The MultiDark Database: Release of the Bolshoi and MultiDark Cosmological Simulations

We present the online MultiDark Database -- a Virtual Observatory-oriented, relational database for hosting various cosmological simulations. The data is accessible via an SQL (Structured Query Language) query interface, which also allows users to directly pose scientific questions, as shown in a number of examples in this paper. Further examples for the usage of the database are given in its extensive online documentation (www.multidark.org). The database is based on the same technology as the Millennium Database, a fact that will greatly facilitate the usage of both suites of cosmological simulations. The first release of the MultiDark Database hosts two 8.6 billion particle cosmological N-body simulations: the Bolshoi (250/h Mpc simulation box, 1/h kpc resolution) and MultiDark Run1 simulation (MDR1, or BigBolshoi, 1000/h Mpc simulation box, 7/h kpc resolution). The extraction methods for halos/subhalos from the raw simulation data, and how this data is structured in the database are explained in this paper. With the first data release, users get full access to halo/subhalo catalogs, various profiles of the halos at redshifts z=0-15, and raw dark matter data for one time-step of the Bolshoi and four time-steps of the MultiDark simulation. Later releases will also include galaxy mock catalogs and additional merging trees for both simulations as well as new large volume simulations with high resolution. This project is further proof of the viability to store and present complex data using relational database technology. We encourage other simulators to publish their results in a similar manner.Comment: 28 pages, 9 figures, submitted to New Astronom

ProtoMD: A Prototyping Toolkit for Multiscale Molecular Dynamics

ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to calibrate parameters needed in traditional CG-MD methods. The toolkit integrates `GROMACS wrapper' to initiate MD simulations, and `MDAnalysis' to analyze and manipulate trajectory files. It facilitates experimentation with a spectrum of coarse-grained variables, prototyping rare events (such as chemical reactions), or simulating nanocharacterization experiments such as terahertz spectroscopy, AFM, nanopore, and time-of-flight mass spectroscopy. ProtoMD is written in python and is freely available under the GNU General Public License from github.com/CTCNano/proto_md

Effect of Multiphase Radiation on Coal Combustion in a Pulverized Coal jet Flame

The accurate modeling of coal combustion requires detailed radiative heat transfer models for both gaseous combustion products and solid coal particles. A multiphase Monte Carlo ray tracing (MCRT) radiation solver is developed in this work to simulate a laboratory-scale pulverized coal flame. The MCRT solver considers radiative interactions between coal particles and three major combustion products (CO2, H2O, and CO). A line-by-line spectral database for the gas phase and a size-dependent nongray correlation for the solid phase are employed to account for the nongray effects. The flame structure is significantly altered by considering nongray radiation and the lift-off height of the flame increases by approximately 35%, compared to the simulation without radiation. Radiation is also found to affect the evolution of coal particles considerably as it takes over as the dominant mode of heat transfer for medium-to-large coal particles downstream of the flame. To investigate the respective effects of spectral models for the gas and solid phases, a Planck-mean-based gray gas model and a size-independent gray particle model are applied in a frozen-field analysis of a steady-state snapshot of the flame. The gray gas approximation considerably underestimates the radiative source terms for both the gas phase and the solid phase. The gray coal approximation also leads to under-prediction of the particle emission and absorption. However, the level of under-prediction is not as significant as that resulting from the employment of the gray gas model. Finally, the effect of the spectral property of ash on radiation is also investigated and found to be insignificant for the present target flame

Plasma Edge Kinetic-MHD Modeling in Tokamaks Using Kepler Workflow for Code Coupling, Data Management and Visualization

A new predictive computer simulation tool targeting the development of the H-mode pedestal at the plasma edge in tokamaks and the triggering and dynamics of edge localized modes (ELMs) is presented in this report. This tool brings together, in a coordinated and effective manner, several first-principles physics simulation codes, stability analysis packages, and data processing and visualization tools. A Kepler workflow is used in order to carry out an edge plasma simulation that loosely couples the kinetic code, XGC0, with an ideal MHD linear stability analysis code, ELITE, and an extended MHD initial value code such as M3D or NIMROD. XGC0 includes the neoclassical ion-electron-neutral dynamics needed to simulate pedestal growth near the separatrix. The Kepler workflow processes the XGC0 simulation results into simple images that can be selected and displayed via the Dashboard, a monitoring tool implemented in AJAX allowing the scientist to track computational resources, examine running and archived jobs, and view key physics data, all within a standard Web browser. The XGC0 simulation is monitored for the conditions needed to trigger an ELM crash by periodically assessing the edge plasma pressure and current density profiles using the ELITE code. If an ELM crash is triggered, the Kepler workflow launches the M3D code on a moderate-size Opteron cluster to simulate the nonlinear ELM crash and to compute the relaxation of plasma profiles after the crash. This process is monitored through periodic outputs of plasma fluid quantities that are automatically visualized with AVS/Express and may be displayed on the Dashboard. Finally, the Kepler workflow archives all data outputs and processed images using HPSS, as well as provenance information about the software and hardware used to create the simulation. The complete process of preparing, executing and monitoring a coupled-code simulation of the edge pressure pedestal buildup and the ELM cycle using the Kepler scientific workflow system is described in this paper