Performance metrics in a hybrid MPI-OpenMP based molecular dynamics simulation with short-range interactions

We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation-intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for parallelizing a generalized MD computation scheme for systems with short range interatomic interactions. The algorithm is discussed in the context of nano-indentation of Chromium films with carbon indenters using the Embedded Atom Method potential for Cr-Cr interaction and the Morse potential for Cr-C interactions. We study the performance of our algorithm for a range of MPI-thread combinations and find the performance to depend strongly on the computational task and load sharing in the multi-core processor. The algorithm scaled poorly with MPI and our hybrid schemes were observed to outperform the pure message passing scheme, despite utilizing the same number of processors or cores in the cluster. Speed-up achieved by our algorithm compared favorably with that achieved by standard MD packages. (C) 2013 Elsevier Inc. All rights reserved.

Quantum chemical study on influence of intermolecular hydrogen bonding on the geometry, the atomic charges and the vibrational dynamics of 2,6-dichlorobenzonitrile

FT-IR (4000-400 cm(-1)) and FT-Raman (4000-200 cm(-1)) spectral measurements on solid 2,6-dichlorobenzonitrile (2,6-DCBN) have been done. The molecular geometry, harmonic vibrational frequencies and bonding features in the ground state have been calculated by density functional theory at the B3LYP/6-311++G (d,p) level. A comparison between the calculated and the experimental results covering the molecular structure has been made. The assignments of the fundamental vibrational modes have been done on the basis of the potential energy distribution (PED). To investigate the influence of intermolecular hydrogen bonding on the geometry, the charge distribution and the vibrational spectrum of 2,6-DCBN; calculations have been done for the monomer as well as the tetramer. The intermolecular interaction energies corrected for basis set superposition error (BSSE) have been calculated using counterpoise method. Based on these results, the correlations between the vibrational modes and the structure of the tetramer have been discussed. Molecular electrostatic potential (MEP) contour map has been plotted in order to predict how different geometries could interact. The Natural Bond Orbital (NBO) analysis has been done for the chemical interpretation of hyperconjugative interactions and electron density transfer between occupied (bonding or lone pair) orbitals to unoccupied (antibonding or Rydberg) orbitals. UV spectrum was measured in methanol solution. The energies and oscillator strengths were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. TD-DFT method has also been used for theoretically studying the hydrogen bonding dynamics by monitoring the spectral shifts of some characteristic vibrational modes involved in the formation of hydrogen bonds in the ground and the first excited state. The C-13 nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge independent atomic orbital (GIAO) method and compared with experimental results. Standard thermodynamic functions have been obtained and changes in thermodynamic properties on going from monomer to tetramer have been presented. (C) 2013 Elsevier B.V. All rights reserved.

A spectral multiscale method for wave propagation analysis: Atomistic-continuum coupled simulation

In this paper, we present a new multiscale method which is capable of coupling atomistic and continuum domains for high frequency wave propagation analysis. The problem of non-physical wave reflection, which occurs due to the change in system description across the interface between two scales, can be satisfactorily overcome by the proposed method. We propose an efficient spectral domain decomposition of the total fine scale displacement along with a potent macroscale equation in the Laplace domain to eliminate the spurious interfacial reflection. We use Laplace transform based spectral finite element method to model the macroscale, which provides the optimum approximations for required dynamic responses of the outer atoms of the simulated microscale region very accurately. This new method shows excellent agreement between the proposed multiscale model and the full molecular dynamics (MD) results. Numerical experiments of wave propagation in a 1D harmonic lattice, a 1D lattice with Lennard-Jones potential, a 2D square Bravais lattice, and a 2D triangular lattice with microcrack demonstrate the accuracy and the robustness of the method. In addition, under certain conditions, this method can simulate complex dynamics of crystalline solids involving different spatial and/or temporal scales with sufficient accuracy and efficiency. (C) 2014 Elsevier B.V. All rights reserved.

