Merge pull request #117 from SSCHAcode/spglib_fix

Fixed the spglib symmetrization to work with spglib beyond 2.2

Author: mesonepigreco

UserGuide/gettingstarted.rst

@@ -309,20 +309,20 @@ This tutorial requires spglib and the ASE packages installed.
    struct.has_unit_cell = True # periodic boundary conditions on
 
    # Lets see the symmetries that prints spglib
-   print("Original space group: ", spglib.get_spacegroup(struct.get_ase_atoms()))
+   print("Original space group: ", spglib.get_spacegroup(struct.get_spglib_cell()))
 
    # The previous command should print
    # Original space group: Im-3m (299)
 
    # Lets store the symmetries and convert from spglib to the CellConstructor
-   syms = spglib.get_symmetry(struct.get_ase_atoms())
+   syms = spglib.get_symmetry(struct.get_spglib_cell())
    cc_syms = CC.symmetries.GetSymmetriesFromSPGLIB(syms)
 
    # We can add a random noise on the atoms
    struct.coords += np.random.normal(0, 0.01, size = (2, 3))
 
    # Let us print again the symmetry group
-   print("Space group with noise: ", spglib.get_spacegroup(struct.get_ase_atoms()))
+   print("Space group with noise: ", spglib.get_spacegroup(struct.get_spglib_cell()))
 
    # This time the code will print
    # Space group with noise: P-1 (2)
@@ -333,7 +333,7 @@ This tutorial requires spglib and the ASE packages installed.
    struct.impose_symmetries(cc_syms)
 
    # The previous command will print details on the symmetrization iterations
-   print("Final group: ", spglib.get_spacegroup(struct.get_ase_atoms()))
+   print("Final group: ", spglib.get_spacegroup(struct.get_spglib_cell()))
    # Now the structure will be again in the Im-3m group.
 
 You can pass to all spglib commands a threshold for the symmetrization. In this case you can also use a large threshold and get the symmetries of the closest larger space group. You can use them to constrain the symmetries.

cellconstructor/Phonons.py

@@ -1371,7 +1371,7 @@ def load_phonopy(self, yaml_filename = "phonopy.yaml", fc_filename = None):
         It needs two files: the file with the structure information,
         and the file with the force constant matrix.
 
-        TODO: Test properly, possible bugs.
+        TODO: Not working!!
 
         Parameters
         ----------
@@ -3214,7 +3214,7 @@ def SymmetrizeSupercell(self, supercell_size = None):
         #qe_sym.SetupQPoint()
         qe_sym.ApplySymmetriesToV2(superdyn.dynmats[0])
 
-        #spgsym = spglib.get_symmetry(superdyn.structure.get_ase_atoms())
+        #spgsym = spglib.get_symmetry(superdyn.structure.get_spglib_cell())
         #syms = symmetries.GetSymmetriesFromSPGLIB(spgsym, False)
         #superdyn.ForceSymmetries(syms)
 
@@ -4804,7 +4804,7 @@ def compute_phonons_finite_displacements_sym(structure, ase_calculator, epsilon=
 
     #print("DEBUG:", debug)
     # Use spglib to get all the symmetry operations
-    symm = spglib.get_symmetry(super_structure.get_ase_atoms())
+    symm = spglib.get_symmetry(super_structure.get_spglib_cell())
     symm = symmetries.GetSymmetriesFromSPGLIB(symm)
     n_syms = len(symm)
 

cellconstructor/Structure.py

@@ -1468,6 +1468,36 @@ def get_ase_atoms(self):
 
         return atm
 
+    
+    def get_spglib_cell(self):
+        """
+        Convert the current structure in a valid spglib cell 
+        for computing the symmetries.
+
+        The spglib cell is a standard tuple containing lattice, positions and 
+        atomic numbers.
+
+        Results
+        -------
+
+            cell : Tuple
+                the standard tuple containing (lattice, positions, numbers) for
+                spglib.
+
+        """
+
+        lattice = np.copy(self.unit_cell)
+
+        # Positions needs to be in fractional atomic units
+        positions = Methods.covariant_coordinates(lattice, self.coords)
+
+        # Numbers: convert atomic labels into integers
+        mapping = {}
+        numbers = [mapping.setdefault(s, len(mapping) + 1) for s in self.atoms]
+
+        cell = (lattice, positions, numbers)
+        return cell
+
     def get_phonopy_calculation(self, supercell = [1,1,1]):
         """
         Convert the CellConstructor structure to a phonopy object 

cellconstructor/symmetries.py

@@ -1277,7 +1277,7 @@ def SetupFromSPGLIB(self):
             raise ImportError("Error, this function works only if spglib is available")
 
