----
 5 files changed, 99 insertions(+), 46 deletions(-)

diff --git a/doc/command-options.md b/doc/command-options.md
index 635150fb..b4957714 100644
--- a/doc/command-options.md
+++ b/doc/command-options.md
@@ -86,8 +86,7 @@ These options have no respective configuration file tags.
 
 This is used to create `FORCES_FC3` from `phono3py_disp.yaml` and force
 calculator outputs containing forces in supercells. `phono3py_disp.yaml` has to
-be located at the current directory. Calculator interface has to be specified
-except for VASP (default) case.
+be located at the current directory.
 
 ```bash
 % phono3py --cf3 disp-{00001..00755}/vasprun.xml
@@ -97,14 +96,26 @@ except for VASP (default) case.
 % phono3py --cf3 supercell_out/disp-{00001..00111}/Si.out
 ```
 
+````{note}
+The calculator interface should be stored in `phono3py_disp.yaml`, so it is not
+needed to set it manually. Command-line-options like `--qe` will be ignored. If
+the calculator interface is missing from `phono3py_disp.yaml` but needed, please
+update the `phono3py` section in the file as follows:
+
+```yaml
+phono3py:
+  calculator: qe
+```
+````
+
 (cf3_file_option)=
 
 ### `--cf3-file` (command option only)
 
 This is used to create `FORCES_FC3` from a text file containing a list of
 calculator output file names. `phono3py_disp.yaml` has to be located at the
-current directory. Calculator interface has to be specified except for VASP
-(default) case.
+current directory. The calculator interface is unnecessary to specify, see the
+note at {ref}`--cf3 <cf3_option>`.
 
 ```bash
 % phono3py --cf3-file file_list.dat
@@ -130,8 +141,9 @@ together with `--cutoff-pair` option.
 
 This is used to create `FORCES_FC2` similarly to `--cf3` option.
 `phono3py_disp.yaml` has to be located at the current directory. This is
-optional. Calculator interface has to be specified except for VASP (default)
-case. `FORCES_FC2` is necessary to run with `--dim-fc2` option.
+optional. `FORCES_FC2` is necessary to run with `--dim-fc2` option. The
+calculator interface is unnecessary to specify, see the note at {ref}`--cf3
+<cf3_option>`.
 
 ```bash
 % phono3py --cf2 disp_fc2-{00001..00002}/vasprun.xml
@@ -142,8 +154,8 @@ case. `FORCES_FC2` is necessary to run with `--dim-fc2` option.
 ### `--cfz` (command option only)
 
 This is used to create `FORCES_FC3` and `FORCES_FC2` subtracting residual forces
-combined with `--cf3` and `--cf2`, respectively. Calculator interface has to be
-specified except for VASP (default) case.
+combined with `--cf3` and `--cf2`, respectively. The calculator interface is
+unnecessary to specify, see the note at {ref}`--cf3 <cf3_option>`.
 
 In the following example, it is supposed that `disp3-00000/vasprun.xml` and
 `disp2-00000/vasprun.xml` contain the forces of the perfect supercells. In ideal
@@ -204,7 +216,6 @@ When using with `--cf2`, `--cf3` has to be specified simultaneously as below,
 % phono3py --cf3 disp-{00001..00755}/vasprun.xml --cf2 disp_fc2-{00001..00002}/vasprun.xml --sp
 ```
 
-
 ## Supercell, primitive cell, masses, magnetic moments
 
 (dim_option)=
@@ -299,6 +310,7 @@ web page](https://phonopy.github.io/phonopy/setting-tags.html#magmom).
 ## Displacement creation
 
 (create_displacements_option)=
+
 ### `-d` (`CREATE_DISPLACEMENTS = .TRUE.`)
 
 **`phono3py-load` doesn't have this option.**
@@ -317,6 +329,7 @@ information about primitive cell (`primitive_matrix` key) in
 ```
 
 (random_displacements_option)=
+
 ### `--rd` (`RANDOM_DISPLACEMENTS`), `--rd-fc2` (`RANDOM_DISPLACEMENTS_FC2`) and `--random-seed` (`RANDOM_SEED`)
 
 **`phono3py-load` doesn't have this option.**
@@ -336,6 +349,7 @@ and/or `--rd-fc2`,
 ```
 
 (amplitude_option)=
+
 ### `--amplitude` (`DISPLACEMENT_DISTANCE`)
 
 **`phono3py-load` doesn't have this option.**
@@ -348,6 +362,7 @@ The default value depends on calculator. See
 {ref}`default_displacement_distance_for_calculator`.
 
 (fc_calculator_option)=
+
 ### `--fc-calc`, `--fc-calculator` (`FC_CALCULATOR`)
 
 Choice of force constants calculator.
@@ -357,14 +372,17 @@ Choice of force constants calculator.
 ```
 
 To use different force constants calculators for fc2 and fc3
+
 ```bash
 % phono3py-load --fc-calc "symfc|" ...
 ```
+
 Those for fc2 and fc3 are seprated by `|` such as `symfc|` . Blank means to
 employ the finite difference method for systematic displacements generated by
 the option `-d`.
 
 (fc_calculator_options_option)=
+
 ### `--fc-calc-opt`, `--fc-calculator-options` (`FC_CALCULATOR_OPTIONS`)
 
 Special options for force constants calculators.
@@ -608,9 +626,9 @@ $$
  \bigl|\Phi_{-\lambda\lambda'\lambda''}\bigl|^2
  \left\{(n_{\lambda'}+ n_{\lambda''}+1)
   \delta(\omega-\omega_{\lambda'}-\omega_{\lambda''}) \right.
-  + (n_{\lambda'}-n_{\lambda''})
+  * (n_{\lambda'}-n_{\lambda''})
  \left[\delta(\omega+\omega_{\lambda'}-\omega_{\lambda''})
-+ \left. \delta(\omega-\omega_{\lambda'}+\omega_{\lambda''})
+* \left. \delta(\omega-\omega_{\lambda'}+\omega_{\lambda''})
 \right]\right\}.
 $$
 
@@ -840,7 +858,7 @@ $$
  \bigl|\Phi_{-\lambda\lambda_1\lambda_2}\bigl|^2
  (n_{\lambda_1}-n_{\lambda_2})
  \left[\delta(\omega+\omega_{\lambda_1}-\omega_{\lambda_2})
- +  \delta(\omega-\omega_{\lambda_1}+\omega_{\lambda_2})
+ *  \delta(\omega-\omega_{\lambda_1}+\omega_{\lambda_2})
  \right]
  \end{align*}
 $$
@@ -854,7 +872,7 @@ $$
  \bigl|\Phi_{-\lambda\lambda_1\lambda_2}\bigl|^2
 (n_{\lambda_1}+ n_{\lambda_2}+1)
  \left[ \delta(\omega-\omega_{\lambda_1}-\omega_{\lambda_2})
- + \delta(\omega + \omega_{\lambda_1} + \omega_{\lambda_2}) \right]
+ * \delta(\omega + \omega_{\lambda_1} + \omega_{\lambda_2}) \right]
  \end{align*},
 $$
 
