September 2010 - Allocations-admins - mailman3.cels.anl.gov

[LCRC Accounts] Yearly Allocation Request from qmc_for_nuclei
by accounts＠lcrc.anl.gov 17 Sep '10

17 Sep '10

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Robert Wiringa Project Name: qmc_for_nuclei Division: PHY Project title: Quantum Monte Carlo Calculations of Light Nuclei Associated funding: DOE Division of Nuclear Physics Other Systems: ANL Blue Gene/P (10M hours for 12C) ANL SiCortex (indeterminate) Science: This project uses Quantum Monte Carlo [Green's function (GFMC), variational (VMC), and auxiliary-field diffusion (AFDMC)] methods to compute ground-state and low-lying excited-state expectation values of energies, densities, structure functions, astrophysical reaction rates, etc., for light nuclei and low-energy scattering reactions involving these nuclei. Realistic two- and three-nucleon potentials are used. Our goal is a description of all of these systems using a Hamiltonian that also provides an excellent description of nucleon-nucleon scattering and nucleonic matter. Such a `standard nuclear model' can then be used, for example, to compute low-energy astrophysical reactions which cannot be experimentally measured. Project description: In FY10 we did not make as much use of Fusion as expected - about 70,000 CPU hours total (counting early FY10 hours on Jazz as half-hours on Fusion), partly because we made extensive use of the MCS SiCortex and ALCF Blue Gene for major parts of our research. We expect to continue using those other resources but the SiCortex time is not guaranteed, and it seems that the machine is getting shaky. In FY11 there will be three staff members and three postdocs working on the project. We would like to do the following: A) GFMC Nucleon-Nucleus Scattering We are continuing our studies of nucleon-nucleus scattering for n+3H, p+3He, n+4He, and p+4He, and for parity-violating (PV) n+4He scattering. Eventually we will continue to larger systems, but there are still some unresolved issues with the 3+1 and 4+1 scattering cases. Based on current experience with Fusion, we will need about 30,000 CPU hours to complete the present studies. B) Transitions in A=8-10 Nuclei We have been studying electromagnetic transitions in 10Be and 10C in collaboration with the PHY low-energy experimental group, funded by a joint LDRD project. These studies show a surprising sensitivity to details of the nuclear Hamiltonian, in particular the three-body forces, which we need to explore further. A new postdoc is arriving this fall who will be studying meson-exchange-current contributions to magnetic moments and transitions in A=8-10 nuclei. We are also starting to provide transition densities in 9Be and 10B to help explain pion inelastic-scattering and new neutrino scattering data. For this work we expect to use 50,000 CPU hours in FY11. C) Unnatural-parity and double-intruder states We have been making GFMC calculations for the unnatural-parity excitations (where one nucleon is excited to the next nuclear shell) in 9Be and VMC calculations for unnatural-parity states in 10Be and 10B. We wish to continue this work in FY11, including double-intruder states in A=10 that have two nucleons excited to the next shell, and the parity-inversion in 11Be, where the 1/2+ intruder state is the ground state. Again, we wish to explore the sensitivity to different nuclear Hamiltonians, and estimate the need for 50,000 CPU hours in FY11. D) Neutron drops We will continue to use Auxiliary Field Diffusion Monte Carlo (AFDMC) and GFMC to compute properties of large systems of neutrons. These will be both neutron drops and neutron matter done in periodic boundary conditions. We have two tasks: 1) to provide guidance to the development of energy density functional theories as part of the UNEDF SciDAC, and 2) to test the effect of three-body forces, fitted to light nuclei, in neutron matter. Based on our work this past year, we estimate 30,000 hours for this work in FY11. The Quantum Monte Carlo methods work very efficiently on parallel processors. We use MPI and see speed-up efficiencies better than 95% for up to 250 CPU's on Fusion, with sustained speeds of 1.8 GFLOPS/CPU. Using ADLB and OpenMP on BG/P we have run efficiently on 130,000 processors. We have already demonstrated that OpenMP also works well for us on Fusion for larger nuclei. This all adds up to 160,000 hours. Project URL: http://www.phy.anl.gov/theory/research/forces.html Current FY Hours Used: undetermined amount New FY Requested allocation: 160000 Justification: Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from stoch_prog
by accounts＠lcrc.anl.gov 17 Sep '10

