An Improved Dynamic Core for a Non-hydrostatic Model System on the Yin-Yang Grid

A 3D dynamic core of the non-hydrostatic model GRAPES（Global/Regional Assimilation and Prediction System） is developed on the Yin-Yang grid to address the polar problem and to enhance the computational efficiency. Three-dimensional Coriolis forcing is introduced to the new core, and full representation of the Coriolis forcing makes it straightforward to share code between the Yin and Yang subdomains. Similar to that in the original GRAPES model, a semi-implicit semi-Lagrangian scheme is adopted for temporal integration and advection with additional arrangement for cross-boundary transport. Under a non-centered second-order temporal and spatial discretization, the dry nonhydrostatic frame is summarized as the solution of an elliptical problem. The resulting Helmholtz equation is solved with the Generalized Conjugate Residual solver in cooperation with the classic Schwarz method. Even though the coefficients of the equation are quite different from those in the original model, the computational procedure of the new core is just the same. The bi-cubic Lagrangian interpolation serves to provide Dirichlet-type boundary conditions with data transfer between the subdomains. The dry core is evaluated with several benchmark test cases, and all the tests display reasonable numerical stability and computing performance. Persistency of the balanced flow and development of both the mountain-induced Rossby wave and Rossby–Haurwitz wave confirms the appropriate installation of the 3D Coriolis terms in the semi-implicit semi-Lagrangian dynamic core on the Yin-Yang grid.

A Neural-network-based Alternative Scheme to Include Nonhydrostatic Processes in an Atmospheric Dynamical Core

Here,a nonhydrostatic alternative scheme(NAS)is proposed for the grey zone where the nonhydrostatic impact on the atmosphere is evident but not large enough to justify the necessity to include an implicit nonhydrostatic solver in an atmospheric dynamical core.The NAS is designed to replace this solver,which can be incorporated into any hydrostatic models so that existing well-developed hydrostatic models can effectively serve for a longer time.Recent advances in machine learning(ML)provide a potential tool for capturing the main complicated nonlinear-nonhydrostatic relationship.In this study,an ML approach called a neural network(NN)was adopted to select leading input features and develop the NAS.The NNs were trained and evaluated with 12-day simulation results of dry baroclinic-wave tests by the Weather Research and Forecasting(WRF)model.The forward time difference of the nonhydrostatic tendency was used as the target variable,and the five selected features were the nonhydrostatic tendency at the last time step,and four hydrostatic variables at the current step including geopotential height,pressure in two different forms,and potential temperature,respectively.Finally,a practical NAS was developed with these features and trained layer by layer at a 20-km horizontal resolution,which can accurately reproduce the temporal variation and vertical distribution of the nonhydrostatic tendency.Corrected by the NN-based NAS,the improved hydrostatic solver at different horizontal resolutions can run stably for at least one month and effectively reduce most of the nonhydrostatic errors in terms of system bias,anomaly root-mean-square error,and the error of the wave spatial pattern,which proves the feasibility and superiority of this scheme.

A dynamic core evolutionary clustering algorithm based on saturated memory

Because the number of clustering cores needs to be set before implementing the K-means algorithm,this type of algorithm often fails in applications with increasing data and changing distribution characteristics.This paper proposes an evolutionary algorithm DCC,which can dynamically adjust the number of clustering cores with data change.DCC algorithm uses the Gaussian function as the activation function of each core.Each clustering core can adjust its center vector and coverage based on the response to the input data and its memory state to better fit the sample clusters in the space.The DCC algorithm model can evolve from 0.After each new sample is added,the winning dynamic core can be adjusted or split by competitive learning,so that the number of clustering cores of the algorithm always maintains a better adaptation relationship with the existing data.Furthermore,because its clustering core can split,it can subdivide the densely distributed data clusters.Finally,detailed experimental results show that the evolutionary clustering algorithm DCC based on the dynamic core method has excellent clustering performance and strong robustness.

Earth's deformation due to the dynamical perturbations of the fluid outer core

The elasto-gravitational deformation response of the Earths solid parts to the perturbations of the pressure and gravity on the core-mantle boundary (CMB) and the solid inner core boundary (ICB), due to the dynamical behaviors of the fluid outer core (FOC), is discussed. The internal load Love numbers, which are formulized in a general form in this study, are employed to describe the Earths deformation. The preliminary reference Earth model (PREM) is used as an example to calculate the internal load Love numbers on the Earths surface, CMB and ICB, respectively. The characteristics of the Earths deformation variation with the depth and the perturbation periods on the boundaries of the FOC are also investigated. The numerical results indicate that the internal load Love numbers decrease quickly with the increasing degree of the spherical harmonics of the displacement and depend strongly on the perturbation frequencies, especially on the high frequencies. The results, obtained in this work, can be used to construct the boundary conditions for the core dynamics of the long-period oscillations of the Earths fluid outer core.

