Hybrid Simulation Scheme Research Articles

Multiparticle collision dynamics simulation of a polymer in a viscous fluid

We perform a hybrid molecular dynamics simulation of a polymer immersed in a viscous liquid. Using the multiparticle collision dynamics algorithm to incorporate the hydrodynamic effects, we examine static and dynamic properties of a self-avoiding flexible polymer. The diffusion coefficient of the polymer is found to be proportional to N −ν , where N is the molecular weight of the polymer and ν = 3/5 is the swelling exponent, as predicted by the Zimm model. The velocity autocorrelation function of the center of mass of the polymer is obtained as a function of time t, which shows an algebraic decay as t −3/2 at long-time scales. Our results confirm the theoretical prediction for the dynamical properties of a polymer and show the validity of the hybrid simulation scheme in studying the dynamics of a polymer in a viscous fluid.

Rapid prototyping of electric vehicle controllers combining Dymola and Simulink

A methodology that allows the rapid prototyping of electric vehicle controllers is presented. A hybrid simulation scheme is implemented. It combines Dymola for the dynamic modelling of the prototype and Simulink for the design of the vehicle controller. This combination allows a complete simulation of the prototype obtaining, as a final product, the source code for the digital controller. The proposed methodology offers flexibility to evaluate different control strategies, modify the physical model, and verify results quickly. Consequently, time and costs of the development process are reduced.

Comparison of 2D Hybrid Simulational and Experimental Results for Dual-Frequency Capacitively Coupled Argon Plasmas

A two-dimensional hybrid simulation scheme is proposed to study the characteristics of dual-frequency (DF) capacitively coupled plasma (CCP) discharge based on the geometry of real device. Given the experimental parameters for argon plasma, the output from the fluid module such as ion density, number flux, electron temperature and the Monte-Carlo collision (MCC) results of ion energy distribution function (IEDF) as well as electron energy distribution function (EEDF) are obtained and discussed in detail. A novel complete floating double probe is designed to measure both density and temperature of electron and a quadrupole mass spectrometer is also equipped for IEDF investigations. The measurements on the density of bulk plasma, electron temperature and IEDF agree well, qualitatively, with the simulated results. A comparison with experimental results indicates that, since the structure of real device is taken into account, this model is capable of describing the global dynamic characteristics occurred in DF-CCP and presenting more reliable results than the model with an ideal chamber structure.

A simple dynamical scale‐coupling method for concurrent simulation of hybridized atomistic/coarse‐grained‐particle system

AbstractWe propose a simple method for dynamical coupling of two sub‐systems with different characteristic scales described with different theoretical models, such as the fine‐scale sub‐system with the atomistic model (AM) such as the empirical inter‐atomic potential and the coarse‐scale sub‐system with the coarse‐grained particle (CGP) method, in a concurrent hybrid simulation scheme. Naive coupling of the different‐scale sub‐systems results in reflection of high wavenumber waves at the interface because of the differences in the phonon Brillouin‐zone and in the dispersion relation. To solve the problem, the present scale‐coupling method introduces (virtual) extra atoms and particles for the AM and the CGP sub‐systems, respectively, beyond the atom–particle interface, and uses the extra atoms and the particles to mutually transfer information of the waves between the two sub‐systems and to suppress the artificial reflection of the incident wave in the whole wavenumber range. As the algorithm in the present scale‐coupling method is local in time and space, it is applicable to hybrid systems with any interface shape at low computation and memory requirement. Accuracy of the present scale‐coupling method is compared with that of the existing methods for a simple model system. The hybrid AM‐CGP simulation of indentation of a graphene nano‐drum using the present scale‐coupling method is performed to demonstrate its accuracy and usefulness through its comparison with the fully atomistic results. Copyright © 2010 John Wiley & Sons, Ltd.

Femtosecond laser ablation of aluminium

We investigate femtosecond laser ablation of aluminium using a hybrid simulation scheme. Two equations are solved simultaneously: one for the electronic system, which accounts for laser energy absorption and heat conduction, the other for the dynamics of the lattice where the ablation process takes place. For the electron-temperature a generalized heat-conduction equation is solved by applying a finite difference scheme. For the lattice properties, e.g. pressure, density or temperature, we use common molecular dynamics. Energy transfer between the subsystems is allowed by introducing an electron–phonon coupling term. This combined treatment of the electronic and atomic systems is an extension of the well known two-temperature model [Anisimov, Kapeliovich, Perel’man, Electron emission from metal surfaces exposed to ultra short laser pulses, JETP Lett. 39 (2)].