17 Sep '10

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Cosmin Petra Project Name: stoch_prog Division: Mathematics and Computer Science Division Project title: Stochastic Programming and Application for Energy Systems Associated funding: DOE-ASCR: Mathematics of Petascale Data Program. Scalable Algorithms for Gaussian Processes. Mihai Anitescu, PI. Other Systems: Science: This project is an optimization framework that exploits the weather forecast information in the operation of energy systems. Our objective is to illustrate how the use of forecast information and high accuracy physics and computations can translate into lower operating costs. We will solve the stochastic unit commitment/energy dispatch problem with network transmission constraints and wind power generation. Project description: In the previous year, we were able to obtain a high level of parallelization in solving stochastic optimization problems. The half-arrow shaped structure these problems have was exploited at the linear algebra layer in an optimization framework based on interior-point methods. We devised a scenario-based decomposition that uses the Schur-complement technique. The code we implemented, PIPS, was able to solve problems up to 189 million variables using 2,048 cores on Fusion with a (strong) scaling efficiency of 78%. The efficiency of the 1024 cores run was slightly better than 90%. We also used Elemental to parallelize dense linear solves with the Schur complement matrix. When solving more complex stochastic optimization problems like the stochastic unit commitment problem with network transmission constraints, the scenario (second stage) subproblems become really large and impose memory related constraints on how many MPI processes can be run on one node. We will follow a mixed approach MPI+SMP to overcome this limitation. On the other hand, the first stage solves involving the Schur complement matrix will be also performed in the same mixed programming model using the built-in features of Elemental. We expect to perform tests involving all Fusion's cores. 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 RANS_REACTOR
by accounts＠lcrc.anl.gov 17 Sep '10

17 Sep '10

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: David Pointer Project Name: RANS_REACTOR Division: NE Project title: Reynolds Averaged Navier Stokes Simulations to Support Advanced Reactor Concept Development Associated funding: DOE-NE GenIV Reactors and Nuclear Energy University Programs Other Systems: Small NE division reserv and eddy clusters MCS cosmea cluster Science: Demonstrate the applicability of finite volume Reynolds Averaged Navier Stokes methods to advanced reactor design analyses; contribute to the advancement of transformational sodium-cooled fast reactor and high-temperature gas-cooled reactor conceptual designs Project description: Computational Methods: The general-purpose commercial CFD code Star-CD is a finite volume formulation code for the analysis of compressible and incompressible flows and heat transfer. Star-CCM+ supports the use of generic polyhedral mesh elements, greatly simplifying the generation of computational meshes for complex geometries. The SIMPLE algorithm is used with Rhie-Chow interpolation for pressure- velocity coupling and algebraic multi-grid preconditioning. A 2nd-order central differencing scheme will be applied to all cases. Scalability: The scalability of the current version of Star-CD has been demonstrated for more than 40,000 cores on the Jaguar Cray XT at ORNL by Steve Behling of CD-adapco group. Simulations Planned (with estimated CPU times based on scoping studies completed on NE division clusters in the prior year): 15 jobs * 2000 node-hours/job = 30000 node hours - Complete solution verification study for OECD T-junction benchmark simulations 5 jobs * 24000 node-hours/job = 120000 node hours - unsteady fluid dynamis and heat transfer simulations for Sodium-cooled Fast Reactor (SFR) core design 10 jobs * 5000 node-hours/job = 50000 node hours - steady state simulations of boiling in PWR fuel assembly for OECD international benchmark study Users: Dave Pointer, Elia Merzari, Jeffrey Smith, Adrian Tentner + 3 Summer Students + 1 (still) unidentified post-doc Project URL: 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 Request: md_pls_dft_for_TiO2
by accounts＠lcrc.anl.gov 17 Sep '10

