2,827 research outputs found
Highly accelerated simulations of glassy dynamics using GPUs: caveats on limited floating-point precision
Modern graphics processing units (GPUs) provide impressive computing
resources, which can be accessed conveniently through the CUDA programming
interface. We describe how GPUs can be used to considerably speed up molecular
dynamics (MD) simulations for system sizes ranging up to about 1 million
particles. Particular emphasis is put on the numerical long-time stability in
terms of energy and momentum conservation, and caveats on limited
floating-point precision are issued. Strict energy conservation over 10^8 MD
steps is obtained by double-single emulation of the floating-point arithmetic
in accuracy-critical parts of the algorithm. For the slow dynamics of a
supercooled binary Lennard-Jones mixture, we demonstrate that the use of
single-floating point precision may result in quantitatively and even
physically wrong results. For simulations of a Lennard-Jones fluid, the
described implementation shows speedup factors of up to 80 compared to a serial
implementation for the CPU, and a single GPU was found to compare with a
parallelised MD simulation using 64 distributed cores.Comment: 12 pages, 7 figures, to appear in Comp. Phys. Comm., HALMD package
licensed under the GPL, see http://research.colberg.org/projects/halm
Tuning the pseudospin polarization of graphene by a pseudo-magnetic field
One of the intriguing characteristics of honeycomb lattices is the appearance
of a pseudo-magnetic field as a result of mechanical deformation. In the case
of graphene, the Landau quantization resulting from this pseudo-magnetic field
has been measured using scanning tunneling microscopy. Here we show that a
signature of the pseudo-magnetic field is a local sublattice symmetry breaking
observable as a redistribution of the local density of states. This can be
interpreted as a polarization of graphene's pseudospin due to a strain induced
pseudo-magnetic field, in analogy to the alignment of a real spin in a magnetic
field. We reveal this sublattice symmetry breaking by tunably straining
graphene using the tip of a scanning tunneling microscope. The tip locally
lifts the graphene membrane from a SiO support, as visible by an increased
slope of the curves. The amount of lifting is consistent with molecular
dynamics calculations, which reveal a deformed graphene area under the tip in
the shape of a Gaussian. The pseudo-magnetic field induced by the deformation
becomes visible as a sublattice symmetry breaking which scales with the lifting
height of the strained deformation and therefore with the pseudo-magnetic field
strength. Its magnitude is quantitatively reproduced by analytic and
tight-binding models, revealing fields of 1000 T. These results might be the
starting point for an effective THz valley filter, as a basic element of
valleytronics.Comment: Revised manuscript: streamlined the abstract and introduction, added
methods to supplement, Nano Letters, 201
Modeling contact formation between atomic-sized gold tips via molecular dynamics
The formation and rupture of atomic-sized contacts is modelled by means of
molecular dynamics simulations. Such nano-contacts are realized in scanning
tunnelling microscope and mechanically controlled break junction experiments.
These instruments routinely measure the conductance across the nano-sized
electrodes as they are brought into contact and separated, permitting
conductance traces to be recorded that are plots of conductance versus the
distance between the electrodes. One interesting feature of the conductance
traces is that for some metals and geometric configurations a jump in the value
of the conductance is observed right before contact between the electrodes, a
phenomenon known as jump-to-contact. This paper considers, from a computational
point of view, the dynamics of contact between two gold nano-electrodes.
Repeated indentation of the two surfaces on each other is performed in two
crystallographic orientations of face-centred cubic gold, namely (001) and
(111). Ultimately, the intention is to identify the structures at the atomic
level at the moment of first contact between the surfaces, since the value of
the conductance is related to the minimum cross-section in the contact region.
Conductance values obtained in this way are determined using first principles
electronic transport calculations, with atomic configurations taken from the
molecular dynamics simulations serving as input structures.Comment: 6 pages, 4 figures, conference submissio
Diffusion-Based Coarse Graining in Hybrid Continuum-Discrete Solvers: Applications in CFD-DEM
In this work, a coarse-graining method previously proposed by the authors in
a companion paper based on solving diffusion equations is applied to CFD-DEM
simulations, where coarse graining is used to obtain solid volume fraction,
particle phase velocity, and fluid-particle interaction forces. By examining
the conservation requirements, the variables to solve diffusion equations for
in CFD-DEM simulations are identified. The algorithm is then implemented into a
CFD-DEM solver based on OpenFOAM and LAMMPS, the former being a
general-purpose, three-dimensional CFD solver based on unstructured meshes.
Numerical simulations are performed for a fluidized bed by using the CFD-DEM
solver with the diffusion-based coarse-graining algorithm. Converged results
are obtained on successively refined meshes, even for meshes with cell sizes
comparable to or smaller than the particle diameter. This is a critical
advantage of the proposed method over many existing coarse-graining methods,
and would be particularly valuable when small cells are required in part of the
CFD mesh to resolve certain flow features such as boundary layers in wall
bounded flows and shear layers in jets and wakes. Moreover, we demonstrate that
the overhead computational costs incurred by the proposed coarse-graining
procedure are a small portion of the total costs in typical CFD-DEM simulations
as long as the number of particles per cell is reasonably large, although
admittedly the computational overhead of the coarse graining often exceeds that
of the CFD solver. Other advantages of the present algorithm include more
robust and physically realistic results, flexibility and easy implementation in
almost any CFD solvers, and clear physical interpretation of the computational
parameter needed in the algorithm. In summary, the diffusion-based method is a
theoretically elegant and practically viable option for CFD-DEM simulations
Role of Internal Motions and Molecular Geometry on the NMR Relaxation of Hydrocarbons
The role of internal motions and molecular geometry on H NMR relaxation
times in hydrocarbons is investigated using MD (molecular dynamics)
simulations of the autocorrelation functions for in{\it tra}molecular
and in{\it ter}molecular H-H dipole-dipole interactions
arising from rotational () and translational () diffusion, respectively.
We show that molecules with increased molecular symmetry such as neopentane,
benzene, and isooctane show better agreement with traditional hard-sphere
models than their corresponding straight-chain -alkane, and furthermore that
spherically-symmetric neopentane agrees well with the Stokes-Einstein theory.
The influence of internal motions on the dynamics and relaxation of
-alkanes are investigated by simulating rigid -alkanes and comparing with
flexible (i.e. non-rigid) -alkanes. Internal motions cause the rotational
and translational correlation-times to get significantly shorter
and the relaxation times to get significantly longer, especially for
longer-chain -alkanes. Site-by-site simulations of H's along the chains
indicate significant variations in and across the chain,
especially for longer-chain -alkanes. The extent of the stretched (i.e.
multi-exponential) decay in the autocorrelation functions are
quantified using inverse Laplace transforms, for both rigid and flexible
molecules, and on a site-by-site bases. Comparison of measurements
with the site-by-site simulations indicate that cross-relaxation (partially)
averages-out the variations in and across the chain of
long-chain -alkanes. This work also has implications on the role of
nano-pore confinement on the NMR relaxation of fluids in the organic-matter
pores of kerogen and bitumen
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