2013 Theory Department Weekly Highlights
March 22~
COMPUTATIONAL PLASMA PHYSICS GROUP
S. Ethier and S. Jardin (along with C.S. Chang, PPPL Theory) participated in the NERSC Program Requirements Review "Large Scale Production Computing and Storage Requirements for Fusion Energy Sciences: Target 2017" in Rockville MD March 19-20. The review brought together the leaders in the FES computational physics community to discuss what computing capabilities would be needed in 2017 in order to conduct their research. More details regarding the review, including the presentations, can be found at:
http://www.nersc.gov/science/hpc-requirements-reviews/FES
B.H. Park, visiting researcher from KSTAR, made a presentation at the weekly CPPG group meeting on "Monte Carlo RF Kick Operator in NUBEAM". The presentation covered the theory and implementation of the RF Kick operator now in a production mode in TRANSP that allows calculation of the effect of the RF fields as calculated by TORIC on the fast ions as calculated by NUBEAM. The talk was broadcast by ReadyTalk to collaborators at ORNL and MIT.
March 15~
THEORY
On March 12, D. Stotler, B. Davis and G. Tchilinguirian ran the Robot Arm competition at the New Jersey Science Olympiad State Tournament. Each of the 20 high school teams participating in Robot Arm designed and built a stationary robot capable of picking up various objects and
placing them in one of four "goal" boxes.
On March 14, X. Li and L. Zakharov visited the Institute of Computational Mathematics and Scientific/Engineering Computing in Beijing. Li gave a talk on "Hiro Currents in Vertical Disruption Events (VDE) and their Simulations". Direct measurements of axisymmetrical Hiro currents during VDE on EAST in May 2012 made it clear that existing disruption simulation codes miss the important effect of Hiro currents and misrepresent the physics of even 2-D vertical instability. New numerical schemes, based on adaptive coordinates, aligned with the magnetic field, should be used to reproduce the Hiro currents. Li presented the steps for development of the VDE simulation code system, which includes the interfacing of the existing core equilibrium code ESC, new plasma edge equilibrium code PEC, and existing conducting shell simulation code SHL. The recently developed PEC is now interfaced with ESC as parallel processes. The details of numerical scheme of PEC, based on Hermite finite elements, were discussed. The special software, CodeBuilder (Cb), which maintains the documentation, communications and the source code consistent with each other, was used for the code development.
On March 14, L. Zakharov gave a talk on "Stationary Flowing Liquid Lithium (FLiLi) System for Tokamaks" to the Professor M.J. Ni group in the College of Physical Sciences, Graduate University of Chinese Academy of Sciences. He explained that unique property of liquid lithium to pump hydrogen isotopes is a key to the plasma regimes relevant to magnetic fusion. Utilization of this property should return magnetic fusion to its original idea of insulation of the high temperature plasma from the wall. The major challenge for using liquid lithium is related to its high chemical activity and interaction with residual outgassing from the wall in the tokamak devices. The talk described how the stationary FLiLi system addresses this technology challenge and make the use of liquid lithium practical and consistent with the safety requirements.
COMPUTATIONAL PLASMA PHYSICS GROUP
Dr. J. Lang, Computational Plasma Physics Group (PPPL), presented a CPPG seminar titled "XGC1 Performance on GPU-CPU Hybrid Architecture". XGC1 is a particle-in-cell code including gyrokinetic ions and drift kinetic electrons, which typically uses 5000 particles per cell and the total number of particles exceeds 20 billion. An electron sub-cycling method was developed to push electrons multiple steps for each ion push, and this takes up most of the computing time (>90%). These computationally heavy pushing subroutines are good fits to the recently developed General Purpose Graphics Processing Unit (GPGPU) technologies. The XGC1 code was recently ported to the GPU based TITAN supercomputer using CUDA FORTRAN. In her talk, she presented the CUDA FORTRAN implementation and optimization in XGC1 and demonstrated its performance improvement in the GPU-CPU hybrid architecture.
A new visualization interface has been developed for exploring three-dimensional data, f(x,y,z) or f(x,y,t). Written in Python and using the Tkinter package, the graphical user interface provides an intuitive approach for positioning and animating slice planes through the data and animating the view of the data volume. The rendering is computed in the VisIt software and animations are saved in QuickTime movie files. These techniques are useful for visualizing density data computed by Nubeam and the full wave solution in reflectometry simulations. The visualization interface was developed by M. Lotocki, M. Knyszek, and J. Miller under the direction of E. Feibush.