17 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: Handan Yildirim Applicant's institution: ANL Applicant's division: CNM Project Name: md_pls_dft_for_TiO2 Project title: First Principles and Classical Molecular Dynamics Calculations of Lithium Intercalation into TiO2 Surfaces and Nanostructures Associated funding: BES Other Systems: Carbon 650 000 Science: First principles calculations based on Density Functional Theory (DFT) and classical Molecular Dynamic (MD) simulations (using polarizable potentials) will be performed to study the atomistic mechanism of Li intercalation into TiO2 surfaces and nanostructures and their corresponding energetics; these studies will be directly relevant to the exploration of the properties of titania as an alternative electrode for energy storage in Li ion batteries. The effort will also consider Li-ion behavior in both crystalline (anatase and rutile) and amorphous TiO2 with the aim of revealing the role of Li behavior in the possible phase transition that has been observed in recent experiments upon Li intercalation into amorphous TiO2. The complex nature of the problem comes from the fact that it requires a detailed understanding of the interplay of several parameters, such as the effect of Li concentration, electric field and the Li dynamics/diffusion, on the possib le phase transition. Thus the present study requires detailed analysis of the energetics and dynamics of Li in TiO2 under various conditions. Note that there is no sufficient detail given in the literature for Li diffusion energetics and dynamics in both crystalline and amorphous TiO2. Our goal is to explore the details of Li diffusion under conditions that are similar to those of the experiments, thus providing a detailed atomistic picture of the key parameters that are responsible for the observed phase transition. Furthermore, throughout the study, we will gain detailed atomistic features of Li intercalation and transport in various TiO2 structures that are missing in the current literature. Project description: The problem is inherently multi-scale in nature, and the ultimate answer to those observed features could only be provided using a multi-scale simulation approach. Thus, we will treat the problem using both DFT and MD simulations. At the first stage of the calculations we will use MD simulations (at low and high temperature – ranging form 300K to 700K) for a long enough time (~ 5ns at the current studies) to observe/learn about the details of the Li diffusion processes in both crystalline and amorphous TiO2 bulk structures at lithium concentrations relevant for battery electrode operation (ranging from 25% to 100% interstitial lithium). Using these observed processes as an input, we will calculate the corresponding energetics, diffusion pathways and dynamics using periodic Density Functional Theory calculations. MD results will also be expected to provide possible differences in the diffusion and dynamics of Li in crystalline and amorphous structur es. On the other hand, using DFT, we will explore detailed electronic structures of the crystalline and amorphous TiO2 to understand and validate the observations obtained from MD simulations for both systems. The second phase of these analyses will be devoted to reveal the effect of nano-structuring and morphology on the above-mentioned properties. For this part of the work, we will explore Li diffusion energetics and dynamics in crystalline and amorphous nanotubes and nanoparticles of TiO2 by changing the size, length and diameter (in the case of tube) of these nanostructures. For this stage, we will vastly benefit from the ability of classical MD simulations that allow simulation of several thousands of atoms. We will explore the size effects on Li intercalation properties. The third stage of the calculations will be devoted to investigating electric field effects on the Li diffusion energetics and dynamics on both crystalline and amorphous TiO2. We will apply an electric field less than the break down potential of TiO2 on both crystalline and amorphous structures, and explore the field effects with low and high Li concentrations. Our goal in this part of the study is to separate the effect of field from that of the concentration and thus to evaluate the role of each parameter in Li diffusion. These calculations are expected to provide further insights into the role of field on both crystalline and amorphous structures thus help to explain the observed amorphous to crystalline phase transition. These calculations will be performed using MD simulations at both low and high temperatures, and for ns range simulation times. In preliminary work, we have obtained several results for the diffusion and absorption of Li in TiO2 Anatase bulk both using DFT and MD simulations. Using DFT (the VASP code), we have calculated three absorption energies and diffusion activation barriers for three diffusion processes of Li. We have analyzed the results of MD simulation at both 500K and 700K to identify the possible Li diffusion processes, and used these processes to calculate the corresponding energetics using DFT. Our preliminary DFT results show that Li prefers to sit at the octahedral site at which it is six- coordinated. The diffusion mechanism of Li is observed to facilitate through hopping from an octahedral to octahedral site that leads to the lowest activation energy barrier as compared to those other two processes. We also note that the existence of Li leads a shift in Fermi level as noted in the literature. Lets us note that the presence of oxygen makes our DFT calculations quite expensive since we need to use large enough energy cut off (500eV is used at the current simulations). For sufficient convergence of the total energy of about 100 atoms system with the chosen parameters requires 100 plus ionic iterations. For the recent simulations, we have mostly used 32 CPU’s per job, and at least 5 jobs, on average, run simultaneously; we expect a similar distribution of jobs when running VASP on Fusion. Depending on the requirement for finer converged energies, we will be adjusting these parameters. Note that we will also be exploring Li adsorption and diffusion on other such systems as Anatase and Rutile surfaces, nanoparticles of several sizes, nanotubes, and amorphous TiO2 thus it is inevitable that we require significant computational resources to complete this part of the proposed study. We have also performed preliminary classical MD simulations to study Li diffusion energetics and dynamics under several conditions using the DL-POLY code. Our preliminary results for Li diffusion in Anatase TiO2 bulk provided several insights for Li behavior in such system. Upon relaxation, we find that Li prefers to sit at the octahedral site as observed in our DFT study. We have performed several MD simulations for single Li diffusion at temperatures ranging from 300K to 700K for simulation times ranging from 500ps to 5ns. We find that it is not possible to observe diffusion at low temperature as 300K due to high correlation time of ~1 microsecond reported. However, the diffusion at higher temperatures (500K and above) is observed, and found to facilitate through hopping between octahedral sites. We have also managed to obtain an amorphous TiO2 starting from Anatase bulk, and the obtained amorphous phase is in very good agreement with that of reported in an experimental stu dy. We are currently exploring several such aspects of Li diffusion (in both crystalline and amorphous structures) as concentration, temperature, and field effects to understand the role of each individual parameter in the experimentally observed phase transition. Note that these simulations have to be performed with a very fine timestep (~0.2 fs in general), thus requires long simulation hours even for 5ns. For the current calculations we have systems of nearly 3000 to 5000 atoms. For 5ns simulation, we need 25 millions simulation step, and note that we are exploring the diffusion events at both low and high temperatures. Lets us note that, for system size of 3000-5000 atoms using 0.2fs time step, the simulation of 5ns at low temperatures with Li loaded in the system requires approximately 10 days using 32 CPU’s. We anticipate that we will be running of about 5 to 10 jobs per day to complete this part of the proposed research. Our simulations also indicate that for the ca lculations with field introduced, the required time step is even finer. Our calculations will be extended to study the same phenomenon for the above-mentioned nanostructruced systems thus we will be in need of significant computational resources for the completion of this proposed study. Project URL: Requested allocation: 550 000 Justification: In roughly three and a half months, we required over 250,000 CPU hours for the combination of MD and DFT calculations that also include testing of classical potential used, and the convergence tests for DFT studies. These calculations have been performed on the CNM’s carbon cluster, but this resource is fully subscribed and is being increasingly used for external user projects. Thus, we require substantial computational resources on Fusion to complete our proposed project. For a full year, we estimate that approximately 550,000 CPU hours will be sufficient. 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 Parallel_Fusion_PDEs
by accounts＠lcrc.anl.gov 17 Sep '10

