Semi-Empirical Shadow Molecular Dynamics: A PyTorch Implementation

Kulichenko, Maksim; Barros, Kipton Marcos; Lubbers, Nicholas Edward; Fedik, Nikita; Zhou, Guoqing; Tretiak, Sergei; Nebgen, Benjamin Tyler; Niklasson, Anders N.

doi:10.1021/acs.jctc.3c00234

Title: Semi-Empirical Shadow Molecular Dynamics: A PyTorch Implementation

Journal Article · 09 May 2023 · Journal of Chemical Theory and Computation

DOI: https://doi.org/10.1021/acs.jctc.3c00234 · OSTI ID:1985863

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Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
NVIDIA Corporation, Santa Clara, CA (United States)

Here, extended Lagrangian Born–Oppenheimer molecular dynamics (XL-BOMD) in its most recent shadow potential energy version has been implemented in the semiempirical PyTorch-based software PySeQM. The implementation includes finite electronic temperatures, canonical density matrix perturbation theory, and an adaptive Krylov subspace approximation for the integration of the electronic equations of motion within the XL-BOMB approach (KSA-XL-BOMD). The PyTorch implementation leverages the use of GPU and machine learning hardware accelerators for the simulations. The new XL-BOMD formulation allows studying more challenging chemical systems with charge instabilities and low electronic energy gaps. The current public release of PySeQM continues our development of modular architecture for large-scale simulations employing semi-empirical quantum-mechanical treatment. Applied to molecular dynamics, simulation of 840 carbon atoms, one integration time step executes in 4 s on a single Nvidia RTX A6000 GPU.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE Laboratory Directed Research and Development (LDRD) Program; USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division (CSGB); USDOE National Nuclear Security Administration (NNSA)

Grant/Contract Number:: 89233218CNA000001

OSTI ID:: 1985863

Report Number(s):: LA-UR-22-33200; {"","Journal ID: ISSN 1549-9618"}

Journal Information:: Journal of Chemical Theory and Computation, Journal Name: Journal of Chemical Theory and Computation Journal Issue: 11 Vol. 19; ISSN 1549-9618

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

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