Fit indices provide helpful information for researchers to assess the fit of their structural equation models to their data. However, like many statistics and methods, researchers can misuse fit ...indices, which suggest the potential for questionable research practices that might arise during the analytic and interpretative processes. In the current paper, the author highlights two critical ethical dilemmas regarding the use of fit indices, which are (1) the selective reporting of fit indices and (2) using fit indices to justify poorly-fitting models. The author highlights the dilemmas and provides potential solutions for researchers and journals to follow to reduce these questionable research practices.
The design and implementation of a new framework for adaptive mesh refinement calculations are described. It is intended primarily for applications in astrophysical fluid dynamics, but its flexible ...and modular design enables its use for a wide variety of physics. The framework works with both uniform and nonuniform grids in Cartesian and curvilinear coordinate systems. It adopts a dynamic execution model based on a simple design called a "task list" that improves parallel performance by overlapping communication and computation, simplifies the inclusion of a diverse range of physics, and even enables multiphysics models involving different physics in different regions of the calculation. We describe physics modules implemented in this framework for both nonrelativistic and relativistic magnetohydrodynamics (MHD). These modules adopt mature and robust algorithms originally developed for the Athena MHD code and incorporate new extensions: support for curvilinear coordinates, higher-order time integrators, more realistic physics such as a general equation of state, and diffusion terms that can be integrated with super-time-stepping algorithms. The modules show excellent performance and scaling, with well over 80% parallel efficiency on over half a million threads. The source code has been made publicly available.
•A fourth-order accurate method for the numerical solution of the equations of ideal magnetohydrodynamics (MHD) is proposed.•The piecewise parabolic method (PPM) in the upwind constrained transport ...framework satisfies the divergence-free constraint.•Modern PPM limiters provide MHD shock-capturing abilities while maintaining full fourth-order accuracy for smooth profiles.•Fourth-order accuracy yields significant improvement in solution errors relative to traditional second-order schemes.
We present a fourth-order accurate finite volume method for the solution of ideal magnetohydrodynamics (MHD). The numerical method combines high-order quadrature rules in the solution of semi-discrete formulations of hyperbolic conservation laws with the upwind constrained transport (UCT) framework to ensure that the divergence-free constraint of the magnetic field is satisfied. A novel implementation of UCT that uses the piecewise parabolic method (PPM) for the reconstruction of magnetic fields at cell corners in 2D is introduced. The resulting scheme can be expressed as the extension of the second-order accurate constrained transport (CT) Godunov-type scheme that is currently used in the Athena astrophysics code. After validating the base algorithm on a series of hydrodynamics test problems, we present the results of multidimensional MHD test problems which demonstrate formal fourth-order convergence for smooth problems, robustness for discontinuous problems, and improved accuracy relative to the second-order scheme.
Extracellular enzymes in soils mediate the decomposition of organic matter and catalyze key transformations in carbon, nitrogen and phosphorus cycling. However, most studies of extracellular enzyme ...activity have focused exclusively on relatively carbon and nutrient-rich surface soils. In tropical forests, several centimeters of nutrient-rich surface soil can overlay meters of resource-poor subsoil, of which the microbial ecology is poorly characterized. The goal of this study was to determine how extracellular enzyme activity changes as a function of depth across two soil orders (Oxisols and Inceptisols) and two forest types that occur at different elevations (Tabonuco, lower elevation; Colorado, higher elevation) at the Luquillo Critical Zone Observatory in northeast Puerto Rico. We excavated three soil pits to 140 cm at four different sites representing the four soil × forest combinations, and measured potential activities of four carbon-acquiring enzymes (α-glucosidase, β-glucosidase, β-xylosidase, cellobiohydrolase), one nitrogen-acquiring enzyme (N-acetyl glucosaminidase) and one organic phosphorus-acquiring enzyme (acid phosphatase) at six discrete depth intervals. We used phospholipid fatty acid (PLFA) analysis to assess viable microbial biomass and community structure. Overall, microbial biomass, specific enzyme activities and community structure were similar across the two soil and forest types, in spite of higher carbon concentrations and C:N ratios in the Colorado forest soil. Soil nutrients, microbial biomass and potential enzyme activities all declined exponentially with depth. However, when normalized to microbial biomass, specific enzyme activities either did not change with depth (β-glucosidase, β-xylosidase, cellobiohydrolase and N-acetyl glucosaminidase) or increased significantly with depth (α-glucosidase and acid phosphatase, P < 0.05). Principal components analysis of PLFA biomarkers revealed shifts in community structure with depth (P < 0.01), driven largely by a decline in fungal:bacterial ratios, an increase in gram positive and actinobacteria biomarkers, and a decrease in gram negative biomarkers. Shifts in community structure, upregulation of enzyme production in response to resource scarcity and decreased enzyme turnover rates may all contribute to high specific enzyme activities in subsoils. Our study indicates that low-carbon tropical subsoils contain small but metabolically active microbial communities, and that specific enzyme activities can be used to examine changes in microbial physiology across orders of magnitude gradients in soil carbon concentrations.
