1,540 research outputs found
Experiences from Software Engineering of Large Scale AMR Multiphysics Code Frameworks
Among the present generation of multiphysics HPC simulation codes there are
many that are built upon general infrastructural frameworks. This is especially
true of the codes that make use of structured adaptive mesh refinement (SAMR)
because of unique demands placed on the housekeeping aspects of the code. They
have varying degrees of abstractions between the infrastructure such as mesh
management and IO and the numerics of the physics solvers. In this experience
report we summarize the experiences and lessons learned from two of such major
software efforts, FLASH and Chombo.Comment: Experience Repor
The Convergence of Particle-in-Cell Schemes for Cosmological Dark Matter Simulations
Particle methods are a ubiquitous tool for solving the Vlasov-Poisson
equation in comoving coordinates, which is used to model the gravitational
evolution of dark matter in an expanding universe. However, these methods are
known to produce poor results on idealized test problems, particularly at late
times, after the particle trajectories have crossed. To investigate this, we
have performed a series of one- and two-dimensional "Zel'dovich Pancake"
calculations using the popular Particle-in-Cell (PIC) method. We find that PIC
can indeed converge on these problems provided the following modifications are
made. The first modification is to regularize the singular initial distribution
function by introducing a small but finite artificial velocity dispersion. This
process is analogous to artificial viscosity in compressible gas dynamics, and,
as with artificial viscosity, the amount of regularization can be tailored so
that its effect outside of a well-defined region - in this case, the
high-density caustics - is small. The second modification is the introduction
of a particle remapping procedure that periodically re-expresses the dark
matter distribution function using a new set of particles. We describe a
remapping algorithm that is third-order accurate and adaptive in phase space.
This procedure prevents the accumulation of numerical errors in integrating the
particle trajectories from growing large enough to significantly degrade the
solution. Once both of these changes are made, PIC converges at second order on
the Zel'dovich Pancake problem, even at late times, after many caustics have
formed. Furthermore, the resulting scheme does not suffer from the unphysical,
small-scale "clumping" phenomenon known to occur on the Pancake problem when
the perturbation wave vector is not aligned with one of the Cartesian
coordinate axes.Comment: 29 pages, 29 figures. Accepted for publication in ApJ. The revised
version includes a discussion of energy conservation in the remapping
procedure, as well as some interpretive differences in the Conclusions made
in response to the referee report. Results themselves are unchange
A 4th-Order Particle-in-Cell Method with Phase-Space Remapping for the Vlasov-Poisson Equation
Numerical solutions to the Vlasov-Poisson system of equations have important
applications to both plasma physics and cosmology. In this paper, we present a
new Particle-in-Cell (PIC) method for solving this system that is 4th-order
accurate in both space and time. Our method is a high-order extension of one
presented previously [B. Wang, G. Miller, and P. Colella, SIAM J. Sci. Comput.,
33 (2011), pp. 3509--3537]. It treats all of the stages of the standard PIC
update - charge deposition, force interpolation, the field solve, and the
particle push - with 4th-order accuracy, and includes a 6th-order accurate
phase-space remapping step for controlling particle noise. We demonstrate the
convergence of our method on a series of one- and two- dimensional
electrostatic plasma test problems, comparing its accuracy to that of a
2nd-order method. As expected, the 4th-order method can achieve comparable
accuracy to the 2nd-order method with many fewer resolution elements.Comment: 18 pages, 10 figures, submitted to SIS
Genomics technology for assessing soil pollution
Transcription and metabolite analysis is a powerful way to reveal physiological shifts in response to environmental pollution. Recent studies on earthworms, including one in BMC Biology, show that the type of pollution and its availability for uptake by organisms can differentially affect transcription and metabolism
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