Merge pull request #446 from phonopy/phonopy-load-symfc

Symfc as default when phonopy-load

.github/workflows/phonopy-pytest-conda-openmp.yml

@@ -18,7 +18,7 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v4

.github/workflows/phonopy-pytest-conda.yml

@@ -18,7 +18,7 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v4

README.md

@@ -12,11 +12,6 @@ http://phonopy.github.io/phonopy/
 
 See https://phonopy.github.io/phonopy/install.html.
 
-## Dependency
-
-It is necessary to install `symfc` and `seekpath` either via pip, conda, etc, to
-utilize the respective additional features.
-
 ## Mailing list for questions
 
 Usual phonopy questions should be sent to phonopy mailing list

doc/install.md

@@ -89,18 +89,15 @@ Prepare the following Python libraries:
 - matplotlib (>=2.2.2)
 - python-yaml (pyyaml >= 5.3)
 - python-h5py (h5py >= 3.0)
-- spglib (>=2.3)
 - scipy
+- spglib (>=2.3)
+- symfc
 
 It is recommended to install seekpath to plot phonon band structure:
 
 - seekpath
 
 
-As an external force constants calculator, installation of symfc is recommended:
-
-- symfc
-
 For the CP2K interface, the following package will be needed to install:
 
 - cp2k-input-tools

doc/phonopy-load.md

@@ -29,8 +29,11 @@ command:
    automatically enabled. This can be disabled by `--nonac` option.
 
 5. When force constants are calculated from displacements and forces dataset,
-   force constants are automatically symmetrized. To disable this, `--no-sym-fc`
-   option is used.
+   force constants are automatically symmetrized. From phonopy v2.30.0, `symfc`
+   is used for the symmetrization. The behavior of the symmetrization before
+   v2.30.0, `--fc-calculator traditional` has to be specified. `--no-sym-fc`
+   option can be used to calculate force constants in the traditional force
+   constants calculator without symmetrization.
 
 6. `--save-params` option is added. With this option, `phonopy_params.yaml` that
    contains most of the information to run phonopy, i.e., crystal structure,

phonopy/api_phonopy.py

@@ -64,7 +64,6 @@
     symmetrize_compact_force_constants,
     symmetrize_force_constants,
 )
-from phonopy.harmonic.force_constants import get_fc2 as get_phonopy_fc2
 from phonopy.interface.calculator import get_default_physical_units
 from phonopy.interface.fc_calculator import get_fc2
 from phonopy.interface.phonopy_yaml import PhonopyYaml
@@ -101,7 +100,7 @@
     isclose,
     shape_supercell_matrix,
 )
-from phonopy.structure.dataset import forces_in_dataset, get_displacements_and_forces
+from phonopy.structure.dataset import forces_in_dataset
 from phonopy.structure.grid_points import length2mesh
 from phonopy.structure.symmetry import Symmetry, symmetrize_borns_and_epsilon
 from phonopy.units import VaspToTHz
@@ -3855,37 +3854,19 @@ def _run_force_constants_from_forces(
         decimals=None,
     ) -> None:
         if self._dataset is not None:
-            if fc_calculator is not None:
-                disps, forces = get_displacements_and_forces(self._dataset)
-                self._force_constants = get_fc2(
-                    self._supercell,
-                    self._primitive,
-                    disps,
-                    forces,
-                    fc_calculator=fc_calculator,
-                    fc_calculator_options=fc_calculator_options,
-                    atom_list=distributed_atom_list,
-                    symmetry=self._symmetry,
-                    symprec=self._symprec,
-                    log_level=self._log_level,
-                )
-            else:
-                if "displacements" in self._dataset:
-                    lines = [
-                        "Type-II dataset for displacements and forces was "
-                        "given. Setting fc_calculator",
-                        "(external force constants calculator) is required "
-                        "to produce force constants.",
-                    ]
-                    raise RuntimeError("\n".join(lines))
-                self._force_constants = get_phonopy_fc2(
-                    self._supercell,
-                    self._symmetry,
-                    self._dataset,
-                    atom_list=distributed_atom_list,
-                    primitive=self._primitive,
-                    decimals=decimals,
-                )
+            self._force_constants = get_fc2(
+                self._supercell,
+                self._primitive,
+                self._dataset,
+                fc_calculator=fc_calculator,
+                fc_calculator_options=fc_calculator_options,
+                atom_list=distributed_atom_list,
+                symmetry=self._symmetry,
+                symprec=self._symprec,
+                log_level=self._log_level,
+            )
+            if decimals:
+                self._force_constants = self._force_constants.round(decimals=decimals)
 