•Measured C, N and P-acquiring enzymes, microbial biomass and community structure with soil depth.•Microbial biomass, enzyme activities, carbon and nutrients decline exponentially with depth.•Biomass-normalized specific enzyme activities either do not decline or increase significantly with depth.•Subsoils contain metabolically active communities that are structurally distinct from surface communities.
ABSTRACT We present a new general relativistic magnetohydrodynamics (GRMHD) code integrated into the Athena++ framework. Improving upon the techniques used in most GRMHD codes, ours allows the use of ...advanced, less diffusive Riemann solvers, in particular HLLC and HLLD. We also employ a staggered-mesh constrained transport algorithm suited for curvilinear coordinate systems in order to maintain the divergence-free constraint of the magnetic field. Our code is designed to work with arbitrary stationary spacetimes in one, two, or three dimensions, and we demonstrate its reliability through a number of tests. We also report on its promising performance and scalability.
Classical hydrodynamics is a remarkably versatile description of the coarse-grained behaviour of many-particle systems once local equilibrium has been established1. The form of the hydrodynamical ...equations is determined primarily by the conserved quantities present in a system. Some quantum spin chains are known to possess, even in the simplest cases, a greatly expanded set of conservation laws, and recent work suggests that these laws strongly modify collective spin dynamics, even at high temperature2,3. Here, by probing the dynamical exponent of the one-dimensional Heisenberg antiferromagnet KCuF3 with neutron scattering, we find evidence that the spin dynamics are well described by the dynamical exponent z = 3/2, which is consistent with the recent theoretical conjecture that the dynamics of this quantum system are described by the Kardar–Parisi–Zhang universality class4,5. This observation shows that low-energy inelastic neutron scattering at moderate temperatures can reveal the details of emergent quantum fluid properties like those arising in non-Fermi liquids in higher dimensions.Quantum systems possessing conserved quantities are expected to show quantum fluid properties governed by hydrodynamic equations. This behaviour is now evidenced in a neutron scattering study on the one-dimensional Heisenberg antiferromagnet KCuF3.
We use global three-dimensional radiation magnetohydrodynamical simulations to study accretion disks onto a black hole with accretion rates varying from to . We initialize the disks with a weakly ...magnetized torus centered at either 50 or 80 gravitational radii, leading to self-consistent turbulence generated by the magnetorotational instability (MRI). The inner regions of all disks have radiation pressure ∼104-106 times the gas pressure. Nonaxisymmetric density waves that steepen into spiral shocks form as gas flows toward the black hole. Maxwell stress from MRI turbulence can be larger than the Reynolds stress only when the net vertical magnetic flux is sufficiently large. Outflows are formed with a speed of ∼0.1-0.4c. When the accretion rate is smaller than , outflows are launched from ∼10 gravitational radii, and the radiative efficiency is ∼5%-7%. For an accretion rate reaching , most of the funnel region near the rotation axis becomes optically thick, and the outflow is launched from beyond 50 gravitational radii. The radiative efficiency is reduced to 1%. We always find that the kinetic energy luminosity associated with the outflow is at most ∼15%-30% of the radiative luminosity. The mass flux in the outflow is ∼15%-50% of the net mass accretion rates. We discuss the implications of our simulation results on the observational properties of these disks.
The global evolution of protoplanetary disks (PPDs) has recently been shown to be largely controlled by the amount of poloidal magnetic flux threading the disk. The amount of magnetic flux must also ...coevolve with the disk, as a result of magnetic flux transport, a process that is poorly understood. In weakly ionized gas as in PPDs, magnetic flux is largely frozen in the electron fluid, except when resistivity is large. When the disk is largely laminar, we show that the relative drift between the electrons and ions (the Hall drift), and the ions and neutral fluids (ambipolar drift) can play a dominant role on the transport of magnetic flux. Using two-dimensional simulations that incorporate the Hall effect and ambipolar diffusion (AD) with prescribed diffusivities, we show that when large-scale poloidal field is aligned with disk rotation, the Hall effect rapidly drags magnetic flux inward at the midplane region, while it slowly pushes flux outward above/below the midplane. This leads to a highly radially elongated field configuration as a global manifestation of the Hall-shear instability. This field configuration further promotes rapid outward flux transport by AD at the midplane, leading to instability saturation. In quasi-steady state, magnetic flux is transported outward at approximately the same rate at all heights, and the rate is comparable to the Hall-free case. For anti-aligned field polarity, the Hall effect consistently transports magnetic flux outward, leading to a largely vertical field configuration in the midplane region. The field lines in the upper layer first bend radially inward and then outward to launch a disk wind. Overall, the net rate of outward flux transport is about twice as fast as that of the aligned case. In addition, the rate of flux transport increases with increasing disk magnetization. The absolute rate of transport is sensitive to disk microphysics, which remains to be explored in future studies.
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