Molecular Dynamics Simulation Program Research Articles

ARGOS, a vectorized general molecular dynamics program

AbstractThe organization of the highly vectorizable molecular dynamics simulation program ARGOS is described. The specific choice of the data structure and the separation of the calculation of interactions involving solutes and solvent molecules allows a considerable improvement in computation speed. Illustrative results are given for the NEC SX‐2/400 supercomputer. For the simulation of a large biological molecule in water a speedup factor of 5 is obtained as a result of vectorization of the code to 87%. The parts of the code used in a simulation of pure water could be vectorized to 98%, leading to an overall speedup factor due to vectorization of 13. The simulation of pure water runs over 300 times faster on the SX‐2/400 than on the VAX 8650.

Depolarized interaction-induced light scattering in dense phases

Depolarized interaction-induced light scattering (DILS) spectra of low density gases are now fully understood. Experimental data from different laboratories are in agreement within experimental error and the comparison among different experimental techniques (namely the depolarization ratio and the second virial Kerr effect) is finally positive (D. A. Dunmur, M. R. Manterfiel and D. J. Robinson, Mol. Phys., 1983, 50, 573). From the pair spectra empirical models of polarizability anisotropy can be derived, which can be used as an input in molecular dynamics (MD) simulation programs in order to extend the comparison between theory and experiment to the dense phase. This has already been done for argon, and the results are that, within one or two standard deviations, the pairwise additivity approximation, either in the total potential-energy function or in the total polarizability anisotropy, accounts for the DILS spectral moments over the whole density range of the fluid phase (F. Barocchi, G. Spinelli and M. Zoppi, Chem. Phys. Lett., 1982, 90, 22; M. Zoppi and G. Spinelli, Phys. Rev. A, 1986, 33, 939). On the other hand, DILS spectra are also present in the solid phase, but they are mixed with other effects such as phonon scattering. The analysis of the available experimental data shows a substantial difference between the correlation functions associated with DILS spectra, in the liquid and solid phase. This difference is attributable in part to the structure of the solid (long-range spatial order) and in part to simple density effects. The aim of this work is to present some preliminary experimental results which could be used to gain a better understanding, on a quantitative basis, of the relative weight of the kinetic and collective behaviour of dense hydrogen, near the liquid-solid transition.

Molecular dynamics simulation of the damage production in Al (110) surface with slow argon ions

We have developed a molecular dynamics simulation program to gain more insight into the sputtering process, especially the damage produced by it. We have studied the sputtering of aluminium (110) surface with argon ions. The Morse pair potentail was used for Al−Al interaction, the Lennard-Jones potential for Ar−Ar interaction and both the Moliere potential and the universal potential of Ziegler et al. for Ar−Al interaction. An electronic friction term proportional to the particle velocities was also used. The studied incident argon ion energies and angles were 200 and 400 eV and 0° (normal), 25°, 45° and 75°, respectively. The calculated sputtering yield and the overall shape and the mean depth of the vacancy profiles agree with the experimental results. The obtained profiles contain a narrow peak within the topmost atomic layers, followed by a weak tail deeper in the material. The intersitial and argon ion distributions are much more spread out at larger depths. The total number of vacancies per incident Ar + ion varies from 0 to 7, increasing as function of Ar + ion energy.