added a min_dist check for the side chains, so they don't overlap with...

added a min_dist check for the side chains, so they don't overlap with themselves or other atoms. the point in the code where this is done can be improved though...

new/codered.py

@@ -192,12 +192,28 @@ class CodeRed:
             ad_structure = surf + Atoms(species, comb)
 
             # calculate and add side chains, if any
+            min_dist_valid = True
             for i in range(len(self.sideChains)):
                 sc = self.sideChains[i].calc_positions(len(surf)+sc_connect_indices[i], ad_structure)
                 ad_structure = ad_structure + sc
 
+                # check minimum distances
+                n_sc_atoms = len(sc)
+                dist_matrix = ad_structure.get_all_distances(mic=True)
+                # 1. check self interaction with periodic images
+                #    (this construct gives all distances between sc_atoms in the combined unit cell)
+                if np.any(dist_matrix[-n_sc_atoms:,-n_sc_atoms:][np.triu_indices(n_sc_atoms,1)] < self.min_dist):
+                    min_dist_valid = False
+                    break
+                # 2. check distance to other atoms
+                #    (this construct gives all distances of sc_atoms to other atoms in the structure)
+                elif np.any(dist_matrix[-n_sc_atoms:,:-n_sc_atoms] < self.min_dist):
+                    min_dist_valid = False
+                    break
+
             # add to structure list
-            structures.append(ad_structure)
+            if min_dist_valid:
+                structures.append(ad_structure)
 
         return structures
 

new/sideChainGen.py

@@ -190,6 +190,8 @@ class SideChain:
         self.mode = mode
         self.nn_cutoff = nn_cutoff
         self.min_dist = min_dist
+        if self.min_dist > self.distance:
+            print('WARNING! The distance attribute should not be smaller than the min_dist attribute!')
 
 
     def calc_positions(self, anchor_index, structure):
@@ -227,6 +229,6 @@ class SideChain:
 
         # calculate and set new positions
         sc_atoms.set_positions(anchor + self.distance*sc_dir + np.dot(sc_atoms.get_positions(),R))
-        
+
         # return the side chain adapted to the given environment
         return sc_atoms