A High-Throughput Multiobjective Genetic-Algorithm Workflow for In Situ Training of Reactive Molecular-Dynamics Force Fields

2016 ◽  
Keyword(s):  
Genetic Algorithm ◽  
Molecular Dynamics ◽  
High Throughput ◽  
Force Fields ◽  
Multiobjective Genetic Algorithm ◽  
Reactive Molecular Dynamics ◽  
In Situ Training

scholarly journals Optimizing the performance of reactive molecular dynamics simulations for many-core architectures

2018 ◽  
Vol 33 (2) ◽  
pp. 304-321 ◽  
Author(s):  
Hasan Metin Aktulga ◽  
Chris Knight ◽  
Paul Coffman ◽  
Kurt A O’Hearn ◽  
Tzu-Ray Shan ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Species ◽  
Trajectory Data ◽  
Reactive Molecular Dynamics ◽  
Species Analysis ◽  
Dynamics Simulations ◽  
Many Core ◽  
Molecular Species Analysis

Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this article, we focus on optimizing the performance of the widely used LAMMPS/ReaxC package for many-core architectures. As hybrid parallelism allows better leverage of the increasing on-node parallelism, we adopt thread parallelism in the construction of bonded and nonbonded lists and in the computation of complex ReaxFF interactions. To mitigate the I/O overheads due to large volumes of trajectory data produced and to save users the burden of post-processing, we also develop a novel in situ tool for molecular species analysis. We analyze the performance of the resulting ReaxC-OMP package on two different architectures: (i) Mira, an IBM Blue Gene/Q system and (ii) Cori-II, a Cray XC-40 sytem with Knights Landing processors. For Pentaerythritol tetranitrate (PETN) systems of sizes ranging from 32 thousand to 16.6 million particles, we observe speedups in the range of 1.5–4.5×. We observe sustained performance improvements for up to 262,144 cores (1,048,576 processes) of Mira and a weak scaling efficiency of 91.5% in large simulations containing 16.6 million particles. The in situ molecular species analysis tool incurs only insignificant overheads across various system sizes and runs configurations.

scholarly journals Nanocellulose/graphene oxide layered membranes: elucidating their behaviour during filtration of water and metal ions in real time

Nanoscale ◽  
2019 ◽  
Vol 11 (46) ◽  
pp. 22413-22422 ◽  
Author(s):  
Luis Valencia ◽  
Susanna Monti ◽  
Sugam Kumar ◽  
Chuantao Zhu ◽  
Peng Liu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Graphene Oxide ◽  
Metal Ions ◽  
Real Time ◽  
Metal Ion ◽  
Computational Simulations ◽  
Reactive Molecular Dynamics

In situ SAXS and reactive molecular dynamics (ReaxFF) computational simulations of water and metal ion interaction with CNF–GO layered membranes.

In Situ Formation of Circular and Branched Oligomers in Localized High Concentration Electrolyte at Lithium−metal Solid Electrolyte Interphase: A Hybrid ab initio and Reactive Molecular Dynamics

2021 ◽  
Author(s):  
Yue Liu ◽  
Qintao Sun ◽  
Peiping Yu ◽  
Bingyun Ma ◽  
Hao Yang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Solid Electrolyte ◽  
Solid Electrolyte Interphase ◽  
Lithium Metal ◽  
High Concentration ◽  
Metal Anode ◽  
Reactive Molecular Dynamics ◽  
Li Metal Anode ◽  
In Situ Formation

Developing advanced electrolytes has been considered as a promising approach to stabilize lithium (Li) metal anode via the formation of stable solid electrolyte interphase (SEI) that can protect Li anode...

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