43 research outputs found
Symfind: Addressing the Fragility of Subhalo Finders and Revealing the Durability of Subhalos
A major question in CDM is what this theory actually predicts for
the properties of subhalo populations. Subhalos are difficult to simulate and
to find within simulations, and this propagates into uncertainty in theoretical
predictions for satellite galaxies. We present Symfind, a new
particle-tracking-based subhalo finder, and demonstrate that it can track
subhalos to orders-of-magnitude lower masses than commonly used halo-finding
tools, with a focus on Rockstar and consistent-trees. These longer survival
mean that at a fixed peak subhalo mass, we find more
subhalos within the virial radius, , and
more subhalos within in the Symphony dark-matter-only
simulation suite. More subhalos are found as resolution is increased. We
perform extensive numerical testing. In agreement with idealized simulations,
we show that the of subhalos is only resolved at high resolutions
(), but that mass loss itself can be
resolved at much more modest particle counts (). We show that Rockstar converges to false solutions for the mass
function, radial distribution, and disruption masses of subhalos. We argue that
our new method can trace resolved subhalos until the point of typical galaxy
disruption without invoking ``orphan'' modeling. We outline a concrete set of
steps for determining whether other subhalo finders meet the same criteria. We
publicly release Symfind catalogs and particle data for the Symphony simulation
suite at \url{http://web.stanford.edu/group/gfc/symphony}.Comment: 45 pages, 19 figure
Rotary Wing Aerodynamics
This book contains state-of-the-art experimental and numerical studies showing the most recent advancements in the field of rotary wing aerodynamics and aeroelasticity, with particular application to the rotorcraft and wind energy research fields
DEANN: Speeding up Kernel-Density Estimation using Approximate Nearest Neighbor Search
Kernel Density Estimation (KDE) is a nonparametric method for estimating the
shape of a density function, given a set of samples from the distribution.
Recently, locality-sensitive hashing, originally proposed as a tool for nearest
neighbor search, has been shown to enable fast KDE data structures. However,
these approaches do not take advantage of the many other advances that have
been made in algorithms for nearest neighbor algorithms. We present an
algorithm called Density Estimation from Approximate Nearest Neighbors (DEANN)
where we apply Approximate Nearest Neighbor (ANN) algorithms as a black box
subroutine to compute an unbiased KDE. The idea is to find points that have a
large contribution to the KDE using ANN, compute their contribution exactly,
and approximate the remainder with Random Sampling (RS). We present a
theoretical argument that supports the idea that an ANN subroutine can speed up
the evaluation. Furthermore, we provide a C++ implementation with a Python
interface that can make use of an arbitrary ANN implementation as a subroutine
for KDE evaluation. We show empirically that our implementation outperforms
state of the art implementations in all high dimensional datasets we
considered, and matches the performance of RS in cases where the ANN yield no
gains in performance.Comment: 24 pages, 1 figure. Submitted for revie
Training very large scale nonlinear SVMs using Alternating Direction Method of Multipliers coupled with the Hierarchically Semi-Separable kernel approximations
Typically, nonlinear Support Vector Machines (SVMs) produce significantly
higher classification quality when compared to linear ones but, at the same
time, their computational complexity is prohibitive for large-scale datasets:
this drawback is essentially related to the necessity to store and manipulate
large, dense and unstructured kernel matrices. Despite the fact that at the
core of training a SVM there is a \textit{simple} convex optimization problem,
the presence of kernel matrices is responsible for dramatic performance
reduction, making SVMs unworkably slow for large problems. Aiming to an
efficient solution of large-scale nonlinear SVM problems, we propose the use of
the \textit{Alternating Direction Method of Multipliers} coupled with
\textit{Hierarchically Semi-Separable} (HSS) kernel approximations. As shown in
this work, the detailed analysis of the interaction among their algorithmic
components unveils a particularly efficient framework and indeed, the presented
experimental results demonstrate a significant speed-up when compared to the
\textit{state-of-the-art} nonlinear SVM libraries (without significantly
affecting the classification accuracy)
Development and Application of Numerical Methods in Biomolecular Solvation
This work addresses the development of fast summation methods for long range particle interactions and their application to problems in biomolecular solvation, which describes the interaction of proteins or other biomolecules with their solvent environment. At the core of this work are treecodes, tree-based fast summation methods which, for N particles, reduce the cost of computing particle interactions from O(N^2) to O(N log N). Background on fast summation methods and treecodes in particular, as well as several treecode improvements developed in the early stages of this work, are presented.
Building on treecodes, dual tree traversal (DTT) methods are another class of tree-based fast summation methods which reduce the cost of computing particle interactions for N particles to O(N). The primary result of this work is the development of an O(N) dual tree traversal fast summation method based on barycentric Lagrange polynomial interpolation (BLDTT). This method is implemented to run across multiple GPU compute nodes in the software package BaryTree. Across different problem sizes, particle distributions, geometries, and interaction kernels, the BLDTT shows consistently better performance than the previously developed barycentric Lagrange treecode (BLTC).
The first major biomolecular solvation application of fast summation methods presented is to the Poisson–Boltzmann implicit solvent model, and in particular, the treecode-accelerated boundary integral Poisson–Boltzmann solver (TABI-PB). The work on TABI-PB consists of three primary projects and an application. The first project investigates the impact of various biomolecular surface meshing codes on TABI-PB, and integrated the NanoShaper software into the package, resulting in significantly better performance. Second, a node patch method for discretizing the system of integral equations is introduced to replace the previous centroid collocation scheme, resulting in faster convergence of solvation energies. Third, a new version of TABI-PB with GPU acceleration based on the BLDTT is developed, resulting in even more scalability. An application investigating the binding of biomolecular complexes is undertaken using the previous Taylor treecode-based version of TABI-PB. In addition to these projects, work performed over the course of this thesis integrated TABI-PB into the popular Adaptive Poisson–Boltzmann Solver (APBS) developed at Pacific Northwest National Laboratory.
The second major application of fast summation methods is to the 3D reference interaction site model (3D-RISM), a statistical-mechanics based continuum solvation model. This work applies cluster-particle Taylor expansion treecodes to treat long-range asymptotic Coulomb-like potentials in 3D-RISM, and results in significant speedups and improved scalability to the 3D-RISM package implemented in AmberTools. Additionally, preliminary work on specialized GPU-accelerated treecodes based on BaryTree
for 3D-RISM long-range asymptotic functions is presented.PHDApplied and Interdisciplinary MathematicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/168120/1/lwwilson_1.pd
Generalized averaged Gaussian quadrature and applications
A simple numerical method for constructing the optimal generalized averaged Gaussian quadrature formulas will be presented. These formulas exist in many cases in which real positive GaussKronrod formulas do not exist, and can be used as an adequate alternative in order to estimate the error of a Gaussian rule. We also investigate the conditions under which the optimal averaged Gaussian quadrature formulas and their truncated variants are internal
MS FT-2-2 7 Orthogonal polynomials and quadrature: Theory, computation, and applications
Quadrature rules find many applications in science and engineering. Their analysis is a classical area of applied mathematics and continues to attract considerable attention. This seminar brings together speakers with expertise in a large variety of quadrature rules. It is the aim of the seminar to provide an overview of recent developments in the analysis of quadrature rules. The computation of error estimates and novel applications also are described