March 8~
THEORY
A. Hakim presented an invited talk "Discontinuous Galerkin Algorithms for (Gyro) Kinetic Simulations of Turbulence in Plasmas" at the SIAM Computational Science and Engineering 2013 conference in Boston, Massachusetts. Latest kinetic simulation results from underdevelopment code, Gkeyll, were presented. While at the conference, a collaborative effort to benchmark fluid aspects of the code against work done by Francois Waelbroeck and co-workers of the Institute of Fusion Studies in Texas (IFS) was begun. In this effort the transport of blobs in tokamak edge will be studied and compared to a code from IFS as well as BOUT++. Results from this work will be jointly presented at the Sherwood conference later this year.
March 1~
THEORY
A paper by L. Peterson and G. Hammett has just been accepted for publication in the SIAM Journal of Scientific Computing, on "Positivity Preservation and Advection Algorithms With Applications To Edge Plasma Turbulence" http://w3.pppl.gov/~hammett/gyrofluid/papers/2013/peterson_positivity.pdf. Peterson is a former PPPL graduate student and now a research physicist in ICF at LLNL.
E.H. Kim gave a seminar entitled “Role of Linear Mode Conversion Role of Linear Mode Conversion on Generation and Propagation of Space Plasma Waves” at Dartmouth College.
A series of innovative research on geometric theory and algorithms for kinetic system has been carried out recently by J. Squire, a third year Ph.D. student at Princeton University’s Graduate Program in Plasma Physics and PPPL’s Theory Department. A geometric integration algorithm of the Vlasov-Maxwell system with a variational particle-in-cell scheme has been developed and successfully tested [Phys. Plasmas 19, 084501 (2012)]. Using the formalism of discrete exterior calculus, the field solver, interpolation scheme, and particle advance algorithm are derived through minimization of a single discrete field theory action. As a consequence of ensuring that the action is invariant under discrete electromagnetic gauge transformations, the integrator exactly conserves Gauss’s law. This intimate link between the gauge properties of a discrete system with its numerical properties has also been discovered for the variational symplectic algorithm of gyrocenter dynamics [Phys. Plasmas 19, 052501 (2012)]. For explicit algorithms, an instability arises because the discrete symplectic structure does not reproduce the continuous structure in the limit of zero step-size. This numerical instability can be avoided by introducing ageneralized gauge transformation that places Lagrangian in an “antisymmetric discretization gauge”, in which the discrete symplectic structure has the correct form. By designing a model discrete Lagrangian, the algorithms can be made approximately gauge invariant as long as scalar and vector potentials are relatively smooth. A gauge invariant discrete Lagrangian is indispensable for particle-in-cell algorithms because it ensures current continuity and preservation of Gauss’s law. On the theoretical side, a new variational principle for the gyrokinetic system has been developed in the Eulerian frame and based on constrained variations of the phase space fluid velocity and particle distribution function [Phys. Plasmas 20, 022501 (2013)]. To explicitly derive the field theoretic Hamiltonian structure of the system, a Legendre transform with a modified Dirac theory of constraints is used to construct meaningful brackets from those obtained directly from Euler-Poincaré theory. Possible applications of these formulations include continuum geometric integration techniques, large-eddy simulation models, and Casimir type stability methods.
COMPUTATIONAL PLASMA PHYSICS GROUP
S. Ethier gave a mini-course entitled "Introduction to Parallel Debugging" as part of the series of mini-courses hosted by the Princeton Institute for Computational Science and Engineering (PICSciE). The lecture introduced the Princeton University participants to different approaches in tackling the task of debugging parallel applications, including the use of open source tools and advanced parallel debuggers, such as Totalview and DDT. The students and researchers attending the lecture were from a wide span of science departments, including chemistry, political sciences, geosciences, physics, and electrical engineering. This shows the major role that advanced parallel computing plays in scientific research across all the departments at the university.