         # Get the symmetries
-        spg_syms = spglib.get_symmetry(self.structure.get_ase_atoms(), symprec = self.threshold)
+        spg_syms = spglib.get_symmetry(self.structure.get_spglib_cell(), symprec = self.threshold)
         symmetries = GetSymmetriesFromSPGLIB(spg_syms, regolarize= False)
 
         trans_irt = 0

tests/TestDiagonalizeSymmetries/test_diagsymmetries.py

@@ -29,7 +29,7 @@ def test_diag_symmetries():
 
     # Get the symmetries
     supercell_s = dyn.structure.generate_supercell(dyn.GetSupercell())
-    spglib_syms = spglib.get_symmetry(dyn.structure.get_ase_atoms())
+    spglib_syms = spglib.get_symmetry(dyn.structure.get_spglib_cell())
     syms = CC.symmetries.GetSymmetriesFromSPGLIB(spglib_syms)
 
     # Get the symmetries on the polarization vectors

tests/TestImposeSymmetries/test_impose_symmetries.py

@@ -32,13 +32,13 @@ def test_impose_symmetry():
     dyn = CC.Phonons.Phonons("old_dyn", full_name=True)
 
     # Print the symmetry group at high threshold
-    GROUP = spglib.get_spacegroup(dyn.structure.get_ase_atoms(), 0.05)
-    s_group_expected = spglib.get_spacegroup(dyn.structure.get_ase_atoms())
+    GROUP = spglib.get_spacegroup(dyn.structure.get_spglib_cell(), 0.05)
+    s_group_expected = spglib.get_spacegroup(dyn.structure.get_spglib_cell())
     print ("Space group with high threshold:", s_group_expected)
     print ("Space group with low threshold:", GROUP)
 
     # Get the symmetries from the new spacegroup
-    symmetries = spglib.get_symmetry(dyn.structure.get_ase_atoms(), symprec = 0.05)
+    symmetries = spglib.get_symmetry(dyn.structure.get_spglib_cell(), symprec = 0.05)
     print("Number of symmetries: {}".format(len(symmetries["rotations"])))
 
     # Transform the spglib symmetries into the CellConstructor data type
@@ -47,7 +47,7 @@ def test_impose_symmetry():
     dyn.structure.impose_symmetries(sym_mats)
 
     # Check once again the symetry
-    s_group_after = spglib.get_spacegroup(dyn.structure.get_ase_atoms())
+    s_group_after = spglib.get_spacegroup(dyn.structure.get_spglib_cell())
     print ("New space group with high threshold:", s_group_after)
 
     assert s_group_after == GROUP

tests/TestModeSymmetries/test_double_symmetrization.py

@@ -31,7 +31,7 @@ def test_double_symmetrization(verbose = False):
     nat = ss.N_atoms
 
     # Get the simmetries
-    spglib_syms = spglib.get_symmetry(ss.get_ase_atoms())
+    spglib_syms = spglib.get_symmetry(ss.get_spglib_cell())
     syms = CC.symmetries.GetSymmetriesFromSPGLIB(spglib_syms)
 
     m = np.tile(ss.get_masses_array(), (3,1)).T.ravel()

tests/TestModeSymmetries/test_mode_symmetries.py

@@ -27,7 +27,7 @@ def test_mode_symmetries(verbose = False):
     ss = dyn.structure.generate_supercell(dyn.GetSupercell())
 
     # Load the symmetries from the structure
-    spglib_sym = spglib.get_symmetry(ss.get_ase_atoms())
+    spglib_sym = spglib.get_symmetry(ss.get_spglib_cell())
     symmetries = CC.symmetries.GetSymmetriesFromSPGLIB(spglib_sym)
 
     # Select only one of the problematic symmetries

tests/TestPhononSupercell/_test_pol_supercell.py

@@ -79,7 +79,7 @@
     print("Please, install spglib if you want to run the test on the symmetries.")
     exit(0)
 
-spglib_sym = spglib.get_symmetry(dyn_realspace.structure.get_ase_atoms())
+spglib_sym = spglib.get_symmetry(dyn_realspace.structure.get_spglib_cell())
 symmetries = CC.symmetries.GetSymmetriesFromSPGLIB(spglib_sym, False)
 
 

tests/TestQStarWithSPGLIB/test_qstar_with_spglib.py

@@ -20,9 +20,9 @@ def test_qstar_with_spglib():
     print("The total number of q:")
     print(len(cmca_dyn.q_tot))
 
-    print("Space group:", spglib.get_spacegroup(cmca_dyn.structure.get_ase_atoms()))
+    print("Space group:", spglib.get_spacegroup(cmca_dyn.structure.get_spglib_cell()))
     print("Number of symmetries:")
-    syms = spglib.get_symmetry(cmca_dyn.structure.get_ase_atoms())
+    syms = spglib.get_symmetry(cmca_dyn.structure.get_spglib_cell())
     print(len(syms["rotations"]))
 
     assert len(cmca_dyn.q_stars) == 8