Now the fix of a frequency works

Author: mesonepigreco

Modules/Ensemble.py

@@ -1706,7 +1706,12 @@ def get_preconditioned_gradient(self, subtract_sscha = True, return_error = Fals
 
         # Dyagonalize
         w, pols = supercell_dyn.DyagDinQ(0)
-        trans = CC.Methods.get_translations(pols, supercell_dyn.structure.get_masses_array())
+
+        if not self.ignore_small_w:
+            trans = CC.Methods.get_translations(pols, supercell_dyn.structure.get_masses_array())
+        else:
+            trans = np.abs(w) < CC.Phonons.__EPSILON_W__
+
         ityp = supercell_dyn.structure.get_ityp() + 1 # Py to fortran convertion
         mass = np.array(list(supercell_dyn.structure.masses.values()))
 
@@ -1893,7 +1898,12 @@ def get_stress_tensor(self, offset_stress = None, add_centroid_contrib = False,
         # Get frequencies and polarization vectors
         super_dyn = self.current_dyn.GenerateSupercellDyn(self.supercell)
         wr, pols = super_dyn.DyagDinQ(0)
-        trans = ~ CC.Methods.get_translations(pols, super_dyn.structure.get_masses_array())
+
+        if not self.ignore_small_w:
+            trans = ~ CC.Methods.get_translations(pols, super_dyn.structure.get_masses_array())
+        else:
+            trans = np.abs(wr) > CC.Phonons.__EPSILON_W__
+
         wr = np.real( wr[trans])
         pols = np.real( pols[:, trans])
 
@@ -2606,7 +2616,10 @@ def get_free_energy_hessian(self, include_v4 = False, get_full_hessian = True, v
 
 
         # Get the translational modes
-        trans = CC.Methods.get_translations(pols, dyn_supercell.structure.get_masses_array())
+        if not self.ignore_small_w:
+            trans = CC.Methods.get_translations(pols, dyn_supercell.structure.get_masses_array())
+        else:
+            trans = np.abs(w) < CC.Phonons.__EPSILON_W__
 
 
         # Get the atomic types

Modules/SchaMinimizer.py

@@ -410,7 +410,7 @@ def minimization_step(self, custom_function_gradient = None):
 
             # Preconditionate the gradient for the wyckoff minimization
             if self.precond_wyck:
-                struct_precond = GetStructPrecond(self.ensemble.current_dyn)
+                struct_precond = GetStructPrecond(self.ensemble.current_dyn, ignore_small_w = self.ensemble.ignore_small_w)
                 struct_grad_precond = struct_precond.dot(struct_grad_reshaped)
                 struct_grad = struct_grad_precond.reshape( (self.dyn.structure.N_atoms, 3))
 
@@ -1298,7 +1298,10 @@ def check_imaginary_frequencies(self):
 
             ss0 = self.ensemble.dyn_0.structure.generate_supercell(self.dyn.GetSupercell())
 
-            trans_mask = ~CC.Methods.get_translations(pold, ss0.get_masses_array())
+            if not self.ensemble.ignore_small_w:
+                trans_mask = ~CC.Methods.get_translations(pold, ss0.get_masses_array())
+            else:
+                trans_mask = np.abs(wold) > CC.Phonons.__EPSILON_W__
 
             old_n_trans = np.sum((~trans_mask).astype(int))
 
@@ -1781,7 +1784,7 @@ def ApplyFCPrecond(current_dyn, matrix, T = 0):
 
 
 
-def GetStructPrecond(current_dyn):
+def GetStructPrecond(current_dyn, ignore_small_w = False):
     r"""
     GET THE PRECONDITIONER FOR THE STRUCTURE MINIMIZATION
     =====================================================
@@ -1824,7 +1827,10 @@ def GetStructPrecond(current_dyn):
     _msi_ = 1 / np.sqrt(_m_)
 
     # Select translations
-    not_trans = ~CC.Methods.get_translations(pols, mass)
+    if not ignore_small_w:
+        not_trans = ~CC.Methods.get_translations(pols, mass)
+    else:
+        not_trans = np.abs(w) > CC.Phonons.__EPSILON_W__
 
     # Delete the translations from the dynamical matrix
     w = w[not_trans]