     def _set_dynamical_matrix(self) -> None:
         import phonopy._phonopy as phonoc

phonopy/cui/phonopy_argparse.py

@@ -778,13 +778,14 @@ def get_parser(fc_symmetry=False, is_nac=False, load_phonopy_yaml=False):
     parser.add_argument(
         "--sigma", dest="sigma", default=None, help="Smearing width for DOS"
     )
-    parser.add_argument(
-        "--symfc",
-        dest="use_symfc",
-        action="store_true",
-        default=None,
-        help="Use symfc for generating force constants",
-    )
+    if not fc_symmetry:
+        parser.add_argument(
+            "--symfc",
+            dest="use_symfc",
+            action="store_true",
+            default=None,
+            help="Use symfc for generating force constants",
+        )
     parser.add_argument(
         "--symmetry",
         dest="is_check_symmetry",

phonopy/cui/phonopy_script.py

@@ -680,7 +680,9 @@ def read_force_sets_from_phonopy_yaml(phpy_yaml):
                 print_error()
             sys.exit(1)
 
-        (fc_calculator, fc_calculator_options) = _get_fc_calculator_params(settings)
+        (fc_calculator, fc_calculator_options) = _get_fc_calculator_params(
+            settings, load_phonopy_yaml=False
+        )
 
         phonon.dataset = force_sets
         if log_level:
@@ -812,7 +814,9 @@ def _store_force_constants(
     if cutoff_radius:
         phonon.set_force_constants_zero_with_radius(cutoff_radius)
 
-    # Enforce space group symmetry to force constants
+    # This enforces space group symmetry to force constants.
+    # The force constants are supposed to be read from a file since otherwise
+    # the force constants are considered to follow space group symmetry.
     if settings.fc_spg_symmetry:
         if log_level:
             print("Force constants are symmetrized by space group operations.")
@@ -830,7 +834,10 @@ def _store_force_constants(
 
     # Imporse translational invariance and index permulation symmetry to
     # force constants
-    if settings.fc_symmetry:
+    fc_calculator, _ = _get_fc_calculator_params(
+        settings, load_phonopy_yaml=load_phonopy_yaml
+    )
+    if settings.fc_symmetry and fc_calculator == "traditional":
         phonon.symmetrize_force_constants()
 
     # Write FORCE_CONSTANTS
@@ -1721,12 +1728,20 @@ def _auto_primitive_axes(primitive_matrix):
     return isinstance(primitive_matrix, str) and primitive_matrix == "auto"
 
 
-def _get_fc_calculator_params(settings):
+def _get_fc_calculator_params(settings, load_phonopy_yaml=True):
     """Return fc_calculator and fc_calculator_params from settings."""
     fc_calculator = None
     if settings.fc_calculator is not None:
         if settings.fc_calculator.lower() in fc_calculator_names:
             fc_calculator = settings.fc_calculator.lower()
+    else:
+        if settings.fc_symmetry:
+            if load_phonopy_yaml:
+                fc_calculator = "symfc"
+            else:
+                fc_calculator = "traditional"
+        else:
+            fc_calculator = "traditional"
 
     fc_calculator_options = None
     if settings.fc_calculator_options is not None:

phonopy/harmonic/force_constants.py

@@ -60,7 +60,6 @@ def get_fc2(
     dataset,
     atom_list=None,
     primitive: Optional[Primitive] = None,
-    decimals=None,
 ):
     """Force constants are computed.
 
