Three-dimensional Lennard-Jones Research Articles

Accurate and Fast Estimation of the Continuum Limit in Path Integral Simulations of Quantum Oscillators and Crystals.

Convergence of imaginary-time path integral results requires a substantial number of beads (n) when quantum effects are significant. Traditional Trotter scaling approaches estimate the continuum limit (n → ∞) through extrapolation; however, their validity is restricted to the asymptotic domain of large n. We introduce an efficient extrapolation approach for quantum oscillators and crystals with harmonic character. The fitting function is inspired by the analytic solution of the harmonic oscillator (HO), or the Einstein crystal for solids. While the formulation is designed for first derivative properties (energy and pressure), its extension to second derivative properties (e.g., heat capacity) is straightforward. We apply the method to a one-dimensional HO and anharmonic oscillator (AO), as well as a three-dimensional Lennard-Jones crystal. Configurations are sampled using path integral molecular dynamics simulations in the canonical ensemble, at a low temperature of T = 0.1 (simulation units). Compared to Trotter extrapolation approaches, the new method demonstrates a substantial accuracy in estimating the continuum limit, using only a few simulations of relatively small system sizes. This efficiency significantly reduces computational cost, providing a powerful tool to facilitate computations for more complex and challenging systems, such as molecules and crystals modeled using ab initio methods.

Perspective: How to overcome dynamical density functional theory

We argue in favour of developing a comprehensive dynamical theory for rationalizing, predicting, designing, and machine learning nonequilibrium phenomena that occur in soft matter. To give guidance for navigating the theoretical and practical challenges that lie ahead, we discuss and exemplify the limitations of dynamical density functional theory (DDFT). Instead of the implied adiabatic sequence of equilibrium states that this approach provides as a makeshift for the true time evolution, we posit that the pending theoretical tasks lie in developing a systematic understanding of the dynamical functional relationships that govern the genuine nonequilibrium physics. While static density functional theory gives a comprehensive account of the equilibrium properties of many-body systems, we argue that power functional theory is the only present contender to shed similar insights into nonequilibrium dynamics, including the recognition and implementation of exact sum rules that result from the Noether theorem. As a demonstration of the power functional point of view, we consider an idealized steady sedimentation flow of the three-dimensional Lennard-Jones fluid and machine-learn the kinematic map from the mean motion to the internal force field. The trained model is capable of both predicting and designing the steady state dynamics universally for various target density modulations. This demonstrates the significant potential of using such techniques in nonequilibrium many-body physics and overcomes both the conceptual constraints of DDFT as well as the limited availability of its analytical functional approximations.

Theory of dynamical stability for two- and three-dimensional Lennard-Jones crystals

The dynamical stability of three-dimensional (3D) Lennard-Jones (LJ) crystals has been studied for many years. The fcc and hcp structures are dynamically stable, while the bcc structure is stable only for long-range LJ potentials that are characterized by relatively small integer pairs $(m,n)$. Here, we study the dynamical stability of two-dimensional (2D) LJ crystals, where the planar hexagonal, the buckled honeycomb, and the buckled square structures are assumed. We demonstrate that the stability property of 2D and 3D LJ crystals can be classified into four groups depending on $(m,n)$. The instabilities of the planar hexagonal, the buckled square, and the bcc structures are investigated within analytical expressions. The structure-stability relationship between the LJ crystals and the elemental metals in the periodic table is also discussed.

Methods to locate saddle points in complex landscapes.

We present a class of simple algorithms that allows us to find the reaction path in systems with a complex potential energy landscape. The approach does not need any knowledge on the product state and does not require the calculation of any second derivatives. The underlying idea is to use two nearby points in the configuration space to locate the path of the slowest ascent. By introducing a weak noise term, the algorithm is able to find even low-lying saddle points that are not directly reachable by means of the slowest ascent path. Since the algorithm only makes use of the value of the potential and its gradient, the computational effort to find saddle points is linear in the number of degrees of freedom if the potential is short-ranged. We test the performance of the algorithm for three potential energy landscapes. For the Müller-Brown surface, we find that the algorithm always finds the correct saddle point. For the modified Müller-Brown surface, which has a saddle point that is not reachable by means of the slowest ascent path, the algorithm is still able to find this saddle point with high probability. For the case of a three-dimensional Lennard-Jones cluster, the algorithm is able to find the lowest energy barrier with high probability, showing that the method is also efficient in landscapes with many dimensions.