An Adaptive Nonhydrostatic Atmospheric Dynamical Core Using a Multi-Moment Constrained Finite Volume Method

An adaptive 2 D nonhydrostatic dynamical core is proposed by using the multi-moment constrained finite-volume(MCV) scheme and the Berger-Oliger adaptive mesh refinement(AMR) algorithm. The MCV scheme takes several pointwise values within each computational cell as the predicted variables to build high-order schemes based on single-cell reconstruction. Two types of moments, such as the volume-integrated average(VIA) and point value(PV), are defined as constraint conditions to derive the updating formulations of the unknowns, and the constraint condition on VIA guarantees the rigorous conservation of the proposed model. In this study, the MCV scheme is implemented on a height-based, terrainfollowing grid with variable resolution to solve the nonhydrostatic governing equations of atmospheric dynamics. The AMR grid of Berger-Oliger consists of several groups of blocks with different resolutions, where the MCV model developed on a fixed structured mesh can be used directly. Numerical formulations are designed to implement the coarsefine interpolation and the flux correction for properly exchanging the solution information among different blocks. Widely used benchmark tests are carried out to evaluate the proposed model. The numerical experiments on uniform and AMR grids indicate that the adaptive model has promising potential for improving computational efficiency without losing accuracy.

Parallelization and I/O Performance Optimization of a Global Nonhydrostatic Dynamical Core Using MPI

The Global-Regional Integrated forecast System(GRIST)is the next-generation weather and climate integrated model dynamic framework developed by Chinese Academy of Meteorological Sciences.In this paper,we present several changes made to the global nonhydrostatic dynamical(GND)core,which is part of the ongoing prototype of GRIST.The changes leveraging MPI and PnetCDF techniques were targeted at the parallelization and performance optimization to the original serial GND core.Meanwhile,some sophisticated data structures and interfaces were designed to adjust flexibly the size of boundary and halo domains according to the variable accuracy in parallel context.In addition,the I/O performance of PnetCDF decreases as the number of MPI processes increases in our experimental environment.Especially when the number exceeds 6000,it caused system-wide outages(SWO).Thus,a grouping solution was proposed to overcome that issue.Several experiments were carried out on the supercomputing platform based on Intel x86 CPUs in the National Supercomputing Center in Wuxi.The results demonstrated that the parallel GND core based on grouping solution achieves good strong scalability and improves the performance significantly,as well as avoiding the SWOs.

On the Dynamics of Vortex Filaments and Their Core Structure

We give a brief review of the asymptotic theory of slender vortex filaments with emphases on (i) the choices of scalings and small parameters characterizing the physical problem,(ii) the key steps in the formulation of the theory and (iii) the assumptions and/or restrictions on the theory of Callegari and Ting (1978).We present highlights of an extension of the 1978 asymptotic theory:the analyses for core structures with axial variation.Making use of the physical insights gained from the analyses,we present a new derivation of the evolution equations for the core structure.The new one is simpler and straightforward and shows the physics clearly.

Verification of a Modified Nonhydrostatic Global Spectral Dynamical Core Based on the Dry-Mass Vertical Coordinate: Three-Dimensional Idealized Test Cases

The newly developed nonhydrostatic(NH)global spectral dynamical core is evaluated by using three-dimensional(3D)benchmark tests with/without moisture.This new dynamical core differs from the original Aladin-NH like one in the combined use of a dry-mass vertical coordinate and a new temperature variable,and thus,it inherently conserves the dry air mass and includes the mass sink effect associated with precipitation flux.Some 3D dry benchmark tests are first conducted,including steady state,dry baroclinic waves,mountain waves in non-sheared and sheared background flows,and a dry Held–Suarez test.The results from these test cases demonstrate that the present dynamical core is accurate and robust in applications on the sphere,especially for addressing the nonhydrostatic effects.Then,three additional moist test cases are conducted to further explore the improvement of the new dynamical core.Importantly,in contrast to the original Aladin-NH like one,the new dynamical core prefers to obtain simulated tropical cyclone with lower pressure,stronger wind speeds,and faster northward movement,which is much closer to the results from the Model for Prediction Across Scales(MPAS),and it also enhances the updrafts and provides enhanced precipitation rate in the tropics,which partially compensates the inefficient vertical transport due to the absence of the deep convection parameterization in the moist Held–Suarez test,thus demonstrating its potential value for full-physics global NH numerical weather prediction application.

Comparison and Analysis of Two Different Calculation Schemes of SLEVE-Hybrid Coordinate in the GRAPES_MESO Model

The calculation scheme of the smoothed-level and hybrid(SLEVE-hybrid for short)coordinates in numerical forecasting model is not limited in number.It is divided into the semi-analytical scheme and the finite differential scheme in terms of the various differential methods of the coordinate deformation variables.Having compared the dynamic equation and the long-time batch simulation results of the two schemes,the present study draws the following conclusions.The first-order finite difference accuracy of the coordinate deformation variables in the finite differential scheme is theoretically lower than that in the semi-analytical scheme.The larger the vertical gradient of the layer thickness is,the larger the relative errors of the finite differential scheme are.The long-time batch simulation test in the GRAPES model dynamic core demonstrates that the bias of the temperature and the geopotential height in the semianalytical scheme is smaller under the default layering,while the simulation difference of the two schemes is greatly reduced when the layering is more uniform.

