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[LCRC Accounts] Yearly Allocation Request from HEIGHTS-3D
by accounts＠lcrc.anl.gov 16 Sep '10

16 Sep '10

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Tatyana Sizyuk Project Name: HEIGHTS-3D Division: MCS Project title: HEIGHTS-3D modeling of plasma material interaction during edge-localized modes (ELM) and disruptions in fusion devices. Advanced 2D and 3D Laser-Produced Plasma Processes modeling for EUV Lithography and other advanced plasma applications. Associated funding: SEMATECH Other Systems: BG/P Science: HEIGHTS package is being developed as a comprehensive tool for simulation and optimization of various interaction processes during intense power deposition of various energy sources such as plasma, laser, and particle beams incident on target materials. The package has several integrated models with detailed description of main processes: energy and particles deposition, material surface and bulk thermal response and melt-layer formation and splashing, vapor and plasma magnetohydrodynamics, nano-scale surface evolution, photon line and continuum radiation transport, atomic and molecular processes of surface materials in the plasma, thermal hydraulic analysis of coolant channels inside the bulk components. HEIGHTS team areas of current analysis and developments include research for the development of magnetic fusion energy (MFE) and inertial fusion energy (IFE) reactors, discharge produced plasma (DPP) and laser produces plasma (LPP) applications at the wide range of energy intensities (e.g., 108 -1013 W/cm2 for LPP devices), different device geometries (e.g., several reactor designs for MFE, IFE, and lithography) and large variation in both time and space scales (nanoseconds to seconds in LPP and MFE respectively; nanometers in plasma facing materials and centimeters/meters in reactor walls and cavity chamber). HEIGHTS package is being updated on continuing basis with frequent add-on of new modules, improving of developed physical models and mathematics, and revising of parallel computing methods. Project description: The following numerical simulations will be carried out in FY2011: 1. We will implement, test, and evaluate parallel efficiency of separate modules and whole package updated to implement Adaptive Mesh Refinement (AMR) technique in the environment of LCRC (Fusion) cluster. 2. Utilizing the updated modules for AMR techniques, HEIGHTS team will prolong simulation of plasma/wall interactions at the steady state and transient conditions in MFE reactors. Modeling results will be compared with previously obtained results and will be benchmarked with recent experimental measurements. 3. We will continue to study the physics of colliding plasmas phenomena using HEIGHTS 3D LPP package. This is a very exciting and relatively unexplored area. We are planning to model various target geometries and target materials for creating colliding plasmas, including different target design and multiple laser beams. Also orthogonally expanding plasmas produced using 2 laser beams and 2 targets will be simulated. Great physics can be discovered in this fascinating area. Calculation time for above-listed numerical simulation experiments varies and depends on many parameters such as: a) geometrical size of the problem; b) required grid refinement details; c) real time of the simulated process; d) required physical dimension of the analyzed system. We would like to request 300,000 allocation hours to conduct various optimizations, benchmarking, and parametric studies of the HEIGHTS 3D packages for several projects during FY2011. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 300000 Justification: Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from EBAC
by accounts＠lcrc.anl.gov 16 Sep '10

16 Sep '10

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Tsung-Shung Lee Project Name: EBAC Division: PHY Project title: Analysis of Nucleon Resonances Associated funding: U.S. Department of Energy, Office of Nuclear Physics Division, under Contract DE-AC02-06CH11357 Other Systems: workstation theory9 of PHY , and NERSC Science: The objective of this project is to extract nucleon resonance information from world data of meson production reactions for advancing our understanding of the origin of hadron matter within Quantum Chromodynamics (QCD), the fundamental theory of strong interactions Project description: The objectives of Analysis of Nucleon Resonances (N*) are twofold. The first is to perform dynamical coupled-channels analysis of meson production reaction data for extracting the parameters of nucleon resonances. The second objective is to develop theoretical interpretations of the determined resonance parameters in terms of hadron structure calculations such as the constituent quark model and Lattice QCD calculations. This project will provide information for understanding the non-perturbative aspects of QCD. In particular, the extracted N-N* form factors will reveal the dynamical origins of quark confinement and the meson cloud associated with the spontaneously breaking of chiral symmetry. This project is needed to reach milestones HP3 and HP7 by 2012 set in DOE's long-range plan of 2010. Project URL: http://ebac-theory.jlab.org Current FY Hours Used: undetermined amount New FY Requested allocation: 350000 Justification: The analysis will be carried out by solving a large set of coupled integral equation in momentum-space an performing chi-squared fits , with about 200 parameters, to very extensive world data of pion-nucleon scattering and electromagnetic meson production reactions. The calculation at each energy and each set of parameters involve an inversion of an about 1000*1000 complex matrix. This has to be repeated The calculation at each energy and each set of parameters involve an inversion of an about 1000*1000 complex matrix. This has to be repeated many times in searching the best-fit parameters in chi-squared fit to very extensive data (about 60,000 data points) using MINUIT Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from pflotran
by accounts＠lcrc.anl.gov 16 Sep '10

