Molecular Simulation in the Canonical Ensemble and Beyond

Jia, Zhidong; Leimkuhler, Benedict

doi:10.1051/m2an:2007019

Cited by 2 publications

(2 citation statements)

References 39 publications

(58 reference statements)

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“…By using Python as a high-level language, looping algorithms such as the Velocity Verlet method [31] (see also e.g. [32,33]) for timestepping or advanced thermostats [34,35] can be implemented very easily, while still generating fast code for the computationally expensive particle loops.…”

Section: Introductionmentioning

confidence: 99%

A domain specific language for performance portable molecular dynamics algorithms

Saunders

Grant

Müller

2018

Computer Physics Communications

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Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be experts both in their own domain (physics/chemistry/biology) and specialists in the low level parallelisation and optimisation of their codes. To address this challenge, we describe a "Separation of Concerns" approach for the development of parallel and optimised MD codes: the science specialist writes code at a high abstraction level in a domain specific language (DSL), which is then translated into efficient computer code by a scientific programmer. In a related context, an abstraction for the solution of partial differential equations with grid based methods has recently been implemented in the (Py)OP2 library. Inspired by this approach, we develop a Python code generation system for molecular dynamics simulations on different parallel architectures, including massively parallel distributed memory systems and GPUs. We demonstrate the efficiency of the auto-generated code by studying its performance and scalability on different hardware and compare it to other state-of-the-art simulation packages. With growing data volumes the extraction of physically meaningful information from the simulation becomes increasingly challenging and requires equally efficient implementations. A particular advantage of our approach is the easy expression of such analysis algorithms. We consider two popular methods for deducing the crystalline structure of a material from the local environment of each atom, show how they can be expressed in our abstraction and implement them in the code generation framework.

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Section: Introductionmentioning

confidence: 99%

A domain specific language for performance portable molecular dynamics algorithms

Saunders

Grant

Müller

2018

Computer Physics Communications

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“…This result is in agreement with the properties obtained in ref. 39 for multi-temperature dynamics. Therefore, the proposed FNH equations can at best approximate a (canonical) equilibrium distribution for finite T, Q 2 .…”

Section: Fast Nosé-hoover Equations Of Motionmentioning

confidence: 99%