Julian H. R. Clarke

A molecular dynamics study of chain configurations in n‐alkane‐like liquids

We present precise measurements of the configurational properties of n‐alkane‐like liquids with 4, 5, 8, 20, 50, and 100 methylene groups. Quantities measured include the distributions of square radii of gyration, square end‐to‐end distances and proportion of conformers. To achieve high precision for n=50 and 100 a Fujitsu AP 1000 massively parallel processing machine with up to 512 processors is used. The results are compared with those obtained for the Flory model of alkane chains in which only correlation between nearest‐neighbor torsion angles are considered; the latter were obtained by Monte Carlo sampling of isolated chains using the pivot algorithm. Discrepancies between the two sets of data are discussed in terms of solvent and end effects. For n=100 full configurational relaxation was not observed within 2 ns.

A direct method of studying reaction rates by equilibrium molecular dynamics: Application to the kinetics of isomerization in liquid n‐butane

In this article we describe a straightforward and general method for studying chemical reaction kinetics in equilibrium systems using molecular dynamics computer simulation. We have applied it to the problem of determining the rate constants for the trans–gauche isomerization processes in liquid n‐butane. The method relies upon the fact that if a dynamic equilibrium exists in the system then it must apply to any chosen subset of the system. The power of the method is demonstrated by its high precision and in the discovery that a mechanism for direct gauche to gauche interconversions through the trans well is required to explain the data. The connection between the method applied here and other approaches to the determination of rate constants is discussed. The correlation function for isomerization dynamics is usually formulated as a collective property of the system. Its use leads to poor statistics when applied to simulation data. It is shown that the relaxation functions are equivalent to single partic...

The preparation of polymer melt samples for computer simulation studies

We have previously proposed a method for preparing dense amorphous polymer samples which was designed to circumvent the need for long periods of relaxation to equilibrium [J. I. McKechnie, D. Brown, and J. H. R. Clarke, Macromolecules 25, 1562 (1992)]. In the current article, we examine in more detail the application of the method to the preparation of polymer melts using precise data from massively parallel simulations. We expose deficiencies in the original method and introduce a modification which improves the equilibration. The limitations of the overall procedure are discussed in detail.

A domain decomposition parallelization strategy for molecular dynamics simulations on distributed memory machines

Abstract An algorithm is described which allows large scale molecular dynamics simulations to be carried out on a distributed memory parallel computer. The method is a development of a spatial decomposition technique already described [S.Y. Liem, D. Brown and J.H.R. Clarke, Comput. Phys. Commun. 67 (1991) 261] but incorporates decomposition of 3-D space in all three dimensions with link-cell and neighbour table techniques for enhanced efficiency. It is shown that communications between processors can be minimized without incurring the penalties associated with redundant force calculations. The method has been tested on a Fujitsu AP1000 parallel machine with up to 512 processor elements.

Molecular orientation correlations and reorientational motions in liquids carbon monoxide, nitrogen and oxygen at 77 K; A Raman and Rayleigh light-scattering study

Reorientational autocorrelation functions have been determined from measurements of depolarized vibrational Raman scattering for liquid carbon monoxide, nitrogen and oxygen at 77 K and atmospheric pressure. The autocorrelation functions, which for these liquids are not significantly affected by vibration-rotation interaction, reveal that free rotation is an important feature of the molecular motion in liquid nitrogen but is less important for carbon monoxide and oxygen. The differences in behaviour are discussed in terms of intermolecular forces. New values for the depolarized Rayleigh scattering cross section have been determined from intensity measurements made relative to the 992 cm-1 Raman line of benzene. These values are compared to those reported previously by the authors using a different intensity standard (Chem. Phys. Lett., 31, 355 (1975)). The scattering cross sections yield the following values , where ϑij is the angle between the major axes of molecules i and j (i≠j) and P 2 indicates the se...

A domain decomposition parallel processing algorithm for molecular dynamics simulations of polymers

Abstract We describe in this paper a domain decomposition molecular dynamics algorithm for use on distributed memory parallel computers which is capable of handling systems containing rigid bond constraints and three- and four-body potentials as well as non-bonded potentials. The algorithm has been successfully implemented on the Fujitsu 1024 processor element AP1000 machine. The performance has been compared with and benchmarked against the alternative cloning method of parallel processing [D. Brown, J.H.R. Clarke, M. Okuda and T. Yamazaki, J. Chem. Phys., 100 (1994) 1684] and results obtained using other scalar and vector machines. Two parallel versions of the SHAKE algorithm, which solves the bond length constraints problem, have been compared with regard to optimising the performance of this procedure.

The polarisability of LiCl as a function of bond distance

Abstract We report a near-Hartree—Fock-limit calculation of the variation of the polarisability of LiCl with bond distance over the range 2 a 0 to 20 a 0 . The results, which are of interest in the IBC model of light scattering, are broadly similar to corresponding calculations on Ne 2 and He 2 .

Equation of state of hard and Weeks–Chandler–Anderson hyperspheres in four and five dimensions

The fifth and sixth virial coefficient for hard hyperspheres in four and five dimensions has been computed using Monte Carlo techniques. It is found that B5/B24 has values 0.035 63±0.000 07 and 0.012 87±0.000 06 and that B6/B25 has values 0.007 691±0.000 028 and 0.000 942±0.000 027 in four and five dimensions, respectively. These values are used to investigate the equation of state of hard and Weeks–Chandler–Anderson (WCA) hyperspheres in four and five dimensions. Molecular dynamics simulations are performed for WCA hyperspheres. When compared to the molecular dynamics calculations, it is found that both the hard hypersphere and WCA equations of state are well described by a variety of theoretical approaches as long as the density is in the low-to-moderate regime. At the highest fluid densities studied, the Luban–Michels procedure provides the best accuracy for hard hyperspheres. The WCA prescription for the scaling of the reference system to a hard hypersphere one is a very good approximation in the flui...

A large scale molecular dynamics study of chain configurations in the n=100 alkane melt

We describe simulations of a polymer melt sample containing 640 chains, each chain being composed of 100 methylene groups. Using these large scale simulations radii of gyration have been calculated with a statistical error of ∼2%. At this level of precision it is shown that even for this modest chain length configurational equilibrium is not achieved in less than 4 ns at 500 K. Values of the square radii of gyration, square end‐to‐end distances and proportion of conformers at equilibrium show good agreement with predictions of the Flory model of alkane chains in which all long range interactions along the chains are ignored. These simulations were performed using a Fujitsu AP1000 massively parallel processing machine with 1024 processors in conjunction with a recently described domain decomposition molecular dynamics algorithm [D. Brown, J. H. R. Clarke, M. Okuda, and T. Yamazaki, Comput. Phys. Commun. 83, 1 (1994)] capable of handling systems containing rigid bond constraints and threea are made with pre...

The rheological properties of model liquid n-hexane determined by non-equilibrium molecular dynamics

Abstract Molecular dynamics computer simulation has been used to study a dense liquid composed of model molecules resembling n-hexane under steady-state she