Correction of diffusion calculations when using two types of non-rectangular simulation boxes in molecular simulations

Cao, Ting; Ji, Xiangfei; Wu, Jinpeng; Zhang, Shiju; Xin, Yang

doi:10.1007/s00894-018-3910-6

Cited by 8 publications

(1 citation statement)

References 31 publications

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“…These might affect the simulation itself (e.g., insufficient sampling of the ensemble [52]) or the scattering pattern calculation (e.g., Bragg peak broadening of a crystalline material [82,84]). The Q-clean method introduced here is currently only implemented for cubic simulation boxes; a future extension could incorporate other shapes of simulation regions like octahedrons or dodecahedrons [85].…”

Section: Structure-atomic and Nanoscopicmentioning

confidence: 99%

Computation of X-ray and Neutron Scattering Patterns to Benchmark Atomistic Simulations against Experiments

Majumdar,

Müller,

Busch

2024

IJMS

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Molecular Dynamics simulations study material structure and dynamics at the atomic level. X-ray and neutron scattering experiments probe exactly the same time- and length scales as the simulations. In order to benchmark simulations against measured scattering data, a program is required that computes scattering patterns from simulations with good single-core performance and support for parallelization. In this work, the existing program Sassena is used as a potent solution to this requirement for a range of scattering methods, covering pico- to nanosecond dynamics, as well as the structure from some Ångströms to hundreds of nanometers. In the case of nanometer-level structures, the finite size of the simulation box, which is referred to as the finite size effect, has to be factored into the computations for which a method is described and implemented into Sassena. Additionally, the single-core and parallelization performance of Sassena is investigated, and several improvements are introduced.

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