Escherized Colloids

A set of computational tools for using isohedral tiles to produce patchy colloids that self-assemble into two-dimensional films with a desired symmetry group and void fraction.

Installation

Getting Started

$ git clone https://github.com/usnistgov/escherized-colloids.git
$ cd escherized_colloids
$ # 1. Perform required installations, see below
$ # 2. Perform optional installations, see below

Dependencies

Tactile (required, included)

This code relies on Prof. Craig Kaplan's tactile library. You can view an interactive version of this library here.

$ git clone https://github.com/isohedral/tactile ./tactile
$ cd tactile; git checkout 33d5b03 # This is the commit used during development
$ cd ../;

JSON (required, included)

JSON support for c++ is provided by here. The lone necessary json.hpp file is shipped with this code in src/, but can be updated from this repo. For example:

$ wget -O src/json.hpp https://github.com/nlohmann/json/releases/download/v3.10.4/json.hpp

OptimLib (required)

Optimizations are performed using the OptimLib library. On Ubuntu you can install the requirements as follows:

$ sudo apt install libopenblas-dev
$ sudo apt install libomp-dev
$ sudo apt install libarmadillo-dev
$ git clone https://github.com/kthohr/optim ./optim
$ cd optim
$ git submodule update --init
$ export ARMA_INCLUDE_PATH=/usr/include/;
$ ./configure ---header-only-version

See here for more details on installing it as a header only library.

When compiling your code, add #define OPTIM_ENABLE_ARMA_WRAPPERS and #include "optim.hpp to your cpp file, and set the include path to the head_only_version directory (e.g.,-I/path/to/optimlib/header_only_version) in your Makefile. See the examples/ directory for example implementations.

You should also perform tests as described here.

GoogleTest (optional)

If you want to run tests to check the code (recommended) you need to install GoogleTest. This installation procedure also requires CMake and superuser privileges. Note: this project currently is set up for c++11, however, googletest >= v1.14 has moved to c++14 by default, so use the last c++11 release (v1.12.1) for backward compatibility.

$ git clone https://github.com/google/googletest.git --branch release-1.12.1 
$ cd googletest
$ mkdir build
$ cd build
$ cmake ..
$ make
$ sudo make install

Once installed, you can automatically execute all tests as follows.

$ cd tests
$ bash auto.sh

pymatgen (optional)

Symmetry checks and manipulations are performed using pymatgen in the design directory. This package must be installed if you intend to use the tools therein.

pre-commit (optional)

This repo uses pre-commit to manage style, as described here. You will need to install cpplint if you want to contribute. If you do not already have pre-commit installed, you will need to do that as well.

$ pip install cpplint

Examples

Some basic examples of using the code to perform some basic manipulations have been provided in the examples/ directory. For example, initializing a colloid by placing a motif inside an isohedral tile, optimizing the tile to fit the motif (``shrinkwrapping''), and creating a unit cell out of motifs.

$ cd examples/initialize_colloid/
$ make
$ bash run.sh # You can change parameters in this file as needed.

How To

A conda environment yaml file is included to reproduce the development environment. You can install this as follows:

$ conda env create -f conda-env.yml
$ conda activate escherc
$ python -m ipykernel install --user --name=escherc

The design procedure is as follows:

• Step 1: Build a new motif or decide on one from the motif_libary/. The Jupyter notebook in the motif_library/ directory (Create_Motifs.ipynb) illustrates how these are built and saved as JSON files.
• Step 2: Use the Design.ipynb notebook in design/ to determine which groups (tiles) are safe, dangerous, or forbidden and decide what you want to create. It is a good idea to check the point symmetry you have assigned to your motif using pymatgen. This optional step is illustrated in the Design.ipynb notebook.
• Step 3: Select a tile, then create a colloid by placing the motif inside of it (e.g., see examples/initialize_colloid/); you can do this in an "optimal" way by optimizing the fit (e.g., see examples/pso_auto/).
• Final check: Create a unit cell (2x2 or greater is usually best) to inspect the design for its symmetry. If you made a safe choice, this should be what you wanted. If you made a dangerous choice, you should double check (e.g., examples/unit_cell/).
• Step 4: See simulations/ directory for tools that use LAMMPS to simulate the self-assembly of these colloidal particles. In particular, the Preparing.ipynb notebook illustrates how to build the simulation scripts (automatically) and also analyze the results.

Citation

Refer to the NIST MIDAS entry for information regarding the citation of this repository.

Contact information

• Nathan A. Mahynski, Material Measurement Laboratory, Chemical Sciences Division, Chemical Informatics Group. Contact: nathan.mahynski@nist.gov

License Information

• See LICENSE.md for more information.
• Any mention of commercial products is for information only; it does not imply recommendation or endorsement by NIST.