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 reactive force-field (ReaxFF) interatomic potential is a powerful computational tool for exploring, developing and optimizing material properties. Methods based on the principles of quantum mechanics (QM), while offering valuable theoretical guidance at the electronic level, are often too computationally intense for simulations that consider the full dynamic evolution of a system. Alternatively, empirical interatomic potentials that are based on classical principles require significantly fewer computational resources, which enables simulations to better describe dynamic processes over longer timeframes and on larger scales. Such methods, however, typically require a predefined connectivity between atoms, precluding simulations that involve reactive events. The ReaxFF method was developed to help bridge this gap. Approaching the gap from the classical side, ReaxFF casts the empirical interatomic potential within a bond-order formalism, thus implicitly describing chemical bonding without expensive QM calculations. This article provides an overview of the development, application, and future directions of the ReaxFF method.

https://biblio.ugent.be/publication/8514189/file/8514192.pdf

The ReaxFF reactive force-field: development, applications and future directions

The tunneling current from a scanning tunneling microscope was used to image and dissociate single O{sub 2} molecules on the Pt(111) surface in the temperature range of 40 to 150K. After dissociation, the two oxygen atoms are found one to three lattice constants apart. The dissociation rate as a function of current was found to vary as I{sup 0.8{plus_minus}0.2} , I{sup 1.8{plus_minus}0.2} , and I{sup 2.9{plus_minus}0.3} for sample biases of 0.4, 0.3, and 0.2V, respectively. These rates are explained using a general model for dissociation induced by intramolecular vibrational excitations via resonant inelastic electron tunneling. {copyright} {ital 1997} {ital The American Physical Society}

Single Molecule Dissociation by Tunneling Electrons

A Guide to Monte Carlo Simulations in Statistical Physics: Reweighting methods

The activation of O2 on metal surfaces is a critical process for heterogeneous catalysis and materials oxidation. Fundamental studies of well-defined metal surfaces using a variety of techniques have given crucial insight into the mechanisms, energetics, and dynamics of O2 adsorption and dissociation. Here, trends in the activation of O2 on transition metal surfaces are discussed, and various O2 adsorption states are described in terms of both electronic structure and geometry. The mechanism and dynamics of O2 dissociation are also reviewed, including the importance of the spin transition. The reactivity of O2 and O toward reactant molecules is also briefly discussed in the context of catalysis. The reactivity of a surface toward O2 generally correlates with the adsorption strength of O, the tendency to oxidize, and the heat of formation of the oxide. Periodic trends can be rationalized in terms of attractive and repulsive interactions with the d-band, such that inert metals tend to feature a full d band ...

O2 Activation by Metal Surfaces: Implications for Bonding and Reactivity on Heterogeneous Catalysts

Accurate modeling of high-temperature hypersonic flows in the atmosphere requires consideration of collision-induced dissociation of molecular species and energy transfer between the translational and internal modes of the gas molecules. Here, we describe a study of the N2 + N2⟶N2 + 2N and N2 + N2⟶4N nitrogen dissociation reactions using the quasiclassical trajectory (QCT) method. The simulations used a new potential energy surface for the N4 system; the surface is an improved version of one that was presented previously. In the QCT calculations, initial conditions were determined based on a two-temperature model that approximately separates the translational-rotational temperature from the vibrational temperature of the N2 diatoms. Five values from 8000 K to 30,000 K were considered for each of the two temperatures. Over 2.4 × 10(9) trajectories were calculated. We present results for ensemble-averaged dissociation rate constants as functions of the translational-rotational temperature T and the vibrational temperature T(v). The rate constant depends more strongly on T when T(v) is low, and it depends more strongly on T(v) when T is low. Quasibound reactant states contribute significantly to the rate constants, as do exchange processes at higher temperatures. We discuss two sets of runs in detail: an equilibrium test set in which T = T(v) and a nonequilibrium test set in which T(v) < T. In the equilibrium test set, high-v and moderately-low-j molecules contribute most significantly to the overall dissociation rate, and this state specificity becomes stronger as the temperature decreases. Dissociating trajectories tend to result in a major loss of vibrational energy and a minor loss of rotational energy. In the nonequilibrium test set, as T(v) decreases while T is fixed, higher-j molecules contribute more significantly to the dissociation rate, dissociating trajectories tend to result in a greater rotational energy loss, and the dissociation probability's dependence on v weakens. In this way, as T(v) decreases, rotational energy appears to compensate for the decline in average vibrational energy in promoting dissociation. In both the equilibrium and nonequilibrium test sets, in every case, the average total internal energy loss in the dissociating trajectories is between 10.2 and 11.0 eV, slightly larger than the equilibrium potential energy change of N2 dissociation.

