This is a highly optimized implementation of the recently proposed symmetric gradient domain machine learning (sGDML) force field model 1 2. It is able to faithfully reproduce detailed global potential energy surfaces (PES) for small- and medium-sized molecules from a limited number of user-provided reference calculations 4.
We provide a set of Python routines to reconstruct and evaluate custom sGDML force fields 3. A user-friendly command-line interface offers assistance through the complete process of model creation, in an effort to make this novel machine learning approach accessible to broad practitioners.
It’s easy to get going!¶
Here is how to reconstruct an ethanol force field using 200 examples from the published benchmark dataset:
$ sgdml-get dataset ethanol_dft $ sgdml all ethanol_dft.npz 200 1000 5000
We use another 1000 points as validation dataset and finally estimate the generalization error of our trained model on additional 5000 geometries. All of these subsets are automatically sampled from the provided bulk dataset
The program output will look something like this:
The sGDML code is developed through our GitHub repository: https://github.com/stefanch/sGDML
Please cite GDML and sGDML as follows:
Chmiela, S., Tkatchenko, A., Sauceda, H. E., Poltavsky, Igor, Schütt, K. T., Müller, K.-R. (2017). Machine Learning of Accurate Energy-conserving Molecular Force Fields. Sci. Adv., 3(5), e1603015.
Chmiela, S., Sauceda, H. E., Müller, K.-R., Tkatchenko, A. (2018). Towards Exact Molecular Dynamics Simulations with Machine-Learned Force Fields. Nat. Commun., 9(1), 3887.
Chmiela, S., Sauceda, H. E., Poltavsky, Igor, Müller, K.-R., Tkatchenko, A. (2019). sGDML: Constructing Accurate and Data Efficient Molecular Force Fields Using Machine Learning. Comput. Phys. Commun., 240, 38-45.
Sauceda, H. E., Chmiela, S., Poltavsky, Igor, Müller, K.-R., Tkatchenko, A. (2019). Molecular Force Fields with Gradient-Domain Machine Learning: Construction and Application to Dynamics of Small Molecules with Coupled Cluster Forces. J. Chem. Phys., 150, 114102.
- Data preparation
- Force field reconstruction
- Force field query
This code is freely available under the terms of the MIT license.