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¶
User Documentation¶
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.
Contents¶
Contributing¶
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.
License Agreement¶
StructOpt is distributed under the MIT license, reproduced below:
Copyright (c) 2016 University of Wisconsin-Madison Computational Materials Group
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.