WIP: Made it so assigned groups always works regardless of size

matscipy/fracture_mechanics/clusters.py

@@ -192,12 +192,18 @@ def generate_3D_cubic_111(cryst_2D, nzlayer, el, a0, lattice, crack_surface,
 def set_groups(a, n, skin_x, skin_y, central_x=-1. / 2, central_y=-1. / 2,
                invert_central=False):
     nx, ny, nz = n
-    sx, sy, sz = a.cell.diagonal()
+    #sx, sy, sz = a.cell.diagonal()
+    #get sx and sy instead from looking directly at atoms
+    sx = np.max(a.positions[:, 0]) - np.min(a.positions[:, 0])
+    sy = np.max(a.positions[:, 1]) - np.min(a.positions[:, 1])
     print('skin_x = {0}*a0, skin_y = {1}*a0'.format(skin_x, skin_y))
     skin_x = skin_x * sx / nx
     skin_y = skin_y * sy / ny
     print('skin_x = {0}, skin_y = {1}'.format(skin_x, skin_y))
-    r = a.positions
+    r = a.get_positions()
+    #shift r such that the min x and y values are 0
+    r[:, 0] -= np.min(r[:, 0])
+    r[:, 1] -= np.min(r[:, 1])
 
     g = np.ones(len(a), dtype=int)
     mask = np.logical_or(

matscipy/fracture_mechanics/thin_strip_utils.py

@@ -233,7 +233,7 @@ def build_thin_strip(self,width,height,thickness,vacuum):
         self.trackable_atoms_mask = crack_slab.arrays['trackable']
         #ase.io.write('1_slab.xyz',crack_slab)
         #set groups (useful later for crack tip determination)
-        set_groups(crack_slab,[nx,ny,nz],20,10)
+        set_groups(crack_slab,[nx,ny,nz],int(nx/5),int(ny/5))
         self.group_array = crack_slab.arrays['groups']
         crack_slab.set_pbc((False,False,True))
         return crack_slab