@@ -122,9 +121,6 @@ def get_fc2(
             atom_list=atom_list,
         )
 
-    if decimals:
-        force_constants = force_constants.round(decimals=decimals)
-
     return force_constants
 
 

phonopy/interface/fc_calculator.py

@@ -43,18 +43,24 @@
 
 from phonopy.structure.atoms import PhonopyAtoms
 from phonopy.structure.cells import Primitive
+from phonopy.structure.dataset import get_displacements_and_forces
 from phonopy.structure.symmetry import Symmetry
 
-fc_calculator_names = {"alm": "ALM", "hiphive": "hiPhive", "symfc": "symfc"}
+fc_calculator_names = {
+    "alm": "ALM",
+    "hiphive": "hiPhive",
+    "symfc": "symfc",
+    "traditional": "traditional",
+    "none": "none",
+}
 
 
 # get_fc2 is called from
 # phonopy.api_phonopy.Phonopy._run_force_constants_from_forces.
 def get_fc2(
     supercell: PhonopyAtoms,
     primitive: Primitive,
-    displacements: np.ndarray,
-    forces: np.ndarray,
+    dataset: dict,
     fc_calculator: Optional[str] = None,
     fc_calculator_options: Optional[str] = None,
     atom_list: Optional[Union[Sequence[int], np.ndarray]] = None,
@@ -73,12 +79,8 @@ def get_fc2(
         Supercell
     primitive : Primitive
         Primitive cell
-    displacements : array_like
-        Displacements of atoms in supercell.
-        shape=(num_snapshots, num_atoms, 3), dtype='double', order='C'
-    forces : array_like
-        Forces of atoms in supercell.
-        shape=(num_snapshots, num_atoms, 3), dtype='double', order='C'
+    dataset : dict
+        Dataset that contains displacements, forces, and optionally energies.
     fc_calculator : str, optional
         Currently only 'alm' is supported. Default is None, meaning invoking
         'alm'.
@@ -108,6 +110,26 @@ def get_fc2(
         shape=(len(atom_list), num_atoms, 3, 3), dtype='double', order='C'.
 
     """
+    displacements, forces = get_displacements_and_forces(dataset)
+    if fc_calculator is None or fc_calculator == "traditional":
+        from phonopy.harmonic.force_constants import get_fc2
+
+        if "displacements" in dataset:
+            lines = [
+                "Type-II dataset for displacements and forces was "
+                "given. Setting fc_calculator",
+                "(external force constants calculator) is required "
+                "to produce force constants.",
+            ]
+            raise RuntimeError("\n".join(lines))
+        return get_fc2(
+            supercell,
+            symmetry,
+            dataset,
+            atom_list=atom_list,
+            primitive=primitive,
+        )
+
     if fc_calculator == "alm" or fc_calculator is None:
         from phonopy.interface.alm import get_fc2
 

phonopy/interface/symfc.py

@@ -110,9 +110,7 @@ def run_symfc(
             " Symfc start "
             "-------------------------------"
         )
-        print(
-            "Symfc is a non-trivial force constants calculator. Please cite the paper:"
-        )
+        print("Symfc is a force constants calculator. See the following paper:")
         print("A. Seko and A. Togo, arXiv:2403.03588.")
         print("Symfc is developed at https://github.com/symfc/symfc.")
         print(f"Computing {_orders} order force constants.", flush=True)

pyproject.toml

@@ -15,7 +15,8 @@ dependencies = [
     "matplotlib>=2.2.2",
     "h5py>=3.0",
     "spglib>=2.3",
-    "scipy"
+    "scipy",
+    "symfc",
 ]
 license = { file = "LICENSE" }
 
@@ -26,9 +27,8 @@ Repository = "https://github.com/phonopy/phonopy"
 [project.optional-dependencies]
 cp2k = ["cp2k-input-tools"]
 seekpath = ["seekpath"]
-symfc = ["symfc"]
 pypolymlp = ["pypolymlp"]
-tools = ["seekpath", "symfc", "pypolymlp"]
+tools = ["seekpath", "pypolymlp"]
 
 [project.scripts]
 phonopy = "phonopy.scripts.phonopy:run"