17 Sep '10

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Lois Curfman McInnes Project Name: Parallel_Fusion_PDEs Division: MCS Project title: Parallel Implicit Algorithms in Edge Fusion Simulations Associated funding: DOE SciDAC program via the FACETS project (FACETS = Framework Application for Core-Edge Transport Simulations) Other Systems: MCS workstations Science: We are developing scalable algorithms for the solution of nonlinear partial differential equations that arise in the multi-institutional SciDAC FACETS (Framework Application for Core-Edge Transport Simulations) project (PI John Cary, Tech-X Corporation). This project's aim is the construction of a multiphysics, parallel framework application, FACETS, that will enable whole-device modeling for the U.S. fusion program and ITER, the next-step fusion confinement device. FACETS will be highly flexible, through use of component technology and object oriented design, to facilitate switching among models. This will enable use of simplified models for rapid turnaround or high-fidelity models to take advantage of the largest supercomputer hardware. Project description: We are developing scalable algorithms for the solution of nonlinear partial differential equations that arise in the multi-institutional SciDAC FACETS (Framework Application for Core-Edge Transport Simulations) project (PI John Cary, Tech-X Corporation). This project's aim is the construction of a multiphysics, parallel framework application, FACETS, that will enable whole-device modeling for the U.S. fusion program and ITER, the next-step fusion confinement device. FACETS will be highly flexible, through use of component technology and object oriented design, to facilitate switching among models. This will enable use of simplified models for rapid turnaround or high-fidelity models to take advantage of the largest supercomputer hardware. An integral part of the FACETS development will be the coupling of existing core and edge simulations, with the transport and wall interactions described by reduced models. Adding more detailed wall interactions will follow. In the out years, we will bring in greater coupling complexity, including the addition of near-first-principles computations of turbulent transport in the core and the edge. This development plan was created to provide early delivery of capability, with continual delivery of new capability throughout the project. Our FACETS work on scalable nonlinear solvers focuses on exploring issues in implicit Newton-based solution strategies in the edge plasma transport applications UEDGE and BOUT++ (LLNL) and the Scalable Nonlinear Equation Solvers (SNES) in the Portable, Extensible Toolkit for Scientific Computing (PETSc, ANL). We are using parallel computing resources @ fusion.lcrc.anl.gov to investigate the efficiency and robustness of various parallel algorithmic options, including different preconditioners and options for matrix-free Newton-Krylov methods. These parallel edge transport codes are now being coupled with core simulations, and we expect to perform experiments for coupled models during FY11. Project URL: http://www.facetsproject.org Current FY Hours Used: undetermined amount New FY Requested allocation: 64000 Justification: Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Request: glassforms
by accounts＠lcrc.anl.gov 17 Sep '10