Extensivity and additivity of the Kolmogorov-Sinai entropy for simple fluids.

According to the van der Waals picture, attractive and repulsive forces play distinct roles in the structure of simple fluids. Here, we examine their roles in dynamics; specifically, in the degree of deterministic chaos using the Kolmogorov-Sinai (KS) entropy rate and the spectra of Lyapunov exponents. With computer simulations of three-dimensional Lennard-Jones and Weeks-Chandler-Andersen fluids, we find repulsive forces dictate these dynamical properties, with attractive forces reducing the KS entropy at a given thermodynamic state. Regardless of interparticle forces, the maximal Lyapunov exponent is intensive for systems ranging from 200 to 2000 particles. Our finite-size scaling analysis also shows that the KS entropy is both extensive (a linear function of system-size) and additive. Both temperature and density control the "dynamical chemical potential," the rate of linear growth of the KS entropy with system size. At fixed system-size, both the KS entropy and the largest exponent exhibit a maximum as a function of density. We attribute the maxima to the competition between two effects: as particles are forced to be in closer proximity, there is an enhancement from the sharp curvature of the repulsive potential and a suppression from the diminishing free volume and particle mobility. The extensivity and additivity of the KS entropy and the intensivity of the largest Lyapunov exponent, however, hold over a range of temperatures and densities across the liquid and liquid-vapor coexistence regimes.

Nonequilibrium temperature measurement in a thermal conduction process.

We identify the temperature being measured by a thermometer in a nonequilibrium scenario by studying heat conduction in a three-dimensional Lennard-Jones (LJ) system whose two ends are kept at different temperatures. It is accomplished by modeling the thermometer particles also with the LJ potential but with added tethers to prevent their rigid body motion. These models of the system and the thermometer mimic a real scenario in which a mechanical thermometer is "inserted" into a system and kept there long enough for the temperature to reach a steady value. The system is divided into five strips, and for each strip the temperature is measured using an embedded thermometer. Unlike previous works, these thermometers are small enough not to alter the steady state of the nonequilibrium system. After showing initial transients, the thermometers eventually show steady-state conditions with the subregions of the system and provide values of the different temperature definitions-kinetic, configurational, dynamical, and higher-order configurational. It is found that their kinetic and the configurational temperatures are close to the system's kinetic temperature except in the two thermostatted regions. In the thermostatted regions, where the system's kinetic and the configurational temperatures are significantly different, the thermometers register a temperature substantially different from either of these two values. With a decrease in the system density and size, these differences between the kinetic and the configurational temperatures of the thermometer become more pronounced.

Finite-size scaling of Lennard-Jones droplet formation at fixed density

We reaccess the droplet condensation-evaporation transition of a three-dimensional Lennard-Jones system upon a temperature change. With the help of parallel multicanonical simulations we obtain precise estimates of the transition temperature and the width of the transition for systems with up to 2048 particles. This allows us to supplement previous observations of finite-size scaling regimes with a clearer picture also for the case of a continuous particle model.

Effects of domain morphology on kinetics of fluid phase separation

Kinetics of phase separation in a three-dimensional single-component Lennard-Jones fluid, that exhibits vapor-liquid transition, is studied via molecular dynamics simulations after quenching homogeneous systems, of different overall densities, inside the coexistence region. For densities close to the vapor branch of the coexistence curve, phase separation progresses via nucleation of liquid droplets and collisions among them. This is different from the evaporation-condensation mechanism proposed by Lifshitz and Slyozov, even though both lead to power-law growth of average domain size, as a function of time, with an exponent α = 1∕3. Beyond a certain threshold value of the overall density, we observe elongated, percolating domain morphology which suddenly enhances the value of α. These results are consistent with some existing theoretical expectations.

Heterogeneous relaxation dynamics in amorphous materials under cyclic loading

Molecular dynamics simulations are performed to investigate heterogeneous dynamics in amorphous glassy materials under oscillatory shear strain. We consider three-dimensional binary Lennard-Jones mixture well below the glass transition temperature. The structural relaxation and dynamical heterogeneity are quantified by means of the self-overlap order parameter and the dynamic susceptibility. We found that at sufficiently small strain amplitudes, the mean square displacement exhibits a broad subdiffusive plateau and the system undergoes nearly reversible deformation over about 10(4) cycles. Upon increasing strain amplitude, the transition to the diffusive regime occurs at shorter time intervals and the relaxation process involves intermittent bursts of large particle displacements. The detailed analysis of particle hopping dynamics and the dynamic susceptibility indicates that mobile particles aggregate into clusters whose sizes increase at larger strain amplitudes. Finally, the correlation between particle mobilities in consecutive time intervals demonstrates that dynamic facilitation becomes increasingly pronounced at larger strain amplitudes.

