PND: Physics-informed neural-network software for molecular dynamics applications

Taufeq Mohammed Razakh; Beibei Wang; Shane Jackson; Rajiv K. Kalia; Aiichiro Nakano; Ken-ichi Nomura; Priya Vashishta

SoftwareX (Jul 2021)

PND: Physics-informed neural-network software for molecular dynamics applications

Taufeq Mohammed Razakh,
Beibei Wang,
Shane Jackson,
Rajiv K. Kalia,
Aiichiro Nakano,
Ken-ichi Nomura,
Priya Vashishta

Affiliations

Taufeq Mohammed Razakh: Collaboratory for Advanced Computing and Simulations, University of Southern California, Los Angeles, CA 90089-0242, USA; Department of Computer Science, University of Southern California, Los Angeles, CA 90089-0781, USA
Beibei Wang: Collaboratory for Advanced Computing and Simulations, University of Southern California, Los Angeles, CA 90089-0242, USA; Department of Physics & Astronomy, University of Southern California, Los Angeles, CA 90089-0484, USA
Shane Jackson: Collaboratory for Advanced Computing and Simulations, University of Southern California, Los Angeles, CA 90089-0242, USA; Department of Physics & Astronomy, University of Southern California, Los Angeles, CA 90089-0484, USA
Rajiv K. Kalia: Collaboratory for Advanced Computing and Simulations, University of Southern California, Los Angeles, CA 90089-0242, USA; Department of Computer Science, University of Southern California, Los Angeles, CA 90089-0781, USA; Department of Physics & Astronomy, University of Southern California, Los Angeles, CA 90089-0484, USA; Department of Chemical Engineering & Materials Science, University of Southern California, Los Angeles, CA 90089-12111, USA
Aiichiro Nakano: Collaboratory for Advanced Computing and Simulations, University of Southern California, Los Angeles, CA 90089-0242, USA; Department of Computer Science, University of Southern California, Los Angeles, CA 90089-0781, USA; Department of Physics & Astronomy, University of Southern California, Los Angeles, CA 90089-0484, USA; Department of Chemical Engineering & Materials Science, University of Southern California, Los Angeles, CA 90089-12111, USA; Department of Quantitative & computational Biology, University of Southern California, Los Angeles, CA 90089-2910, USA
Ken-ichi Nomura: Collaboratory for Advanced Computing and Simulations, University of Southern California, Los Angeles, CA 90089-0242, USA; Department of Chemical Engineering & Materials Science, University of Southern California, Los Angeles, CA 90089-12111, USA; Corresponding author at: Collaboratory for Advanced Computing and Simulations, University of Southern California, Los Angeles, CA 90089-0242, USA.
Priya Vashishta: Collaboratory for Advanced Computing and Simulations, University of Southern California, Los Angeles, CA 90089-0242, USA; Department of Computer Science, University of Southern California, Los Angeles, CA 90089-0781, USA; Department of Physics & Astronomy, University of Southern California, Los Angeles, CA 90089-0484, USA; Department of Chemical Engineering & Materials Science, University of Southern California, Los Angeles, CA 90089-12111, USA

Journal volume & issue: Vol. 15
p. 100789

Abstract

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We have developed PND, a differential equation solver software based on a physics-informed neural network (PINN) for molecular dynamics simulators. Based on automatic differentiation technique provided by PyTorch, our software allows users to flexibly implement equation of motion for atoms, initial and boundary conditions, and conservation laws as loss function to train the network. PND comes with a parallel molecular dynamic engine in order to examine and optimize loss function design, and different conservation laws and boundary conditions, and hyperparameters, thereby accelerating PINN-based development for molecular applications.

Published in SoftwareX

ISSN: 2352-7110 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Science: Mathematics: Instruments and machines: Electronic computers. Computer science: Computer software
Website: http://www.journals.elsevier.com/softwarex/

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