17 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: Haiying He Applicant's institution: ANL Applicant's division: Materials Science Project Name: glassforms Project title: First-principles Calculations of Mineral and Glass Dissolution under Various pH Conditions Associated funding: DOE Other Systems: Science: The dissolution behavior of minerals and glasses has been found to strongly depend on the pH value of the aqueous environment. The delicate balance of ions at the solid-water interface in aqueous solutions is still a big challenge both for accurate computational modeling and for unambiguous experimental measurements. This project aims to develop physical models to simulate the water-silicate (either in crystalline or glass forms) interface at the atomic level under various pH conditions and to calculate the rates of dissolution for Si, Al and other constituting elements under acidic, neutral and basic conditions. These studies are based on first-principles calculations. The calculated reaction barriers together with the surface model can then be used to estimate the overall dissolution rates and compare with experimental values. These data will also serve as a valuable dataset to feed into micro-kinetic models for better understanding of the dissolut ion behavior and prediction of dissolution rates. Project description: As a model system, we have chosen first to study the dissolution of a mineral – orthoclase (KAlSi3O8) under various pH conditions and then to extend our knowledge to other minerals or glasses. The first part is to develop a physical model to predict the hydrogen coverage on a surface as a function of the pH value of the aqueous solution. This is done by calculating the variation of free energy as one brings a proton from solution to the surface. First-principles calculations are employed for the surfaces and tabulated ionization potential and solvation energy data for aqueous protons. The surface Si sites are, for instance, categorized into three types – neutral (≡SiOH), protonated (≡SiOH2+) and deprotonated (≡SiO-). The second part is to calculate the reaction barrier of breaking the Si-O-Si bond or the Si-O-Al bond at different surface sites. The energy required to break the Si-O-Si(Al) bond is also different depending upon their coordina tion number to the bulk. The properties that we are going to calculate in this part include structures and energies of reactants, intermediates and products, as well as reaction barriers (based on the Nudge Elastic Band method). The calculated reaction barriers together with the surface site distribution determined from the surface model can then be used to estimate the dissolution rates. We will be able to validate our theoretical results by comparison with experimental measurements at ANL. We will also consider different surface orientations and defective surfaces. Therefore, the calculations will determine dependence of reaction rates on changes in pH values, surface orientations, and the presence of defects on surface. This project primarily uses the density-functional-theory (DFT) implemented electronic structure code VASP. The system sizes of our calculations are usually around 100-200 atoms. VASP has been tested to scale very well in parallel processing on Fusion. The optimum number of processors used for these systems is 32-64 processors per calculation. Project URL: Requested allocation: 783,360 Justification: The first-principles calculations will be carried out using the electronic-structure code VASP. A single optimization calculation takes 48 hours on 32 processors. We are considering 10 perfect and defective surfaces/interfaces, each requiring 15 optimization calculations to derive their free energies as a function of pH, thereby to determine the surface structure interfaced with solvent. Therefore, the total required computer time for this part is 230,400. The second part is to calculate the detailed reaction pathways under acidic, neutral and basic conditions. The energy required to break the Si-O-Si(Al) bond is again differentiated by their coordination numbers with the bulk material (varying from 1 to 4). It takes about 48 hours on 160 processors (5 images) to calculate a reaction barrier. Therefore, the total estimated computer time for this part is 552,960. In sum, the total requested allocation for this project is 783,360 processor hours. 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 Chaos
by accounts＠lcrc.anl.gov 17 Sep '10