@@ -922,11 +940,11 @@ $$
  \bigl|\Phi_{-\lambda\lambda_1\lambda_2}\bigl|^2 &
  \left\{(n_{\lambda_1}+ n_{\lambda_2}+1)
  \left[ \delta(\omega-\omega_{\lambda_1}-\omega_{\lambda_2})
- + \delta(\omega+\omega_{\lambda_1}+\omega_{\lambda_2}) \right] \right.
+ * \delta(\omega+\omega_{\lambda_1}+\omega_{\lambda_2}) \right] \right.
  \\
  & + (n_{\lambda_1}-n_{\lambda_2})
  \left[\delta(\omega+\omega_{\lambda_1}-\omega_{\lambda_2})
- + \left. \delta(\omega-\omega_{\lambda_1}+\omega_{\lambda_2})
+ * \left. \delta(\omega-\omega_{\lambda_1}+\omega_{\lambda_2})
  \right]\right\},
 \end{align*}
 $$
@@ -941,14 +959,14 @@ $$
  \left\{
  \left[ \frac{(n_{\lambda_1}+ n_{\lambda_2}+1)}{
  (\omega-\omega_{\lambda_1}-\omega_{\lambda_2})_\mathrm{p}}
- + \frac{(n_{\lambda_1}+ n_{\lambda_2}+1)}{
+ * \frac{(n_{\lambda_1}+ n_{\lambda_2}+1)}{
  (\omega+\omega_{\lambda_1}+\omega_{\lambda_2})_\mathrm{p}}
  \right]
  \right. \\
   & + \left[
  \frac{(n_{\lambda_1}-n_{\lambda_2})}{(\omega +
  \omega_{\lambda_1} - \omega_{\lambda_2})_\mathrm{p}}
- + \left. \frac{(n_{\lambda_1}-n_{\lambda_2})}{(\omega -
+ * \left. \frac{(n_{\lambda_1}-n_{\lambda_2})}{(\omega -
  \omega_{\lambda_1} + \omega_{\lambda_2})_\mathrm{p}}
  \right]\right\},
 \end{align*}
@@ -1012,7 +1030,7 @@ A_\lambda(\omega) = \frac{1}{\pi} \frac{4\Omega^2_\lambda
  \Gamma_\lambda(\omega)}
  {\left[\omega^2 - \Omega^2_\lambda -
  2\Omega_\lambda \Delta_\lambda(\omega) \right]^2
- + \left[ 2\Omega_\lambda
+ * \left[ 2\Omega_\lambda
  \Gamma_\lambda(\omega) \right]^2},
 $$
 
@@ -1348,12 +1366,12 @@ Using this option, output file names are slightly modified. For example, with
 
 This rule is applied to
 
-+ `fc3.hdf5`
-+ `fc2.hdf5`
-+ `kappa-xxx.hdf5`
-+ `phonon-xxx.hdf5`
-+ `pp-xxx.hdf5`
-+ `gamma_detail-xxx.hdf5` (write only)
+* `fc3.hdf5`
+* `fc2.hdf5`
+* `kappa-xxx.hdf5`
+* `phonon-xxx.hdf5`
+* `pp-xxx.hdf5`
+* `gamma_detail-xxx.hdf5` (write only)
 
 (input_filename_option)=
 
@@ -1367,11 +1385,11 @@ specifying `-i iso --fc3`, a file name `fc3.iso.hdf5` is read instead of
 
 This rule is applied to
 
-+ `fc3.hdf5`
-+ `fc2.hdf5`
-+ `kappa-xxx.hdf5`
-+ `phonon-xxx.hdf5`
-+ `pp-xxx.hdf5`
+* `fc3.hdf5`
+* `fc2.hdf5`
+* `kappa-xxx.hdf5`
+* `phonon-xxx.hdf5`
+* `pp-xxx.hdf5`
 
 ### `--io` (command option only)
 
diff --git a/phono3py/cui/create_force_constants.py b/phono3py/cui/create_force_constants.py
index c4a41cd3..7d33ec6c 100644
--- a/phono3py/cui/create_force_constants.py
+++ b/phono3py/cui/create_force_constants.py
@@ -259,7 +259,6 @@ def parse_forces(
             distance_to_A=physical_units["distance_to_A"],
             force_to_eVperA=physical_units["force_to_eVperA"],
         )
-
     assert dataset is not None
 
     if "natom" in dataset and dataset["natom"] != natom:
@@ -273,6 +272,12 @@ def parse_forces(
             f'Displacement dataset for {fc_type} was read from "{filename_read_from}".'
         )
 
+    if calculator is not None and log_level:
+        print(
+            f"Displacements and forces were converted from {calculator} "
+            "unit to A and eV/A."
+        )
+
     # Overwrite dataset['cutoff_distance'] when necessary.
     if fc_type == "fc3" and cutoff_pair_distance:
         if "cutoff_distance" not in dataset or (
diff --git a/phono3py/cui/create_force_sets.py b/phono3py/cui/create_force_sets.py
index 57c69570..84bec1ff 100644
--- a/phono3py/cui/create_force_sets.py
+++ b/phono3py/cui/create_force_sets.py
@@ -44,7 +44,7 @@
 from phonopy.cui.create_force_sets import check_number_of_force_files
 from phonopy.cui.load_helper import get_nac_params
 from phonopy.cui.phonopy_script import file_exists, files_exist, print_error
-from phonopy.file_IO import parse_FORCE_SETS, write_FORCE_SETS
+from phonopy.file_IO import is_file_phonopy_yaml, parse_FORCE_SETS, write_FORCE_SETS
 from phonopy.interface.calculator import get_calc_dataset
 
 from phono3py.file_IO import (
@@ -72,10 +72,24 @@ def create_FORCES_FC3_and_FORCES_FC2(
 
     """
     interface_mode = settings.calculator
+
     disp_filename_candidates = [
         "phono3py_disp.yaml",
     ]
-    if cell_filename is not None:
+
+    if log_level:
+        print("")
+
+    if (
+        log_level
+        and cell_filename is not None
+        and not is_file_phonopy_yaml(cell_filename, keyword="phono3py")
+    ):
+        print(f'*Unnecessary to specify "{cell_filename}".')
+
+    if cell_filename is not None and is_file_phonopy_yaml(
+        cell_filename, keyword="phono3py"
+    ):
         disp_filename_candidates.insert(0, cell_filename)
     disp_filenames = files_exist(
         disp_filename_candidates, log_level=log_level, is_any=True
@@ -86,6 +100,10 @@ def create_FORCES_FC3_and_FORCES_FC2(
     if ph3py_yaml.calculator is not None:
         interface_mode = ph3py_yaml.calculator  # overwrite
 
+    if interface_mode is not None:
+        if log_level:
+            print(f"Calculator interface: {interface_mode}")
+
     if settings.create_forces_fc3 or settings.create_forces_fc3_file:
         calc_dataset_fc3 = _get_force_sets_fc3(
             settings, ph3py_yaml.dataset, disp_filename, interface_mode, log_level
@@ -172,7 +190,9 @@ def create_FORCE_SETS_from_FORCES_FCx(
     phonon_smat, input_filename: Optional[str], cell_filename: Optional[str], log_level
 ):
     """Convert FORCES_FC3 or FORCES_FC2 to FORCE_SETS."""
-    if cell_filename is not None:
+    if cell_filename is not None and is_file_phonopy_yaml(
+        cell_filename, keyword="phono3py"
+    ):
         disp_filename = cell_filename
     elif input_filename is None:
         disp_filename = "phono3py_disp.yaml"
@@ -286,7 +306,6 @@ def _get_force_sets_fc3(
     settings, disp_dataset, disp_filename, interface_mode, log_level
 ) -> dict:
     if log_level:
-        print("")
         print(f'FC3 Displacement dataset was read from "{disp_filename}".')
 