Nonlinear response and crowding effects in microrheology

The mobility of tagged particles in a microrheological setup has been investigated via molecular dynamics simulations of a three-dimensional Lennard-Jones binary mixture. After coupling a small number of particles to a constant external driving force, the drift velocity and other observables of the dragged probe particles are reported in the linear and nonlinear response regime. In the nonlinear regime significant crowding effects are observed, thereby creating stringlike structures. Formation of the strings further enhances the nonlinear effects. A systematic study of these effects' dependence on temperature and total number of driven probe atoms is presented.

Phase diagram and universality of the Lennard-Jones gas-liquid system

The gas-liquid phase transition of the three-dimensional Lennard-Jones particles system is studied by molecular dynamics simulations. The gas and liquid densities in the coexisting state are determined with high accuracy. The critical point is determined by the block density analysis of the Binder parameter with the aid of the law of rectilinear diameter. From the critical behavior of the gas-liquid coexisting density, the critical exponent of the order parameter is estimated to be β = 0.3285(7). Surface tension is estimated from interface broadening behavior due to capillary waves. From the critical behavior of the surface tension, the critical exponent of the correlation length is estimated to be ν = 0.63(4). The obtained values of β and ν are consistent with those of the Ising universality class.

On the potential energy landscape of supercooled liquids and glasses

The activation-relaxation technique (ART), a saddle-point search method, is applied to determine the potential energy landscape around supercooled and glassy configurations of a three-dimensional binary Lennard-Jones system. We show a strong relation between the distribution of activation energies around a given glassy configuration and its history, in particular, the cooling rate used to produce the glass and whether or not the glass was plastically deformed prior to sampling. We also compare the thermally activated transitions found by ART around a supercooled configuration with the succession of transitions undergone by the same supercooled liquid during a time trajectory simulated by molecular dynamics. We find that ART is biased towards more heterogeneous transitions with higher activation energies and more broken bonds than the MD simulation.

Communication: The application of the global isomorphism to the study of liquid-vapor equilibrium in two and three-dimensional Lennard-Jones fluids

We analyze the interrelation between the coexistence curve of the Lennard-Jones fluid and the Ising model in two and three dimensions within the global isomorphism approach proposed earlier [V. L. Kulinskii, J. Phys. Chem. B 114, 2852 (2010)]. In case of two dimensions, we use the exact Onsager result to construct the binodal of the corresponding Lennard-Jones fluid and compare it with the results of the simulations. In the three-dimensional case, we use available numerical results for the Ising model for the corresponding mapping. The possibility to observe the singularity of the binodal diameter is discussed.

Accelerated molecular dynamics simulation of low-velocity frictional sliding

Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of atomic force microscope (AFM) experiments and to lower the sliding speeds below those in a conventional MD simulation. In this study the hyperdynamics method, originally devised to extend MD time scales for non-driven systems, is applied to the frictional sliding system. This technique is combined with a parallel algorithm that simultaneously simulates the system over a range of slider positions so that the overall acceleration rate is approximately the number of processors multiplied by the boost factor from the hyperdynamics method. The new methodologies are tested using two-dimensional and three-dimensional Lennard-Jones AFM models. Direct comparison with the results from conventional MD shows close agreement validating the methods. The acceleration rate achieved in this study is four orders of magnitude in 2D and three orders of magnitude in 3D.

Parallel canonical Monte Carlo simulations through sequential updating of particles

In canonical Monte Carlo simulations, sequential updating of particles is equivalent to random updating due to particle indistinguishability. In contrast, in grand canonical Monte Carlo simulations, sequential implementation of the particle transfer steps in a dense grid of distinct points in space improves both the serial and the parallel efficiency of the simulation. The main advantage of sequential updating in parallel canonical Monte Carlo simulations is the reduction in interprocessor communication, which is usually a slow process. In this work, we propose a parallelization method for canonical Monte Carlo simulations via domain decomposition techniques and sequential updating of particles. Each domain is further divided into a middle and two outer sections. Information exchange is required after the completion of the updating of the outer regions. During the updating of the middle section, communication does not occur unless a particle moves out of this section. Results on two- and three-dimensional Lennard-Jones fluids indicate a nearly perfect improvement in parallel efficiency for large systems.