February 22~
THEORY
Discovery of new modes of intense beam propagation in alternating-gradient accelerators. Highintensity charged particle beams have a wide range of applications ranging from basic scientific research in high energy and nuclear physics and ion-beam-driven high energy density matter to practical applications such as heavy ion fusion energy and medical accelerators. To accelerate and transport high-intensity beams, it is critical to understand in what modes the beams can propagate through an alternating-gradient focusing channel. Up to now, the only known class of exactly soluble modes of intense beam propagation including self-electric and self-magnetic field effects is the Kapchinskij-Vladimirskij (KV) distribution discovered in 1959. Recent research at Princeton University’s Plasma Physics Laboratory reveals that there exists a much larger class of self-consistent modes of intense beam propagation in alternating-gradient accelerator systems [Phys. Rev. Lett. 110, 064803 (2013)]. For each of the classical KV solutions, the beam propagation dynamics is specified by two free parameters, i.e., two emittances in the transverse plane. For the newly discovered class of beam modes, which include the classical KV solutions as a sub-class, each mode is specified by ten free parameters. Because the space domain of free parameters has been extended from two-dimensional to ten-dimensional, the new propagation modes that have been discovered enable a large increase in flexibility in the amount of beam control and steering capability. For example, the new modes allow the beam to tumble (rotate) in the transverse plane perpendicular to the propagation direction, which can be utilized as a beam smoothing technique for accelerator applications where smooth illumination is required, such as in the case of heavy ion fusion and medical accelerators. Theoretically, the new modes have been discovered by generalizing the one-dimensional Courant-Snyder theory for charged particles in an alternating-gradient focusing lattice and the associated one-dimensional envelope equation (also known as the Milne-Pinney equation) to a higher-dimensional, non-Abelian space. In particular, the one-dimensional Courant-Snyder invariant (also known as the Lewis invariant in quantum mechanics) is generalized to higher dimensions, and the new class of solutions of the nonlinear Vlasov-Maxwell equations is constructed after applying the Cholesky decomposition technique. [H. Qin and R. C. Davidson, Phys. Rev. Lett. 110, 064803 (2013)]
J. Johnson participated in the STORM kick-off meeting in Brussels, Belgium February 20-21. STORM is a FP7 project involving seven partners from EU and USA to understand turbulence, intermittency, and nonlinearity in Heliospheric plasmas.
W. Tang was invited to serve on the Advisory Board for the DOE-ASCR SciDAC-3 Institute: "Scalable Data Management, Analysis, and Visualization Institute" (SDAV) led by Arie Shoshani of LBNL and attended its initial meeting on February 20. He also participated in the associated SDAV All Hands Meeting February 20-22 in San Francisco, California.
COMPUTATIONAL PLASMA PHYSICS GROUP
A. Kritz, T. Rafiq, and A. Pankin from Lehigh University visited PPPL February 15 to discuss their experience with PTRANSP and to learn to use the new solver in TRANSP, PT_SOLVER. S. Ethier attended the annual NERSC Users Group meeting held in Oakland, California, on February 12-15. The first day was dedicated to the business meeting, during which the NERSC staff present the status and plans for the supercomputer center, and seek feedback from the user community on how to best support and enhance scientific discovery through high performance computation and storage. The second day took place at LBNL and focused on trends in HPC, as well as scientific and HPC accomplishments by NERSC users. The final two days were dedicated to training, for both beginners and experienced users, with a focus on NERSC's new Cray XC30 supercomputer, Edison. Documents for the presentations can be found at https://www.nersc.gov/users/NUG/annual-meetings/2013/ .
Fedruary 15~
THEORY
The Theory Department Plasma Material Interaction (PMI) Working Group met on February 8 to discuss the prospects for using small plasma experiments to advance the development of PMI theory and models. Presentations on pertinent experimental devices at PPPL and elsewhere were made by Y. Raitses, I. Kaganovich, and T. Abrams.
Visiting research scholar Jinxing Zheng who is being hosted by J. Breslau continued his research on stellarator coil design with a study of the relationship between the radius of curvature and the maximum field produced by the coils. He has also practiced exercising the COILOPT code by re-deriving a set of optimized coils for the reference plasma configuration of the NCSX device. On February 15, J. Breslau presented an invited talk on "Spline Representations for More Efficient Stellarator Coil Design" at the Workshop on Exploratory Topics in Plasma and Fusion Research (EPR2013) in Forth Worth. The talk described a new software tool developed by Dr. Breslau that computes optimized stellarator coil shapes modeled by spline curves that accurately produce a target plasma configuration while being much easier to construct and maintain than those computed using previous techniques. H. Mynick also attended the Workshop and presented a paper, "Progress in Turbulent Optimization of Toroidal Configurations".
