finalize spg_symmetry_table and prep for v0.6.6

doc/Usage.rst

@@ -864,8 +864,8 @@ To access the pyxtal structure
 	    H3C4O4       @ [ 0.5328  0.0993  0.0601]  WP [4a] Site [1] Euler [   0.0    0.0    0.0]
 
 
-Site Symmetry
---------------------------------
+Space Group and Site Symmetry table
+-----------------------------------
 
 PyXtal provides a
 `site_symmetry <pyxtal.symmetry.html#pyxtal.symmetry.site_symmetry>`_ class to handle the conversion of site symmetry symbols and operations.
@@ -972,7 +972,7 @@ Possible combinations include
     ['1', '-1', '2', 'm', '3', '-3', '6', '-6', '6/m']
 
 
-Finally, a one-hot matrix representation `(15, 13)` can also be obtained via 
+The one-hot matrix representation `(15, 13)` can also be obtained via 
 
 .. code-block:: Python
 
@@ -997,3 +997,48 @@ Finally, a one-hot matrix representation `(15, 13)` can also be obtained via
      [1 0 0 0 0 0 0 0 0 0 0 0 0] # 1
      [1 0 0 0 0 0 0 0 0 0 0 0 0] # 1
     ]
+
+
+Finally, the both Group and Wyckoff_position classes support the access of the symmetry element analysis via
+
+.. code-block:: Python
+
+    from pyxtal.symmetry import Group
+    g = Group(14)
+    ss_spg = g.get_spg_symmetry_object()
+    print('Space group symmetry table', g.number, g.symbol)
+    ss_spg.to_beautiful_matrix_representation()
+
+    for wp in g:
+        print('\nWp symmetry table', wp.get_label())
+        ss_wp = wp.get_site_symmetry_object()
+        ss_wp.to_beautiful_matrix_representation()
+
+::
+
+    Space group symmetry table 14 P21/c
+    Order    Axis       1    -1   2    2_1  m    a    b    c    n    d    3    3_1  3_2  4    -4   4_1  4_2  4_3  -3   6    6_1  6_2  6_3  6_4  6_5  -6   
+       0 ( 0  1  0):    1    1    0    1    0    0    0    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
+    
+    Wp symmetry table 4e
+    Order    Axis       1    -1   2    m    3    4    -4   -3   6    -6   
+       0 ( 0  1  0):    1    0    0    0    0    0    0    0    0    0      1
+    
+    Wp symmetry table 2d
+    Order    Axis       1    -1   2    m    3    4    -4   -3   6    -6   
+       0 ( 0  1  0):    1    1    0    0    0    0    0    0    0    0     -1
+    
+    Wp symmetry table 2c
+    Order    Axis       1    -1   2    m    3    4    -4   -3   6    -6   
+       0 ( 0  1  0):    1    1    0    0    0    0    0    0    0    0     -1
+    
+    Wp symmetry table 2b
+    Order    Axis       1    -1   2    m    3    4    -4   -3   6    -6   
+       0 ( 0  1  0):    1    1    0    0    0    0    0    0    0    0     -1
+    
+    Wp symmetry table 2a
+    Order    Axis       1    -1   2    m    3    4    -4   -3   6    -6   
+       0 ( 0  1  0):    1    1    0    0    0    0    0    0    0    0     -1
+    
+
+Note that the space group symmetry has 26 symmetry elements as it includes additional screw axis (`2_1`, `3_1`, `3_2`, `4_1`, `4_2`, `4_3`, `6_1`, `6_2`, `6_3, `6_4`, `6_5`) and glide plane (`a`, `b`, `c`, `d`, `n`) operations.

pyxtal/db.py

@@ -438,15 +438,25 @@ def clean_structures(self, dtol=1e-3, etol=1e-3):
         print("The following structures were deleted", to_delete)
         self.db.delete(to_delete)
 