     if "first_atoms" in disp_dataset:  # type-1
diff --git a/phono3py/cui/phono3py_script.py b/phono3py/cui/phono3py_script.py
index 943b9311..36ad6b5a 100644
--- a/phono3py/cui/phono3py_script.py
+++ b/phono3py/cui/phono3py_script.py
@@ -281,7 +281,7 @@ def read_phono3py_settings(args, argparse_control, log_level):
                     args=args, default_settings=argparse_control
                 )
                 cell_filename = args.filename[0]
-            else:
+            else:  # args.filename[0] is assumed to be phono3py-conf file.
                 phono3py_conf_parser = Phono3pyConfParser(
                     filename=args.filename[0],
                     args=args,
@@ -1033,6 +1033,7 @@ def main(**argparse_control):
             unitcell_filename,
             input_filename,
             output_filename,
+            interface_mode,
         )
 
         if phono3py.supercell.magnetic_moments is None:
diff --git a/phono3py/cui/show_log.py b/phono3py/cui/show_log.py
index 650a5657..c03f90b6 100644
--- a/phono3py/cui/show_log.py
+++ b/phono3py/cui/show_log.py
@@ -46,7 +46,13 @@
 
 
 def show_general_settings(
-    settings, run_mode, phono3py, cell_filename, input_filename, output_filename
+    settings,
+    run_mode,
+    phono3py,
+    cell_filename,
+    input_filename,
+    output_filename,
+    interface_mode,
 ):
     """Show general setting information."""
     is_primitive_axes_auto = (
@@ -58,28 +64,32 @@ def show_general_settings(
     phonon_supercell_matrix = phono3py.phonon_supercell_matrix
 
     print("-" * 29 + " General settings " + "-" * 29)
-    print("Run mode: %s" % run_mode)
+    if run_mode:
+        print("Run mode: {run_mode}")
     if output_filename:
-        print("Output filename is modified by %s." % output_filename)
+        print(f"Output filename is modified by {output_filename}.")
     if input_filename:
-        print("Input filename is modified by %s." % input_filename)
+        print(f"Input filename is modified by {input_filename}.")
     if settings.hdf5_compression:
-        print("HDF5 data compression filter: %s" % settings.hdf5_compression)
-
-    if phono3py.calculator:
-        print("Calculator interface: %s" % phono3py.calculator)
-    print('Crystal structure was read from "%s".' % cell_filename)
+        print(f"HDF5 data compression filter: {settings.hdf5_compression}")
+    if interface_mode:
+        print(
+            f'Crystal structure was read from "{cell_filename}" '
+            f"in {interface_mode} unit."
+        )
+    else:
+        print(f'Crystal structure was read from "{cell_filename}".')
 
     print_supercell_matrix(supercell_matrix, phonon_supercell_matrix)
 
     if is_primitive_axes_auto:
         print("Primitive matrix (Auto):")
         for v in primitive_matrix:
-            print("  %s" % v)
+            print(f"  {v}")
     elif primitive_matrix is not None:
         print("Primitive matrix:")
         for v in primitive_matrix:
-            print("  %s" % v)
+            print(f"  {v}")
 
 
 def print_supercell_matrix(

From 2457584692235252fda96d1d26780047cab819b4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 2 Sep 2024 23:08:39 +0000
Subject: [PATCH 05/13] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.6.2 → v0.6.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.2...v0.6.3)
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index a5b78599..6ec4db59 100644
--- 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: v0.6.2
+  rev: v0.6.3
   hooks:
   - id: ruff
     args: [ "--fix", "--show-fixes" ]

From b7fea1a068afd53772b400bb0c7d217c1855bcf5 Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Tue, 3 Sep 2024 20:12:59 +0900
Subject: [PATCH 06/13] Update for reading pypolymlp MLPs from file

---
 phono3py/api_phono3py.py                 |  7 ++++++-
 phono3py/cui/create_force_constants.py   | 21 ++++++++++++++-------
 phono3py/cui/load.py                     |  7 ++++---
 phono3py/phonon3/displacement_fc3.py     |  2 +-
 phono3py/phonon3/reciprocal_to_normal.py |  2 +-
 5 files changed, 26 insertions(+), 13 deletions(-)

diff --git a/phono3py/api_phono3py.py b/phono3py/api_phono3py.py
index 00d54efe..41f971cb 100644
--- a/phono3py/api_phono3py.py
+++ b/phono3py/api_phono3py.py
@@ -60,6 +60,7 @@
     PypolymlpParams,
     develop_polymlp,
     evalulate_polymlp,
+    load_polymlp,
     parse_mlp_params,
 )
 from phonopy.structure.atoms import PhonopyAtoms
@@ -2226,8 +2227,12 @@ def develop_mlp(
             verbose=self._log_level - 1 > 0,
         )
 
+    def load_mlp(self, filename: str = "pypolymlp.mlp"):
+        """Load machine learning potential of pypolymlp."""
+        self._mlp = load_polymlp(filename=filename)
+
     def evaluate_mlp(self):
-        """Evaluate the machine learning potential of pypolymlp.
+        """Evaluate machine learning potential of pypolymlp.
 
         This method calculates the supercell energies and forces from the MLP
         for the displacements in self._dataset of type 2. The results are stored
diff --git a/phono3py/cui/create_force_constants.py b/phono3py/cui/create_force_constants.py
index 7d33ec6c..99eb892c 100644
--- a/phono3py/cui/create_force_constants.py
+++ b/phono3py/cui/create_force_constants.py
@@ -502,7 +502,8 @@ def _read_dataset_fc3(
         file_exists(e.filename, log_level=log_level)
 
     if use_pypolymlp:
-        phono3py.mlp_dataset = dataset
+        if forces_in_dataset(dataset):
+            phono3py.mlp_dataset = dataset
         run_pypolymlp_to_compute_forces(
             phono3py,
             mlp_params,
@@ -521,6 +522,7 @@ def run_pypolymlp_to_compute_forces(
     displacement_distance: Optional[float] = None,
     number_of_snapshots: Optional[int] = None,
     random_seed: Optional[int] = None,
+    mlp_filename: str = "pypolymlp.mlp",
     log_level: int = 0,
 ):
     """Run pypolymlp to compute forces."""
@@ -536,10 +538,18 @@ def run_pypolymlp_to_compute_forces(
                     print(f"  {k}: {v}")
     if log_level > 1:
         print("")
-    if log_level:
-        print("Developing MLPs by pypolymlp...", flush=True)
 
-    ph3py.develop_mlp(params=mlp_params)
+    if forces_in_dataset(ph3py.mlp_dataset):
+        if log_level:
+            print("Developing MLPs by pypolymlp...", flush=True)
+        ph3py.develop_mlp(params=mlp_params)
+    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.')
 
     if log_level:
         print("-" * 30 + " pypolymlp end " + "-" * 31, flush=True)
@@ -577,9 +587,6 @@ def run_pypolymlp_to_compute_forces(
             flush=True,
         )
 
-    if ph3py.mlp_dataset is None:
-        msg = "mlp_dataset has to be set before calling this method."
-        raise RuntimeError(msg)
     if ph3py.supercells_with_displacements is None:
         raise RuntimeError("Displacements are not set. Run generate_displacements.")
 
diff --git a/phono3py/cui/load.py b/phono3py/cui/load.py
index f87d6e2c..e4dda9d0 100644
--- a/phono3py/cui/load.py
+++ b/phono3py/cui/load.py
@@ -416,7 +416,8 @@ def set_dataset_and_force_constants(
     )
     if not read_fc["fc3"]:
         if use_pypolymlp:
-            ph3py.mlp_dataset = dataset
+            if forces_in_dataset(dataset):
+                ph3py.mlp_dataset = dataset
         else:
             ph3py.dataset = dataset
     read_fc["fc2"], phonon_dataset = _get_dataset_phonon_dataset_or_fc2(
@@ -461,8 +462,8 @@ def compute_force_constants_from_datasets(
     """
     fc3_calculator = extract_fc2_fc3_calculators(fc_calculator, 3)
     fc2_calculator = extract_fc2_fc3_calculators(fc_calculator, 2)
-    if not read_fc["fc3"] and (ph3py.dataset or ph3py.mlp_dataset):
-        if use_pypolymlp and forces_in_dataset(ph3py.mlp_dataset):
+    if not read_fc["fc3"]:
+        if use_pypolymlp:
             run_pypolymlp_to_compute_forces(
                 ph3py,
                 mlp_params=mlp_params,
diff --git a/phono3py/phonon3/displacement_fc3.py b/phono3py/phonon3/displacement_fc3.py
index f769c900..9afd6eac 100644
--- a/phono3py/phonon3/displacement_fc3.py
+++ b/phono3py/phonon3/displacement_fc3.py
@@ -272,7 +272,7 @@ def get_bond_symmetry(
 def get_least_orbits(atom_index, cell, site_symmetry, symprec=1e-5):
     """Find least orbits for a centering atom."""
     orbits = _get_orbits(atom_index, cell, site_symmetry, symprec)
-    mapping = np.arange(cell.get_number_of_atoms())
+    mapping = np.arange(len(cell))
 
     for i, orb in enumerate(orbits):
         for num in np.unique(orb):
diff --git a/phono3py/phonon3/reciprocal_to_normal.py b/phono3py/phonon3/reciprocal_to_normal.py
index 9cf2970e..4db52090 100644
--- a/phono3py/phonon3/reciprocal_to_normal.py
+++ b/phono3py/phonon3/reciprocal_to_normal.py
@@ -88,7 +88,7 @@ def _reciprocal_to_normal(self, grid_triplet):
                 self._fc3_normal[i, j, k] = fc3_elem / fff
 
     def _sum_in_atoms(self, band_indices, eigvecs):
-        num_atom = self._primitive.get_number_of_atoms()
+        num_atom = len(self._primitive)
         (e1, e2, e3) = eigvecs
         (b1, b2, b3) = band_indices
 