Sensitivity of Precipitation in Aqua-Planet Experiments with an AGCM

The sensitivity of precipitation was studied by conducting control aqua-planet experiments(APEs) with a model to determine atmospheric general circulation.The model includes two versions: that with a spectral dynamical core(SAMIL) and that with a finite-volume dynamical core(FAMIL).Three factors were investigated including dynamical core,time-step length,and horizontal resolution.Numerical results show that the dynamical core significantly affects the structure of zonal averaged precipitation.FAMIL exhibited an equatorial precipitation belt with a single narrow peak,and SAMIL showed a broader belt with double peaks.Moreover,the time step of the model physics is shown to affect the zonal-averaged tropical convective precipitation ratio such that a longer time step leads to more production and consumption of convective available potential energy and convection initiated away from the equator,which corresponds to equatorial double peaks of precipitation.Further,precipitation is determined to be sensitive to horizontal resolution such that higher horizontal resolution allows for more small-scale kinetic energy to be resolved and leads to a broader probability distribution of low-level vertical velocity.This process results in heavier rainfall and convective precipitation extremes in the tropics.Abstract The sensitivity of precipitation was studied by conducting control aqua-planet experiments(APEs)with a model to determine atmospheric general circulation.The model includes two versions:that with a spectral dynamical core(SAMIL)and that with a finite-volume dynamical core(FAMIL).Three factors were investigated including dynamical core,time-step length,and horizontal resolution.Numerical results show that the dynamical core significantly affects the structure of zonal averaged precipitation.FAMIL exhibited an equatorial precipitation belt with a single narrow peak,and SAMIL showed a broader belt with double peaks.Moreover,the time step of the model physics is shown to affect the zonal-averaged tropical convective precipitation ratio such that a longer time step leads to more production and consumption of convective available potential energy and convection initiated away from the equator,which corresponds to equatorial double peaks of precipitation.Further,precipitation is determined to be sensitive to horizontal resolution such that higher horizontal resolution allows for more small-scale kinetic energy to be resolved and leads to a broader probability distribution of low-level vertical velocity.This process results in heavier rainfall and convective precipitation extremes in the tropics.

Foreword: East-West Asymmetry of the Inner Core and Earth Rotational Dynamics

In the last several years since 2004 an important new finding has been unveiled by combined efforts due to Japanese （Satoru Tanaka）, French （Renaud Deguen, Y Albousierre and Marc Monnereau）, American and Chinese geophysicists （Xiaodong Song and Vernon F Cormier） who employed from unambi- guous detailed seismological evidence and explained by clear theoretical and sound laboratory arguments drawn from fluid dynamics that there exists a strong East-West hemi-spherical asymmetry on the inner- outer core boundary,

Plasmaspheric trough evolution under different conditions of subauroral ion drift

The statistical characteristics of the subauroral ion drift (SAID) in the ionosphere and the plasmaspheric trough evolution under different conditions of SAID were investigated in this paper, based on 566 SAID events observed by Akebono, Astrid-2, DE-2, and Freja satellites. The relationships between the latitudinal location of SAID and the Kp, AL, and Dst indices for these events were also discussed. It was found that the SAID events happened mainly at invariant latitude (ILAT) of 60.4° and magnetic local time (MLT) of 21.6 MLT and that 92.4% of the events happened when the Kp index was below 5.0, indicating a medium geomagnetic activity. The latitudinal half-width of SAID varied from 0.5° to 3.0° with a typical half-width of 1.0°. The SAID would happen at low latitudes if the geomagnetic activity was high. The effects of SAID on equatorial outer plas- masphere trough evolutions were studied with the dynamic global core plasma model (DGCPM) driven by the statistical results of SAID signatures. It was noted that locations, shapes and density of troughs vary with ILAT, MLT, latitudinal width, cross polar cap potential and lifetime of SAID events. The evolution of a trough is determined by the extent of SAID electric field penetrating into plasmasphere and not all SAID events can result in trough formations.

A Brief Review of Software Tools for Pangenomics

Since the proposal for pangenomic study, there have been a dozen software tools actively in use for pangenomic analysis. By the end of 2014, Panseq and the pan-genomes analysis pipeline（PGAP） ranked as the top two most popular packages according to cumulative citations of peerreviewed scientific publications. The functions of the software packages and tools, albeit variable among them, include categorizing orthologous genes, calculating pangenomic profiles, integrating gene annotations, and constructing phylogenies. As epigenomic elements are being gradually revealed in prokaryotes, it is expected that pangenomic databases and toolkits have to be extended to handle information of detailed functional annotations for genes and non-protein-coding sequences including non-coding RNAs, insertion elements, and conserved structural elements. To develop better bioinformatic tools, user feedback and integration of novel features are both of essence.