17 Sep '10

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Mark Paul Project Name: Chaos Division: MCS Project title: Spatiotemporal chaos and turbulence in fluids Associated funding: DOE DE-FG03-98ER14891, DE-FG02-98ER14892, NSF CTS-0604376, NSF CBET-0747727. Other Systems: NERSC, Virginia Tech's System X, ops.phys.oxy.edu (128 node linux cluster at Occidental College) Science: This work is a computational effort to push as deeply as is currently possible toward a quantitative understanding of how complex dynamics (i.e., spatiotemporal chaos and turbulence) arise in spatially-extended nonequilibrium systems that are at the frontiers of numerous science and technological problems. Project description: This is a continuing project and with this year's allocation request we propose to continue along directions begun in the previous request. All of our calculations use spectral element methods to explore the spatiotemporal chaos and turbulence of fluid systems. The code nek5000 has previously demonstrated scalability and efficiency for the specific problems that we are interested in. Using previous allocations we have made significant progress on the numerical simulation of Rayleigh-Benard convection for experimentally realistic conditions. Rayleigh-Benard convection is the buoyancy induced convection that occurs when a fluid layer is heated uniformly from below. We are most interested in cases where the fluid dynamics of the convection layer is chaotic or turbulent. Specifically, the code integrates the three-dimensional time-dependent Boussinesq equations, any associated reaction-diffusion-advection equations for the transport of scalar quantities of interest, and the linearized tangent-space equations for computing Lyapunov diagnostics. The code is geometrically flexible and can handle a number of experimentally appropriate boundary conditions. The Lyapunov diagnostics we can compute include the spectrum of Lyapunov exponents and vectors that can be used to provide fundamental insights into the complex dynamics that include the fractal dimension and the location of fast growing perturbations. In this allocation we propose to explore the following problems. 1) Transport in chaotic flow fields In this project we are interested in exploring the transport enhancement of a scalar species when the underlying fluid dynamics are spatiotemporally chaotic. There are a number of situations in which this is important and we will explore two in particular. First, is the combustion of premixed gases in a chaotic flow field. Second, is the motion of swimming microorganisms in a fluid layer. Both of these situations can be described by an additional reaction-diffusion-advection equation that is solved simultaneously with the Boussinesq equations that describe the fluid motion of Rayleigh-Benard convection. The nek5000 code already has this capability and our proposed work does not involve significant additional code development. We began this work in the previous allocation. Over the past year we have explored a number of validation cases to ensure the accuracy of the code for the parameter space that we are interested in. In this renewal request we will first compute the transport of a passive scalar quantity in a large shallow fluid layer that is undergoing spiral defect chaos. The motivation behind this is two-fold. First, to connect our work with previous calculations in the literature (Chiam et al, Physical Review E, 036205, 2005). And second, is to provide a baseline computation of the passive transport of a scalar quantity. This baseline computation will be important for comparison as we begin to explore the cases where the scalar quantity is not passive but active; in the case of combustion the scalar quantity will also react, in the case of bioconvection the scalar quantity will also be able to swim. The bulk of our computations will be done on exploring a broad range of parameter space for these two active transport situations. 2) Turbulent thermal convection. We will continue our three-dimensional numerical simulations of fully turbulent Rayleigh-Benard convection cells. Many experiments are currently being performed in this regime, but this system is not well understood theoretically. Thermal plumes are present in turbulent convection as a means of heat transport. However, a large-scale circulation (LSC) has been found, which sweeps the thermal plumes along like leaves in a wind. This LSC also undergoes chaotic, abrupt reversals. Visualizations are extremely difficult in experiments, so numerical simulations are essential for bridging the gap between experiment and theory. Heat transport measurements can also be determined from these simulations and compared to experiments and theoretical predictions. Thin thermal and viscous boundary layers are also present, and we are performing a detailed analysis of these boundary layers, which are key to understanding the nature of turbulence in these cells. Finally Lyapunov exponents can be computed for these systems and a correlation is expected between the time dependence of the LSC and the time dependence of one of the Lyapunov exponents. Turbulent Rayleigh-Benard systems have application to such diverse phenomena as weather forecasting and the reversal of the earth's magnetic field. We have been successful in observing turbulence and the LSC in our simulations of systems with Prandtl numbers of 0.4 and 0.7 and for Rayleigh numbers between 10E6 and 10E8. Successful convergence tests and checks with experiments were performed last year. We are also in the process of analyzing the data. We would like to continue our explorations for even higher Rayleigh number this year, to solidify our conclusions at lower Rayleigh number. More information can be found at the following URL's Janet Scheel http://faculty.oxy.edu/jscheel/research.html Mark Paul http://www.me.vt.edu/mpaul Paul Fischer http://www.mcs.anl.gov/~fischer/ Allocation request: 150,000 Transport in chaotic convection 150,000 Turbulent thermal convection 300,000 Total Request Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 300000 Justification: None required for our request. Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from Chaos
by accounts＠lcrc.anl.gov 17 Sep '10