From 9fa805b1b5fa3d24ec994355ee4b305392660685 Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Wed, 4 Sep 2024 17:29:31 +0900
Subject: [PATCH 07/13] Refactoring of calculation using pypolymlp

---
 phono3py/api_phono3py.py               | 41 ++++++++++++++++------
 phono3py/cui/create_force_constants.py | 48 ++++++++++----------------
 phono3py/cui/phono3py_script.py        |  7 ++--
 3 files changed, 52 insertions(+), 44 deletions(-)

diff --git a/phono3py/api_phono3py.py b/phono3py/api_phono3py.py
index 00d54efe..d26d3bb5 100644
--- a/phono3py/api_phono3py.py
+++ b/phono3py/api_phono3py.py
@@ -2208,16 +2208,37 @@ def develop_mlp(
         else:
             _params = params
 
-        disps = self._mlp_dataset["displacements"]
-        forces = self._mlp_dataset["forces"]
-        energies = self._mlp_dataset["supercell_energies"]
-        n = int(len(disps) * (1 - test_size))
-        train_data = PypolymlpData(
-            displacements=disps[:n], forces=forces[:n], supercell_energies=energies[:n]
-        )
-        test_data = PypolymlpData(
-            displacements=disps[n:], forces=forces[n:], supercell_energies=energies[n:]
-        )
+        if _params.ntrain is not None and _params.ntest is not None:
+            ntrain = _params.ntrain
+            ntest = _params.ntest
+            disps = self._mlp_dataset["displacements"]
+            forces = self._mlp_dataset["forces"]
+            energies = self._mlp_dataset["supercell_energies"]
+            train_data = PypolymlpData(
+                displacements=disps[:ntrain],
+                forces=forces[:ntrain],
+                supercell_energies=energies[:ntrain],
+            )
+            test_data = PypolymlpData(
+                displacements=disps[-ntest:],
+                forces=forces[-ntest:],
+                supercell_energies=energies[-ntest:],
+            )
+        else:
+            disps = self._mlp_dataset["displacements"]
+            forces = self._mlp_dataset["forces"]
+            energies = self._mlp_dataset["supercell_energies"]
+            n = int(len(disps) * (1 - test_size))
+            train_data = PypolymlpData(
+                displacements=disps[:n],
+                forces=forces[:n],
+                supercell_energies=energies[:n],
+            )
+            test_data = PypolymlpData(
+                displacements=disps[n:],
+                forces=forces[n:],
+                supercell_energies=energies[n:],
+            )
         self._mlp = develop_polymlp(
             self._supercell,
             train_data,
diff --git a/phono3py/cui/create_force_constants.py b/phono3py/cui/create_force_constants.py
index c4a41cd3..c118334a 100644
--- a/phono3py/cui/create_force_constants.py
+++ b/phono3py/cui/create_force_constants.py
@@ -118,19 +118,28 @@ def create_phono3py_force_constants(
         if settings.read_fc3:
             _read_phono3py_fc3(phono3py, symmetrize_fc3r, input_filename, log_level)
         else:  # fc3 from FORCES_FC3 or ph3py_yaml
-            _read_dataset_fc3(
+            dataset = _read_dataset_fc3(
                 phono3py,
                 ph3py_yaml,
                 phono3py_yaml_filename,
                 settings.cutoff_pair_distance,
                 calculator,
-                settings.use_pypolymlp,
-                settings.mlp_params,
-                settings.displacement_distance,
-                settings.random_displacements,
-                settings.random_seed,
                 log_level,
             )
+
+            if settings.use_pypolymlp:
+                phono3py.mlp_dataset = dataset
+                run_pypolymlp_to_compute_forces(
+                    phono3py,
+                    settings.mlp_params,
+                    displacement_distance=settings.displacement_distance,
+                    number_of_snapshots=settings.random_displacements,
+                    random_seed=settings.random_seed,
+                    log_level=log_level,
+                )
+            else:
+                phono3py.dataset = dataset
+
             phono3py.produce_fc3(
                 symmetrize_fc3r=symmetrize_fc3r,
                 is_compact_fc=settings.is_compact_fc,
@@ -214,7 +223,7 @@ def parse_forces(
     fc_type: Literal["fc3", "phonon_fc2"] = "fc3",
     calculator: Optional[str] = None,
     log_level=0,
-):
+) -> dict:
     """Read displacements and forces.
 
     Physical units of displacements and forces are converted following the
@@ -454,13 +463,8 @@ def _read_dataset_fc3(
     phono3py_yaml_filename: Optional[str],
     cutoff_pair_distance: Optional[float],
     calculator: Optional[str],
-    use_pypolymlp: bool,
-    mlp_params: Union[str, dict, PypolymlpParams],
-    displacement_distance: Optional[float],
-    number_of_snapshots: Optional[int],
-    random_seed: Optional[int],
     log_level: int,
-):
+) -> dict:
     """Read or calculate fc3.
 
     Note
@@ -496,18 +500,7 @@ def _read_dataset_fc3(
         # from _get_type2_dataset
         file_exists(e.filename, log_level=log_level)
 
-    if use_pypolymlp:
-        phono3py.mlp_dataset = dataset
-        run_pypolymlp_to_compute_forces(
-            phono3py,
-            mlp_params,
-            displacement_distance=displacement_distance,
-            number_of_snapshots=number_of_snapshots,
-            random_seed=random_seed,
-            log_level=log_level,
-        )
-    else:
-        phono3py.dataset = dataset
+    return dataset
 
 
 def run_pypolymlp_to_compute_forces(
@@ -529,8 +522,6 @@ def run_pypolymlp_to_compute_forces(
             for k, v in asdict(parse_mlp_params(mlp_params)).items():
                 if v is not None:
                     print(f"  {k}: {v}")
-    if log_level > 1:
-        print("")
     if log_level:
         print("Developing MLPs by pypolymlp...", flush=True)
 
@@ -579,6 +570,7 @@ def run_pypolymlp_to_compute_forces(
         raise RuntimeError("Displacements are not set. Run generate_displacements.")
 
     ph3py.evaluate_mlp()
+    ph3py.save("phono3py_mlp_eval_dataset.yaml")
 
 
 def run_pypolymlp_to_compute_phonon_forces(
@@ -601,8 +593,6 @@ def run_pypolymlp_to_compute_phonon_forces(
                 for k, v in asdict(parse_mlp_params(mlp_params)).items():
                     if v is not None:
                         print(f"  {k}: {v}")
-        if log_level > 1:
-            print("")
         if log_level:
             print("Developing MLPs by pypolymlp...", flush=True)
 
diff --git a/phono3py/cui/phono3py_script.py b/phono3py/cui/phono3py_script.py
index 943b9311..886fa0df 100644
--- a/phono3py/cui/phono3py_script.py
+++ b/phono3py/cui/phono3py_script.py
@@ -165,16 +165,13 @@ def finalize_phono3py(
 