A novel method for studying the buckling of nanotubes considering geometrical imperfections

Buckling of nanotubes has been studied using many methods such as molecular dynamics (MD), molecular mechanics, and continuum-based shell theories. In MD, motion of the individual atoms is tracked under applied temperature and pressure, ensuring a reliable estimate of the material response. The response thus simulated varies for individual nanotubes and is only as accurate as the force field used to model the atomic interactions. On the other hand, there exists a rich literature on the understanding of continuum mechanics-based shell theories. Based on the observations on the behavior of nanotubes, there have been a number of shell theory-based approaches to study the buckling of nanotubes. Although some of these methods yield a reasonable estimate of the buckling stress, investigation and comparison of buckled mode shapes obtained from continuum analysis and MD are sparse. Previous studies show that the direct application of shell theories to study nanotube buckling often leads to erroneous results. The present study reveals that a major source of this error can be attributed to the departure of the shape of the nanotube from a perfect cylindrical shell. Analogous to the shell buckling in the macro-scale, in this work, the nanotube is modeled as a thin-shell with initial imperfection. Then, a nonlinear buckling analysis is carried out using the Riks method. It is observed that this proposed approach yields significantly improved estimate of the buckling stress and mode shapes. It is also shown that the present method can account for the variation of buckling stress as a function of the temperature considered. Hence, this can prove to be a robust method for a continuum analysis of nanosystems taking in the effect of variation of temperature as well.

Discrete Vortex Method-Based Model for Ground-Effect Studies

A discrete vortex method-based model has been proposed for two-dimensional/three-dimensional ground-effect prediction. The model merely requires two-dimensional sectional aerodynamics in free flight. This free-flight data can be obtained either from experiments or a high-fidelity computational fluid dynamics solver. The first step of this two-step model involves a constrained optimization procedure that modifies the vortex distribution on the camber line as obtained from a discrete vortex method to match the free-flight data from experiments/computational fluid dynamics. In the second step, the vortex distribution thus obtained is further modified to account for the presence of the ground plane within a discrete vortex method-based framework. Whereas the predictability of the lift appears as a natural extension, the drag predictability within a potential flow framework is achieved through the introduction of what are referred to as drag panels. The need for the use of the generalized Kutta-Joukowski theorem is emphasized. The extension of the model to three dimensions is by the way of using the numerical lifting-line theory that allows for wing sweep. The model is extensively validated for both two-dimensional and three-dimensional ground-effect studies. The work also demonstrates the ability of the model to predict lift and drag coefficients of a high-lift wing in ground effect to about 2 and 8% accuracy, respectively, as compared to the results obtained using a Reynolds-averaged Navier-Stokes solver involving grids with several million volumes. The model shows a lot of promise in design, particularly during the early phase.

Wave propagation analysis in adhesively bonded composite joints using the wavelet spectral finite element method

A wavelet spectral finite element (WSFE) model is developed for studying transient dynamics and wave propagation in adhesively bonded composite joints. The adherands are formulated as shear deformable beams using the first order shear deformation theory (FSDT) to obtain accurate results for high frequency wave propagation. Equations of motion governing wave motion in the bonded beams are derived using Hamilton's principle. The adhesive layer is modeled as a line of continuously distributed tension/compression and shear springs. Daubechies compactly supported wavelet scaling functions are used to transform the governing partial differential equations from time domain to frequency domain. The dynamic stiffness matrix is derived under the spectral finite element framework relating the nodal forces and displacements in the transformed frequency domain. Time domain results for wave propagation in a lap joint are validated with conventional finite element simulations using Abaqus. Frequency domain spectrum and dispersion relation results are presented and discussed. The developed WSFE model yields efficient and accurate analysis of wave propagation in adhesively-bonded composite joints. (C) 2014 Elsevier Ltd. All rights reserved.

SIMULATION STUDY OF THE ADSORPTION DYNAMICS OF CYLINDRICAL SILICA GEL PARTICLES

The paper presents a simulation study of loose cylindrically shaped particles packed within a copper plate and aluminum fins. The model presented solves coupled heat and mass transfer equations using the finite volume method based on ANSY S FLUENT medium. Three different arrangements of cylindrical particles are considered. The model is validated with experimental data. It is found that the arrangements which represented monolayer configurations are only marginally better in heat transfer and uptake efficiency than the tri-layer configuration in the presence of fins. However, there is an appreciable difference in the uptake curve between monoand tri-layer configurations in the absence of fins. Finally, it is found that the fin pitch also plays an important role in determining the time constant for the adsorber design.