COMPUTATIONAL PLASMA PHYSICS GROUP
During the week of February 4-8, Irena Johnson organized an on-site Python Programming Training, which included nine scientists, eight from the Theory Department. Python, is a popular modern object oriented computing language that has the advantage of being open source, easily readable, efficient, portable and scalable to large projects. Those who attended acquired valuable skills that will facilitate improved code development for data management and visualization. On February 13, the entire PPPL TRANSP group (with R. Budny and S. Kaye) held a two-hour video conference call with the JET TRANSP team including I. Voisekhovitch, J. Conboy, and M. Romanelli. The JET side discussed their usage patterns for TRANSP and some JET-specific modifications that they have made. The PPPL team discussed the progress during the last year and future plans in the areas of (1) the new PT_SOLVER, (2) new free-boundary equilibrium capabilities, (3) new NUBEAM capabilities including NUBEAM/RF coupling, and (4) new parallelization options. Plans were made regarding incorporating the JET modifications in to the PPPL code version, and working with JET physicists to utilize some of the newly installed capabilities as they are released.
February 8~
THEORY
Recently, a series of innovative research on the theoretical foundation of modern gyrokinetic theory has been carried out by J. Burby, a third year Ph.D. student at Princeton University’s Graduate Program in Plasma Physics and PPPL’s Theory Department. Using the methods and techniques of differential geometry, Burby proved that in general the gyrocenter phase space coordinates do not exist globally [Phys. Plasmas 19, 052106 (2012)]. However, this does not imply that gyrokinetic theory is invalid in general. He showed that the fundamental justification of the gyrokinetic theory is due to the existence of asymptotic gyro-symmetry, which is a global and coordinate independent fact when the space-time scalelength of the magnetic field is larger than that of the gyromotion of a charged particle. To a more practical side, the application of the methods of differential geometry reveals that the toroidal precession of a charged particle in a toroidal confinement device is a geometric phase [Phys. Plasmas 20, 012511 (2013)], similar to the well-known Berry’s phase in quantum system. Such a revelation enables a general coordinate independent expression of the toroidal precession in tokamaks and quasisymmetric stellarators alike, which can be implemented as an accurate and efficient algorithm for numerical simulations.
On February 5, Dr. Seung-Hoe Ku gave a theory seminar entitled "Introduction to XGC." The presentation focused on basic properties and capabilities of the XGC ( X-point Gyrokinetic Code) code such as the model equations, geometry, collision operators, logical wall-sheath, and the full/delta/total-f numerical techniques. Physical results of global simulations of ITG turbulence, neutral atomic physics, and intrinsic rotation were also discussed. Some of the mentioned future work included simulations of electrostatic turbulence in L-mode, and L-H transition and comparisons with experiments; and enhancement of electromagnetic capability to include low-m/n tearing modes.
February 1~
COMPUTATIONAL PLASMA PHYSICS GROUP
TRANSP off-site collaborators presently authenticate with PKI FusionGrid credentials issued by the ESnet Certificate Authority (CA), a parallel service to the more widely used DOEGrids CA, to submit jobs to the PPPL computer system. Both DOEGrids CA and ESnet CA will cease providing PKI services on March 23, and are transitioning services to a new CA managed by the Open Science Grid (OSG). However, OSG will not support storing credentials on a "MyProxy" server since this does not comply with IGTF policies. Now Certificates will be stored on the user's computer. All TRANSP collaborators have been notified of the changes and instructions and tools have been provided on the TRANSP Website. The TRANSP Production service is now managing and accepting both types of FusionGrid credentials (user-managed and MyProxy-managed) until such time as the old ones gradually expire. Several groups of users have already made the change and have not reported any undue difficulties. Any questions regarding the transition should be referred to Tina Ludescher at ludescher@pppl.gov.
January 25~
THEORY
A paper co-authored by A. Hakim on non-linear simulations of RF propagation has appeared in Physics of Plasmas. In this, both PIC and non-neutral, multi-fluid models are used to study nonlinear wave coupling of IBWs in the edge of a tokamak plasma, leading to a characterization of parametric decay instabilities, a serious parasitic loss mechanism in RF heating systems. The paper is now online at : http://pop.aip.org/resource/1/phpaen/v20/i1/p012116_s1
On January 24, S. Klasky gave a theory seminar entitled "Accelerating Scientific Knowledge Discovery in DOE science." The presentation focused on the effect of data I/O management on code performance and scalability. Efforts in the development of ADIOS, the open source data management framework whose purpose is to increase I/O efficiency of massively parallel codes, while being easy to implement, were also discussed.
January 18~
THEORY
A. Bhattacharjee has been invited to serve on the Standing Committee on Solar and Space Physics (CSSP) of the National Academies for a term effective immediately and ending June 2014.
