sgdml 0.5.2

Reference implementation of the GDML and sGDML force field models.

Symmetric Gradient Domain Machine Learning (sGDML)

For more details visit: sgdml.org
Documentation can be found here: docs.sgdml.org

Requirements:

• Python 3.7+
• PyTorch (>=1.8)
• NumPy (>=1.19)
• SciPy (>=1.1)

Optional:

• ASE (>=3.16.2) (to run atomistic simulations)

Getting started

Stable release

Most systems come with the default package manager for Python pip already preinstalled. Install sgdml by simply calling:

$ pip install sgdml

The sgdml command-line interface and the corresponding Python API can now be used from anywhere on the system.

Development version

(1) Clone the repository

$ git clone https://github.com/stefanch/sGDML.git
$ cd sGDML

...or update your existing local copy with

$ git pull origin master

(2) Install

$ pip install -e .

Using the flag --user, you can tell pip to install the package to the current users's home directory, instead of system-wide. This option might require you to update your system's PATH variable accordingly.

Optional dependencies

Some functionality of this package relies on third-party libraries that are not installed by default. These optional dependencies (or "package extras") are specified during installation using the "square bracket syntax":

$ pip install sgdml[<optional1>]

Atomic Simulation Environment (ASE)

If you are interested in interfacing with ASE to perform atomistic simulations (see here for examples), use the ase keyword:

$ pip install sgdml[ase]

Reconstruct your first force field

Download one of the example datasets:

$ sgdml-get dataset ethanol_dft

Train a force field model:

$ sgdml all ethanol_dft.npz 200 1000 5000

Query a force field

import numpy as np
from sgdml.predict import GDMLPredict
from sgdml.utils import io

r,_ = io.read_xyz('geometries/ethanol.xyz') # 9 atoms
print(r.shape) # (1,27)

model = np.load('models/ethanol.npz')
gdml = GDMLPredict(model)
e,f = gdml.predict(r)
print(e.shape) # (1,)
print(f.shape) # (1,27)

Authors

• Stefan Chmiela
• Jan Hermann

We appreciate and welcome contributions and would like to thank the following people for participating in this project:

• Huziel Sauceda
• Igor Poltavsky
• Luis Gálvez
• Danny Panknin
• Grégory Fonseca

References

• [1] Chmiela, S., Tkatchenko, A., Sauceda, H. E., Poltavsky, I., Schütt, K. T., Müller, K.-R., Machine Learning of Accurate Energy-conserving Molecular Force Fields. Science Advances, 3(5), e1603015 (2017)
  10.1126/sciadv.1603015

• [2] Chmiela, S., Sauceda, H. E., Müller, K.-R., & Tkatchenko, A., Towards Exact Molecular Dynamics Simulations with Machine-Learned Force Fields. Nature Communications, 9(1), 3887 (2018)
  10.1038/s41467-018-06169-2

• [3] Chmiela, S., Sauceda, H. E., Poltavsky, I., Müller, K.-R., & Tkatchenko, A., sGDML: Constructing Accurate and Data Efficient Molecular Force Fields Using Machine Learning. Computer Physics Communications, 240, 38-45 (2019) 10.1016/j.cpc.2019.02.007