     _physical_units = get_default_physical_units(phono3py.calculator)
 
-    write_force_sets = phono3py.mlp is not None
-    _write_displacements = write_displacements or phono3py.mlp is not None
-
     ph3py_yaml = Phono3pyYaml(
         configuration=confs_dict,
         calculator=phono3py.calculator,
         physical_units=_physical_units,
         settings={
-            "force_sets": write_force_sets,
-            "displacements": _write_displacements,
+            "force_sets": False,
+            "displacements": write_displacements,
         },
     )
     ph3py_yaml.set_phonon_info(phono3py)

From a178e369fbbe89618d3e216c979c1bdda46731fc Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Thu, 5 Sep 2024 10:58:29 +0900
Subject: [PATCH 08/13] Add pypolymlp CLI test

---
 phono3py/api_phono3py.py               |  6 ++-
 phono3py/cui/create_force_constants.py |  6 ++-
 phono3py/cui/phono3py_script.py        |  8 ++++
 test/api/test_api_phono3py.py          |  1 +
 test/cui/test_phono3py_load_script.py  | 52 ++++++++++++++++++++++++++
 5 files changed, 70 insertions(+), 3 deletions(-)

diff --git a/phono3py/api_phono3py.py b/phono3py/api_phono3py.py
index 4dc46d22..9ded6132 100644
--- a/phono3py/api_phono3py.py
+++ b/phono3py/api_phono3py.py
@@ -2209,7 +2209,11 @@ def develop_mlp(
         else:
             _params = params
 
-        if _params.ntrain is not None and _params.ntest is not None:
+        if (
+            _params is not None
+            and _params.ntrain is not None
+            and _params.ntest is not None
+        ):
             ntrain = _params.ntrain
             ntest = _params.ntest
             disps = self._mlp_dataset["displacements"]
diff --git a/phono3py/cui/create_force_constants.py b/phono3py/cui/create_force_constants.py
index c68c836a..94c82b46 100644
--- a/phono3py/cui/create_force_constants.py
+++ b/phono3py/cui/create_force_constants.py
@@ -514,7 +514,7 @@ def run_pypolymlp_to_compute_forces(
     displacement_distance: Optional[float] = None,
     number_of_snapshots: Optional[int] = None,
     random_seed: Optional[int] = None,
-    mlp_filename: str = "pypolymlp.mlp",
+    mlp_filename: str = "phono3py.pmlp",
     log_level: int = 0,
 ):
     """Run pypolymlp to compute forces."""
@@ -533,6 +533,9 @@ def run_pypolymlp_to_compute_forces(
         if log_level:
             print("Developing MLPs by pypolymlp...", flush=True)
         ph3py.develop_mlp(params=mlp_params)
+        ph3py.mlp.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:
@@ -581,7 +584,6 @@ def run_pypolymlp_to_compute_forces(
         raise RuntimeError("Displacements are not set. Run generate_displacements.")
 
     ph3py.evaluate_mlp()
-    ph3py.save("phono3py_mlp_eval_dataset.yaml")
 
 
 def run_pypolymlp_to_compute_phonon_forces(
diff --git a/phono3py/cui/phono3py_script.py b/phono3py/cui/phono3py_script.py
index 3d767e3e..2f699db2 100644
--- a/phono3py/cui/phono3py_script.py
+++ b/phono3py/cui/phono3py_script.py
@@ -163,6 +163,14 @@ def finalize_phono3py(
     else:
         yaml_filename = filename
 
+    if phono3py.mlp_dataset is not None:
+        mlp_eval_filename = "phono3py_mlp_eval_dataset.yaml"
+        if log_level:
+            print(
+                f'Dataset generated using MMLPs was written in "{mlp_eval_filename}".'
+            )
+        phono3py.save(mlp_eval_filename)
+
     _physical_units = get_default_physical_units(phono3py.calculator)
 
     ph3py_yaml = Phono3pyYaml(
diff --git a/test/api/test_api_phono3py.py b/test/api/test_api_phono3py.py
index beb63677..98fb2bfa 100644
--- a/test/api/test_api_phono3py.py
+++ b/test/api/test_api_phono3py.py
@@ -173,6 +173,7 @@ def test_type2_forces_energies_setter_Si(si_111_222_rd: Phono3py):
 def test_use_pypolymlp_mgo(mgo_222rd_444rd: Phono3py):
     """Test use_pypolymlp in produce_fc3."""
     pytest.importorskip("pypolymlp")
+    pytest.importorskip("symfc")
 
     ph3_in = mgo_222rd_444rd
     ph3 = Phono3py(
diff --git a/test/cui/test_phono3py_load_script.py b/test/cui/test_phono3py_load_script.py
index 4437e06d..cd8a4d32 100644
--- a/test/cui/test_phono3py_load_script.py
+++ b/test/cui/test_phono3py_load_script.py
@@ -36,6 +36,7 @@ class MockArgs:
     is_bterta: Optional[bool] = None
     mesh_numbers: Optional[Sequence] = None
     temperatures: Optional[Sequence] = None
+    use_pypolymlp: bool = False
     input_filename = None
     output_filename = None
     input_output_filename = None
@@ -114,6 +115,54 @@ def test_phono3py_with_QE_calculator(load_phono3py_yaml):
             file_path.unlink()
 
 
+def test_phono3py_load_with_pypolymlp_si():
+    """Test phono3py-load script with pypolymlp.
+
+    First run generates phono3py.pmlp.
+    Second run uses phono3py.pmlp.
+
+    """
+    pytest.importorskip("pypolymlp")
+    pytest.importorskip("symfc")
+
+    argparse_control = _get_phono3py_load_args(
+        cwd / ".." / "phono3py_params_Si-111-222-rd.yaml.xz",
+        fc_calculator="symfc",
+        use_pypolymlp=True,
+    )
+
+    with pytest.raises(SystemExit) as excinfo:
+        main(**argparse_control)
+    assert excinfo.value.code == 0
+
+    # phono3py.yaml and fc2.hd5 are used in the next run. So they are not deleted.
+    for created_filename in ("fc3.hdf5", "phono3py_mlp_eval_dataset.yaml"):
+        file_path = pathlib.Path(cwd_called / created_filename)
+        if file_path.exists():
+            file_path.unlink()
+
+    argparse_control = _get_phono3py_load_args(
+        cwd / "phono3py.yaml",
+        fc_calculator="symfc",
+        use_pypolymlp=True,
+    )
+
+    with pytest.raises(SystemExit) as excinfo:
+        main(**argparse_control)
+    assert excinfo.value.code == 0
+
+    for created_filename in (
+        "phono3py.yaml",
+        "fc2.hdf5",
+        "fc3.hdf5",
+        "phono3py.pmlp",
+        "phono3py_mlp_eval_dataset.yaml",
+    ):
+        file_path = pathlib.Path(cwd_called / created_filename)
+        if file_path.exists():
+            file_path.unlink()
+
+
 def _get_phono3py_load_args(
     phono3py_yaml_filepath: Union[str, pathlib.Path],
     fc_calculator: Optional[str] = None,
@@ -121,6 +170,7 @@ def _get_phono3py_load_args(
     is_bterta: bool = False,
     temperatures: Optional[Sequence] = None,
     mesh_numbers: Optional[Sequence] = None,
+    use_pypolymlp: bool = False,
 ):
     # Mock of ArgumentParser.args.
     if load_phono3py_yaml:
@@ -130,6 +180,7 @@ def _get_phono3py_load_args(
             is_bterta=is_bterta,
             temperatures=temperatures,
             mesh_numbers=mesh_numbers,
+            use_pypolymlp=use_pypolymlp,
             log_level=1,
         )
     else:
@@ -141,6 +192,7 @@ def _get_phono3py_load_args(
             is_bterta=is_bterta,
             temperatures=temperatures,
             mesh_numbers=mesh_numbers,
+            use_pypolymlp=use_pypolymlp,
         )
 