-    def clean_structures_pmg(self, dtol=5e-2, criteria=None, max_sim=None):
+    def clean_structures_pmg(self, dtol=5e-2, criteria=None):
         """
         Clean up the db by removing the duplicate structures
         Here we check the follow criteria
             - same density
             - pymatgen check
 
+        criteria should look like the following,
+        {'CN': {'C': 3},
+         'cutoff': 1.8,
+         'MAX_energy': -8.00,
+         #'MAX_similarity': 0.2,
+         'BAD_topology': ['hcb'],
+         'BAD_dimension': [0, 2],
+        }
+
         Args:
             dtol (float): tolerance of density
+            criteria (dict): including
         """
 
         unique_rows = []
@@ -460,10 +470,29 @@ def clean_structures_pmg(self, dtol=5e-2, criteria=None, max_sim=None):
                 if not xtal.check_validity(criteria, True):
                     unique = False
                     print('Found unsatisfied criteria', row.id, row.space_group_number, row.wps)
-            if max_sim is not None:
-                if hasattr(row, 'similarity') and row.similarity > max_sim:
-                    unique = False
-                    print('Found unsatisfied similarity', row.id, row.similarity, row.space_group_number, row.wps)
+
+                if unique:
+                    if 'MAX_energy' in criteria and hasattr(row, 'ff_energy') \
+                        and row.ff_energy > criteria['MAX_energy']:
+                        unique = False
+                        print('Found unsatisfied energy', row.id, row.ff_energy, row.space_group_number, row.wps)
+                if unique:
+                    if 'MAX_similarity' in criteria and hasattr(row, 'similarity') \
+                        and row.similarity > criteria['MAX_similarity']:
+                        unique = False
+                        print('Found unsatisfied similarity', row.id, row.similarity, row.space_group_number, row.wps)
+                if unique:
+                    if 'BAD_topology' in criteria and hasattr(row, 'topology') \
+                        and row.topology[:3] in criteria['BAD_topology']:
+                        unique = False
+                        print('Found unsatisfied topology', row.id, row.topology, row.space_group_number, row.wps)
+                if unique:
+                    if 'BAD_dimension' in criteria and hasattr(row, 'dimension') \
+                        and row.dimension in criteria['BAD_dimension']:
+                        unique = False
+                        print('Found unsatisfied dimension', row.id, row.topology, row.space_group_number, row.wps)
+
+
             if unique:
                 for prop in unique_rows:
                     (rowid, den) = prop
@@ -482,7 +511,6 @@ def clean_structures_pmg(self, dtol=5e-2, criteria=None, max_sim=None):
         self.db.delete(to_delete)
 
 
-
     def update_row_topology(self, StructureType='Auto', overwrite=True):
         """
         Update row topology base on the CrystalNets.jl

pyxtal/symmetry.py

@@ -553,6 +553,34 @@ def list_wyckoff_combinations(self, numIons, quick=False, numWp=(None, None), Nm
 
         return combinations, has_freedom, indices
 
+    def get_spg_symmetry_object(self):
+        """
+        Generate the symmetry table for the given space group
+        It only supports space group now!
+        """
+
+        if self.dim == 3:
+            l_type, bravis = self.lattice_type, self.symbol[0]
+            wp = self.get_wyckoff_position(0)
+
+            if 143 <= self.number <= 194:
+                ops = wp.get_euclidean_ops()
+                hexagonal = True
+            else:
+                ops = wp.ops
+
+            if bravis in ['A', 'B', 'C', 'I']:
+                ops = ops[:int(len(ops)/2)]
+            elif bravis == 'R':
+                ops = ops[:int(len(ops)/3)]
+            elif bravis == 'F':
+                ops = ops[:int(len(ops)/4)]
+
+            return site_symmetry(ops, l_type, bravis, True)
+            #ss.to_beautiful_matrix_representation()
+        else:
+            raise ValueError("Only supports space group symmetry")
+
     def get_wyckoff_position(self, index):
         """
         Returns a single Wyckoff_position object.
@@ -2894,7 +2922,7 @@ def set_table(self, skip=False):
                 if num_symmetries > 0:
                     strs = '{:4d} ({:2d} {:2d} {:2d}): '.format(direction_id, *axis)
                     for sym in matrix[i]:
-                        strs +="{:4d}".format(sym)
+                        strs +="{:4d} ".format(sym)
                     #strs += "{:4d}{:4d}{:4d}{:4d}{:4d}{:4d}{:4d}{:4d}{:4d}{:4d}".format(*matrix[i])
                     if not self.parse_trans:
                         symbol, _ = self.get_highest_symmetry(matrix[i])
@@ -3101,7 +3129,7 @@ def to_beautiful_matrix_representation(self, skip=True):
             symbols = ['1', '-1', '2', 'm', '3', '4', '-4', '-3', '6', '-6']
 