A Suite of Hybrid Simulation Schemes for Nano-to-Micrometer Scale Processes at Solid-Fluid Interfaces

Computer simulation of a variety of solid-fluid interfaces in nano-to-micrometer scales has attracted much attention in recent years. We have been developing the hybrid simulation schemes to apply them to the interfaces at realistic settings without losing physical accuracies, by concurrently coupling the electronic density-functional theory (DFT), the molecular dynamics (MD), the recursive coarse-grained particle (RCGP) method, and the lattice Boltzmann equation (LBE) method. In the hybrid DFT-MD simulation scheme, multiple DFT regions each of which is composed of a relatively small number of atoms are embedded in a system of classical MD atoms. For robust coupling of the DFT and MD regions with reasonable mechanical accuracies the buffered-cluster method is adopted, which requires no link-atoms and is applicable to a wide range of materials and settings. The sizes and number of the DFT regions change adaptively to trace the chemical reactions during the simulation run. The hybrid DFT-MD simulation scheme is successfully applied to various interesting processes including the atomic-scale friction between nano-scale objects. Useful MD simulation requires realistic, dynamic boundary conditions to the atoms. We develop the RCGP method to coarse-grain the atomic system in the solid phase, in which each particle represents a group of the atoms and the inter-particle interaction is constructed by renormalizing the inter-atomic interaction in a recursive manner under the assumption of the local statistical equilibrium. The RCGP method has attractive features such as its natural incorporation of the atomic phonons in the thermal equilibrium and its potential suitableness to connection to the atomistic system. In the hybrid RCGP-MD simulation scheme, the overall shape of the total system calculated with the RCGP method gives the dynamics boundary conditions to the MD regions. A nano-thrusting simulation of a structured Al system that demonstrates reasonable coupling of the RCGP and MD regions is presented. A hybrid RCGP-LBE simulation scheme has been developed to study interaction between the fluid motion and the elastic body in realistic settings. The dynamics of the fluid is simulated by the LBE with the dynamic boundary conditions relating to the moving solid body. The solid body is coarse-grained with the RCGP method. A hybrid RCGP-LBE simulation of a deformable nano-rod in the Poiseuille flow is performed to confirm the fluidsolid coupling scheme.

Hybrid Simulations for Desinging of Nano-Interfacial Structures

There is growing demand to perform dynamic, atomistic computer-simulation of nano-scaled interfaces. For dynamic simulation of interesting processes at the nano-interfaces, we have been developing the hybrid simulation schemes by concurrently coupling the quantum description as the electronic density-functional theory and the classical description as the classical molecular dynamics. A quantum (QM) region composed of a relatively small number of atoms, is embedded with the novel buffered-cluster method in a classical (CL) region of atoms interacting through an empirical inter-atomic potential. The hybrid QM-CL simulation scheme is applied to various kinds of nano-processes including implantation of oxygen atoms to a Si slab relating to SIMOX technology.

A coupled finite-element, boundary-integral method for simulating ultrasonic flowmeters

Today's most popular technology of ultrasonic flow measurement is based on the transit-time principle. In this paper, a numerical simulation technique applicable to the analysis of transit-time flowmeters is presented. A flowmeter represents a large simulation problem that also requires computation of acoustic fields in moving media. For this purpose, a novel boundary integral method, the Helmholtz integral-ray tracing method (HIRM), is derived and validated. HIRM is applicable to acoustic radiation problems in arbitrary mean flows at low Mach numbers and significantly reduces the memory demands in comparison with the finite-element method (FEM). It relies on an approximate free-space Green's function which makes use of the ray tracing technique. For simulation of practical acoustic devices, a hybrid simulation scheme consisting of FEM and HIRM is proposed. The coupling of FEM and HIRM is facilitated by means of absorbing boundaries in combination with a new, reflection-free, acoustic-source formulation. Using the coupled FEM-HIRM scheme, a full three-dimensional (3-D) simulation of a complete transit-time flowmeter is performed for the first time. The obtained simulation results are in good agreement with measurements both at zero flow and under flow conditions.

Electrophoretic properties of highly charged colloids: A hybrid molecular dynamics∕lattice Boltzmann simulation study