17 Sep '10

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Mark Paul Project Name: Chaos Division: MCS Project title: Spatiotemporal chaos and turbulence in fluids Associated funding: DOE DE-FG03-98ER14891, DE-FG02-98ER14892, NSF CTS-0604376, NSF CBET-0747727. Other Systems: NERSC, Virginia Tech's System X, ops.phys.oxy.edu (128 node linux cluster at Occidental College) Science: This work is a computational effort to push as deeply as is currently possible toward a quantitative understanding of how complex dynamics (i.e., spatiotemporal chaos and turbulence) arise in spatially-extended nonequilibrium systems that are at the frontiers of numerous science and technological problems. Project description: This is a continuing project and with this year's allocation request we propose to continue along directions begun in the previous request. All of our calculations use spectral element methods to explore the spatiotemporal chaos and turbulence of fluid systems. The code nek5000 has previously demonstrated scalability and efficiency for the specific problems that we are interested in. Using previous allocations we have made significant progress on the numerical simulation of Rayleigh-Benard convection for experimentally realistic conditions. Rayleigh-Benard convection is the buoyancy induced convection that occurs when a fluid layer is heated uniformly from below. We are most interested in cases where the fluid dynamics of the convection layer is chaotic or turbulent. Specifically, the code integrates the three-dimensional time-dependent Boussinesq equations, any associated reaction-diffusion-advection equations for the transport of scalar quantities of interest, and the linearized tangent-space equations for computing Lyapunov diagnostics. The code is geometrically flexible and can handle a number of experimentally appropriate boundary conditions. The Lyapunov diagnostics we can compute include the spectrum of Lyapunov exponents and vectors that can be used to provide fundamental insights into the complex dynamics that include the fractal dimension and the location of fast growing perturbations. In this allocation we propose to explore the following problems. 1) Transport in chaotic flow fields In this project we are interested in exploring the transport enhancement of a scalar species when the underlying fluid dynamics are spatiotemporally chaotic. There are a number of situations in which this is important and we will explore two in particular. First, is the combustion of premixed gases in a chaotic flow field. Second, is the motion of swimming microorganisms in a fluid layer. Both of these situations can be described by an additional reaction-diffusion-advection equation that is solved simultaneously with the Boussinesq equations that describe the fluid motion of Rayleigh-Benard convection. The nek5000 code already has this capability and our proposed work does not involve significant additional code development. We began this work in the previous allocation. Over the past year we have explored a number of validation cases to ensure the accuracy of the code for the parameter space that we are interested in. In this renewal request we will first compute the transport of a passive scalar quantity in a large shallow fluid layer that is undergoing spiral defect chaos. The motivation behind this is two-fold. First, to connect our work with previous calculations in the literature (Chiam et al, Physical Review E, 036205, 2005). And second, is to provide a baseline computation of the passive transport of a scalar quantity. This baseline computation will be important for comparison as we begin to explore the cases where the scalar quantity is not passive but active; in the case of combustion the scalar quantity will also react, in the case of bioconvection the scalar quantity will also be able to swim. The bulk of our computations will be done on exploring a broad range of parameter space for these two active transport situations. 2) Turbulent thermal convection. We will continue our three-dimensional numerical simulations of fully turbulent Rayleigh-Benard convection cells. Many experiments are currently being performed in this regime, but this system is not well understood theoretically. Thermal plumes are present in turbulent convection as a means of heat transport. However, a large-scale circulation (LSC) has been found, which sweeps the thermal plumes along like leaves in a wind. This LSC also undergoes chaotic, abrupt reversals. Visualizations are extremely difficult in experiments, so numerical simulations are essential for bridging the gap between experiment and theory. Heat transport measurements can also be determined from these simulations and compared to experiments and theoretical predictions. Thin thermal and viscous boundary layers are also present, and we are performing a detailed analysis of these boundary layers, which are key to understanding the nature of turbulence in these cells. Finally Lyapunov exponents can be computed for these systems and a correlation is expected between the time dependence of the LSC and the time dependence of one of the Lyapunov exponents. Turbulent Rayleigh-Benard systems have application to such diverse phenomena as weather forecasting and the reversal of the earth's magnetic field. We have been successful in observing turbulence and the LSC in our simulations of systems with Prandtl numbers of 0.4 and 0.7 and for Rayleigh numbers between 10E6 and 10E8. Successful convergence tests and checks with experiments were performed last year. We are also in the process of analyzing the data. We would like to continue our explorations for even higher Rayleigh number this year, to solidify our conclusions at lower Rayleigh number. More information can be found at the following URL's Janet Scheel http://faculty.oxy.edu/jscheel/research.html Mark Paul http://www.me.vt.edu/mpaul Paul Fischer http://www.mcs.anl.gov/~fischer/ Allocation request: 150,000 Transport in chaotic convection 150,000 Turbulent thermal convection 300,000 Total Request Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 300000 Justification: None required for our request. Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from CEES-Si
by accounts＠lcrc.anl.gov 17 Sep '10

