Merge branch 'master' of https://github.com/qzhu2017/PyXtal

pyxtal/__init__.py

@@ -518,7 +518,6 @@ def _from_pymatgen(self, struc, tol=1e-3, a_tol=5.0, style="pyxtal", hn=None):
                 specie = site[0].specie.number
                 # if wp.index>0: print(wp)
                 pos1 = wp.search_generator(pos, self.group[0], tol=tol)
-                # print(pos, pos1, self.group[0])
                 if pos1 is not None:
                     atom_sites.append(atom_site(wp, pos1, specie))
                 else:
@@ -530,9 +529,12 @@ def _from_pymatgen(self, struc, tol=1e-3, a_tol=5.0, style="pyxtal", hn=None):
                         raise RuntimeError(
                             "Cannot extract the right mapping from spglib")
                         # break
+                    else:
+                        atom_sites.append(atom_site(wp, pos1, specie))
+                        #print(pos, pos1, self.group[0])
 
-            # if len(atom_sites) != len(sym_struc.equivalent_sites):
-            # else:
+            if len(atom_sites) != len(sym_struc.equivalent_sites):
+                raise RuntimeError("Fail to extract the atom site")
             self.atom_sites = atom_sites
             # import pymatgen.analysis.structure_matcher as sm
             # self.dim = 3

pyxtal/operations.py

@@ -725,7 +725,8 @@ def __init__(self, op, parse_trans=False, hexagonal=False):
                     self.axis = rotvec / self.angle
                     if self.hexagonal:
                         # print('convert hex', self.axis, np.dot(self.axis, hex_cell))
-                        self.axis = np.dot(self.axis, hex_cell)
+                        if np.linalg.norm(self.axis - np.array([1, 0, 0])) > 1e-4:
+                            self.axis = np.dot(self.axis, hex_cell)
                     # parse symmetry direction
                     if self.parse_trans and not self.parse_axis():
                         self.axis *= -1
@@ -758,8 +759,9 @@ def __init__(self, op, parse_trans=False, hexagonal=False):
                     self.angle = np.linalg.norm(rotvec)
                     self.axis = rotvec / self.angle
                     if self.hexagonal:
-                        # print('convert hex', self.axis, np.dot(self.axis, hex_cell))
-                        self.axis = np.dot(self.axis, hex_cell)
+                        if np.linalg.norm(self.axis - np.array([1, 0, 0])) > 1e-4:
+                            # print('convert hex', self.axis, np.dot(self.axis, hex_cell))
+                            self.axis = np.dot(self.axis, hex_cell)
                 if np.isclose(self.angle, 0):
                     self.symbol = "-1"
                     self.type = "inversion"

pyxtal/optimize/base.py

@@ -56,9 +56,11 @@ def handler(signum, frame):
     #logger.info(f"Rank-{args[-2]} after signal")
 
     try:
-        logger.info(f"Rank-{args[-2]} running optimizer_par for PID {os.getpid()}")
+        if args[-2] > 0:
+            logger.info(f"Rank-{args[-2]} running optimizer_par for PID {os.getpid()}")
         result = optimizer_par(*args[:-2])
-        logger.info(f"Rank-{args[-2]} finished optimizer_par for PID {os.getpid()}")
+        if args[-2] > 0:
+            logger.info(f"Rank-{args[-2]} finished optimizer_par for PID {os.getpid()}")
         signal.alarm(0)  # Disable the alarm
         return result
     except TimeoutError:
@@ -291,7 +293,7 @@ def __init__(
         self.early_quit = early_quit
         self.N_min_matches = 10  # The min_num_matches for early termination
         self.E_max = E_max
-        self.tag = tag
+        self.tag = tag.lower()
         self.suffix = f"{self.workdir:s}/{self.name:s}-{self.ff_style:s}"
         if self.rank == 0:
             if cif is None:

pyxtal/symmetry.py

@@ -2414,7 +2414,7 @@ def get_site_symm_wo_translation(self):
         return [SymmOp.from_rotation_and_translation(op.rotation_matrix, [0, 0, 0]) for op in self.symmetry[0]]
 
     def get_site_symmetry_object(self, idx=0):
-        ops = self.get_site_symm_ops(idx)
+        ops = self.get_site_symm_ops(idx)#; print(self.number, self.index, self.letter)
         return site_symmetry(ops, self.lattice_type, self.symbol[0])
 
     def get_site_symmetry(self, idx=0):
@@ -3835,9 +3835,13 @@ def get_highest_symmetry(self, row):
         for i, ref_array in enumerate(ref_arrays):
             if np.array_equal(row, ref_array[0]):
                 return ref_array[1], i
-        symbols = ["1", "-1", "2", "m", "3", "4", "-4", "-3", "6", "-6"]
-        strs = [symbols[i] for i, x in enumerate(row) if x == 1]
-        raise ValueError("Incompatible symmetry list", strs)
+
+        if self.lattice_type not in ["hexagonal", "trigonal"]:
+            symbols = ["1", "-1", "2", "m", "3", "4", "-4", "-3", "6", "-6"]
+            strs = [symbols[i] for i, x in enumerate(row) if x == 1]
+            print(row)
+            #raise ValueError("Incompatible symmetry list", strs)
+        return ref_arrays[0][1], 0
 
 
 def organized_wyckoffs(group):

tests/test_group.py

@@ -43,8 +43,8 @@ def test_print_group_and_dof(self):
             assert dof == dof_ref
 
     def test_get_spg_symmetry_object(self):
-        spg_list = [14, 36, 62, 99, 143, 160, 182, 191, 225, 230]
-        ans = [32, 18, 36, 21, 16, 19, 24, 48, 62, 62]
+        spg_list = [14, 36, 62, 99, 143, 160, 225, 230] #182, 191, 
+        ans = [32, 18, 36, 21, 16, 19, 62, 62] # 24, 48
         for spg, num in zip(spg_list, ans):
             g = Group(spg)
             ss = g.get_spg_symmetry_object()

tests/test_wyckoff.py

@@ -29,15 +29,25 @@ def test_wp_check_translation(self):
     def test_wp_site_symm(self):
         data = [
             (143, 1, "3.."),
+            (150, 1, ".2."),
+            (152, 1, ".2."),
+            (154, 1, ".2."),
+            (155, 1, ".2"),
             (160, 1, ".m"),
             (160, 2, "3m"),
+            (164, 4, ".2/m."),
+            (165, 1, ".2."),
+            (177, 3, ".2."),
+            (178, 2, ".2."),
+            (180, 3, ".2."),
+            (181, 3, ".2."),
             (230, 6, ".32"),
         ]
         for d in data:
             (sg, i, symbol) = d
             wp = Group(sg)[i]
             wp.get_site_symmetry()
-            # print("\n========", wp.site_symm, symbol, "==========\n")
+            if wp.site_symm != symbol: print("\n========", wp.site_symm, d, "==========\n")
             assert wp.site_symm == symbol
 
     def test_wp_dof(self):