Plus-minus random directional displacements

phonopy/api_phonopy.py

@@ -36,6 +36,7 @@
 import sys
 import textwrap
 import warnings
+from typing import Optional, Union
 
 import numpy as np
 
@@ -885,14 +886,14 @@ class Phonopy:
 
     def generate_displacements(
         self,
-        distance=0.01,
-        is_plusminus="auto",
-        is_diagonal=True,
-        is_trigonal=False,
-        number_of_snapshots=None,
-        random_seed=None,
-        temperature=None,
-        cutoff_frequency=None,
+        distance: float = 0.01,
+        is_plusminus: Union[str, bool] = "auto",
+        is_diagonal: bool = True,
+        is_trigonal: bool = False,
+        number_of_snapshots: Optional[int] = None,
+        random_seed: Optional[int] = None,
+        temperature: Optional[float] = None,
+        cutoff_frequency: Optional[float] = None,
     ):
         """Generate displacement dataset.
 
@@ -945,16 +946,14 @@ class Phonopy:
             this value.
 
         """
-        if (
-            np.issubdtype(type(number_of_snapshots), np.integer)
-            and number_of_snapshots > 0
-        ):  # noqa: E129
+        if number_of_snapshots is not None and number_of_snapshots > 0:
             if temperature is None:
                 displacement_dataset = get_random_displacements_dataset(
                     number_of_snapshots,
                     distance,
                     len(self._supercell),
                     random_seed=random_seed,
+                    is_plusminus=(is_plusminus is True),
                 )
             else:
                 self.run_random_displacements(
@@ -3262,11 +3261,11 @@ class Phonopy:
 
     def run_random_displacements(
         self,
-        temperature,
-        number_of_snapshots=1,
-        random_seed=None,
-        dist_func=None,
-        cutoff_frequency=None,
+        temperature: float,
+        number_of_snapshots: int = 1,
+        random_seed: Optional[int] = None,
+        dist_func: Optional[str] = None,
+        cutoff_frequency: Optional[float] = None,
     ):
         """Generate random displacements from phonon structure.
 
@@ -3434,7 +3433,7 @@ class Phonopy:
             self._dynamical_matrix.is_nac()
             and self._dynamical_matrix.nac_method == "gonze"
             and self._gv_delta_q is None
-        ):  # noqa E129
+        ):
             if self._log_level:
                 msg = "Group velocity calculation:\n"
                 text = (

phonopy/harmonic/displacement.py

@@ -33,6 +33,8 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
+from typing import Optional
+
 import numpy as np
 
 directions_axis = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
@@ -238,14 +240,14 @@ def _determinant(a, b, c):
 
 
 def get_random_displacements_dataset(
-    num_supercells, distance, num_atoms, random_seed=None
+    num_supercells: int,
+    distance: float,
+    num_atoms: int,
+    random_seed: Optional[int] = None,
+    is_plusminus: bool = False,
 ):
     """Return random displacements at constant displacement distance."""
-    if (
-        np.issubdtype(type(random_seed), np.integer)
-        and random_seed >= 0
-        and random_seed < 2**32
-    ):
+    if random_seed is not None and random_seed >= 0 and random_seed < 2**32:
         seed = random_seed
     else:
         seed = None
@@ -257,6 +259,9 @@ def get_random_displacements_dataset(
     supercell_disps = np.array(
         disps.reshape(num_supercells, num_atoms, 3), dtype="double", order="C"
     )
+    if is_plusminus is True:
+        supercell_disps = np.concatenate((supercell_disps, -supercell_disps), axis=0)
+
     dataset = {"displacements": supercell_disps}
 
     if seed is not None:

phonopy/phonon/random_displacements.py

@@ -33,6 +33,8 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
+from typing import Optional, Tuple
+
 import numpy as np
 
 from phonopy.harmonic.dynamical_matrix import get_dynamical_matrix
@@ -185,7 +187,13 @@ class RandomDisplacements:
         self._uu = None
         self._uu_inv = None
 
-    def run(self, T, number_of_snapshots=1, random_seed=None, randn=None):
+    def run(
+        self,
+        T: float,
+        number_of_snapshots: int = 1,
+        random_seed: Optional[int] = None,
+        randn: Optional[Tuple] = None,
+    ):
         """Calculate random displacements.
 
         Parameters

test/harmonic/test_displacements.py

@@ -70,6 +70,51 @@ def test_tio2(ph_tio2: Phonopy):
     ph_tio2.dataset = dataset
 
 
+def test_tio2_random_disp(ph_tio2: Phonopy):
+    """Test random displacements of TiO2."""
+    dataset = deepcopy(ph_tio2.dataset)
+    disp_ref = [
+        [0, 0.01, 0.0, 0.0],
+        [0, 0.0, 0.01, 0.0],
+        [0, 0.0, 0.0, 0.01],
+        [0, 0.0, 0.0, -0.01],
+        [72, 0.01, 0.0, 0.0],
+        [72, 0.0, 0.0, 0.01],
+    ]
+    np.testing.assert_allclose(ph_tio2.displacements, disp_ref, atol=1e-8)
+    ph_tio2.generate_displacements(number_of_snapshots=4, distance=0.03)
+    d = ph_tio2.displacements
+    np.testing.assert_allclose(np.linalg.norm(d, axis=2).ravel(), 0.03, atol=1e-8)
+    ph_tio2.dataset = dataset
+
+
+def test_tio2_random_disp_plusminus(ph_tio2: Phonopy):
+    """Test random plus-minus displacements of TiO2.
+
+    Note
+    ----
+    Displacements of last 4 supercells are minus of those of first 4 supercells.
+
+    """
+    dataset = deepcopy(ph_tio2.dataset)
+    disp_ref = [
+        [0, 0.01, 0.0, 0.0],
+        [0, 0.0, 0.01, 0.0],
+        [0, 0.0, 0.0, 0.01],
+        [0, 0.0, 0.0, -0.01],
+        [72, 0.01, 0.0, 0.0],
+        [72, 0.0, 0.0, 0.01],
+    ]
+    np.testing.assert_allclose(ph_tio2.displacements, disp_ref, atol=1e-8)
+    ph_tio2.generate_displacements(
+        number_of_snapshots=4, distance=0.03, is_plusminus=True
+    )
+    d = ph_tio2.displacements
+    np.testing.assert_allclose(d[:4], -d[4:], atol=1e-8)
+    np.testing.assert_allclose(np.linalg.norm(d, axis=2).ravel(), 0.03, atol=1e-8)
+    ph_tio2.dataset = dataset
+
+
 def test_zr3n4(ph_zr3n4: Phonopy):
     """Test displacements of Zr3N4."""
     dataset = deepcopy(ph_zr3n4.dataset)