Add utility and fix bug with dual_monoalyer (#31)

* fix inaccuracy in separation value in dual_monolayer

* add utitil to calculate boundary position of a compound

surface_coatings/monolayer.py

@@ -1,6 +1,7 @@
 """Routines to create (dual) monolayer systems."""
 from copy import deepcopy
 from warnings import warn
+from surface_coatings.utils.utils import boundary_positions
 
 import mbuild as mb
 import numpy as np
@@ -166,8 +167,10 @@ def __init__(
 
         bot_box = bottom.get_boundingbox()
         top_box = top.get_boundingbox()
-        z_val = bot_box.lengths[2]
-        top.translate([0, 0, z_val + separation])
+        top_min, top_max = boundary_positions(top)
+        bot_min, bot_max = boundary_positions(bottom)
+
+        top.translate([0, 0, bot_max[2] - top_min[2] + separation])
 
         if surface_idx:
             if isinstance(surface_idx, dict):

surface_coatings/utils/utils.py

@@ -0,0 +1,22 @@
+import numpy as np
+import mbuild as mb
+
+
+def boundary_positions(compounds):
+    xs, ys, zs = list(), list(), list()
+    if isinstance(compounds, mb.Compound):
+        for part in compounds.particles():
+            xs.append(part.pos[0])
+            ys.append(part.pos[1])
+            zs.append(part.pos[2])
+    elif isinstance(compounds, (list, tuple)):
+        for molecule in compounds:
+            for part in molecule.particles():
+                xs.append(part.pos[0])
+                ys.append(part.pos[1])
+                zs.append(part.pos[2])
+
+    minima = (min(xs), min(ys), min(zs))
+    maxima = (max(xs), max(ys), max(zs))
+    return np.array(minima), np.array(maxima)
+