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The Discrete Element Method is widely employed for simulating granular flows, but conventional integration techniques may produce unphysical results for simulations with static friction when particle size ratios exceed R ≈ 3. These inaccuracies arise under certain circumstances because some variables in the velocity-Verlet algorithm are calculated at the half-timestep, while others are computed at the full timestep. To correct this, we develop an improved velocity-Verlet integration algorithm to ensure physically accurate outcomes up to the largest size ratios examined (R = 100). The implementation of this improved synchronized_verlet integration method within the LAMMPS framework is detailed, and its effectiveness is validated through a simple three-particle test case and a more general example of granular flow in mixtures with large size-ratios, for which we provide general guidelines for selecting simulation parameters and accurately modeling inelasticity in large particle size-ratio simulations.
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Machine learning for parameter auto-tuning in molecular dynamics simulations: Efficient dynamics of ions near polarizable nanoparticles
Simulating the dynamics of ions near polarizable nanoparticles (NPs) using coarse-grained models is extremely challenging due to the need to solve the Poisson equation at every simulation timestep. Recently, a molecular dynamics (MD) method based on a dynamical optimization framework bypassed this obstacle by representing the polarization charge density as virtual dynamic variables and evolving them in parallel with the physical dynamics of ions. We highlight the computational gains accessible with the integration of machine learning (ML) methods for parameter prediction in MD simulations by demonstrating how they were realized in MD simulations of ions near polarizable NPs. An artificial neural network–based regression model was integrated with MD simulation and predicted the optimal simulation timestep and optimization parameters characterizing the virtual system with 94.3% success. The ML-enabled auto-tuning of parameters generated accurate dynamics of ions for ≈ 10 million steps while improving the stability of the simulation by over an order of magnitude. The integration of ML-enhanced framework with hybrid Open Multi-Processing / Message Passing Interface (OpenMP/MPI) parallelization techniques reduced the computational time of simulating systems with thousands of ions and induced charges from thousands of hours to tens of hours, yielding a maximum speedup of ≈ 3 from ML-only acceleration and a maximum speedup of ≈ 600 from the combination of ML and parallel computing methods. Extraction of ionic structure in concentrated electrolytes near oil–water emulsions demonstrates the success of the method. The approach can be generalized to select optimal parameters in other MD applications and energy minimization problems.
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- Award ID(s):
- 1720625
- PAR ID:
- 10549252
- Publisher / Repository:
- SAGE Publications
- Date Published:
- Journal Name:
- The International Journal of High Performance Computing Applications
- Volume:
- 34
- Issue:
- 3
- ISSN:
- 1094-3420
- Format(s):
- Medium: X Size: p. 357-374
- Size(s):
- p. 357-374
- Sponsoring Org:
- National Science Foundation
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