     # See phono3py-load script.

From 92932847d6f3584cbea22010f8f13e7ded8647c2 Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Thu, 5 Sep 2024 13:08:31 +0900
Subject: [PATCH 09/13] Fix test

---
 .github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml | 2 +-
 .github/workflows/phono3py-pytest-conda-mkl-v2.yml         | 2 +-
 .github/workflows/phono3py-pytest-conda-mkl.yml            | 2 +-
 .github/workflows/phono3py-pytest-conda-numpy2.yml         | 2 +-
 .github/workflows/phono3py-pytest-conda-phphmtblas.yml     | 2 +-
 .github/workflows/phono3py-pytest-conda.yml                | 2 +-
 phono3py/api_phono3py.py                                   | 2 +-
 test/cui/test_phono3py_load_script.py                      | 2 +-
 8 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml b/.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml
index f32a9b58..a262cdf6 100644
--- a/.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml
+++ b/.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml
@@ -35,7 +35,7 @@ jobs:
     - name: Install phonopy develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        git clone https://github.com/phonopy/phonopy.git
         cd phonopy
         pip install -e . -vvv
         cd ..
diff --git a/.github/workflows/phono3py-pytest-conda-mkl-v2.yml b/.github/workflows/phono3py-pytest-conda-mkl-v2.yml
index 7a285923..a6d5c8d5 100644
--- a/.github/workflows/phono3py-pytest-conda-mkl-v2.yml
+++ b/.github/workflows/phono3py-pytest-conda-mkl-v2.yml
@@ -35,7 +35,7 @@ jobs:
     - name: Install phonopy develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        git clone https://github.com/phonopy/phonopy.git
         cd phonopy
         pip install -e . -vvv
         cd ..
diff --git a/.github/workflows/phono3py-pytest-conda-mkl.yml b/.github/workflows/phono3py-pytest-conda-mkl.yml
index a9be299a..f42b8264 100644
--- a/.github/workflows/phono3py-pytest-conda-mkl.yml
+++ b/.github/workflows/phono3py-pytest-conda-mkl.yml
@@ -35,7 +35,7 @@ jobs:
     - name: Install phonopy develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        git clone https://github.com/phonopy/phonopy.git
         cd phonopy
         pip install -e . -vvv
         cd ..
diff --git a/.github/workflows/phono3py-pytest-conda-numpy2.yml b/.github/workflows/phono3py-pytest-conda-numpy2.yml
index fdb106b2..6265efaf 100644
--- a/.github/workflows/phono3py-pytest-conda-numpy2.yml
+++ b/.github/workflows/phono3py-pytest-conda-numpy2.yml
@@ -35,7 +35,7 @@ jobs:
     - name: Install symfc develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/symfc/symfc.git
+        git clone https://github.com/symfc/symfc.git
         cd symfc
         pip install -e . -vvv
         cd ..
diff --git a/.github/workflows/phono3py-pytest-conda-phphmtblas.yml b/.github/workflows/phono3py-pytest-conda-phphmtblas.yml
index 59f41d31..5c2dc672 100644
--- a/.github/workflows/phono3py-pytest-conda-phphmtblas.yml
+++ b/.github/workflows/phono3py-pytest-conda-phphmtblas.yml
@@ -35,7 +35,7 @@ jobs:
     - name: Install phonopy develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        git clone https://github.com/phonopy/phonopy.git
         cd phonopy
         pip install -e . -vvv
         cd ..
diff --git a/.github/workflows/phono3py-pytest-conda.yml b/.github/workflows/phono3py-pytest-conda.yml
index ad620453..1df4515a 100644
--- a/.github/workflows/phono3py-pytest-conda.yml
+++ b/.github/workflows/phono3py-pytest-conda.yml
@@ -28,7 +28,7 @@ jobs:
     - name: Install phonopy develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        git clone https://github.com/phonopy/phonopy.git
         cd phonopy
         pip install -e . -vvv
         cd ..
diff --git a/phono3py/api_phono3py.py b/phono3py/api_phono3py.py
index 9ded6132..b42d4a16 100644
--- a/phono3py/api_phono3py.py
+++ b/phono3py/api_phono3py.py
@@ -2252,7 +2252,7 @@ def develop_mlp(
             verbose=self._log_level - 1 > 0,
         )
 
-    def load_mlp(self, filename: str = "pypolymlp.mlp"):
+    def load_mlp(self, filename: str = "phono3py.pmlp"):
         """Load machine learning potential of pypolymlp."""
         self._mlp = load_polymlp(filename=filename)
 
diff --git a/test/cui/test_phono3py_load_script.py b/test/cui/test_phono3py_load_script.py
index cd8a4d32..c3b751b1 100644
--- a/test/cui/test_phono3py_load_script.py
+++ b/test/cui/test_phono3py_load_script.py
@@ -142,7 +142,7 @@ def test_phono3py_load_with_pypolymlp_si():
             file_path.unlink()
 
     argparse_control = _get_phono3py_load_args(
-        cwd / "phono3py.yaml",
+        cwd_called / "phono3py.yaml",
         fc_calculator="symfc",
         use_pypolymlp=True,
     )

From 998a660e6a8d3865825432ea13158bcb64de6aeb Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Thu, 5 Sep 2024 13:14:21 +0900
Subject: [PATCH 10/13] Fix github workflows

---
 .github/workflows/phono3py-pytest-conda-numpy2.yml     | 2 +-
 .github/workflows/phono3py-pytest-conda-phphmtblas.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/phono3py-pytest-conda-numpy2.yml b/.github/workflows/phono3py-pytest-conda-numpy2.yml
index 6265efaf..85aee8be 100644
--- a/.github/workflows/phono3py-pytest-conda-numpy2.yml
+++ b/.github/workflows/phono3py-pytest-conda-numpy2.yml
@@ -42,7 +42,7 @@ jobs:
     - name: Install phonopy develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        git clone https://github.com/phonopy/phonopy.git
         cd phonopy
         pip install -e . -vvv
         cd ..
diff --git a/.github/workflows/phono3py-pytest-conda-phphmtblas.yml b/.github/workflows/phono3py-pytest-conda-phphmtblas.yml
index 5c2dc672..5771b33b 100644
--- a/.github/workflows/phono3py-pytest-conda-phphmtblas.yml
+++ b/.github/workflows/phono3py-pytest-conda-phphmtblas.yml
@@ -28,7 +28,7 @@ jobs:
     - name: Install symfc develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/symfc/symfc.git
+        git clone https://github.com/symfc/symfc.git
         cd symfc
         pip install -e . -vvv
         cd ..

From 9b23427cbf162433e51ca6c65364a8a42e27cda4 Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Thu, 5 Sep 2024 16:38:13 +0900
Subject: [PATCH 11/13] Separate detail of Phono3py.develop_mlp() into a
 function in phonopy

---
 phono3py/api_phono3py.py | 51 +++++-----------------------------------
 1 file changed, 6 insertions(+), 45 deletions(-)

diff --git a/phono3py/api_phono3py.py b/phono3py/api_phono3py.py
index b42d4a16..c1d8da07 100644
--- a/phono3py/api_phono3py.py
+++ b/phono3py/api_phono3py.py
@@ -58,6 +58,7 @@
 from phonopy.interface.pypolymlp import (
     PypolymlpData,
     PypolymlpParams,
+    develop_mlp_by_pypolymlp,
     develop_polymlp,
     evalulate_polymlp,
     load_polymlp,
@@ -2204,52 +2205,12 @@ def develop_mlp(
         if self._mlp_dataset is None:
             raise RuntimeError("MLP dataset is not set.")
 