Recent PPPL kinetic studies of a collisionless plasma slab bounded by dielectric walls with strong secondary electron emission (SEE) predicted a strongly anisotropic, non-monotonic electron velocity distribution function (EVDF), which is depleted in the loss cone. This EVDF reduces the electron wall losses compared to Maxwellian plasmas. Sheath oscillations occur due to coupling of the sheath potential and non-Maxwellian electron energy distribution function when there are intense electron beams emitted from the walls. In a bounded plasma where the electrons impacting the walls produce more than one secondary electron on average no classical Debye sheath or space-charge limited sheath exists. Ions are not drawn to the walls and electrons are not repelled. Hence, the plasma electrons travel unobstructed to the walls, producing extreme particle and energy fluxes. Strong dependence of the wall potential on SEE allows for active control of plasma properties by judicious choice of the wall material. These results are published by M. D. Campanell, A.V. Khrabrov and I. D. Kaganovich, in papers Phys. Rev. Lett. 108,
255001 (2012),Phys. Rev. Lett. 108, 235001 (2012), and Phys. Plasmas 19, 123513 (2012).
January 11~
THEORY
On January 11, Dr. Will Fox gave a theory seminar entitled "Magnetic Reconnection and Laboratory Astrophysics Experiments with Laser-produced Plasmas." Magnetic reconnection experiments using magnetized high-energy-density plasma bubbles produced by ablating a target with a high intensity lasers were described along with the underlying theory. Results obtained from recent experiments on the OMEGA EP facility were discussed and compared with 2D collisional PIC (particle-in-cell) simulations.
A. Bhattacharjee gave an invited talk on the "Physics of Explosive Events Within the Heliosphere" in the Conference on Space Weather at the Annual Meeting of the American Meteorological Society, Austin, Texas, January 6-10.
Dec. 21- Jan. 4~
THEORY
Y.-M. Huang of the University of New Hampshire (UNH) and A. Bhattacharjee of PPPL have published a new study on the "Distribution of Plasmoids in High-Lundquist-Number Reconnection" in Physical Review Letters on December 28, (PRL, 265002, 2012). Over the last three years or so, there has been much interest in the discovery that the secondary instability of thin current sheets in large systems, above a critical value of the Lundquist number, produces a new regime of fast reconnection in which the reconnection rate, within the framework of resistive MHD, becomes independent on the Lundquist number (to a first approximation). By means of an analytic phenomenological model and direct numerical simulations, Huang and Bhattacharjee have obtained a distribution function of plasmoids in a thin current sheet in 2D as a function of the magnetic flux. This distribution function shows a power-law behavior that differs from other recent theoretical predictions. The predictions of the model are presently being tested by laboratory experiments as well as observations of post-flare heliospheric current sheets by graduate student Lijia Guo of UNH, who is presently at Princeton University as a visiting student. The plasmoid instability and its consequences for fast reconnection was also the subject of an invited paper at the 2013 DPP-APS meeting by Huang, an account of which has been submitted recently to the Physics of Plasmas ( http://arxiv.org/abs/1301.0331).
On January 3, Dr. Robert Leamon gave a theory seminar entitled "On the Modulation of the Solar Activity Cycles." The talk addressed the origin of the 11-year sunspot cycle by tying it to the temporally overlapping activity bands of the 22-year magnetic activity cycle. Importance of the temporal asymmetry of solar activity between the Northern and Southern hemispheres was emphasized. The decadal variation in flux distribution on the solar disk which impacts plasma energetics on small scale and on the large scale, such as cosmic ray flux, was attributed to the
lead/lag between the two hemispheres (and their phasing).
COMPUTATIONAL PLASMA PHYSICS GROUP
The National Energy Research Supercomputer Center (NERSC) announced its 2013 allocation awards in late December 2012. PPPL researchers received a total of 68,120,000 CPU hours in 8 different awards. The projects, PIs, and awards were as follows: Center for Integrated Computation and Analysis of Reconnection and Turbulence, A. Bhattacharjee (4,000k); Nonlinear Delta-f Particle Simulation of Collective Effects for Heavy Ion Fusion Drivers and High Intensity Particle Accelerators, R. Davidson (50k); Simulations of Field-Reversed Configuration and Other Compact Tori Plasmas, R. Davidson (70k); Center for Edge Physics Simulation, C. S. Chang (25,000k); Center for Simulation of Energetic Particles, G. Fu (6,000k); 3D Extended MHD simulation of fusion plasmas, S. Jardin (10,000k); Turbulent Transport and Multiscale Gyrokinetic Simulation, W. Lee (15,000k); Experimental Tests of Gyrokinetic Simulations of Microturbulence, D. Mikkelsen (8,000k).
