continue to fix #273 with speed up

pyxtal/symmetry.py

@@ -1331,6 +1331,24 @@ def get_min_supergroup(self, group_type="t", G=None):
             msg = "Only supports the supergroups for space group"
             raise NotImplementedError(msg)
 
+    @classmethod
+    def _get_max_subgroup_numbers(cls, number, max_cell=9):
+        """
+        Returns the minimal supergroups as a dictionary
+        """
+        groups = []
+        sub_k = Group._get_max_k_subgroup(number)
+        sub_t = Group._get_max_t_subgroup(number)
+        k = sub_k["subgroup"]
+        t = sub_t["subgroup"]
+        for i, n in enumerate(t):
+            if np.linalg.det(sub_t["transformation"][i][:3, :3]) <= max_cell:
+                groups.append(n)
+        for i, n in enumerate(k):
+            if np.linalg.det(sub_k["transformation"][i][:3, :3]) <= max_cell:
+                groups.append(n)
+        return groups
+
     def get_max_subgroup_numbers(self, max_cell=9):
         """
         Returns the minimal supergroups as a dictionary
@@ -1550,8 +1568,8 @@ def search_supergroup_paths(self, H, max_layer=5):
             groups = []
             subgroups = []
             for g in previous_layer_groups:
-                subgroup_numbers = np.unique(
-                    Group(g, quick=True).get_max_subgroup_numbers())
+                #subgroup_numbers = np.unique(Group(g, quick=True).get_max_subgroup_numbers())
+                subgroup_numbers = np.unique(Group._get_max_subgroup_numbers(g))
 
                 # If a subgroup list has been found with H
                 # trace a path through the dictionary to build the path
@@ -1605,6 +1623,7 @@ def search_supergroup_paths(self, H, max_layer=5):
     #            path_list.append((g_type, id, p))
     #            g0 = g1
     #    return path_list
+
     def path_to_subgroup(self, H):
         """
         For a given a path, extract the
@@ -1693,7 +1712,6 @@ def path_to_general_wp(self, index=1, max_steps=1):
         Find the path to transform the special wp into general site
 
         Args:
-            group: Group object
             index: the index of starting wp
             max_steps: the number of steps to search
 
@@ -1748,11 +1766,11 @@ def path_to_general_wp(self, index=1, max_steps=1):
                 [
                     deepcopy(p)[1:]
                     for p in potential
-                    if (len(set(p[-1][3])) == 1 and p[-1][3][0][-1] == Group(p[-1][2])[0].letter)
+                    if (len(set(p[-1][3])) == 1 and p[-1][3][0][-1] == Wyckoff_position.from_group_and_index(p[-1][2], 0).letter)
                 ]
             )
             potential = [
-                p for p in potential if not (len(set(p[-1][3])) == 1 and p[-1][3][0][-1] == Group(p[-1][2])[0].letter)
+                p for p in potential if not (len(set(p[-1][3])) == 1 and p[-1][3][0][-1] == Wyckoff_position.from_group_and_index(p[-1][2], 0).letter)
             ]
 
         return solutions
@@ -2325,7 +2343,11 @@ def transform_from_matrix(self, trans=None, reset=True, update=False):
                 trans = np.array([[1, 0, 1], [0, 1, 0], [1, 0, 1]])
 
         if 2 < self.number < 16:
-            ops = Group(self.number)[self.index] if reset else self.ops
+            #ops = Group(self.number)[self.index] if reset else self.ops
+            if reset:
+                ops = Wyckoff_position.from_group_and_index(self.number, self.index)
+            else:
+                ops = self.ops
 
             for j, op in enumerate(ops):
                 vec = op.translation_vector.dot(trans)

tests/test_group.py

@@ -134,5 +134,10 @@ def test_get_wyckoff_position_from_xyz(self):
             else:
                 assert wp.get_label() == wp0
 
+    def test_short_path_to_general_wp():
+        data = [('t', 0, 141, ['16h']), ('t', 6, 122, ['16e'])]
+        G = Group(227)
+        assert G.short_path_to_general_wp(4) == data
+
 if __name__ == "__main__":
     unittest.main()

tests/test_mem.py

@@ -0,0 +1,24 @@
+import psutil
+import os
+
+def print_memory_usage():
+    process = psutil.Process(os.getpid())
+    mem_info = process.memory_info()
+    print(f"Memory usage: {mem_info.rss / 1024 ** 2:.2f} MB")  # RSS is the Resident Set Size
+
+if __name__ == "__main__":
+    print_memory_usage()
+    from pyxtal.symmetry import Group
+    print_memory_usage()
+    g = Group(4, quick=True)
+    print_memory_usage()
+    g = Group(227)
+    print_memory_usage()
+
+    from pyxtal import pyxtal
+    xtal = pyxtal()
+    xtal.from_spg_wps_rep(194, ['2c', '2b'], [2.46, 6.70])
+    print_memory_usage()
+
+    xtal.subgroup_once()
+    print_memory_usage()