Estimating successive pK(a) values of polyprotic acids from ab initio molecular dynamics using metadynamics: the dissociation of phthalic acid and its isomers

Estimation of the dissociation constant, or pK(a), of weak acids continues to be a central goal in theoretical chemistry. Here we show that ab initio Car-Parrinello molecular dynamics simulations in conjunction with metadynamics calculations of the free energy profile of the dissociation reaction can provide reasonable estimates of the successive pK(a) values of polyprotic acids. We use the distance-dependent coordination number of the protons bound to the hydroxyl oxygen of the carboxylic group as the collective variable to explore the free energy profile of the dissociation process. Water molecules, sufficient to complete three hydration shells surrounding the acid molecule, were included explicitly in the computation procedure. Two distinct minima corresponding to the dissociated and un-dissociated states of the acid are observed and the difference in their free energy values provides the estimate for pK(a), the acid dissociation constant. We show that the method predicts the pK(a) value of benzoic acid in good agreement with experiment and then show using phthalic acid (benzene dicarboxylic acid) as a test system that both the first and second pK(a) values as well, as the subtle difference in their values for different isomers can be predicted in reasonable agreement with experimental data.

CROSS-SECTIONAL ANALYSIS OF PRE-TWISTED THICK BEAMS USING VARIATIONAL ASYMPTOTIC METHOD

An asymptotically-exact methodology is presented for obtaining the cross-sectional stiffness matrix of a pre-twisted moderately-thick beam having rectangular cross sections and made of transversely isotropic materials. The anisotropic beam is modeled from 3-D elasticity, without any further assumptions. The beam is allowed to have large displacements and rotations, but small strain is assumed. The strain energy of the beam is computed making use of the constitutive law and the kinematical relations derived with the inclusion of geometrical nonlinearities and initial twist. Large displacements and rotations are allowed, but small strain is assumed. The Variational Asymptotic Method is used to minimize the energy functional, thereby reducing the cross section to a point on the reference line with appropriate properties, yielding a 1-D constitutive law. In this method as applied herein, the 2-D cross-sectional analysis is performed asymptotically by taking advantage of a material small parameter and two geometric small parameters. 3-D strain components are derived using kinematics and arranged as orders of the small parameters. Warping functions are obtained by the minimization of strain energy subject to certain set of constraints that renders the 1-D strain measures well-defined. Closed-form expressions are derived for the 3-D non-linear warping and stress fields. The model is capable of predicting interlaminar and transverse shear stresses accurately up to first order.

Ab Initio Molecular Dynamics Simulations of Amino Acids in Aqueous Solutions: Estimating pK(a) Values from Metadynamics Sampling

Changes in the protonation and deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. Here, we report calculations of the free-energy profile for the protonation deprotonation reaction of the 20 canonical alpha amino acids in aqueous solutions using ab initio Car-Parrinello molecular dynamics simulations coupled with metad-ynamics sampling. We show here that the calculated change in free energy of the dissociation reaction provides estimates of the multiple pK(a) values of the amino acids that are in good agreement with experiment. We use the bond-length-dependent number of the protons coordinated to the hydroxyl oxygen of the carboxylic and the amine groups as the collective variables to explore the free-energy profiles of the Bronsted acid-base chemistry of amino acids in aqueous solutions. We ensure that the amino acid undergoing dissociation is solvated by at least three hydrations shells with all water molecules included in the simulations. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pK(a) values with a mean relative error, with respect to experimental results, of 0.2 pK(a) units.

Kinematics and dynamics of Jansen leg mechanism: A bond graph approach

The Jansen mechanism is a one degree-of-freedom, planar, 12-link, leg mechanism that can be used in mobile robotic applications and in gait analysis. This paper presents the kinematics and dynamics of the Jansen leg mechanism. The forward kinematics, accomplished using circle intersection method, determines the trajectories of various points on the mechanism in the chassis (stationary link) reference frame. From the foot point trajectory, the step length is shown to vary linearly while step height varies non-linearly with change in crank radius. A dynamic model for the Jansen leg mechanism is proposed using bond graph approach with modulated multiport transformers. For given ground reaction force pattern and crank angular speed, this model helps determine the motor torque profile as well as the link and joint stresses. The model can therefore be used to rate the actuator torque and in design of the hardware and controller for such a system. The kinematics of the mechanism can also be obtained from this dynamic model. The proposed model is thus a useful tool for analysis and design of systems based on the Jansen leg mechanism. (C) 2015 Elsevier B.V. All rights reserved.