Exponential Distributions of Collective Flow-Event Properties in Viscous Liquid Dynamics

We study the statistics of flow events in the inherent dynamics in supercooled two- and three-dimensional binary Lennard-Jones liquids. Distributions of changes of the collective quantities energy, pressure, and shear stress become exponential at low temperatures, as does that of the event "size" S identical with summation operator[under ][over ]d_{i};{2}. We show how the S distribution controls the others, while itself following from exponential tails in the distributions of (1) single particle displacements d, involving a Lindemann-like length d_{L} and (2) the number of active particles (with d>d_{L}).

Lyapunov modes in three-dimensional Lennard-Jones fluids

Recent studies on the phase-space dynamics of a one-dimensional Lennard-Jones fluid reveal the existence of regular collective perturbations associated with the smallest positive Lyapunov exponents of the system, called hydrodynamic Lyapunov modes, which previously could only be identified in hard-core fluids. In this work we present a systematic study of the Lyapunov exponents and Lyapunov vectors, i.e. perturbations along each direction of phase space, of a three-dimensional Lennard-Jones fluid. By performing the Fourier transform of the spatial density of the coordinate part of the Lyapunov vector components and then time-averaging this result we find convincing signatures of longitudinal modes, with inconclusive evidence of transverse modes for all studied densities. Furthermore, the longitudinal modes can be more clearly identified for the higher density values. Thus, according to our results, the mixing of modes induced by both the dynamics and the dimensionality induces a hitherto unknown type of order in the tangent space of the model herein studied at high density values.

A Classical Picture of the Role of Vacancies and Interstitials in Helium-4

Motivated by experimental hints for supersolidity in Helium-4, we perform Monte Carlo simulations of vacancies and interstitials in a classical two-and three-dimensional Lennard-Jones solid. We confirm a strong binding energy of vacancies which is of the order of the Lennard-Jones attraction. This is reminiscent of what has been found for vacancies in Quantum Monte Carlo simulations. In addition, we find a strong attraction and large binding energy of interstitials in two-dimensional simulations. This is mainly due to the formation of a pair of dislocations by clustering interstitials, which minimizes the elastic deformation energy. We interpret the results in light of the properties of Helium-4.

Spatial updating grand canonical Monte Carlo algorithms for fluid simulation: Generalization to continuous potentials and parallel implementation

Spatial updating grand canonical Monte Carlo algorithms are generalizations of random and sequential updating algorithms for lattice systems to continuum fluid models. The elementary steps, insertions or removals, are constructed by generating points in space either at random (random updating) or in a prescribed order (sequential updating). These algorithms have previously been developed only for systems of impenetrable spheres for which no particle overlap occurs. In this work, spatial updating grand canonical algorithms are generalized to continuous, soft-core potentials to account for overlapping configurations. Results on two- and three-dimensional Lennard-Jones fluids indicate that spatial updating grand canonical algorithms, both random and sequential, converge faster than standard grand canonical algorithms. Spatial algorithms based on sequential updating not only exhibit the fastest convergence but also are ideal for parallel implementation due to the absence of strict detailed balance and the nature of the updating that minimizes interprocessor communication. Parallel simulation results for three-dimensional Lennard-Jones fluids show a substantial reduction of simulation time for systems of moderate and large size. The efficiency improvement by parallel processing through domain decomposition is always in addition to the efficiency improvement by sequential updating.

DYNAMICS AND STRUCTURE OF GAS-LIQUID INTERFACE

The structure and the dynamics of the gas-liquid phase interface of the three-dimensional Lennard-Jones (12-6) particle system are studied using nonequilibrium molecular dynamics simulation. Heat flux maintains the system into a gas-liquid coexisting state with a steady interface. In the steady state, the interface shows an asymmetric structure and this is well described by a free energy density model with an asymmetric double-well form. When the system approaches to the steady state, a gas of the temperature profile appears between each phase and the gap value is relaxed to that in the steady state following [Formula: see text] for large t . It is observed that heat resistance exists in gas-liquid interface in this scale.