LiquidLib: A comprehensive toolbox for analyzing classical and ab initio molecular dynamics simulations of liquids and liquid-like matter with applications to neutron scattering experiments

Walter, Nathan P.; Jaiswal, Abhishek; Cai, Zhikun; Zhang, Yang

doi:10.1016/j.cpc.2018.03.005

Cited by 49 publications

(36 citation statements)

References 11 publications

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“…All the MD simulations and analyses were implemented using the GROMACS program, 31,32 except that the static structural factors and bond order parameters were analyzed by using the LiquidLib program. 33 Otherwise specially stated, the trajectories of last 10 ns at various temperatures are used to perform the analyses. In experiments, PEO is known as a crystallizable polymer.…”

Section: Computational Detailsmentioning

confidence: 99%

Free Surface-Induced Glass-Transition Temperature Suppression of Simulated Polymer Chains

2019

J. Phys. Chem. C

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Glass-transition temperatures (T g’s) in poly(ethylene oxide) chains of 250 monomers as typical examples have been extensively simulated with the systematically coarse-grained potentials. The studied model systems include two 1-chain systems without and with the periodic boundary condition and two 8-chain systems in the NVT and NPT ensembles, which are labeled as nopbc, pbc, NVT, and NPT, respectively. The absence of crystallization and instead the occurrence of glass transition are first confirmed for all these systems during quick cooling from a high temperature to a low temperature. One unambiguous trend is then obtained for the dynamical T g: T g(nopbc) < T g(pbc) < T g(NVT) < T g(NPT). The T g reductions in the former three systems compared to the last one accord with the greater chain motions at both rubbery and glassy states, which, in turn, is caused by the free surfaces in different degrees. The free surfaces and glass transition for these systems can be obviously revealed by the density maps. It is also found that the dynamical T g for any system is insensible to either initial configuration or ultimate conformation. In other words, this work provides some new insights into glass transition of confined polymers.

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Section: Computational Detailsmentioning

confidence: 99%

Free Surface-Induced Glass-Transition Temperature Suppression of Simulated Polymer Chains

2019

J. Phys. Chem. C

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“…To access shorter times to complement the NSE data, Fourier deconvoluted time-of-flight spectra measured on the AMATERAS neutron spectrometer 44 , 45 at the J-PARC facility were compared with the ISFs collected on the WASP spectrometer. Nuclear neutron scattering is composed of a coherent component yielding information on the relative position and motion of couples of atoms, and an incoherent component related to the single particle dynamics of the atoms 24 , 49 . Polarized diffraction that can separate coherent and incoherent contributions to the scattering signal was performed for CKN on the NGA-NSE spectrometer at the NCNR.…”

Section: Resultsmentioning

confidence: 99%

Q-dependent collective relaxation dynamics of glass-forming liquid Ca0.4K0.6(NO3)1.4 investigated by wide-angle neutron spin-echo

et al. 2022

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The relaxation behavior of glass formers exhibits spatial heterogeneity and dramatically changes upon cooling towards the glass transition. However, the underlying mechanisms of the dynamics at different microscopic length scales are not fully understood. Employing the recently developed wide-angle neutron spin-echo spectroscopy technique, we measured the Q-dependent coherent intermediate scattering function of a prototypical ionic glass former Ca0.4K0.6(NO3)1.4, in the highly viscous liquid state. In contrast to the structure modulated dynamics for Q < 2.4 Å−1, i.e., at and below the structure factor main peak, for Q > 2.4 Å−1, beyond the first minimum above the structure factor main peak, the stretching exponent exhibits no temperature dependence and concomitantly the relaxation time shows smaller deviations from Arrhenius behavior. This finding indicates a change in the dominant relaxation mechanisms around a characteristic length of 2π/(2.4 Å−1) ≈ 2.6 Å, below which the relaxation process exhibits a temperature independent distribution and more Arrhenius-like behavior.

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“…The dynamic structure function is defined as 26 where g d ij ( r , t ) is the distinct van Hove correlation function computed with periodic boundary conditions from our in-house modified version of LiquiLib toolbox normalized so that at time 0 it becomes the pair distribution function g ij ( r ) and at long time it goes to 1. 62 In Equation (1) x i , x j are the corresponding atomic mol fractions, f i ( q ), f j ( q ) are the X-ray atomic form factors, and W ( r ) is a Lorch function. Just like the structure function S ( q ), the dynamic structure function can also be partitioned into convenient additive subcomponents 19 , 20 , 31 − 43 that provide useful information about the correlation of specific subgroups of atoms in the liquid; in this work, we focus mostly on its cationic head–anion subcomponent, S H–A ( q , t ).…”

Section: Methodsmentioning

confidence: 99%

Relationship between the Relaxation of Ionic Liquid Structural Motifs and That of the Shear Viscosity

2021

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In a set of recent articles, we have highlighted that friction is highly inhomogeneous in a typical ionic liquid (IL) with charge networks that are stiff and charge-depleted regions that are soft. This has consequences not only for the dynamics of ILs but also for the transport properties of solutes dissolved in them. In this article, we explore whether the family of alkylimidazolium ILs coupled with bis(trifluoromethylsulfonyl)imide (with similar Coulombic interactions but different alkyl tails), when dynamically “equalized” by having a similar shear viscosity, display q -dependent structural relaxation time scales that are the same across the family. Our results show that this is not the case, and in fact, the relaxation of in-network charge alternation appears to be significantly affected by the presence of separate polar and apolar domains. However, we also find that if one was to assign weight factors to the relaxation of the structural motifs, charge alternation always contributes about the same amount (between 62.1 and 66.3%) across systems to the running integral of the stress tensor correlation function from which the shear viscosity is derived. Adjacency correlations between positive and negative moieties also contribute an identical amount if a prepeak is not present (about 38%) and a slightly smaller amount (about 28%) when intermediate range order exists. The prepeak only contributes about 6% to viscoelastic relaxation, highlighting that the dynamics of the smaller scale motifs is the most important.

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LiquidLib: A comprehensive toolbox for analyzing classical and ab initio molecular dynamics simulations of liquids and liquid-like matter with applications to neutron scattering experiments

Cited by 49 publications

References 11 publications

Free Surface-Induced Glass-Transition Temperature Suppression of Simulated Polymer Chains

Free Surface-Induced Glass-Transition Temperature Suppression of Simulated Polymer Chains

Q-dependent collective relaxation dynamics of glass-forming liquid Ca0.4K0.6(NO3)1.4 investigated by wide-angle neutron spin-echo

Relationship between the Relaxation of Ionic Liquid Structural Motifs and That of the Shear Viscosity

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