enable asu option for from_random

Author: qzhu2017

pyxtal/__init__.py

@@ -292,6 +292,7 @@ def from_random(
         random_state=None,
         tm=None,
         use_hall=False,
+        use_asu=False,
     ):
         """
         The main function to generate random crystals.
@@ -318,6 +319,7 @@ def from_random(
             random_state (optional): numpy random state
             tm (optional): Tol_matrix define the distances
             use_hall (bool): whether to use Hall number. Default is False
+            use_asu (bool): whether to generate points within ASU. Default is False
 
         Returns:
             Crystal structure object if successful
@@ -370,6 +372,7 @@ def from_random(
                     tm=tm,
                     use_hall=use_hall,
                     random_state=random_state,
+                    use_asu=use_asu,
                 )
             if force_pass or struc.valid:
                 quit = True

pyxtal/crystal.py

@@ -61,6 +61,7 @@ def __init__(
         tm=None,
         use_hall=False,
         random_state: int | None | Generator = None,
+        use_asu: bool = False,
     ):
         # Initialize
         self.rng = np.random.default_rng(random_state)
@@ -71,6 +72,7 @@ def __init__(
         self.valid = False
         self.factor = factor
         self.min_density = 0.75
+        self.use_asu = use_asu
 
         # Dimesion
         self.dim = dim
@@ -377,7 +379,13 @@ def _set_ion_wyckoffs(self, numIon, specie, cell, wyks):
             else:
                 if site is not None:
                     wp = self.group[site]
-                    pt = self.lattice.generate_point()
+                    if self.use_asu:
+                        xmin, xmax, ymin, ymax, zmin, zmax = self.group.get_ASU()
+                        # Generate a random point based on (min, max) ranges
+                        pt = self.rng.uniform([xmin, ymin, zmin], [xmax, ymax, zmax])
+                    else:
+                        pt = self.lattice.generate_point()
+
                     # avoid using the merge function
                     if len(wp.short_distances(pt, cell, tol)) > 0:
                         # print('bad pt', pt, wp.short_distances(pt, cell, tol))
@@ -392,7 +400,12 @@ def _set_ion_wyckoffs(self, numIon, specie, cell, wyks):
                     if wp is not False:
                         # print(wp.letter)
                         # Generate a list of coords from ops
-                        pt = self.lattice.generate_point()
+                        if self.use_asu:
+                            xmin, xmax, ymin, ymax, zmin, zmax = self.group.get_ASU()
+                            # Generate a random point based on (min, max) ranges
+                            pt = self.rng.uniform([xmin, ymin, zmin], [xmax, ymax, zmax])
+                        else:
+                            pt = self.lattice.generate_point()
                         pt, wp, _ = wp.merge(pt, cell, tol, group=self.group)
                 # print('good pt', pt)
                 if wp is not False:

tests/test_crystal.py

@@ -58,11 +58,15 @@ def test_single_specie(self):
         os.remove("tmp-3d.cif")
         assert struc.valid
 
+
     def test_mutiple_species(self):
         struc = pyxtal()
         struc.from_random(3, 99, ["Ba", "Ti", "O"], [1, 1, 3], 1.2)
         assert struc.valid
 
+        struc.from_random(3, 99, ["Ba", "Ti", "O"], [1, 1, 3], 1.2, use_asu=True)
+        assert struc.valid
+
     def test_preassigned_sites(self):
         sites = [["1b"], ["1b"], ["2c", "1b"]]
         struc = pyxtal()
@@ -73,6 +77,12 @@ def test_preassigned_sites(self):
         struc.from_random(3, 225, ["C"], [12], 1.0, sites=[["4a", "8c"]])
         assert struc.valid
 
+        struc.from_random(3, 99, ["Ba", "Ti", "O"], [1, 1, 3], 1.0, sites=sites, use_asu=True)
+        assert struc.valid
+
+        struc.from_random(3, 225, ["C"], [12], 1.0, sites=[["4a", "8c"]], use_asu=True)
+        assert struc.valid
+
     def test_read(self):
         # test reading xtal from cif
         for name in ["FAU", "NaSb3F10", "PVO", "lt_quartz"]: