Yu Xie^1*, Jonathan Vandermause^1*, Lixin Sun^1*, Andrea Cepellotti^1*, Boris Kozinsky^1,2*

1 John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA

2 Robert Bosch LLC, Research and Technology Center, Cambridge, Massachusetts 02142, USA

* Corresponding authors emails: xiey@g.harvard.edu, jonathan_vandermause@g.harvard.edu, lixinsun@g.harvard.edu, acepellotti@seas.harvard.edu, bkoz@g.harvard.edu

DOI10.24435/materialscloud:7k-9g [version v1]

Publication date: Aug 03, 2020

How to cite this record

Yu Xie, Jonathan Vandermause, Lixin Sun, Andrea Cepellotti, Boris Kozinsky, Fast Bayesian force fields from active learning and mapped Gaussian processes: application to structural phase transition of stanene, Materials Cloud Archive 2020.90 (2020), doi: 10.24435/materialscloud:7k-9g.

Description

Gaussian process (GP) regression is one promising technique of constructing machine learning force fields with built-in uncertainty quantification, which can be used to monitor the quality of model predictions. A current limitation of existing GP force fields is that the prediction cost grows linearly with the size of the training data set, making accurate GP predictions slow. In this work, we exploit the special structure of the kernel function to construct a mapping of the trained Gaussian process model, including both forces and their uncertainty predictions, onto spline functions of low-dimensional structural features. This method is incorporated in the Bayesian active learning workflow for training of Bayesian force fields. To demonstrate the capabilities of this method, we construct a force field for stanene and perform large scale dynamics simulation of its structural evolution. We provide a fully open-source implementation of our method, as well as the training and testing examples with the stanene dataset.

Materials Cloud sections using this data

Files

File name	Size	Description
README.txt MD5md5:341a49a9f0fae27ff5e71615cdbd5584	733 Bytes	README
flare.zip MD5md5:62cbb48b16b2703d0eb31dfc7cc4341a	94.1 KiB	Python code of this method, including building spline interpolations and Bayesian active learning
data.zip MD5md5:a147d2f8a8d8f2479110735a4159f61d	374.8 KiB	The extracted training and testing data of stanene
Atoms10k_Temp500K.zip MD5md5:a595dc4a44ed4f193fb5c633c2ac5109	88.3 MiB	Large-scale molecular dynamics simulation of melting process of stanene, including MGP pair style coefficient file, LAMMPS input, data, log and trajectory files
LMP.zip MD5md5:980dac59df745cebcd8acb74f3616a27	3.4 MiB	LAMMPS source code of MGP pair style, also including an executable

License

Files and data are licensed under the terms of the following license: Creative Commons Attribution 4.0 International.
Metadata, except for email addresses, are licensed under the Creative Commons Attribution Share-Alike 4.0 International license.

External references

Keywords

machine learning molecular dynamics Bayesian inference stanene phase transition