16 Sep '10

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Boyana Norris Project Name: pflotran Division: MCS Project title: PFLOTRAN Performance Analysis and Tuning Associated funding: Performance Engineering Research Institute (PERI) SciDAC2 Project Other Systems: Jazz, Surveyor, Intrepid Science: performance analysis and automated tuning Project description: PFLOTRAN is a massively parallel code developed at LANL for the accurate prediction of multiscale subsurface processes. PFLOTRAN has many applications and guides safer industrial techniques; for example, it can help geoscientists determine how carbon dioxide flows through aquifers and deep geologic formations during carbon-capture and storage. PFLOTRAN's performance has been studied extensively on Intrepid and Jaguar (Cray XT/5), but no performance studies on Intel-based clusters have been performed. The efficiency of the code is a small fraction of the peak on both BG/P and Cray XT/5. In the first year of this project, we focused mainly on analyzing and improving the performance of the sequential portions of key computational kernels (matrix-vector product, triangular linear solution, and some of the chemistry computations), which required many single-core runs of these kernels. During the next year, we plan to study and possibly improve the scalability of the Jacobian computation and the linear system solution. We'll also investigate approaches for managing the load imbalance between the flow and transport stages. This will require a number of parallel scaling runs. We will use input decks that can run on different ranges of cores, from one node to the whole machine. We'll target runtimes of less than an hour in most cases (by changing the number of time evolution steps). Project URL: http://www.peri-scidac.org/perci/ Current FY Hours Used: undetermined amount New FY Requested allocation: 200000 Justification: Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 16 Sep '10

16 Sep '10

Hello, A change in allocation has been requested: Requester: norris (Boyana Norris) Project: pflotran Title: PFLOTRAN Performance Analysis and Tuning Description: PFLOTRAN is a massively parallel code developed at LANL for the accurate prediction of multiscale subsurface processes. PFLOTRAN has many applications and guides safer industrial techniques; for example, it can help geoscientists determine how carbon dioxide flows through aquifers and deep geologic formations during carbon-capture and storage. PFLOTRAN's performance has been studied extensively on Intrepid and Jaguar (Cray XT/5), but no performance studies on Intel-based clusters have been performed. The efficiency of the code is a small fraction of the peak on both BG/P and Cray XT/5. In addition to analyzing the parallel performance of two test cases, we will investigate applying autotuning tools we are developing as part of PERI to improve the single-node performance, as well as try to reduce the impact of global synchronizations. Current: undetermined amount Justification: Each simulation requires approximately 2 TB of memory and takes 10 minutes to 30 minutes on a Cray XT/5 on up to 16K cores. Thus, the largest-scale runs will require approximately 1280 processor-hours. Some autotuning approaches require the empirical exploration of a potentially large parameter space, so hundreds or thousands of runs may be required. While some of those runs would involve smaller isolated benchmarks, we will have to perform a large number of full simulation runs. We believe that we'd require between 500 and 1000 runs, taking varying times, with worst case of approximately 1280 processor-hours. Therefore we request 640,000 processor/hours for the year. Requested: 110000 A specific reason has been given: In the first year of this project, I focused mainly on analyzing and improving the performance of the sequential portions of key computational kernels (matrix-vector product, triangular linear solution, and some of the chemistry computations). During the next year, I plan to look at the lack of scalability of some of the linear solvers and the parallel imbalance between the flow and transport stages. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 16 Sep '10

16 Sep '10

Hello, A change in allocation has been requested: Requester: norris (Boyana Norris) Project: pflotran Title: PFLOTRAN Performance Analysis and Tuning Description: PFLOTRAN is a massively parallel code developed at LANL for the accurate prediction of multiscale subsurface processes. PFLOTRAN has many applications and guides safer industrial techniques; for example, it can help geoscientists determine how carbon dioxide flows through aquifers and deep geologic formations during carbon-capture and storage. PFLOTRAN's performance has been studied extensively on Intrepid and Jaguar (Cray XT/5), but no performance studies on Intel-based clusters have been performed. The efficiency of the code is a small fraction of the peak on both BG/P and Cray XT/5. In addition to analyzing the parallel performance of two test cases, we will investigate applying autotuning tools we are developing as part of PERI to improve the single-node performance, as well as try to reduce the impact of global synchronizations. Current: undetermined amount Justification: Each simulation requires approximately 2 TB of memory and takes 10 minutes to 30 minutes on a Cray XT/5 on up to 16K cores. Thus, the largest-scale runs will require approximately 1280 processor-hours. Some autotuning approaches require the empirical exploration of a potentially large parameter space, so hundreds or thousands of runs may be required. While some of those runs would involve smaller isolated benchmarks, we will have to perform a large number of full simulation runs. We believe that we'd require between 500 and 1000 runs, taking varying times, with worst case of approximately 1280 processor-hours. Therefore we request 640,000 processor/hours for the year. Requested: 110000 A specific reason has been given: In the first year of this project, I focused mainly on analyzing and improving the performance of the sequential portions of key computational kernels (matrix-vector product, triangular linear solution, and some of the chemistry computations). During the next year, I plan to look at the lack of scalability of some of the linear solvers and the parallel imbalance between the flow and transport stages. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from DFT_corrosion
by accounts＠lcrc.anl.gov 16 Sep '10

