1,613 research outputs found
Implicit-explicit multirate infinitesimal GARK methods
This work focuses on the development of a new class of high-order accurate
methods for multirate time integration of systems of ordinary differential
equations. Unlike other recent work in this area, the proposed methods support
mixed implicit-explicit (IMEX) treatment of the slow time scale. In addition to
allowing this slow time scale flexibility, the proposed methods utilize a
so-called `infinitesimal' formulation for the fast time scale through
definition of a sequence of modified `fast' initial-value problems, that may be
solved using any viable algorithm. We name the proposed class as
implicit-explicit multirate infinitesimal generalized-structure additive
Runge--Kutta (IMEX-MRI-GARK) methods. In addition to defining these methods, we
prove that they may be viewed as specific instances of generalized-structure
additive Runge--Kutta (GARK) methods, and derive a set of order conditions on
the IMEX-MRI-GARK coefficients to guarantee both third and fourth order
accuracy for the overall multirate method. Additionally, we provide three
specific IMEX-MRI-GARK methods, two of order three and one of order four. We
conclude with numerical simulations on two multirate test problems,
demonstrating the methods' predicted convergence rates and comparing their
efficiency against both legacy IMEX multirate schemes and recent third and
fourth order implicit MRI-GARK methods
Digital Preservation and Access of Natural Resources Documents
Digitization and preservation of natural resource documents were reviewed and the current status of digitization presented for a North American university. It is important to present the status of the digitation process for natural resources and to advocate for increased collections of digital material for ease of reference and exchange of information. Digital collections need to include both published documents and ancillary material for research projects and data for future use and interpretation. The methods in this paper can be applied to other natural resource collections increasing their use and distribution. The process of decision making for documents and their preservation and inclusion in ScholarWorks is presented as a part of the Forest Sciences Commons as a subset of the Life Sciences Commons of the Digital Commons Open Network launched and maintained by bepress. Digitization has increased the roles and skillsets needed for librarians and from libraries. This creates new challenges and opportunities for the library as publisher and as an advocate for open access. Digital curation melds together digitization and knowledge management and enhances community engagement. Digitization of collections are reviewed and natural resource documentation presented for faculty publications, Research Projects and Centers, eBooks, Journals, Galleries and electronic Theses and Dissertations (ETDs). Recommendations are made to increase the digital curation of the collection by encouraging community participation and use. Digital archives are important to natural resource professionals as society-ready natural resource graduates need to deal effectively with complex ecological, economic and social issues of current natural resources management. Natural resource research for the future needs to ensure that professionals have a greater breath of knowledge as they interpret and apply new knowledge, understanding, and technology to complex, transdisciplinary social and biological issues and challenges
FMRI Clustering and False Positive Rates
Recently, Eklund et al. (2016) analyzed clustering methods in standard FMRI
packages: AFNI (which we maintain), FSL, and SPM [1]. They claimed: 1) false
positive rates (FPRs) in traditional approaches are greatly inflated,
questioning the validity of "countless published fMRI studies"; 2)
nonparametric methods produce valid, but slightly conservative, FPRs; 3) a
common flawed assumption is that the spatial autocorrelation function (ACF) of
FMRI noise is Gaussian-shaped; and 4) a 15-year-old bug in AFNI's 3dClustSim
significantly contributed to producing "particularly high" FPRs compared to
other software. We repeated simulations from [1] (Beijing-Zang data [2], see
[3]), and comment on each point briefly.Comment: 3 pages, 1 figure. A Letter accepted in PNA
Fully-Coupled Simulation of Cosmic Reionization. I: Numerical Methods and Tests
We describe an extension of the Enzo code to enable fully-coupled radiation
hydrodynamical simulation of inhomogeneous reionization in large cosmological volumes with thousands to millions of point sources. We
solve all dynamical, radiative transfer, thermal, and ionization processes
self-consistently on the same mesh, as opposed to a postprocessing approach
which coarse-grains the radiative transfer. We do, however, employ a simple
subgrid model for star formation which we calibrate to observations. Radiation
transport is done in the grey flux-limited diffusion (FLD) approximation, which
is solved by implicit time integration split off from the gas energy and
ionization equations, which are solved separately. This results in a faster and
more robust scheme for cosmological applications compared to the earlier
method. The FLD equation is solved using the hypre optimally scalable geometric
multigrid solver from LLNL. By treating the ionizing radiation as a grid field
as opposed to rays, our method is scalable with respect to the number of
ionizing sources, limited only by the parallel scaling properties of the
radiation solver. We test the speed and accuracy of our approach on a number of
standard verification and validation tests. We show by direct comparison with
Enzo's adaptive ray tracing method Moray that the well-known inability of FLD
to cast a shadow behind opaque clouds has a minor effect on the evolution of
ionized volume and mass fractions in a reionization simulation validation test.
We illustrate an application of our method to the problem of inhomogeneous
reionization in a 80 Mpc comoving box resolved with Eulerian grid
cells and dark matter particles.Comment: 32 pages, 23 figures. ApJ Supp accepted. New title and substantial
revisions re. v
Cosmological Radiation Hydrodynamics with ENZO
We describe an extension of the cosmological hydrodynamics code ENZO to
include the self-consistent transport of ionizing radiation modeled in the
flux-limited diffusion approximation. A novel feature of our algorithm is a
coupled implicit solution of radiation transport, ionization kinetics, and gas
photoheating, making the timestepping for this portion of the calculation
resolution independent. The implicit system is coupled to the explicit
cosmological hydrodynamics through operator splitting and solved with scalable
multigrid methods. We summarize the numerical method, present a verification
test on cosmological Stromgren spheres, and then apply it to the problem of
cosmological hydrogen reionization.Comment: 14 pages, 3 figures, to appear in Recent Directions in Astrophysical
Quantitative Spectroscopy and Radiation Hydrodynamics, Ed. I. Hubeny,
American Institute of Physics (2009
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