-        if params is not None:
-            _params = parse_mlp_params(params)
-        else:
-            _params = params
-
-        if (
-            _params is not None
-            and _params.ntrain is not None
-            and _params.ntest is not None
-        ):
-            ntrain = _params.ntrain
-            ntest = _params.ntest
-            disps = self._mlp_dataset["displacements"]
-            forces = self._mlp_dataset["forces"]
-            energies = self._mlp_dataset["supercell_energies"]
-            train_data = PypolymlpData(
-                displacements=disps[:ntrain],
-                forces=forces[:ntrain],
-                supercell_energies=energies[:ntrain],
-            )
-            test_data = PypolymlpData(
-                displacements=disps[-ntest:],
-                forces=forces[-ntest:],
-                supercell_energies=energies[-ntest:],
-            )
-        else:
-            disps = self._mlp_dataset["displacements"]
-            forces = self._mlp_dataset["forces"]
-            energies = self._mlp_dataset["supercell_energies"]
-            n = int(len(disps) * (1 - test_size))
-            train_data = PypolymlpData(
-                displacements=disps[:n],
-                forces=forces[:n],
-                supercell_energies=energies[:n],
-            )
-            test_data = PypolymlpData(
-                displacements=disps[n:],
-                forces=forces[n:],
-                supercell_energies=energies[n:],
-            )
-        self._mlp = develop_polymlp(
+        self._mlp = develop_mlp_by_pypolymlp(
+            self._mlp_dataset,
             self._supercell,
-            train_data,
-            test_data,
-            params=_params,
-            verbose=self._log_level - 1 > 0,
+            params=params,
+            test_size=test_size,
+            log_level=self._log_level,
         )
 
     def load_mlp(self, filename: str = "phono3py.pmlp"):

From cd61548dbaa84ad296150ea3e0c50b569613d02e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 9 Sep 2024 23:14:46 +0000
Subject: [PATCH 12/13] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.6.3 → v0.6.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.3...v0.6.4)
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6ec4db59..b76dcf07 100644
--- 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: v0.6.3
+  rev: v0.6.4
   hooks:
   - id: ruff
     args: [ "--fix", "--show-fixes" ]

From 704de3e4d0ee1cb11113f46ee1834237fe29cc12 Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Fri, 13 Sep 2024 15:09:53 +0900
Subject: [PATCH 13/13] Set version 3.5.0

---
 doc/changelog.md    |   4 +
 doc/conf.py         |   4 +-
 doc/index.md        |   5 +-
 phono3py/version.py |   2 +-
 pyproject.toml      |   2 +-
 setup-legacy.cfg    |   7 -
 setup-legacy.py     | 340 --------------------------------------------
 7 files changed, 9 insertions(+), 355 deletions(-)
 delete mode 100644 setup-legacy.cfg
 delete mode 100644 setup-legacy.py

diff --git a/doc/changelog.md b/doc/changelog.md
index b703de32..25cf858f 100644
--- a/doc/changelog.md
+++ b/doc/changelog.md
@@ -2,6 +2,10 @@
 
 # Change Log
 
+## Sep-13-2024: Version 3.5
+
+- Maintenance release.
+
 ## Aug-23-2024: Version 3.4
 
 - Update for spglib v2.5 and for following the change in phonopy.
diff --git a/doc/conf.py b/doc/conf.py
index d091ca08..cb1804de 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -58,9 +58,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = "3.4"
+version = "3.5"
 # The full version, including alpha/beta/rc tags.
-release = "3.4.0"
+release = "3.5.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/doc/index.md b/doc/index.md
index 0ec63523..d7272258 100644
--- a/doc/index.md
+++ b/doc/index.md
@@ -30,11 +30,8 @@ Papers that may introduce phono3py:
   [JPCM.35.353001](https://iopscience.iop.org/article/10.1088/1361-648X/acd831)
   (open access)
 
