sgdml 0.3.2

Reference implementation of the GDML and sGDML force field models.

Symmetric Gradient Domain Machine Learning (sGDML)

For more details visit: http://sgdml.org/

Documentation can be found here: http://sgdml.org/doc/

Requirements:

• Python 2.7/3.7
• NumPy (>=1.13.0)
• SciPy
• PyTorch (optional)

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, we 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.

...with GPU support

For GPU support, the optional PyTorch dependency needs to be installed.

pip install -e .[torch]

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('examples/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)

...with GPU support

Setting use_torch=True when instantiating the predictor redirects all calculations to PyTorch.

gdml = GDMLPredict(model, use_torch=True)

NOTE: PyTorch must be installed with GPU support, otherwise the CPU is used. However, we recommend performing CPU calculations without PyTorch for optimal performance.

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

• [4] Sauceda, H. E., Chmiela, S., Poltavsky, I., Müller, K.-R., & Tkatchenko, A., Molecular Force Fields with Gradient-Domain Machine Learning: Construction and Application to Dynamics of Small Molecules with Coupled Cluster Forces. The Journal of Chemical Physics, 150, 114102 (2019) 10.1063/1.5078687