         for symbol in symbols:
-            strs += '{:4s}'.format(symbol)
+            strs += '{:<4s} '.format(symbol)
         print(strs)
         if not hasattr(self, 'table'): self.set_table(skip)
         for row in self.table:
@@ -4070,45 +4098,31 @@ def get_symmetry_directions(lattice_type, symbol='P', unique_axis='b'):
 
 if __name__ == "__main__":
     print("Test pyxtal.wp.site symmetry")
-    for i in [14, 36, 62, 99, 143, 160, 182, 191, 225, 230]:
+    spg_list = [14, 36, 62, 99, 143, 160, 182, 191, 225, 230]
+    for i in spg_list:
         g = Group(i)
         for wp in g:
             wp.get_site_symmetry()
             print("{:4d} {:10s} {:10s}".format(wp.number, wp.get_label(), wp.site_symm))
 
     print("Test pyxtal.wp.site symmetry representation")
-    for i in range(1, 231): #[14, 36, 62, 99, 143, 160, 182, 191, 225, 230]:
+    for i in spg_list:
         g = Group(i)
         for wp in g:
-            #ss = site_symmetry(wp.get_site_symm_ops(), g.lattice_type, g.symbol[0])
             if wp.index > 0:
                 for idx in range(1): #wp.multiplicity):
                     ss = wp.get_site_symmetry_object(idx)
                     print('\n{:4d} {:10s} {:10s}'.format(wp.number, wp.get_label(), ss.name), ss.hm_symbols)
                     #ss.to_beautiful_matrix_representation(skip=True)
                     #print(ss.to_matrix_representation())
                     #print(ss.to_one_hot())
-                    #if ss.name == '1':
-                    #    print("Problem exit")
 
     print("Test pyxtal.wp.site space group")
-    for i in range(1, 231):
+    for i in spg_list:
         g = Group(i)
         print('\n', g.number, g.symbol)
-        wp = g[0]
-        if 143 <= i <= 194:
-            ops = wp.get_euclidean_ops()
-            hexagonal = True
-        else:
-            ops = wp.ops
-            hexagonal = False
-
-        if g.symbol[0] in ['A', 'B', 'C', 'I']:
-            ops = ops[:int(len(ops)/2)]
-        elif g.symbol[0] == 'R':
-            ops = ops[:int(len(ops)/3)]
-        elif g.symbol[0] == 'F':
-            ops = ops[:int(len(ops)/4)]
-
-        ss = site_symmetry(ops, g.lattice_type, g.symbol[0], True)
+        ss = g.get_spg_symmetry_object()
         ss.to_beautiful_matrix_representation()
+        #matrix = ss.to_matrix_representation_spg()
+        #print(matrix)
+        #print(sum(sum(matrix)))

pyxtal/test_all.py

@@ -54,6 +54,15 @@ def test_print_group_and_dof(self):
             dof = g.get_lattice_dof()
             self.assertTrue(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]
+        for spg, num in zip(spg_list, ans):
+            g = Group(spg)
+            ss = g.get_spg_symmetry_object()
+            matrix = ss.to_matrix_representation_spg()
+            self.assertTrue(num == sum(sum(matrix)))
+
     def test_short_path(self):
         g = Group(217)
         path = g.short_path_to_general_wp(7)