Computational Tools
FLASH
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FLASH-is a modular, adaptive-mesh, parallel simulation code capable of handling general flow problems found in many physical, astrophysical and laboratory environments. In order to achieve this goal the code provides a set of algorithmic modules to compute equations of classic and relativistic hydrodynamics and magnetohydrodynamics that are coupled with general equations of state, material property models, various networks of atomic and nuclear reactions and self-gravity. The code is designed to allow users to configure problems, change algorithms and add new physics modules with minimal effort. It uses the PARAMESH library to manage a block-structured adaptive grid and the MPI library to achieve portability and scalability on a variety of different parallel computers.

GENE
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The gyrokinetic turbulence code GENE is a publicly available, massively parallel Vlasov solver which computes the fully electromagnetic gyrokinetic Vlasov and field equations. Modes of operation include radially global versus local flux tube; and initial value versus eigenvalue, where the latter can access all stable and unstable eigenvalues of the system. General magnetic geometry allows for experimental tokamak equilibria, 3D stellarator equilibria, standardized s-alpha and Miller, as well as slab computations for astrophysical applications. Also included is the GENE Diagnostics Tool, which supplies standard and complex analyses of the various output data from GENE through an easy-to-use graphical interface.

VPIC
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This fully kinetic particle-in-cell code VPIC solves the relativistic Vlasov-Maxwell system of equations using an explicit charge-conserving algorithm [Bowers et al., 2008]. The code has been carefully optimized to exploit petascale architectures [Bowers et al. 2009] and has demonstrated scaling up to 720k cores . In addition, the VPIC code features flexible treatment of boundary conditions and a Monte-Carlo treatment of Coulomb collisions [Daughton et al 09a,b]. It has been applied to a wide range of problems including laser-plasma interactions, magnetic reconnection in space and laboratory plasmas, particle acceleration and turbulence.

References:

Bowers, K.J., B. J. Albright, L. Yin, B. Bergen and T. J. T. Kwan, Ultrahigh performance three-dimensional electromagnetic relativistic kinetic plasma simulation, Phys. Plasmas 15, 055703, 2008

Bowers, K.J., B.J. Albright, L. Yin, W. Daughton, V. Roytershteyn, B. Bergen and T.J.T. Kwan, Advances in petascale kinetic simulations with VPIC and Roadrunner, Journal of Physics: Conference Series 180, 012055, 2009

Daughton, W., V. Roytershteyn, B. J. Albright, H. Karimabadi, L. Yin, and Kevin J. Bowers, Transition from collisional to kinetic regimes in large-scale reconnection layers, Phys. Rev. Lett. 103, 065004, 2009a

Daughton, V. Roytershteyn, B. J. Albright, H. Karimabadi, L. Yin, and Kevin J. Bowers, Influence of Coulomb collisions on the structure of reconnection layers, Phys. Plasmas 16, 072117, 2009b

LA-COMPASS
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The Los Alamos COMPutational Atrophysical Simulation Suites (LA-COMPASS) (Li & Li, Technical Reports, LANL, 2003, 2009, 2012) is a collection of several modern, high resolution, Godunov-type, hydrodynamics and magnetohydrodynamics codes that have been developed at LANL over the past decade, mostly supported by LANL's internal funding sources. All these codes are fully parallelized and optimized via hybrid MPI+OPENMP for large-scale parallel computers with multi-cores. This code has been successfully used to model astrophysical jets in both non-relativistic and relativistic lmits [Li et al. Astrophysical J. (2006); Guan et al. Astrophysical J. (2014)]. It has also been used to model the laboratory jet experiments at Caltech [X. Zhai et al. Astrophysical J. (2014)]. Additionally, it has the adaptive mesh refinement capability that allows better spatial resolution where capturing energy cascade to small scales is important, which also enable us to compare simulations with observations on multi-spatial and temporal scales.

PLUTO
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PLUTO is a freely-distributed software for the numerical solution of mixed hyperbolic/parabolic systems of partial differential equations (conservation laws) targeting high Mach number flows in astrophysical fluid dynamics. The code is designed with a modular and flexible structure whereby different numerical algorithms can be separately combined to solve systems of conservation laws using the finite volume or finite difference approach based on Godunov-type schemes.

NIMROD
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The NIMROD code solves the nonlinear equations of extended MHD as an initial problem. Problems can be solved in either two or three dimensions. In three dimensions the geometry is restricted to have at least one periodic coordinate, but is otherwise arbitrary. (In these cases the dynamics remains fully three dimensional.) The extended MHD model includes both ideal and resistive MHD, and two-fluid (Hall and diamagnetic) and FLR (ion gyro-viscosity) corrections to Ohm's law, along with anisotropic thermal conductivity. The spatial representation uses high (arbitrary) order finite elements for the non-periodic coordinates, and a dealised pseudo-spectral method (with FFTs) for the periodic coordinate. The time advance algorithm is an extension of that used in the DEBS code [D. D. Schnack, et al., J. Comp. Phys. 70, 330 (1987)]. In particular, it uses a more accurate semi-implicit operator, and introduces improved time centering for the two-fluid and gyro-viscous terms. Like DEBS, it is efficient and accurate for problems related to deviations from equilibrium in spatially and temporally stiff systems; it is not designed for problems that are dominated by advection (e.g., strong turbulence and shock waves). It has been applied to studies of several magnetic fusion laboratory concepts, and to some astrophysical problems. The basic algorithm is described in C. R. Sovinec, A. H. Glasser, T.A. Gianakon, D. C. Barnes, R. A. Nebel, S. E. Kruger, D. D. Schnack, S. J. Plimpton, A. Tarditi, M. S. Chu, and the NIMROD Team, J. Comp. Phys. 195, 355 (2004).

DEBS
The DEBS code solves the three-dimensional, compressible, non-linear, resistive MHD equations as an initial value problem in doubly periodic cylindrical geometry. It uses a staggered finite-difference grid in the radial coordinate, and de-aliased pseudo-spectral representations (with FFTs) for the periodic theta and z coordinates. The time advance incorporates a centered leapfrog method for wave-like terms, and a predictor-corrector method (with upwind radial differencing) for the advective terms. A semi-implicit algorithm provides unconditional numerical stability with respect to waves. The time step is only limited by advective stability and accuracy. The algorithm is efficient and accurate for problems related to deviations from equilibrium in spatially and temporally stiff systems; it is not designed for problems that are dominated by advection (e.g., strong turbulence and shock waves).

Options include:
a) ideal MHD;
b) fully three-dimensional temperature dependent resistivity;
b) simple viscosity;
c) anisotropic thermal conductivity;
d) independently rotating inner and outer boundaries (for studying rotational stability, for example);
e) mean flows;
f) imposed external fields (e.g., field errors);
g) multiple non-ideal (resistive) outer boundaries;
h) linear stability;
i) hydrodynamics (no magnetic field).

DEBS has been extensively used and benchmarked for over a decade by laboratory plasma research groups. The algorithm is documented in D. D. Schnack, Z. Mikic, D. S. Harned, E. J. Caramana, and D. C. Barnes, J. Comp. Phys. 70, 330 (1987). Significant applications of DEBS are described in the book S. Ortolani and D. D. Schnack, ''Magnetohydrodynamics of Plasma Relaxation'', World Scientific Press, Singapore, 1993.