HSMA: An O(N) electrostatics package implemented in LAMMPS

Liang, Jiuyang; Yuan, Jiaxing; Xu, Zhenli

doi:10.1016/j.cpc.2022.108332

Cited by 5 publications

(4 citation statements)

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“…It will be also great significance for broader use of the algorithm if there is a version with the graphic processing units, and we are working on it currently. Moreover, extension of the method to quasi-2D systems with planar interfaces, in particular with the dielectric mismatch, ,, is straightforward and shall be studied in our subsequent work. The IRBE method is expected to play an important role for simulating problems in applications in chemical physics, materials, and biological systems.…”

Section: Discussionmentioning

confidence: 99%

“…The remaining part is short ranged and can be calculated by the cutoff scheme similar to the LJ interactions. It is mentioned that there are other kinds of powerful and linear-scaling method for fast evaluation of the electrostatic interactions, including fast multipole methods, , multigrids, and Maxwell-equation molecular dynamics, where the fast multipole methods are particularly efficient for systems for large scale problems and for the case of inhomogeneous particle distribution. , These fundamental methods for computing forces are all required to combine with modern distributed architectures, i.e., the well-known 3D domain decomposition. ,, The advances on domain decomposition, building neighbor lists, and time integration are contributed to the latest topics of algorithm development.…”

Section: Introductionmentioning

confidence: 99%

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Improved Random Batch Ewald Method in Molecular Dynamics Simulations

Liang

Zhao

2022

J. Phys. Chem. A

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The random batch Ewald (RBE) is an efficient and accurate method for molecular dynamics (MD) simulations of physical systems at the nano/microscale. The method shows great potential to solve the computational bottleneck of long-range interactions, motivating a necessity to accelerate short-range components of the nonbonded interactions for a further speedup of MD simulations. In this work, we present an improved RBE method for the nonbonding interactions by introducing the random batch idea to constructing neighbor lists for the treatment of both the short-range part of the Ewald splitting and the Lennard−Jones potential. The efficiency that the novel neighbor list algorithm owes to the stochastic minibatch strategy can significantly reduce the total number of neighbors. We obtain the error estimate and convergence by theoretical analysis and implement the improved RBE method in the LAMMPS package. Benchmark simulations are performed to demonstrate the accuracy and stability of the algorithm. Numerical tests on computer performance by conducting large-scaled MD simulations for systems including up to 0.1 billion water molecules are run on massive clusters with up to 50000 CPU cores, demonstrating the attractive features such as the high parallel scalability and memory-saving of the method in comparison to the existing methods.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Improved Random Batch Ewald Method in Molecular Dynamics Simulations

Liang

Zhao

2022

J. Phys. Chem. A

Self Cite

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“…It will be also great significance for broader use of the algorithm if there is a version with the graphic processing units, and we are working on it currently. Moreover, extension of the method to quasi-2D systems with planar interfaces, in particular with the dielectric mismatch [55,26,56] is straightforward and shall be studied in our subsequent work. The IRBE method is expected to play an important role for simulating problems in applications at chemical physics, materials and biological systems.…”

Section: Discussionmentioning

confidence: 99%

“…The remaining part is short ranged and can be calculated by the cutoff scheme similar to the LJ interactions. It is mentioned that there are other kinds of powerful and linear-scaling method for fast evaluating electrostatic interactions, including fast multipole methods [22,23], multigrids and Maxwell-equation molecular dynamics [24], where the fast multipole methods are particulary efficient for systems for large scale problems and for the case of inhomogeneous particle distribution [25,26]. These fundamental methods for computing forces are all required to combine with modern distributed architectures, i.e., the well-known 3D domain decomposition [14,27,28].…”

Section: Introductionmentioning

confidence: 99%

Improved random batch Ewald method in molecular dynamics simulations

Liang,

Xu,

Zhao

2022

Preprint

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The random batch Ewald (RBE) is an efficient and accurate method for molecular dynamics (MD) simulations of physical systems at the nano-/micro-scale. The method shows great potential to solve the computational bottleneck of long-range interactions, motivating a necessity to accelerating short-range components of the non-bonded interactions for a further speedup of MD simulations. In this work, we present an improved RBE method for the non-bonding interactions by introducing the random batch idea to constructing neighbor lists for the treatment of both the short-range part of the Ewald splitting and the Lennard-Jones potential. The efficiency of the novel neighbor list algorithm owes to the stochastic minibatch strategy which can significantly reduce the total number of neighbors. We implement the improved RBE method in the LAMMPS package. The accuracy and stability of the algorithm are demonstrated by both theoretical analysis and benchmark simulations. Numerical tests on computer performance by conducting large-scaled MD simulations for systems including up to 0.1 billion water molecules, run on massive cluster with up to 50 thousand CPU cores, demonstrating the attractive features such as the high parallel scalability and memory-saving of the method in comparison to the existing methods.

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