16 Sep '10

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Jeffrey Greeley Project Name: DFT_corrosion Division: CNM Project title: First principles studies of lithiation and corrosion of metal and oxide surfaces Associated funding: DOE-BES Other Systems: I have access to the CNM's cluster, carbon, as a staff member. Research staff nominally split about 30% of carbon's resources, but given the recent, rapid increases in the number of staff and postdocs, this resource has become substantially strained. Science: This project uses periodic, planewave Density Functional Theory (DFT) calculations, combined with atomistic thermodynamic models, to probe both the lithiation and corrosion of metal and oxide surfaces. Lithiation and corrosion are distinct electrochemical processes (relevant to the operation of lithium ion batteries and to the durability of fuel cell electrodes, respectively), but they are also simultaneously relevant to the surface chemistry of lithium air batteries, which operate by growing, and subsequently decomposing, lithium oxide or peroxide structures on catalytic metal/oxide substrates. The primary goal of this project will be to perform detailed studies of the surface chemistry and physics of the latter (Li air battery) systems. An important secondary goal, however, will be to extend earlier work on the competition between oxidation and dissolution of platinum surfaces to alloy surfaces. These calculations, in turn, are relevant to the stability of met allic electrodes under both Li air battery and fuel cell operating conditions. Project description: For sustainable future energy needs, truly transformational technologies are needed to power both small-scale portable electronic devices, as well as medium-large scale transportation devices. While battery technology has seen improvement in the last 2-3 decades with the advent of the Li-ion battery for portable electronics, significant enhancements in battery energy density are still needed for transportation and other applications. An exciting alternative to this technology, particularly for large systems, is the Li-air battery, which may offer energy storage densities of comparable levels to that of gasoline. However, significant technical challenges relating to battery power and efficiency, battery recharge ability, and electrolyte stability must be addressed before Li-air batteries can truly compete with existing technologies. A particular catalytic challenge associated with Li-air systems concerns the performance of the Li2O2/Li2O cathode. At this electrode, oxygen combines with lithium ions and electrons migrating from the anode to produce either lithium peroxide or lithium oxide. While the formation of these oxidic species (termed “discharge” of the battery) is rapid and proceeds at voltages close to the appropriate equilibrium potential, the reverse process (decomposition of the oxidic species, or “charging” of the battery) suffers from significant kinetic inhibitions and requires large overpotentials. Most catalytic studies of Li-air focus, therefore, on finding catalytic electrode materials that facilitate oxide/peroxide decomposition and avoid fouling of the cathode due to excessive solid oxide/peroxide accumulation. In spite of a decade of research in this area, however, the fundamental atomic-scale mechanisms of Li-O2 reactions with catalytic species is poorly understood, and there is an urgent need to perform careful studies on model catalytic systems to elucidate the basic chemistry and physi cs that governs these systems. We intend to use periodic DFT calculations to study the surface catalytic chemistry of Li air batteries on transition metal surfaces. The periodic DFT calculations, in conjunction with physical-chemical descriptor models, to characterize the reaction thermodynamics and kinetics of Lix-Oy based species with single-component and binary alloys of transition metal (TM) surfaces. Binding energies and reaction barriers for a variety of intermediate and product species will be determined on the TM surfaces; these species will include Li, O, LiO, O2, LiO2, Li2O2, Li2O, Li3O2, Li2O4, Li3O4, Li4O4, and Li2. We will perform such calculations on both the low index, defect-free fcc(111) or hcp(0001) surfaces of Co, Ru, Os, Cu, Ni, Ag, Pd, Rh, Ir, Pt, and Au. Additionally, we will augment such calculations with calculations on stepped fcc(211) surfaces; these calculations will allow us to understand the effects on reaction energies of representative structures (primarily facets and edg es) of metallic nanoparticles. The DFT calculations, performed at the vacuum-solid interface, will be supplemented with simple thermodynamic corrections to estimate reaction free energy diagrams as a function of the electrode potential. The results will be used to propose rate-limiting steps and selective product distributions on the various surfaces, together with screening criteria for improved materials for control of Lix-Oy species production and decomposition. Finally, we will take calculations based on the resulting “best materials” identified in our analysis further; in this further work, we will extend our calculations to identify the thermodynamic properties of Lix-Oy-TM cluster, film, island, and bulk-like nanoparticle growth on the TM surfaces. Such work will be invaluable in identifying key mechanistic phenomena on model catalysts for lithium-air batteries. An important secondary goal of the proposed work will involve studies of oxidation and dissolution of metal alloy surfaces. This work, which is relevant to the long-term durability of both Li air and fuel cell electrodes under harsh electrochemical operating conditions, is an extension of earlier studies on the competition between oxidation and dissolution of platinum surfaces. The first step will be to determine the binding energies of atomic O and OH, as a function of coverage, on a single-crystal kinked metal surfaces. We will focus on metal overlayers (wherein a single layer of an alloying metal is deposited on a bulk metallic substrate) and will consider primarily fcc(763) kinks. Numerous configurations will be considered for each adsorbate coverage, and the lowest-energy configurations at each coverage will be input into an atomistic thermodynamic formalism (essentially a simplified Grand Canonical Monte Carlo technique) to determine the O coverage as a function of e lectrode potential. These results will then be compared to tabulated values of the equilibrium dissolution potential of the relevant overlayer metals as a function of the metal ion concentration in the surrounding solution; with this analysis, it will be possible to estimate the approximate coverages of surface O and OH that are present at the thermodynmically reversible potential on these surfaces, thereby providing important insights into the interplay between surface oxidation and platinum loss by dissolution. By studying how O and OH decorate the step edges at these higher potentials, it will also be possible to obtain semi-quantitative insight into passivation and place exchange mechanisms that may be operative in various potential ranges. These computational studies will be performed in collaboration with Nenad Markovic (ANL/MSD). The computational requirements of the proposed research will be substantial. Test calculations with the Dacapo code have indicated that the p(3x3) unit cells to be used for the Li air studies require approximately 5 hours per total geometric optimization on 24 cores on computer clusters similar to Fusion. We estimate that a total of 10 transition metals, with about 250 total optimizations required per metal, will be considered, giving a total of 300,000 requested core hours. The explicitly corrosion component of the project will also be substantial, likely requiring about 200,000 core hours. We are therefore requesting 500,000 core hours for the proposed project. Dacapo and VASP have been running successfully on Fusion, and GPAW has been recently installed on the system by John Low. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 500000 Justification: The computational requirements of the proposed research will be substantial. Test calculations with the Dacapo code have indicated that the p(3x3) unit cells to be used for the Li air studies require approximately 5 hours per total geometric optimization on 24 cores on computer clusters similar to Fusion. We estimate that a total of 10 transition metals, with about 250 total optimizations required per metal, will be considered, giving a total of 300,000 requested core hours. The explicitly corrosion component of the project will also be substantial, likely requiring about 200,000 core hours. We are therefore requesting 500,000 core hours for the proposed project. Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Request: IMPROPER11
by accounts＠lcrc.anl.gov 15 Sep '10

