Welcome to StructOpt’s documentation!¶
StructOpt is a reverse structure determination toolkit.
What is reverse structure determination?¶
Reverse structure determination is a type of structural refinement that iteratively modifies and optimizes a structural model. In atomistic simulations, the positions of the atoms are moved within the model at every step. After the atoms have moved, the structure is evaluated to see how “good” it is. If the structure is “better” than the previous step, the moved atoms are more likely to persist into the next generation. This process is repeated many times until acceptable structure(s) have been generated.
Many different metrics can be used to determine how “good” a structure is, and this is often material-dependent. The average energy per atom is one commonly used metric, and others include fits to experimental data (e.g. S(q) or g(r) data), medium-range order information available via FEM measurements, average coordination number, and bond angle constraints.
The specific algorithms that can be used in reverse structure determination are numerous and include Monte Carlo, Genetic Algorithm, and Particle Swarm.
Overview of StructOpt¶
StructOpt is a structure optimization framework that incorportates multiple forward simulation techniques into its optimization scheme with the goal of identifying stable and realistic atomic structures. It is designed with modularity in mind, and encourages simplicity in both its codebase and usage without sacrificing powerful functionality. Nearly any forward simulation technique that takes an atomic model as input and outputs a fitness value can be integrated into this framework.
This documentation serves as both a user and developer guide for StructOpt.
StructOpt serves the purpose of structure refinment for multiple different materials including nanoparticles, defects, and metallic glasses. As such, it is highly customizable and extendable. There are many different types of simulations that can be set up, which requires getting to know the relevent parameters. Multiple examples are included in this documentation and comments (via issues on our github page) are welcome.
The Examples section provides multiple examples of basic StructOpt configurations. Details on the inputs and outputs can be found in the parameters and Outputs sections, respectively. Details on the many options currently available for StructOpt are provided in the parameters section of this document. An explanation of commonly generated errors and troubleshooting advice is provided in the section entitled Troubleshooting.
Bug fixes and error reports are always welcome. We accept PRs and will try to fix issues that have detailed descriptions and are reproducable in a timely fashion.
If you have a forward simulation module that you wish to contribute, please make an issue and the correct people will get email notifications so we can respond.
StructOpt is distributed under the MIT license, reproduced below:
Copyright (c) 2016 University of Wisconsin-Madison Computational Materials Group
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