Using computer simulations, the electrophoretic motion of a positively charged colloid (macroion) in an electrolyte solution is studied in the framework of the primitive model. In this model, the electrolyte is considered as a system of negatively and positively charged microions (counterions and coions, respectively) that are immersed into a structureless medium. Hydrodynamic interactions are fully taken into account by applying a hybrid simulation scheme, where the charged ions (i.e., macroion and electrolyte), propagated via molecular dynamics, are coupled to a lattice Boltzmann (LB) fluid. In a recent electrophoretic experiment by Martin-Molina et al. [J. Phys. Chem. B 106, 6881 (2002)], it was shown that, for multivalent salt ions, the mobility mu initially increases with charge density sigma, reaches a maximum, and then decreases with further increase of sigma. The aim of the present work is to elucidate the behavior of mu at high values of sigma. Even for the case of monovalent microions, a decrease of mu with sigma is found. A dynamic Stern layer is defined that includes all the counterions that move with the macroion while subjected to an external electrical field. The number of counterions in the Stern layer, q(0), is a crucial parameter for the behavior of mu at high values of sigma. In this case, the mobility mu depends primarily on the ratio q(0)/Q (with Q the valency of the macroion). The previous contention that the increase in the distortion of the electric double layer (EDL) with increasing sigma leads to the lowering of mu does not hold for high sigma. In fact, it is shown that the deformation of the EDL decreases with the increase of sigma. The role of hydrodynamic interactions is inferred from direct comparisons to Langevin simulations where the coupling to the LB fluid is switched off. Moreover, systems with divalent counterions are considered. In this case, at high values of sigma the phenomenon of charge inversion is found.

Concurrent Coupling of Electronic-Density-Functional, Molecular Dynamics, and Coarse-Grained Particles Schemes for Multiscale Simulation of Nanostructured Materials

Feature sizes of useful electronic devices are becoming smaller and reaching nanometer ranges. There is increasing demand to perform dynamic simulations of such nano-devices with realistic sizes. To date, various kinds of simulation methods have been used for materials and devices including the density-functional theory (DFT) and the molecular dynamics (MD) for atomistic mechanics and the finite element method for continuum mechanics. We review recent progresses in our multiscale, hybrid simulation schemes that combine those methods. The coarse-grained particles (CG) method originally proposed by Rudd and Broughton [Phys. Rev. B58 (1998), p. R5893] has features suitable to such hybridization. We improve the CG method so that it is applicable to realistic nanostructured materials with large deformations. A novel hybridization scheme that couples the DFT method with the MD method is presented, which is applicable to virtually any selection of the DFT region in a wide range of materials. Hybrid DFT-MD simulations of the H2O reaction with nanostructured Si and alumina systems under stresses are performed, to demonstrate significant effects of stress on the chemical reaction.

Buffered-cluster method for hybridization of density-functional theory and classical molecular dynamics: Application to stress-dependent reaction ofH2Oon nanostructured Si

A hybrid density-functional-theory and molecular-dynamics simulation scheme was proposed [Ogata et al., Comput. Phys. Commun. 149, 30 (2002)] in which a total atomistic system is partitioned, in real space, into the quantum (QM) region whose electronic structure is calculated with the density-functional theory and the classical (CL) region treated with the interatomic potential for the molecular dynamics. In the scheme, the link-atom method that uses hydrogen atoms for termination of the QM atoms is adopted to couple the QM and CL regions mechanically. A proper choice of the QM region that retains the original atomic configuration is limited in the link-atom method. In this paper we propose a coupling method, called the buffered-cluster method, with the introduction of buffer atoms to minimize possible effects arising from the finiteness of the size of the QM region. The buffered-cluster method is applicable to any reasonable choice of the QM region in a wide range of ceramics and semiconductor materials. The accuracy of the buffered-cluster method is analyzed by applying it to crystalline Si and alumina systems, to find little differences around the QM-CL boundaries in both relaxed configuration of the atoms and recoil forces on them due to their trial displacements. The insensitivity of the atomic forces to the choice of the QM region in the buffered-cluster method makes it possible to rechoose the QM region adaptively during the hybrid simulation run for fast computation. The hybrid simulation scheme with the buffered-cluster method is applied to analyze adsorption and dissociation processes of an ${\mathrm{H}}_{2}\mathrm{O}$ molecule on a notched Si-slab system with or without strains, in which the ${\mathrm{H}}_{2}\mathrm{O}$ interacts with the notch-bottom facet of $\mathrm{Si}(100)\text{\ensuremath{-}}(2\ifmmode\times\else\texttimes\fi{}1)$ dimer structure. The QM region is chosen in the system to cover the reaction region. Energy variations along the reaction paths show that the adsorption energy and the dissociation barrier of the ${\mathrm{H}}_{2}\mathrm{O}$ molecule on the Si(100) facet in the system are sensitive to the stain. The adsorption energy decreases substantially, while the dissociation barrier with H transferred to a nearby dimer increases, when the system is stretched. We perform hybrid simulation runs with the buffered-cluster method to study the adsorption and dissociation dynamics of the ${\mathrm{H}}_{2}\mathrm{O}$ molecule with the facet of $\mathrm{Si}(100)\text{\ensuremath{-}}(2\ifmmode\times\else\texttimes\fi{}1)$ in the nanostructured Si system at both stretched and unstrained conditions, in which the QM region is rechosen dynamically to trace the reaction atoms. The probability of the ${\mathrm{H}}_{2}\mathrm{O}$ dissociation and the following H-transfer path depend significantly on the strain applied to the system and on the initial conditions of the molecule.