15 Sep '10

Hello, A new project on the LCRC cluster has been requested. Please forward the information on to the LCRC Allocation sub-committee. Applicant's name: James Rondinelli Applicant's institution: ANL Applicant's division: X-Ray Science Division (XSD) Project Name: IMPROPER11 Project title: Chemical-activated hidden lattice couplings in ultra short perovskite superlattices Associated funding: None; this research project is part of a collaboration with Prof. Craig Fennie at Cornell University (Ithaca, NY) Other Systems: The PI has access to the Center for Nanoscale Materials (CNM) computational facilities. A 100,000 hour allocation for the current year at that facility is dedicated to the investigation of isosymmetric phase transitions in perovskite oxides from first-principles. Science: Complex oxide heteroepitaxy of ultra-short period superlattices provides an elegant route to access latent correlated functionalities derived from artificial elastic, structural, and electronic boundary conditions that are restricted from bulk equilibrium phase diagrams. Such artificially structured ABO3 perovskite materials are amenable to chemical and electrostatic doping for tuning exotic phase diagrams and are suggested to be digital analogues of more complex, and often incompletely, ordered quaternary, oxides. A crucial aspect often overlooked in digitally ordered ultra-short superlattices is that the superlattice geometry and cation ordering leads to a reduction in the atomic site symmetry of the functional atoms. The consequences of such changes in point symmetry are naturally described within a Ginzburg-Landau free energy functional framework. This methodology allows one to identify new symmetry allowed free energy invariants activated by the additional boundary conditions. Motivated by the recent observation of a potentially useful and emergent trilinear coupling in ferroelectric/paraelectric perovskite superlattices, this research project aims to establish a generic framework and set of design rules that guide the choice of materials which show “improper" transitions among three active modes [1]. Manipulating trilinear order parameter couplings or mutually coupled phase transitions in perovskite oxide superlattices are a practical route to achieve control of the non-polar BO6 corner-connected octahedral blocks—which are intimately linked to the magnetic superexchange interactions, orbital bandwidths, and critical superconducting temperatures—through alternative external fields [2,3]. Our goals are to: 1. Identify and understand the trilinear lattice couplings available in ultra-short superlattices from first-principles calculations; 2. Use Ginzburg-Landau theory to identify the symmetry allowed order parameter invariants; 3. Perform first principles calculations (with this allocation) to identify the microscopic mechanism responsible for the activated lattice coupling; and 4. Explore the strength of this coupling with these calculations for a series of material systems; our aim is to suggest which artificially layered heterostructure is the most promising to explore experimentally. This computational research project offers to shed light on an unexplored route that directly activates structurally-driven electronic phase transitions forbidden in the bulk phase diagram of the constituent materials because of symmetry restrictions that prohibit orbital mixing. The work stands to have substantial impact in the field of rational materials design. References: [1] E. Bousquet, M. Dawber, N. Stucki, C. Lichtensteiger, P. Hermet, S. Gariglio, J.-M. Triscone, and P. Ghosez, Nature 452, 732 (2008). [2] M. Rini, R. Tobey, N. Dean, J. Itatani, Y. Tomioka, Y. Tokura, R.W. Schoenlein, and A. Cavalleri, Nature 449, 72 (2007) [3] J.M. Rondinelli and N.A. Spaldin, Phys. Rev. B. 81, 085109 (2010) Project description: All of our investigations employ plane-wave density-functional theory (DFT) to explore and characterize the allowed free energy invariants from first principles [1,2] with recent developments in materials theory understanding of structural phase transitions in perovskite oxides. This investigation combines calculations of materials exhibiting different order parameters (electric polarization, non-polar structural distortions, and magnetization) and their subsequent response to different perturbations on those order parameters (strain, magnetic field, and electric field) to exploit emergent functionalities in artificially structured oxides. Our ultimate goal is to combine multiple functionalities for the design of practical devices based on these couplings. Ab initio theory plays a central role in the research effort aimed at the rational design of materials with multiple functionalities. In particular, first-principles (parameter-free) calculations are excellent compliments to experimental discovery efforts because of their ability to study ideal, defect-free films; additionally, unlike experimental studies, our calculations can treat bi-axial strain present in heteroepitaxial films as a continuous variable since we do not rely on the availability of suitable and chemically compatible substrates. Furthermore, with first-principles calculations we can, with relative ease, decouple the effects of strain from those of interface chemistry, to isolate the microscopic origin for changes in functionality. We plan to employ two codes for our investigations: (1) the commercially available VASP code [3-5], which tends to be most useful for studying materials with complex magnetic structures and their responses, due to the ability to simultaneously use spin-orbit coupling, non-collinear magnetism and LDA+U, and (2) the open-source Abinit package [6,7], which we use primarily to characterize structures, ferroelectricity and responses of materials within a perturbation theory framework. Both codes are based on the plane-wave formalism with PAW potentials for efficient separation of the core and valence electrons. Code Scalability and Efficiency: The scaling of these codes on clusters at national computation facilities is well documented. The PI has not used the LCRC (FUSION) facility before, but all approximate timings and computation hours used to estimate