Merge pull request #10 from pierre-24/fix_deprecations

Fix deprecations

Author: pierre-24

phonopy_vibspec/phonons_analyzer.py

@@ -67,7 +67,7 @@ def __init__(
         dm = self.phonopy.dynamical_matrix.dynamical_matrix
         eigv, eigf = numpy.linalg.eigh(dm)
 
-        self.N = self.structure.get_number_of_atoms()
+        self.N = len(self.structure)
         l_logger.info('Analyze {} modes (including acoustic)'.format(3 * self.N))
         self.frequencies = numpy.sqrt(numpy.abs(eigv.real)) * numpy.sign(eigv.real)
         self.frequencies *= VaspToCm  # in [cm⁻¹]
@@ -90,12 +90,12 @@ def __init__(
 
         try:
             self.phonopy.set_irreps(q)
-            self.irreps = phonon.get_irreps()
+            self.irreps = phonon.irreps
 
-            # TODO: that's internal API, so subject to change!
-            for label, dgset in zip(self.irreps._get_ir_labels(), self.irreps._degenerate_sets):
-                for j in dgset:
-                    self.irrep_labels[j] = label
+            if self.irreps._ir_labels is not None:
+                for label, dgset in zip(self.irreps._ir_labels, self.irreps.band_indices):
+                    for j in dgset:
+                        self.irrep_labels[j] = label
         except RuntimeError as e:
             l_logger.warn('Error while computing irreps ({}). Incorrect labels will be assigned.'.format(e))
 
@@ -210,9 +210,7 @@ def prepare_raman(
 
             for i, (value, _) in enumerate(stencil):
                 displaced_geometry = base_geometry.copy()
-                displaced_geometry.set_positions(
-                    base_geometry.positions + value * step * self.eigendisps[mode]
-                )
+                displaced_geometry.positions = base_geometry.positions + value * step * self.eigendisps[mode]
 
                 path = directory / self.DC_GEOMETRY_TEMPLATE.format(mode + 1, i + 1)  # 1-based output
                 l_logger.debug('Write displaced geometry for (mode={}, step={}) in `{}`'.format(mode, i, path))

phonopy_vibspec/scripts/mode_analysis.py

@@ -1,5 +1,5 @@
 """
-Create a VESTA file containing the eigenvector for each mode
+Analyze the translational/rotational/vibrational contribution to each mode
 """
 
 import argparse
@@ -58,7 +58,7 @@ def main():
         '-f', '--fix-geometry', action='store_true', help='unwrap the cell and move atoms close together')
 
     parser.add_argument(
-        '-I', '--intertia', action='store_true', help='use Inertia tensor for rotations')
+        '-I', '--inertia', action='store_true', help='use Inertia tensor for rotations')
     parser.add_argument('-C', '--center', type=ArgGetVector(3), help='set the center')
 
     args = parser.parse_args()
@@ -127,7 +127,7 @@ def main():
         for i in range(3):
             ri = r - rot_projs[i].dot(r)
             ri /= numpy.linalg.norm(ri)
-            vec_rots[i][iatm * 3:(iatm + 1) * 3] = numpy.linalg.cross(ri, principal_axes[i])
+            vec_rots[i][iatm * 3:(iatm + 1) * 3] = numpy.cross(ri, principal_axes[i])
 
     for i in range(3):
         vec_rots[i] /= numpy.linalg.norm(vec_rots[i])