Add smooth silica surface (#4)

* add smooth silica surface

* update README

* Update entry points

* Fix import bug

* fix test

README.md

@@ -0,0 +1,52 @@
+# Surface Coatings
+
+## Overview 
+Surface Coatings (`surface_coatings`) is an [mBuild](https://mbuild.mosdef.org/) recipe to construct monolayer systems,
+i.e., surfaces coated with monolayers. 
+Recipes are desgined to be add-ons to [mBuild](https://mbuild.mosdef.org/),
+allowing users to construct classes of chemical sysetms utilizing routines developed earlier using [mBuild](https://mbuild.mosdef.org/).
+
+
+## Installation 
+The `surface_coatings` can be install using `pip`. While its dependencies can be found in `environment.yml`.
+```bash
+conda env update --file environemnt.yml
+pip install .
+```
+
+## Example Usage 
+```python
+import mbuild as mb 
+from mbuild.lib.molecules import WaterSPC as H2O
+from surface_coatings.surfaces import SiicaInterfaceCarve
+from surface_coatings.chains import Alkylsilane
+from surface_coatings import Monolayer, DualMonolayer, SolvatedMonolayer, SolvatedDualMonolayer
+
+silane_chain = Alkylsilane()
+silica_surface = SiicaInterfaceCarve()
+
+silica_monolayer = Monolayer(surface=silica_surface, 
+                             chains=silane_chain, 
+                             n_chains=100, 
+                             tile_x=1, 
+                             tile_y=1)
+silica.visualize()
+
+# Create a dual monolayer with the created monolayer
+dual_monolayer = DualMonolayer(top=mb.clone(silica_monolayer),
+                               bottom=mb.cone(silica_monolayer),
+                               separation=3)
+dual_monolayer.visualize()
+
+# Solvate a monolayer system
+solvated_monolayer = SolvatedMonolayer(monolayer=mb.clone(silica_monolayer), 
+                                       solvent=H2O())
+
+solvated_monolayer.visualize()
+
+# Solvate a dual monolayer system 
+solvated_dual_monolayer = SolvatedDualMonolayer(dual_monolayer=dual_monolayer, 
+                                                solvent=H2O())
+solvated_dual_monolayer.visualize()
+
+```

setup.py

@@ -9,7 +9,10 @@
       zip_safe=False,
       entry_points={
             "mbuild.plugins": [
-                ""
+                "Monolayer = surface_coatings.monolayer:Monolayer",
+                "DualMonolayer = surface_coatings.monolayer:DualMonolayer",
+                "SolvatedMonolayer = surface_coatings.solvated_monolayer:SolvatedMonolayer",
+                "SolvatedDualMonolayer = surface_coatings.solvated_monolayer:SolvatedDualMonolayer",
             ]
         }
     )

surface_coatings/chains/alkylsilane.py

@@ -36,4 +36,4 @@ def __init__(self, chain_length=17, terminal_group="methyl"):
         self.add(silane, 'silane')
         mb.force_overlap(self['silane'], self['silane']['up'], self['alkane']['down'])
 
-        self.add(silane['down'], 'down', con tainment=False)
+        self.add(silane['down'], 'down', containment=False)

surface_coatings/monolayer.py

@@ -3,7 +3,6 @@
 
 import mbuild as mb
 from mbuild.lib.atoms import H
-from mbuild.lib.recipes import Monolayer
 
 
 class Monolayer(mb.Compound):

surface_coatings/surfaces/__init__.py

@@ -1,2 +1,3 @@
 from .silicon_interface import SiliconInterface
 from .silica_interface_carve import SilicaInterfaceCarve
+from .silica_interface import SilicaInterface

surface_coatings/surfaces/silica_interface.py

@@ -0,0 +1,20 @@
+import mbuild as mb
+from mbuild.lib.surfaces import Betacristobalite
+
+class SilicaInterface(mb.Compound):
+    def __init__(self, tile_x=1, tile_y=1):
+        super(SilicaInterface, self).__init__()
+        silica_crystal = Betacristobalite()
+        tiled_compound = mb.lib.recipes.TiledCompound(mb.clone(silica_crystal),
+                                                      n_tiles=(tile_x, tile_y, 1))
+        self.add(tiled_compound, "TiledCompound")
+        self._transfer_ports()
+        self.periodicity = (True, True, False)
+
+    def _transfer_ports(self):
+        """Transfer available ports from TiledCompound to parents level"""
+        for port in self["TiledCompound"].available_ports():
+            clone_port = mb.clone(port)
+            clone_port.anchor = port.anchor
+            self.remove(port)
+            self.add(clone_port)

surface_coatings/tests/test_surfaces.py

@@ -1,5 +1,5 @@
 import mbuild as mb
-from surface_coatings.surfaces import SiliconInterface, SilicaInterfaceCarve
+from surface_coatings.surfaces import SiliconInterface, SilicaInterfaceCarve, SilicaInterface
 
 
 class TestSystem(object):
@@ -8,5 +8,9 @@ def test_silicon_interface(self):
         assert silicon_surface.periodicity == (True, True, False)
 
     def test_silica_interface_carve(self):
-        silica_surface = SilicaInterfaceCarve)
+        silica_surface_carve = SilicaInterfaceCarve()
+        assert silica_surface_carve.periodicity == (True, True, False)
+
+    def test_silica_interface(self):
+        silica_surface = SilicaInterface()
         assert silica_surface.periodicity == (True, True, False)