the current allocation size are from benchmarks obtained with a highly-optimized VASP code at the National Center for Supercomputing Applications (NCSA) on the COBALT machine. Similar optimization should be readily achieved on the FUSION machine. Benchmarks for the efficiency and parallelization of the VASP code for the CARBON machine at the CNM (Argonne) are available at https://wiki.anl.gov/cnm/HPC/Benchmarks/Generation_1_vs_2. All available data indicate that the codes scales linearly up to 132 processors. Both codes also have a range of parallelization strategies that can be selected for efficiency based on the size of the calculation and the machine architecture. Minimal communications and near-perfect scaling can be achieved by parallelizing over k-points and electron bands. However, calculations of very large systems, which tend to be memory intensive, are best parallelized over the FFT (plane wave) mesh, at the expense of increased communications. In VASP, the strategy can be readily tuned between two extremes with a single parameter [8]. The LCRC system (FUSION cluster) is ideally suited for our first-principles calculations for two reasons: (i) the nodes are both individually efficient and are linked by high-speed interconnects, which enables us to make use of the excellent scalability and optimization of the MPI-based density-functional codes to be used for these projects, and (ii) the short queue times enable enable efficient completion of our project goals, which typically require running a large number of small 8-32 processor (1-4 node) calculations. Software requirements: Both codes require a FORTRAN 90 Compiler and MPI software for parallel execution. System optimized BLAS and LaPACK libraries (such as MKL or GoTo) are also needed for execution. Experiments planned: The computational portion of this research project address items (3) and (4) described in the Scientific Section of the proposal. The first-principles calculations will be performed to understand the fundamental origin for our predicted trilinear lattice couplings. We will focus on the trilinear invariant of the form P(z)Phi(z+)Phi(z-), which couples a ferroelectric polarization P(z) along the superlattice direction with structural phonon modes [Phi(z+) and Phi(z-)]that describe different BO6 octahedral rotation patterns about the same axis. By systematically changing the chemical composition of the superlattice, we will attempt to disentangle the competing interactions and microscopic origins for the trilinear term which is forbidden in the bulk systems. For this study we will examine ultra-short period superlattices composed of the following ABO3 perovskites: • (LaGaO3)1/(BiGaO3)1 -- (SL1 = LGO/BGO) • (BiFeO3)/(BiGaO3)1 -- (SL2 = BFO/BGO) We will first examine if our computational methods can accurately reproduce the known structural phases of each material that comprise the superlattice. To do so, we will calculate the phonon modes for each material using density functional perturbation theory in the high symmetry cubic phase; we will then systematically “freeze in” each mode to obtain the ground state structures (see the next portion for an example of such an experiment). The initial first step is critical to verifying the predicative power of our computational models. Once we have successfully obtained the correct ground state structures, we will then evaluate if the trilinear coupling term is active in SL1 and SL2. To do so, we will evaluate the change in the free energy equation of state as a function of the soft (and unstable) phonon modes obtained for the individual components of the superlattice. We will calculate specifically how the polarization arises from a coupling to the Phi(z+)Phi(z-) order parameter by increasing the strength of the interaction—practically this is accomplished by increasing the amplitude of the Phi(z+)Phi(z-) structural distortion. Each oxide is anticipated to exhibit certain allowed invariants in the 1/1 period superlattices based on our phenomological studies. The intellectual challenge in these calculations is that each subsequent system (and therefore superlattice) is more complex than the previous due to additional spin degrees of freedom and the fact that DFT studies of multiple order parameters are not routine: • LaGaO3 : non-magnetic dielectric with large octahedral rotations • BiGaO3 : ferroelectric with an anomalously large tetragonality • BiFeO3 : antiferromagnetic-ferroelectric; the quintessential room temperature multiferroic. Upon completion of the first portion of the project, we will then study how strain can be used to tune the energy barrier between different structural phases so as to enhance the coupling strength of the trilinear invariant. Technical details: We outline below how our calculations will proceed to investigate the presence and magnitude of the trilinear coupling term in the chemically different superlattices outlined above. First we will examine how the energetics of of the ideal high-symmetry tetragonal superlattices evolve by ``freezing-in'' linear combinations of the soft phonon modes obtained from our structural study on each component. Based on the know structural phase diagrams, we anticipate most of the eigendisplacments obtained from the calculations will be octahedral rotations that are associated with a symmetry-adapted mode that transforms according to the 3-dimensional irreducible representation R4+ of the parent cubic phase. This is highly desirable since these symmetry modes provide an effective order parameter to map onto our phenomenologically obtained Ginzburg-Landau free energy functional. In order to get an idea of how the calculations will proceed, we describe in more detail the general procedure: the calculations are started by freezing-in the R4+ distortions [9] with amplitudes ranging from 0 to 25% at 5% intervals (5 calculations per mode direction). Each structural distortion requires an integer multiple increase in the primitive unit cell so as to accommodate the atomic displacement pattern associated with the phonon mode and the periodic boundary conditions used in the calculations. Since the computational cost of each calculation approximately scales as (N2)Ln(N), where