pass tol value in random

Author: qzhu2017

pyxtal/crystal.py

@@ -415,7 +415,7 @@ def _set_ion_wyckoffs(self, numIon, specie, cell, wyks):
                     new_site = atom_site(wp, pt, specie)
 
             # Check current WP against existing WP's
-            if self.check_wp(wyckoff_sites_tmp, wyks, cell, new_site):
+            if self.check_wp(wyckoff_sites_tmp, wyks, cell, new_site, tol):
                 if sites_list is not None and len(sites_list) > 0:
                     sites_list.pop(0)
                 wyckoff_sites_tmp.append(new_site)
@@ -430,12 +430,12 @@ def _set_ion_wyckoffs(self, numIon, specie, cell, wyks):
 
         return None
 
-    def check_wp(self, wyckoff_sites_tmp, wyks, cell, new_site):
+    def check_wp(self, wyckoff_sites_tmp, wyks, cell, new_site, tol):
         # Check current WP against existing WP's
         if new_site is None:
             return False
 
-        return all(new_site.check_with_ws2(ws, cell, self.tol_matrix) for ws in wyckoff_sites_tmp + wyks)
+        return all(new_site.check_with_ws2(ws, cell, tol) for ws in wyckoff_sites_tmp + wyks)
 
     def _check_consistency(self, site, numIon):
         num = 0

pyxtal/wyckoff_site.py

@@ -247,16 +247,18 @@ def get_disp(self, pos, lattice, translation):
         # print("++++", id, dists[id], id, diffs[id], translation) #; import sys; sys.exit()
         return diffs[id], dists[id]
 
-    def check_with_ws2(self, ws2, lattice, tm, same_group=True):
+    def check_with_ws2(self, ws2, lattice, tol, same_group=True):
         """
         Given two Wyckoff sites, checks the inter-atomic distances between them.
 
         Args:
             - ws2: a different WP object (will always return False if
             two identical WS's are provided)
             - lattice: a 3x3 cell matrix
+            - tol: tolerance value for distance checking
             - same_group: whether or not two WS's are in the same structure.
             Default value True reduces the calculation cost
+
         Returns:
             True or False
         """
@@ -265,10 +267,8 @@ def check_with_ws2(self, ws2, lattice, tm, same_group=True):
         if self.PBC != ws2.PBC:
             raise ValueError("PBC values do not match between Wyckoff sites")
 
-        # Get tolerance
-        tol = tm.get_tol(self.specie, ws2.specie)
         # Symmetry shortcut method: check only some atoms
-        if same_group is True:
+        if same_group:
             # We can either check one atom in WS1 against all WS2, or vice-versa
             # Check which option is faster
             if self.multiplicity > ws2.multiplicity: