Merge branch 'develop' into publish-gh-pages

.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: v0.6.3
   hooks:
   - id: ruff
     args: [ "--fix", "--show-fixes" ]

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)
 

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

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 (
@@ -497,7 +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,
@@ -516,6 +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."""
@@ -531,10 +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)
@@ -572,9 +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.")
 

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