N is the number of atoms, we have used approximate timings done on the NCSA COBALT machine to estimate the number of CPU hours needed to study the three perovskite materials. Since the PI has not used the FUSION cluster, the timings are only approximately accurate since the machines are of comparable speed. Using these estimated timings we request 7,560 CPU hours for this portion of th e project. LaGaO3 and BiGaO3 will each require approximately 1,890 hours and BiFeO3 will require 3,780 to properly treat the material’s antiferromagnetic order. [The magnetic order in the BFO compound doubles the CPU time due to the fact that two (spin “up” and spin “down”) independent electronic wavefunction manifolds need to be calculated.] Next, starting from the lowest energy configurations we relax the internal coordinates through a conjugate-gradient algorithm which requires a line minimization and proceeds based on calculated forces and total energies. For example, relaxing a monoclinic structure C2/c structure requires the optimization of 15 free internal parameters. We have performed a test of this calculation on the COBALT machine (NCSA) and find that on average 245 CPU hours are necessary to reach a converged structure. On average these calculations require 230 electronic steps, with a computational cost of 465 s/step. Once we have the ionic ground state, we plan to calculate the Born-effective-charges (BECs) to evaluate the complete polarization of each superlattice. This type of calculation allows us to access not only the ionic displacement contribution to the cell polarization but also the electronic term which originates from a redistribution of charge (or hybridization) among the electronic orbitals. Calculation of the BECs along the superlattice growth direction requires one self-consistent electronic calculation (120 CPU hour per calculation per ionic degree of freedom) and three non-self-consistent Berry-phase calculations leading to 640 CPU hours for a prototypical 40-atom simulation cell. For each non magnetic bulk system we require 4,890 CPU hours: 1,890 for the structural study, and 1,000 * (3 atoms for the BECs). The magnetic BiFeO3 material will require twice as much time (9,780). The 3 different bulk systems therefore require a total of ~20,000 CPU hours. For the two superlattices, we will need an additional 30,000 CPU hours in total to study the free energy evolution and electric polarization dependence with respect to the octahedral mode amplitudes. For the non-magnetic and magnetic superlattices we require approximately 10,000 CPU hours and 20,000 CPU hours, respectively. These numbers are based on the estimated described above. Next the in-plane lattice parameters of the superlattices will be varied to simulate growth on various substrate materials which are experimentally available. We propose investigating 5 different strain states: -3, -1.5, 0, +1.5, and +3% to map out a complete phase diagram. (Negative values indicate compression of the lattice, while positive values indicate a tensile strain state.) We then will re-compute the change in free energy with strain and the octahedral modes for each bulk material and superlattice: this gives 4 strain states times five systems (2 superlattices + 3 bulk phases). This gives a total of 20 additional calculations requiring approximately 80,000 CPU hours. We obtain this number based on the PI’s prior experience that only two modes will be of interest in the strained superlattices rather than the 5 modes considered in more exploratory zero strain study. Once we have optimized the internal degrees of freedom and the forces are converged to within an accur acy of 1meV Å-1, we then relax the out-of-plane lattice constant since it will typically decrease due to volume conservation (Poisson effects). Such calculations will also require further relaxations (~80 steps per lattice constant) until the equilibrium length is determined. Based on our estimates with 20 different structures requiring minimization, we request in additional 16,750 CPU hours. We also desire 1,000 CPU hours for optimization and testing of the VASP and Abinit codes (2,000 CPU hours total). The total requested allocation is then divided as follows: 20,000 (Bulk systems) + 30,000 (superlattices at zero strain) + 96,750 [(80,000) superlattices under strain(16,750)] + 2,000 (testing) = 148,750 CPU hours. Project Members: All calculations will be performed by the PI (Rondinelli), while exchange of ideas and data analysis will be done in collaboration with Fennie at Cornell University. References: [1] P. Hohenberg and W. Kohn. Phys. Rev., 136:B864–B871, 1964; W. Kohn and L. J. Sham. Phys. Rev., 140:A1133–A1138, 1965. [2] S. R. Phillpot and S. B. Sinnott. Science, 325, 1634 (2009). [3] G. Kresse and J. Furthmuller, Phys. Rev. B 54, 11169 (1996). [4] G. Kresse and D. Joubert, Phys. Rev. B 59, 1758 (1999). [5] The PI holds a license for this software and can be compiled and optimized for the FUSION architecture. [6] The ABINIT code is a common project of the Université Catholique de Louvain, Corning Incorporated, and other contributors (http://www.abinit.org.) [7] X. Gonze, Phys. Rev. B 55, 10337 (1997); X. Gonze and C. Lee, Phys. Rev. B 55, 10355(1997); X. Gonze et al., Comput. Mater. Sci. 25, 478 (2002). [8] The parallelization tags are described in detail at http://cms.mpi.univie.ac.at/vasp/vasp/Parallelisation_NPAR_tag_LPLANE_tag.h…. [9] A supplemental table of the R4+ modes is available upon request. It includes an estimate of the number of CPU hours required to obtain a self-consistent charge density. Project URL: Requested allocation: 148750 Justification: The requester has used 0 hours of their initial startup project. In addition to approving an initial amount, please specify a Category and Subcategory for this project. For a list of the current selection of approved categories, please see: https://wiki.lcrc.anl.gov/wiki/Processes/Categories Once the Allocation committee has approved the project, please go to the Project Management page to create it: https://accounts.lcrc.anl.gov/projects.php Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Request: genomic_distribution
by accounts＠lcrc.anl.gov 15 Sep '10

