unitcell != supercell

phonopy_vibspec/phonons_analyzer.py

@@ -27,7 +27,7 @@ class PhononsAnalyzer:
 
     def __init__(self, phonon: phonopy.Phonopy):
         self.phonotopy = phonon
-        self.supercell = phonon.supercell
+        self.unitcell = phonon.unitcell
 
         # get eigenvalues and eigenvectors at gamma point
         # See https://github.com/phonopy/phonopy/issues/308#issuecomment-1769736200
@@ -39,7 +39,7 @@ def __init__(self, phonon: phonopy.Phonopy):
 
         mesh_dict = phonon.get_mesh_dict()
 
-        self.N = self.supercell.get_number_of_atoms()
+        self.N = self.unitcell.get_number_of_atoms()
         l_logger.info('Analyze {} modes (including acoustic)'.format(3 * self.N))
         self.frequencies = mesh_dict['frequencies'][0] * THZ_TO_INV_CM  # in [cm⁻¹]
 
@@ -50,7 +50,7 @@ def __init__(self, phonon: phonopy.Phonopy):
         self.eigenvectors = mesh_dict['eigenvectors'][0].real.T  # in  [Å sqrt(AMU)]
 
         # compute displacements with Eq. 4 of 10.1039/C7CP01680H
-        sqrt_masses = numpy.repeat(numpy.sqrt(self.supercell.masses), 3)
+        sqrt_masses = numpy.repeat(numpy.sqrt(self.unitcell.masses), 3)
         self.eigendisps = (self.eigenvectors / sqrt_masses[numpy.newaxis, :]).reshape(-1, self.N, 3)  # in [Å]
 
         # get irreps
@@ -144,7 +144,7 @@ def prepare_raman(
         mode_calcs = []
         steps = []
 
-        base_geometry = self.phonotopy.unitcell
+        base_geometry = self.unitcell
 
         for mode in modes:
             if mode < 0 or mode >= 3 * self.N:

tests/conftest.py

@@ -6,3 +6,9 @@
 def context_SiO2(monkeypatch):
     dir_ = pathlib.Path(__file__).parent / 'tests_files/SiO2'
     monkeypatch.chdir(dir_)
+
+
+@pytest.fixture
+def context_SiO2_supercell(monkeypatch):
+    dir_ = pathlib.Path(__file__).parent / 'tests_files/SiO2_supercell'
+    monkeypatch.chdir(dir_)

tests/test_vibspec.py

@@ -151,3 +151,14 @@ def test_raman_spectrum_extract_dielectrics(context_SiO2):
             assert raman_intensities[i] != pytest.approx(.0, abs=1e-3)
         else:
             assert raman_intensities[i] == pytest.approx(.0, abs=1e-3)
+
+
+def test_infrared_SiO2_supercell(context_SiO2_supercell):
+    phonons = PhononsAnalyzer.from_phonopy(
+        phonopy_yaml='phonopy_disp.yaml',
+        force_constants_filename='force_constants.hdf5',
+        born_filename='BORN'
+    )
+
+    # get spectrum
+    spectrum = phonons.infrared_spectrum()

tests/tests_files/SiO2_supercell/BORN

@@ -0,0 +1,4 @@
+# epsilon and Z* of atoms 1 4
+   2.48082155   -0.00000000    0.00000000    0.00000000    2.48082155    0.00000000    0.00000000    0.00000000    2.51333836 
+   2.98054793   -0.00000000    0.00000000   -0.00000000    3.62049126   -0.32132376    0.00000000    0.27802860    3.42535654 
+  -1.31115748   -0.49333488   -0.31019627   -0.43614151   -1.98936212   -0.67895864   -0.24344107   -0.72145846   -1.71267827