-
-## Documentation
-
 ```{toctree}
-:maxdepth: 1
+:hidden:
 install
 workflow
 examples
diff --git a/phono3py/version.py b/phono3py/version.py
index cb1c9419..d6368a53 100644
--- a/phono3py/version.py
+++ b/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__ = "3.4.0"
+__version__ = "3.5.0"
diff --git a/pyproject.toml b/pyproject.toml
index c9709b36..af837355 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,7 +16,7 @@ dependencies = [
     "matplotlib>=2.2.2",
     "h5py>=3.0",
     "spglib>=2.3",
-    "phonopy>=2.27,<2.28",
+    "phonopy>=2.28,<2.29",
 ]
 license = { file = "LICENSE" }
 
diff --git a/setup-legacy.cfg b/setup-legacy.cfg
deleted file mode 100644
index 01d3497b..00000000
--- a/setup-legacy.cfg
+++ /dev/null
@@ -1,7 +0,0 @@
-[options]
-package_dir=
-    =.
-packages=find:
-
-[options.packages.find]
-where=.
diff --git a/setup-legacy.py b/setup-legacy.py
deleted file mode 100644
index 1784f761..00000000
--- a/setup-legacy.py
+++ /dev/null
@@ -1,340 +0,0 @@
-"""Phono3py setup.py.
-
-Cmake handles automatic finding of library.
-Custom settings should be written in site.cfg.
-
-To fully customize using site.cfg,
-set PHONO3PY_USE_CMAKE=false to avoid running cmake.
-
-"""
-
-import os
-import pathlib
-import shutil
-import subprocess
-
-import numpy
-import setuptools
-
-if (
-    "PHONO3PY_USE_CMAKE" in os.environ
-    and os.environ["PHONO3PY_USE_CMAKE"].lower() == "false"
-):
-    use_cmake = False
-else:
-    use_cmake = True
-
-
-def _run_cmake(build_dir):
-    build_dir.mkdir()
-    args = [
-        "cmake",
-        "-S",
-        ".",
-        "-B",
-        "_build",
-        "-DPHONONCALC=on",
-        "-DPHPHCALC=on",
-        "-DCMAKE_INSTALL_PREFIX=.",
-    ]
-    if (
-        "PHPHCALC_USE_MTBLAS" in os.environ
-        and os.environ["PHPHCALC_USE_MTBLAS"].lower() == "true"
-    ):
-        args.append("-DPHPHCALC_USE_MTBLAS=on")
-
-    # if "CONDA_PREFIX" in os.environ:
-    #     args.append("-DUSE_CONDA_PATH=on")
-    # if "CC" in os.environ:
-    #     args.append(f'-DCMAKE_C_COMPILER={os.environ["CC"]}')
-
-    cmake_output = subprocess.check_output(args)
-    print(cmake_output.decode("utf-8"))
-    subprocess.check_call(["cmake", "--build", "_build", "-v"])
-    return cmake_output
-
-
-def _clean_cmake(build_dir):
-    if build_dir.exists():
-        shutil.rmtree(build_dir)
-
-
-def _get_params_from_site_cfg():
-    """Read extra_compile_args and extra_link_args.
-
-    Examples
-    --------
-    # For macOS
-    extra_compile_args = -fopenmp=libomp
-    extra_link_args = -lomp -lopenblas
-
-    # For linux
-    extra_compile_args = -fopenmp
-    extra_link_args = -lgomp  -lopenblas -lpthread
-
-    """
-    params = {
-        "define_macros": [],
-        "extra_link_args": [],
-        "extra_compile_args": [],
-        "extra_objects": [],
-        "include_dirs": [],
-    }
-    use_mkl_lapacke = False
-    use_threaded_blas = False
-
-    site_cfg_file = pathlib.Path.cwd() / "site.cfg"
-    if not site_cfg_file.exists():
-        return params
-
-    with open(site_cfg_file) as f:
-        lines = [line.strip().split("=", maxsplit=1) for line in f]
-
-        for line in lines:
-            if len(line) < 2:
-                continue
-            key = line[0].strip()
-            val = line[1].strip()
-            if key not in params:
-                continue
-            if key == "define_macros":
-                pair = val.split(maxsplit=1)
-                if pair[1].lower() == "none":
-                    pair[1] = None
-                params[key].append(tuple(pair))
-            else:
-                if "mkl" in val:
-                    use_mkl_lapacke = True
-                if "openblas" in val:
-                    use_threaded_blas = True
-                params[key] += val.split()
-
-    if use_mkl_lapacke:
-        params["define_macros"].append(("MKL_LAPACKE", None))
-    if use_threaded_blas:
-        params["define_macros"].append(("MULTITHREADED_BLAS", None))
-    if "THM_EPSILON" not in [macro[0] for macro in params["define_macros"]]:
-        params["define_macros"].append(("THM_EPSILON", "1e-10"))
-
-    print("=============================================")
-    print("Parameters found in site.cfg")
-    for key, val in params.items():
-        print(f"{key}: {val}")
-    print("=============================================")
-    return params
-
-
-def _get_extensions(build_dir):
-    """Return python extension setting.
-
-    User customization by site.cfg file
-    -----------------------------------
-    See _get_params_from_site_cfg().
-
-    Automatic search using cmake
-    ----------------------------
-    Invoked by environment variable unless PHONO3PY_USE_CMAKE=false.
-
-    """
-    params = _get_params_from_site_cfg()
-    extra_objects_ph3py = []
-    extra_objects_phcalc = []
-
-    if not use_cmake or not shutil.which("cmake"):
-        print("** Setup without using cmake **")
-        sources_ph3py = [
-            "c/_phono3py.c",
-            "c/bzgrid.c",
-            "c/collision_matrix.c",
-            "c/fc3.c",
-            "c/grgrid.c",
-            "c/imag_self_energy_with_g.c",
-            "c/interaction.c",
-            "c/isotope.c",
-            "c/lagrid.c",
-            "c/lapack_wrapper.c",
-            "c/phono3py.c",
-            "c/phonoc_utils.c",
-            "c/pp_collision.c",
-            "c/real_self_energy.c",
-            "c/real_to_reciprocal.c",
-            "c/reciprocal_to_normal.c",
-            "c/snf3x3.c",
-            "c/tetrahedron_method.c",
-            "c/triplet.c",
-            "c/triplet_grid.c",
-            "c/triplet_iw.c",
-        ]
-        sources_phcalc = [
-            "c/_phononcalc.c",
-            "c/dynmat.c",
-            "c/lapack_wrapper.c",
-            "c/phonon.c",
-            "c/phononcalc.c",
-        ]
-    else:
-        print("** Setup using cmake **")
-        use_mkl_lapacke = False
-        found_extra_link_args = []
-        found_extra_compile_args = []
-        sources_ph3py = ["c/_phono3py.c"]
-        sources_phcalc = ["c/_phononcalc.c"]
-        cmake_output = _run_cmake(build_dir)
-        found_flags = {}
-        found_libs = {}
-        for line in cmake_output.decode("utf-8").split("\n"):
-            for key in ["BLAS", "LAPACK", "OpenMP"]:
-                if f"{key} libs" in line and len(line.split()) > 3:
-                    found_libs[key] = line.split()[3].split(";")
-                if f"{key} flags" in line and len(line.split()) > 3:
-                    found_flags[key] = line.split()[3].split(";")
-        for _, value in found_libs.items():
-            found_extra_link_args += value
-            for element in value:
-                if "libmkl" in element:
-                    use_mkl_lapacke = True
-        for _, value in found_flags.items():
-            found_extra_compile_args += value
-        if use_mkl_lapacke:
-            params["define_macros"].append(("MKL_LAPACKE", None))
-
-        libph3py = list((pathlib.Path.cwd() / "_build").glob("*ph3py.*"))
-        if libph3py:
-            print("=============================================")
-            print(f"Phono3py library: {libph3py[0]}")
-            print("=============================================")
-            extra_objects_ph3py += [str(libph3py[0])]
-
-        libphcalc = list((pathlib.Path.cwd() / "_build").glob("*phcalc.*"))
-        if libphcalc:
-            print("=============================================")
-            print(f"Phonon library: {libphcalc[0]}")
-            print("=============================================")
-            extra_objects_phcalc += [str(libphcalc[0])]
-
-        params["extra_link_args"] += found_extra_link_args
-        params["extra_compile_args"] += found_extra_compile_args
-
-        print("=============================================")
-        print("Parameters found by cmake")
-        print("extra_compile_args: ", found_extra_compile_args)
-        print("extra_link_args: ", found_extra_link_args)
-        print("define_macros: ", params["define_macros"])
-        print("=============================================")
-        print()
-
-    extensions = []
-    params["define_macros"].append(("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION"))
-    params["include_dirs"] += ["c", numpy.get_include()]
-
-    extensions.append(
-        setuptools.Extension(
-            "phono3py._phono3py",
-            sources=sources_ph3py,
-            extra_link_args=params["extra_link_args"],
-            include_dirs=params["include_dirs"],
-            extra_compile_args=params["extra_compile_args"],
-            extra_objects=params["extra_objects"] + extra_objects_ph3py,
-            define_macros=params["define_macros"],
-        )
-    )
-
-    extensions.append(
-        setuptools.Extension(
-            "phono3py._phononcalc",
-            sources=sources_phcalc,
-            extra_link_args=params["extra_link_args"],
-            include_dirs=params["include_dirs"],
-            extra_compile_args=params["extra_compile_args"],
-            extra_objects=params["extra_objects"] + extra_objects_phcalc,
-            define_macros=params["define_macros"],
-        )
-    )
-    return extensions
-
-
-def _get_version() -> str:
-    git_num = None
-    version_nums = [None, None, None]
-    with open("phono3py/version.py") as w:
-        for line in w:
-            if "__version__" in line:
-                for i, num in enumerate(line.split()[2].strip('"').split(".")):
-                    version_nums[i] = num
-                break
-
-    # To deploy to pypi by travis-CI
-    if os.path.isfile("__nanoversion__.txt"):
-        nanoversion = 0
-        with open("__nanoversion__.txt") as nv:
-            try:
-                for line in nv:
-                    nanoversion = int(line.strip())
-                    break
-            except ValueError:
-                nanoversion = 0
-        if nanoversion != 0:
-            version_nums.append(nanoversion)
-    elif git_num:
-        version_nums.append(git_num)
-
-    if None in version_nums:
-        print("Failed to get version number in setup.py.")
-        raise
-
-    version = ".".join(["%s" % n for n in version_nums[:3]])
-    if len(version_nums) > 3:
-        version += "-%s" % version_nums[3]
-    return version
-
-
-def main(build_dir):
-    """Run setuptools."""
-    version = _get_version()
-
-    packages_phono3py = [
-        "phono3py",
-        "phono3py.conductivity",
-        "phono3py.cui",
-        "phono3py.interface",
-        "phono3py.other",
-        "phono3py.phonon",
-        "phono3py.phonon3",
-        "phono3py.sscha",
-    ]
-    scripts_phono3py = [
-        "scripts/phono3py",
-        "scripts/phono3py-load",
-        "scripts/phono3py-kaccum",
-        "scripts/phono3py-kdeplot",
-        "scripts/phono3py-coleigplot",
-    ]
-
-    setuptools.setup(
-        name="phono3py",
-        version=version,
-        description="This is the phono3py module.",
-        author="Atsushi Togo",
-        author_email="atz.togo@gmail.com",
-        url="http://phonopy.github.io/phono3py/",
-        packages=packages_phono3py,
-        python_requires=">=3.8",
-        install_requires=[
-            "numpy>=1.17.0",
-            "scipy",
-            "PyYAML>=5.3",
-            "matplotlib>=2.2.2",
-            "h5py>=3.0",
-            "spglib>=2.0",
-            "phonopy>=2.25,<2.26",
-        ],
-        provides=["phono3py"],
-        scripts=scripts_phono3py,
-        ext_modules=_get_extensions(build_dir),
-    )
-    _clean_cmake(build_dir)
-
-
-if __name__ == "__main__":
-    build_dir = pathlib.Path.cwd() / "_build"
-    main(build_dir)