15 Sep '10

Hello, A new project on the LCRC cluster has been requested. Please forward the information on to the LCRC Allocation sub-committee. Applicant's name: William Trimble Applicant's institution: ANL Applicant's division: PHY Project Name: genomic_distribution Project title: Distribution of kmers in metagenomic data Associated funding: Other Systems: Science: Next-generation sequencing technologies are currently producing data from nucleotide sequences extracted from the environment at an unprecedented rate. It is possible that probabilistic models of the character of DNA sequences can be used to substantially reduce the computational burden of sequence similarity and de novo assembly. This project aims to do exploratory work in characterizing the probabilistic properties of real and artificial metagenomic data and their usefullness in handling the same. Project description: The large size (few 10s of GB) of current metagenomic datasets makes them cumbersome to handle on desktop machines. Basic characterization of the sequences can be accomplished in a parallel manner by simply splitting the input data into pieces. Planned experiments include generating artificial metagenomic datasets labeled with reading-frame data using complete genomes, training probabilistic models on the composition of the so-generated fragments, and testing the performance of reading-frame classifying algorithms on the results. To test the same algorithms on real metagenomic data requires annotating the fragments by similarity searching or de-novo alignment, both of which are computationally intensive. Project URL: Requested allocation: 30000 Justification: The requester has used 0 hours of their initial startup project. In addition to approving an initial amount, please specify a Category and Subcategory for this project. For a list of the current selection of approved categories, please see: https://wiki.lcrc.anl.gov/wiki/Processes/Categories Once the Allocation committee has approved the project, please go to the Project Management page to create it: https://accounts.lcrc.anl.gov/projects.php Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from ApsRenewalLattice
by accounts＠lcrc.anl.gov 14 Sep '10

