Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

The stability of two-dimensional (2D) layers and membranes is subject of a long standing theoretical debate. According to the so called Mermin-Wagner theorem, long wavelength fluctuations destroy the long-range order for 2D crystals. Similarly, 2D membranes embedded in a 3D space have a tendency to be crumpled. These dangerous fluctuations can, however, be suppressed by anharmonic coupling between bending and stretching modes making that a two-dimensional membrane can exist but should present strong height fluctuations. The discovery of graphene, the first truly 2D crystal and the recent experimental observation of ripples in freely hanging graphene makes these issues especially important. Beside the academic interest, understanding the mechanisms of stability of graphene is crucial for understanding electronic transport in this material that is attracting so much interest for its unusual Dirac spectrum and electronic properties. Here we address the nature of these height fluctuations by means of straightforward atomistic Monte Carlo simulations based on a very accurate many-body interatomic potential for carbon. We find that ripples spontaneously appear due to thermal fluctuations with a size distribution peaked around 70 \AA which is compatible with experimental findings (50-100 \AA) but not with the current understanding of stability of flexible membranes. This unexpected result seems to be due to the multiplicity of chemical bonding in carbon.

Intrinsic ripples in graphene

Discrete Solitons in Optics

https://iopscience.iop.org/article/10.3367/UFNe.2016.02.037729/pdf

Discrete breathers in crystals

Strong metal–support interactions (SMSIs) are crucial for the preparation of supported metal catalysts. A prevailing view is that the redox feature of the metal oxide support is the driving force behind SMSI construction. Herein we demonstrate CO2-induced SMSIs between irreducible oxide MgO and noble gold nanoparticles, presenting electronic and geometric features that are similar to those of classical SMSIs. The key to these interactions is activating the oxide surface by a reversible reaction, MgO + CO2 ⇆ MgCO3, which leads to migration of the support onto the gold nanoparticles to form thin overlayers. The overlayer is permeable to the reactant molecules, stable under the oxidation conditions and even water tolerant, resulting in sinter-resistant gold nanoparticle catalysts. This investigation provides an approach for the rational design and optimization of supported metal catalysts based on irreducible oxides, and deepens our understanding of the mechanism of SMSI formation. The strong metal–support interaction is an important phenomenon for the modulation of a catalyst´s performance but is traditionally restricted to reducible oxide supports. Here, a CO2-induced strong metal–support interaction is reported for gold nanoparticles supported on non-reducible MgO to yield a superior oxidation catalyst.

Strong metal–support interactions on gold nanoparticle catalysts achieved through Le Chatelier’s principle

It is found that in some metals, an intrinsic localized mode may exist with frequency above the top of the phonon spectrum. The necessary condition, requiring a sufficiently high ratio of quartic to cubic anharmonicity, may be fulfilled because of screening of the interaction between ions by free electrons. Starting from the known literature values of the pair potentials, we have found that in Ni and Nb the derived localized mode condition is fulfilled. Molecular-dynamics simulations of the nonlinear dynamics of Ni and Nb confirmed that high-frequency intrinsic localized modes may exist in these metals.

Prediction of high frequency intrinsic localized modes in Ni and Nb

MD simulations of recoil processes following the scattering of X-rays or neutrons have been performed in ionic crystals and metals. At small energies (<10 eV) the recoil can induce intrinsic localized modes (ILMs) and linear local modes associated with them. As a rule, the frequencies of such modes are located in the gaps of the phonon spectrum. However, in metallic Ni, Nb and Fe, due to the renormalization of atomic interactions by free electrons, the frequencies mentioned are found to be positioned above the phonon spectrum. It has been shown that these ILMs are highly mobile and can efficiently transfer a concentrated vibrational energy to large distances along crystallographic directions. If the recoil energy exceeds tens of eVs, vacancies and interstitials can be formed, being strongly dependent on the direction of the recoil momentum. In NaCl-type lattices the recoil in (110) direction can produce a vacancy and a crowdion, while in the case of a recoil in (100) and in (111) directions a bi-vacancy and a crowdion can be formed.

Theory and MD simulations of intrinsic localized modes and defect formation in solids

Molecular dynamics (MD) simulations of recoil processes following the scattering of x-rays or neutrons have been performed in ionic crystals and metals. At small energies (< 10 eV) the recoil can induce intrinsic localized modes (ILMs) and linear local modes associated with these modes. As a rule, the frequencies of such modes are located in the gaps of the phonon spectrum. However, in metallic Ni, Nb and Fe, due to the renormalization of atomic interactions by free electrons, the frequencies mentioned are found to be positioned above the phonon spectrum. It has been shown that these ILMs are highly mobile and can efficiently transfer a concentrated vibrational energy over large distances along crystallographic directions. If the recoil energy exceeds tens of eVs, vacancies and interstitials can be formed, which are strongly dependent on the direction of the recoil momentum. In NaCl-type lattices the recoil in (110) direction can produce a vacancy and a crowdion, while in the case of a recoil in (100) and in (111) directions a bi-vacancy and a crowdion can be formed.

https://iopscience.iop.org/article/10.1088/0031-8949/89/04/044003/pdf

M. Klopov

Papers

Prediction of high frequency intrinsic localized modes in Ni and Nb

Theory and MD simulations of intrinsic localized modes and defect formation in solids

Theory and molecular dynamics simulations of intrinsic localized modes and defect formation in solids

Materials properties of magnesium and calcium hydroxides from first-principles calculations

Transverse intrinsic localized modes in monatomic chain and in graphene