85 research outputs found
Enhanced molecular dynamics performance with a programmable graphics processor
Design considerations for molecular dynamics algorithms capable of taking
advantage of the computational power of a graphics processing unit (GPU) are
described. Accommodating the constraints of scalable streaming-multiprocessor
hardware necessitates a reformulation of the underlying algorithm. Performance
measurements demonstrate the considerable benefit and cost-effectiveness of
such an approach, which produces a factor of 2.5 speed improvement over
previous work for the case of the soft-sphere potential.Comment: 20 pages (v2: minor additions and changes; v3: corrected typos
Modeling growth of 60-unit shells in solution: Early results
AbstractCurrent research into supramolecular assembly using molecular dynamics simulation is summarized. Ongoing simulations are aimed at exploring the nature of the growth pathways of larger shells than considered previously, under reversible bonding conditions and in the presence of an explicit solvent
Dynamics of polymer chain collapse into compact states
Molecular dynamics simulation methods are used to study the folding of
polymer chains into packed cubic states. The polymer model, based on a chain of
linked sites moving in the continuum, includes both excluded volume and
torsional interactions. Different native-state packing arrangements and chain
lengths are explored; the organization of the native state is found to affect
both the ability of the chain to fold successfully and the nature of the
folding pathway as the system is gradually cooled. An order parameter based on
contact counts is used to provide information about the folding process, with
contacts additionally classified according to criteria such as core and surface
sites or local and distant site pairs. Fully detailed contact maps and their
evolution are also examined.Comment: 11 pages, 11 figures (some low resolution
Star-graph expansions for bond-diluted Potts models
We derive high-temperature series expansions for the free energy and the
susceptibility of random-bond -state Potts models on hypercubic lattices
using a star-graph expansion technique. This method enables the exact
calculation of quenched disorder averages for arbitrary uncorrelated coupling
distributions. Moreover, we can keep the disorder strength as well as the
dimension as symbolic parameters. By applying several series analysis
techniques to the new series expansions, one can scan large regions of the
parameter space for any value of . For the bond-diluted 4-state
Potts model in three dimensions, which exhibits a rather strong first-order
phase transition in the undiluted case, we present results for the transition
temperature and the effective critical exponent as a function of
as obtained from the analysis of susceptibility series up to order 18. A
comparison with recent Monte Carlo data (Chatelain {\em et al.}, Phys. Rev.
E64, 036120(2001)) shows signals for the softening to a second-order transition
at finite disorder strength.Comment: 8 pages, 6 figure
Molecular dynamics in arbitrary geometries : parallel evaluation of pair forces
A new algorithm for calculating intermolecular pair forces in molecular dynamics (MD) simulations on a distributed parallel computer is presented. The arbitrary interacting cells algorithm (AICA) is designed to operate on geometrical domains defined by an unstructured, arbitrary polyhedral mesh that has been spatially decomposed into irregular portions for parallelisation. It is intended for nano scale fluid mechanics simulation by MD in complex geometries, and to provide the MD component of a hybrid MD/continuum simulation. The spatial relationship of the cells of the mesh is calculated at the start of the simulation and only the molecules contained in cells that have part of their surface closer than the cut-off radius of the intermolecular pair potential are required to interact. AICA has been implemented in the open source C++ code OpenFOAM, and its accuracy has been indirectly verified against a published MD code. The same system simulated in serial and in parallel on 12 and 32 processors gives the same results. Performance tests show that there is an optimal number of cells in a mesh for maximum speed of calculating intermolecular forces, and that having a large number of empty cells in the mesh does not add a significant computational overhead
Algorithm for numerical integration of the rigid-body equations of motion
A new algorithm for numerical integration of the rigid-body equations of
motion is proposed. The algorithm uses the leapfrog scheme and the quantities
involved are angular velocities and orientational variables which can be
expressed in terms of either principal axes or quaternions. Due to specific
features of the algorithm, orthonormality and unit norms of the orientational
variables are integrals of motion, despite an approximate character of the
produced trajectories. It is shown that the method presented appears to be the
most efficient among all known algorithms of such a kind.Comment: 4 pages, 1 figur
Spin dynamics simulations of the magnetic dynamics of RbMnF and direct comparison with experiment
Spin-dynamics techniques have been used to perform large-scale simulations of
the dynamic behavior of the classical Heisenberg antiferromagnet in simple
cubic lattices with linear sizes . This system is widely recognized
as an appropriate model for the magnetic properties of RbMnF.
Time-evolutions of spin configurations were determined numerically from coupled
equations of motion for individual spins using a new algorithm implemented by
Krech {\it etal}, which is based on fourth-order Suzuki-Trotter decompositions
of exponential operators. The dynamic structure factor was calculated from the
space- and time-displaced spin-spin correlation function. The crossover from
hydrodynamic to critical behavior of the dispersion curve and spin-wave
half-width was studied as the temperature was increased towards the critical
temperature. The dynamic critical exponent was estimated to be , which is slightly lower than the dynamic scaling prediction, but in
good agreement with a recent experimental value. Direct, quantitative
comparisons of both the dispersion curve and the lineshapes obtained from our
simulations with very recent experimental results for RbMnF are presented.Comment: 30 pages, RevTex, 9 figures, to appear in PR
Self-avoiding walks and connective constants in small-world networks
Long-distance characteristics of small-world networks have been studied by
means of self-avoiding walks (SAW's). We consider networks generated by
rewiring links in one- and two-dimensional regular lattices. The number of
SAW's was obtained from numerical simulations as a function of the number
of steps on the considered networks. The so-called connective constant,
, which characterizes the long-distance
behavior of the walks, increases continuously with disorder strength (or
rewiring probability, ). For small , one has a linear relation , and being constants dependent on the underlying
lattice. Close to one finds the behavior expected for random graphs. An
analytical approach is given to account for the results derived from numerical
simulations. Both methods yield results agreeing with each other for small ,
and differ for close to 1, because of the different connectivity
distributions resulting in both cases.Comment: 7 pages, 5 figure
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