Extra methods for adding boundary conditions to the AdAtom object

core/adAtom.py

 import numpy as np
+from ..utils.boundaryCondition import *
 
 
 class AdAtom:
@@ -10,10 +11,34 @@ class AdAtom:
         self.mesh = []
 
 
-    def add_boundaryCondition(self, bc):
+    def add_boundary_condition(self, bc):
         self.bcs.append(bc)
 
 
+    def add_position_condition(self, position_min=0.0, position_max=1.0):
+        pc = PositionCondition(self, position_min, position_max)
+        self.add_boundary_condition(pc)
+
+
+    def add_distance_condition(self, neighbour, distance_min=0.0, distance_max=np.infty):
+        dc = DistanceCondition(self, neighbour, distance_min, distance_max)
+        self.add_boundary_condition(dc)
+
+
+    def add_angle_condition(self, neighbourA, neighbourB, angle_min=0.0, angle_max=180.0, center=1):
+        if center==0:
+            ac = AngleCondition(neighbourA, self, neighbourB, angle_min, angle_max)
+        elif center==1:
+            ac = AngleCondition(self, neighbourA, neighbourB, angle_min, angle_max)
+        elif center==2:
+            ac = AngleCondition(neighbourA, neighbourB, self, angle_min, angle_max)
+        else:
+            print("ERROR! Invalid argument for center!")
+            return
+
+        self.add_boundary_condition(ac)
+
+
     def get_position_conditions(self):
         pos_bcs = []
         for bc in self.bcs:

core/codered.py

 import numpy as np
 from ase import Atoms
-from adAtom import AdAtom
+from .adAtom import AdAtom
 from ..utils.boundaryCondition import *
 
 
@@ -93,6 +93,9 @@ class CodeRed:
         while self.current_index < self.n_adAtoms:
             # get current atom
             adatom = self.adAtoms[self.current_index]
+
+            # create some informative output
+            print("Creating positions for ad-atom with index {:d}, species: {:s}, label: {:s}".format(self.current_index, adatom.species, adatom.label))
             
             # make sure it has a mesh
             if (adatom.mesh==[] or len(adatom.mesh)==0):
@@ -146,7 +149,12 @@ class CodeRed:
                 if len(self.combinations)==0:
                     return
 
-            # ...?
+            #TODO: include dihedral conditions
     
             # finally increase current index by 1 (only happens if everything worked out)
             self.current_index += 1
+
+        # generate informative output
+        print("Done! Generated {:d} structures in total.".format(len(self.combinations)))
+
+        return self.combinations

utils/boundaryCondition.py

@@ -66,7 +66,7 @@ class AngleCondition(BoundaryCondition):
     """
     Derived class for angle boundary conditions.
     """
-    def __init__(self, atomA='X', atomB='Y', atomC='Z', minAng=0.0, maxAng=180.0, center=1):
+    def __init__(self, atomA='X', atomB='Y', atomC='Z', minAng=0.0, maxAng=180.0):
         self.bc_type = 'ang'
         self.atoms = [atomA, atomB, atomC]
         self.minValue = minAng