An improved potential energy surface and multi-temperature quasiclassical trajectory calculations of N2 + N2 dissociation reactions

The direct molecular simulation (DMS) approach is used to predict the internal energy relaxation and dissociation dynamics of high-temperature nitrogen. An ab initio potential energy surface (PES) is used to calculate the dynamics of two interacting nitrogen molecules by providing forces between the four atoms. In the near-equilibrium limit, it is shown that DMS reproduces the results obtained from well-established quasiclassical trajectory (QCT) analysis, verifying the validity of the approach. DMS is used to predict the vibrational relaxation time constant for N2–N2 collisions and its temperature dependence, which are in close agreement with existing experiments and theory. Using both QCT and DMS with the same PES, we find that dissociation significantly depletes the upper vibrational energy levels. As a result, across a wide temperature range, the dissociation rate is found to be approximately 4–5 times lower compared to the rates computed using QCT with Boltzmann energy distributions. DMS calculations predict a quasi-steady-state distribution of rotational and vibrational energies in which the rate of depletion of high-energy states due to dissociation is balanced by their rate of repopulation due to collisional processes. The DMS approach simulates the evolution of internal energy distributions and their coupling to dissociation without the need to precompute rates or cross sections for all possible energy transitions. These benchmark results could be used to develop new computational fluid dynamics models for high-enthalpy flow applications.

Direct molecular simulation of nitrogen dissociation based on an ab initio potential energy surface

We present a microscopic description for the response of crystalline Si nanospheres up to 10 nm in radius for various uniaxial compression levels The behavior at low compressions closely resembles the Hertzian predictions At higher compressions the creation of a new beta-tin phase in the particle core leads to (i) volumetric changes (ii) an increase in elastic moduli, and (iii) significant hardening Further, (iv) a reversible character of the transformation is obtained with molecular dynamics simulations The agreement of (i)-(iv) with recent experimental findings challenges the current exclusive view of a dislocation plasticity response in somewhat larger nanoparticles The phase-transition path should dominate in ultrasmall structures, where dislocation activity is prohibited

Phase-transition plasticity response in uniaxially compressed silicon nanospheres

Nitrogen dissociation is studied using direct molecular simulation with a new potential-energy surface. Both ${N}_{2}$ - ${N}_{2}$ and $N$ - ${N}_{2}$ processes are simulated as they concurrently take place in an evolving nonequilibrium gas system. The coupling between vibrational excitation and dissociation is quantified leading to several new insights.

Dynamics of nitrogen dissociation from direct molecular simulation

/pdf/phase-transition-plasticity-response-in-uniaxially-z6p9xgrwru.pdf

Paolo Valentini

Papers

An improved potential energy surface and multi-temperature quasiclassical trajectory calculations of N2 + N2 dissociation reactions

Direct molecular simulation of nitrogen dissociation based on an ab initio potential energy surface

Phase-transition plasticity response in uniaxially compressed silicon nanospheres

Dynamics of nitrogen dissociation from direct molecular simulation

Phase Transition Plasticity Response in Uniaxially Compressed Silicon Nanospheres