Linear prediction of force time series to accelerate molecular dynamics simulations

We have recently proposed a molecular dynamics simulation scheme in which the time-consuming evaluation of non-bonding forces is periodically replaced by linear prediction of the latter from previous values [B. Brutovsky, T. Mülders, G.R. Kneller, J. Chem. Phys. 118 (2003) 6179]. For a simple molecular liquid, consisting of linear molecules with an internal vibrational degree of freedom, the method yields a speedup of up to 7 compared to conventional simulations. The hybrid simulation scheme preserves all essential structural and dynamical quantities. We show here that the linear predictor can be considered as an optimal integrator for finite time steps whose coefficients approach those of a discrete Taylor series if the simulation step tends to zero. The short time dynamics and the structure of the liquid are preserved for much longer periods if linear prediction is used instead of Taylor expansion to predict the non-bonding forces.

Hybrid method for simulating front propagation in reaction-diffusion systems.

We study the propagation of pulled fronts in the A<--> A+A microscopic reaction-diffusion process using Monte Carlo simulations. In the mean field approximation the process is described by the deterministic Fisher-Kolmogorov-Petrovsky-Piscounov equation. In particular, we concentrate on the corrections to the deterministic behavior due to the number of particles per correlated volume Omega. By means of a hybrid simulation scheme, we manage to reach large macroscopic values of Omega, which allows us to show the importance in the dynamics of microscopic pulled fronts of the interplay of microscopic fluctuations and their macroscopic relaxation.

Metal ablation by picosecond laser pulses: A hybrid simulation

We investigate picosecond laser ablation of metals using a hybrid simulation scheme. Laser energy input into the electron system and heat conduction within it are modeled using a finite-difference scheme for solving the heat conduction equation. Atom motion in the near-surface part (72 nm) of the sample is modeled using molecular dynamics. Energy transfer between the electronic and atomic subsystems due to electron-phonon coupling is taken into account. For the special case of 0.5 ps UV laser irradiation of copper, we investigate the fluence dependence of the ablation yield, the temperature and pressure evolution in the target, and the ablation mechanism.

Sheath structure and ion current onto a patterned surface immersed in a plasma at floating potential

Using a two-dimensional hybrid simulation scheme, we have studied the processes occurring above a patterned surface immersed in a plasma at floating potential, focussing on the structure of the two-dimensional plasma wall sheath and the uniformity of the ion current onto the wall in steady state. The surface consists of a periodic alternation of a trench and a ridge. We discuss the sheath structure by comparing it to that in front of a planar target. It is found that the sheath is not conformal since the trench widths studied are not large compared to the sheath width. Thus, the electrical potential and the ion and electron densities in the trench show characteristic differences to those of the planar sheath. We show that, in all cases, the ion dose is strongly non-uniform on the target surface. This non-uniformity is traced back to the enhanced electrical fields at the convex corners of the ridge and to the aspect ratio of the surface structure.

A two-dimensional hybrid simulation of ionic fluids

The Monte Carlo method is conventionally used to study properties of ionic fluids, and is known to be rather inefficient. In this paper, a hybrid simulation scheme, which is an amalgamation of the particle-mesh scheme and the Monte Carlo method, is used to study two-dimensional ionic fluids. The results are compared with those obtained using the Perram scheme, which is known to be one of the most efficient 2-D schemes but which cannot be applied to 3-D problems. The computational costs for both methods are about the same. It is anticipated that the proposed hybrid scheme, which may be easily extended to study 3-D problems, will bring about substantial savings over other conventional 3-D schemes, such as those using Ewald summation.

Fermi acceleration at shock waves and the galactic cosmic ray spectrum: numerical simulations

A hybrid simulation scheme is applied to treat first-order Fermi acceleration in the neighborhood of shock waves. A steady-state hydrodynamic approximation that describes the shock transition is used to evaluate the evolution in position, phase, and pitch angle of relativistic test particles. The relativistic test particles are followed to obtain the distribution function for a specific time after injection. The hydrodynamic model has four components: the main background plasma, a minor relativistic particle population, an oblique averaged magnetic field, and self-generated MHD waves. Various physical parameters are analyzed as a function of time for different approximations to the diffusion coefficients and spectral indexes for the power law MHD turbulent spectrum (normalized to the wave pressure obtained from the hydrodynamic approximation). Results are applied to a proposed scenario of the main global acceleration mechanism of galactic cosmic rays from a few GeVs to 10/sup 5/-10/sup 6/ GeV. >