Nonlinear Dynamics of a Rotating Flexible Link

This paper deals with the study of the nonlinear dynamics of a rotating flexible link modeled as a one dimensional beam, undergoing large deformation and with geometric nonlinearities. The partial differential equation of motion is discretized using a finite element approach to yield four nonlinear, nonautonomous and coupled ordinary differential equations (ODEs). The equations are nondimensionalized using two characteristic velocities-the speed of sound in the material and a velocity associated with the transverse bending vibration of the beam. The method of multiple scales is used to perform a detailed study of the system. A set of four autonomous equations of the first-order are derived considering primary resonances of the external excitation and one-to-one internal resonances between the natural frequencies of the equations. Numerical simulations show that for certain ranges of values of these characteristic velocities, the slow flow equations can exhibit chaotic motions. The numerical simulations and the results are related to a rotating wind turbine blade and the approach can be used for the study of the nonlinear dynamics of a single link flexible manipulator.

A hybrid finite element formulation for flexible multibody dynamics

This work deals with the transient analysis of flexible multibody systems within a hybrid finite element framework. Hybrid finite elements are based on a two-field variational formulation in which the displacements and stresses are interpolated separately yielding very good coarse mesh accuracy. Most of the literature on flexible multibody systems uses beam-theory-based formulations. In contrast, the use of hybrid finite elements uses continuum-based elements, thus avoiding the problems associated with rotational degrees of freedom. In particular, any given three-dimensional constitutive relations can be directly used within the framework of this formulation. Since the coarse mesh accuracy as compared to a conventional displacement-based formulation is very high, the scheme is cost effective as well. A general formulation is developed for the constrained motion of a given point on a line manifold, using a total Lagrangian method. The multipoint constraint equations are implemented using Lagrange multipliers. Various kinds of joints such as cylindrical, prismatic, and screw joints are implemented within this general framework. Hinge joints such as spherical, universal, and revolute joints are obtained simply by using shared nodes between the bodies. In addition to joints, the formulation and implementation details for a DC motor actuator and for prescribed relative rotation are also presented. Several example problems illustrate the efficacy of the developed formulation.

Structure and Dynamics of Octamethylcyclotetrasiloxane Confined between Mica Surfaces

Using a molecular model for octamethylcydotetrasiloxane (OMCTS), molecular dynamics simulations are carried out to probe the phase state of OMCTS confined between two mica surfaces in equilibrium With a reservoir. Molecular dynamics simulations are carried out for elevations ranging from 5 to 35 K above the melting point for the OMCTS model used in this study. The Helmholtz free energy is, computed for a specific confinement using the :two-phase thermodynamic (2PT) method. Analysis of the in-plane pair correlation functions did not reveal signatures of freezing even under an extreme confinement of two layers. OMCTS is found to orient with a wide distribution of orientations with respect to the mica surface, with a distinct preference for the surface parallel configuration in the contact layers. The self-intermediate scattering function is found to decay with increasing relaxation times as the surface separation is decreased, and the two-step relaxation in the scattering function, a signature of glassy dynamics, distinctly evolves as the temperature is lowered. However, even at 5 K above the melting point, we did not observe a freezing transition and the self-intermediate scattering functions relax within 200 ps for the seven-layered confined system. The self diffusivity and relaxation times obtained from the Kohlrausch-Williams-Watts stretched exponential fits to the late alpha-relaxation exhibit power law scalings with the packing fraction as predicted by mode coupling theory. A distinct discontinuity in the Helmholtz free energy, potential energy, and a sharp change in the local bond order parameter, Q(4), was observed at 230 K for a five-layered system upon cooling, indicative of a first-order transition. A freezing point depression of about 30 K was observed for this five-layered confined system, and at the lower temperatures, contact layers were found to be disordered with long-range order present only in the inner layers. These dynamical signatures indicate that confined OMCTS undergoes a slowdown akin to a fluid approaching a glass transition upon increasing confinement, and freezing under confinement would require substantial subcooling below the bulk melting point of OMCTS.