14 Sep '10

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Michael Borland Project Name: ApsRenewalLattice Division: ASD Project title: Development of accelerator lattices for the APS Renewal Associated funding: Other Systems: ASD "weed" cluster, operated by ASD/AOP group. weed has 56 Nehelem processors with a lustre filesystem and infiniband network. I typically have access to about 50% of the cluster full time. I was also granted an allocation of 32M core hours on intrepid. Science: As part of the APS Renewal, the accelerator lattice (the location and powering of the magnets) will be modified to incorporate a number of long straight sections for insertion devices and other purposes, such as Short-Pulse X-rays (SPX). This involves breaking the symmetry of the ring, which has serious implications for particle stability. Using simulation-based techniques developed at APS, we can tune the nonlinear elements to improve the dynamic and momentum aperture. Rapid turn-around is essential in order to respond to requests from the APS user community for evaluation of new options. In addition, simulations related to SPX beam dynamics will be performed. Project description: Because of an allocation of 32 M hours received on intrepid, we will make use of fusion primarily for simulation of the SPX system, which is a related aspect of the APS upgrade. Simulations include on-going analysis of sensitivity to static and dynamic errors. We will also begin modeling of the impact of collective effects in the presence of a chirped beam. The computational methods for the SPX sensitivity are relatively simple, involving tracking a large (e.g, 10k) number of simulation particles to find the perturbed equilibrium. These simulations are to a large degree "embarrassingly parallel," as very little communication is required between processors. The simulations essentially consist of perturbing some aspect of the accelerator (e.g., a cavity phase or voltage) and tracking to find an equilibrium response. We also perform analysis of the response to time-dependent modulations. Simulations with single-bunch collective effects are similar, but involve more interprocess communication, although it is still quite limited. In these simulations, we track with various levels of beam intensity under various conditions to determine single-bunch instability limits. In addition to the single-bunch limits, we will use multi-bunch tracking simulation to find coupled-bunch instability limits. The parameters of these simulations need to be determined by some initial runs, but are about an order of magnitude more intensive than the single-bunch simulations. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 400000 Justification: Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from Hydrogen_production
by accounts＠lcrc.anl.gov 14 Sep '10

14 Sep '10

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Faisal Mehmood Project Name: Hydrogen_production Division: MSD Project title: Hydrogen Production from Methanol decomposition on subnanometer Metal Clusters. Associated funding: BES Other Systems: PNNL-Chinook, CNM-Carbon, LCRC-Jazz Science: The proposed research work will improve our fundamental understanding of structure and activity/reactivity of catalyst particles of subnanometer sizes supported on metal oxides. It has been shown experimentally from various studies including that of Argonne scientists (Vajda et al) that subnanometer metal particle exhibit novel catalytic properties that tremendously increase the activity of various industrial reactions. The role of these small metal clusters on reactions involving hydrogen production from hydrogen-rich molecules has not be studied in past. One of the major goals of this work is to use computational methods such as density functional theory to study the structure of these subnanometer clusters and to develop a greater understating of reaction mechanism for hydrogen production that is challenge that needs to be addressed for development of fuel cells. Project description: The understanding of methanol decomposition reaction (CH3OH  CO + 2H2) is a key for hydrogen production from renewable resources such as natural gas, wood waste, municipal waste, etc. There are number of experimental and theoretical studies that have shown Pd-based catalyst to be quite effective for methanol decomposition. In the proposed work I plan to take advantage of FUSION by applying state-of-the-art first principles methods to investigate the stability of larger mono- and bimetallic alloys. Combinations of bimetallic alloys will be searched covering a significant portion of the late transition metals series for hydrogen production from hydrogen rich molecules that has direct relevance to Department of Energy’s mission of discover abundant energy sources. Many hydrogen-rich molecules can provide abundant sources of fuels if an efficient method of hydrogen production can be found. To accomplish these goals, the proposed research is divided into the following specific tasks to be accomplished: 1. Thermodynamics and kinetics of C-H, O-H and C-O bond activation in will be calculated based on binding energy spectrum using first-principles methods. To discover new catalyst, minimum energy pathways will be identified on various sizes mono- and bimetallic clusters. 2. A number of correlations between binding energies will be derived. A scaling model will be developed for estimating dehydrogenation reaction energies on bimetallic cluster alloys. The model will be tested against full DFT calculations for reactions of hydrocarbons and alcohols for selected cases. 3. New catalysts will be identified with desired properties that include low C-H and activation energy barriers. 4. Scaling results will be confirmed/tested by doing rigorous exact DFT calculations of the selected system. Based on these exact calculations scaling models will be improved. 5. Based on DFT studying synthesis of new materials will be proposed. By combining results of detailed DFT calculations for both the thermochemistry and kinetics of all the elementary steps with the experimental data a microkinetic model for many reactions that have application related to hydrogen production and generation. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 800000 Justification: I will be running VASP jobs that scales well for node 2-6 (16-48 cores). For scaling calculations, I have already done many calculations for adsorption energies of many molecules (C, O, H, CO, OH, CH, CH2, CH3, CHOH, COH, HCO, CH2OH, CH3OH, CH3O, CH2O) on M4 (M= Co, Rh, Ir, Pd, Pt, Cu, Ag, Au) cluster and their various combinations. The model proposed from these calculations is now needed to be tested for selected cases for full nudged elastic band (NEB) calculations. There are about 20 different pathways in dehydrogenation of methanol to CO and H2. Each step would require at least 12000 core hours as follows: For each step i.e each NEB job with at least 5 intermediate points between initial and final step and each point running on 48 cores would need at 48 hours to fully converge that is ~ 12000 core hours. 12000 hours * 20 dehydrogenation steps (NEB jobs) = 240000 core hours. There would be at least 3 - 6 metal or alloy systems for which complete NEB calculations will be required. Thank You, The LCRC Accounts System

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