README.md

Surface Coatings

Overview

Surface Coatings (surface_coatings) is an mBuild recipe to construct monolayer systems, i.e., surfaces coated with monolayer films. Recipes are designed to be add-ons to mBuild, allowing users to construct classes of chemical systems utilizing routines developed earlier using mBuild.

Installation

The surface_coatings can be install using pip. While its dependencies can be found in environment.yml.

conda env update --file environment.yml
conda activate surface_coatings
pip install .

Example Usage

import mbuild as mb 
from mbuild.lib.molecules import WaterSPC as H2O
from surface_coatings.surfaces import SilicaInterfaceCarve
from surface_coatings.chains import Alkylsilane
from surface_coatings import Monolayer, DualMonolayer, SolvatedMonolayer, SolvatedDualMonolayer

silane_chain = Alkylsilane()
silica_surface = SilicaInterfaceCarve()

silica_monolayer = Monolayer(surface=silica_surface, 
                             chains=[silane_chain], 
                             n_chains=100, 
                             tile_x=1, 
                             tile_y=1)
silica_monolayer.visualize()

# Create a dual monolayer with the created monolayer
dual_monolayer = DualMonolayer(top=mb.clone(silica_monolayer),
                               bottom=mb.clone(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()