17 Sep '10

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Maria Chan Project Name: CEES-Si Division: CNM Project title: Investigations of silicon surfaces and interfaces for lithium ion batteries Associated funding: DOE Energy Frontier Research Center -- Center for Electrical Energy Storage (CEES) Other Systems: CNM Carbon Science: This project uses density functional theory (DFT) to investigate silicon as an anode material for lithium ion batteries. Silicon is attractive as an alternative to carbon-based anode materials due to enhanced safety and superior capacity. A key question that arises in the design and operation of Si-based anodes concerns the ability of these anodes to ad(b)sorb lithium ions; numerous studies suggest that the Si lithiation process involves a rich combination of adsorption and absorption phenomena, together with surface reconstructions, highly localized volumetric expansions of the Si lattice, and phase transitions between crystalline and amorphous structures. At the atomic and nanoscales, however, even the simplest details of these processes remain poorly understood. We aim to providing atomistic insights on these processes by carrying out DFT studies of the adsorption, initial stages of insertion, vibrational spectra, and diffusion of Li in the surfaces, interfaces b etween phases, and nanowires. Furthermore, we will consider the effects of surface and subsurface impurities. This will aid the design of optimal surface and interfacial structures for battery performance and stability. Project description: We will use total energy DFT calculations to evaluate the adsorption and absorption energy and nudged elastic band migration barriers of Li on and near Si (100), (111) and (110) surfaces with low energy reconstructions. We will also calculate the effects of adsorbed and substitutional impurities on the energetics and kinetics. I will consider 6 types of impurities, 2-3 types of reconstruction per surface orientation, and 10-20 Li position, and combinations thereof. This will amount to 1000-2000 calculations of 100-200 core-hours each. Vibrational frequencies from DFT forces dynamical matrices will be computed in order to aid comparisons with experiments. In addition, energetics and kinetics of Li in nanowires, at the interface between crystalline and amorphous silicon, and between Si and inorganic minerals found to be present at electrode interfaces, will be studied. Interface and nanowire calculations will each consume 500-2000 core-hours and 50-10 0 calculations will be performed. Using the projector-augmented wave method, only valence electrons will be included which reduces computational costs. We will use well-established DFT codes VASP and GPAW, which use a plane wave basis set and real space grids respectively. For large systems such as nanostructures, VASP has been tested on Fusion for computation involving systems with up to 7000 electrons. For routine surface calculations, hard scaling efficiency of 70%-80% has been demonstrated for 64 to 128 cores compared to 8 cores, thus enabling efficient calculations of large numbers of configurations. Please note that I am requesting an allocation for FY2011 significantly higher than that will have been used by the end of FY2010 because my FY2010 allocation did not start until March 2010 and from March to September 2010 I still have access to other machines from previous affiliations that I will no longer have access to in FY2011. Project URL: http://www.anl.gov/energy-storage-science/ 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 intermetallic
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: Randall Meyer Project Name: intermetallic Division: CSE Project title: Fundamental studies of disparate metals in p/d alloys Associated funding: NSF Other Systems: NCSA 100,000 hr/yr Science: The project will use the VASP (Vienna Ab Initio Simulation Package) code to study the formation of unique phases in nanoalloys. Experimentally our group is working with Jeff Miller and Chris Marshall to synthesize alloy nanoparticles involving a d-band transition metal and a "p-electron" metal such as Ga, Ge or Sn. One interesting aspect of these alloys is that they form intermetallics as opposed to homogeneous alloys. However, it is not known how surface segregation may manifest itself in these systems. The primary aim of the proposed theoretical work is to understand the thermodynamics of nanoparticles relative to bulk phases in an effort to understand how to improve catalyst selectivity. Project description: project has moved in two directions simultaneously over the last year. First, we have finally completed a study of water gas shift catalysis over PdZn(111) and NiZn(111). NiZn and PdZn were chosen for examination as candidates for replacement of copper for low temperature water gas shift as their density of states profiles mirror that of copper. At least three distinct catalytic mechanisms are possible: 1) a redox mechanism whereby CO reacts with O on the surface or 2) a mechanism by which formate (HCOO) produced from CO and OH decomposes or 3) a mechanism which involves a carboxyl (OCOH) intermediate formed from hydroxyl and CO. Rodriguez and Liu had previously found that while the reaction went through carboxyl on Au, the reaction was a redox reaction on Cu. In both cases, the formation of formate was thermodynamically favorable, but formate is far too stable dehydrogenate to release CO2. The redox and carboxyl mechanisms can be compared Redox CO + * ↔ CO* H2O + * ↔ H2O* H2O* + * ↔ OH* + H* OH* ↔ O* + H* OH* + OH* ↔ H2O* + O* CO* + O* ↔ CO2* + * CO2* ↔ CO2 + * H* + H* ↔ H2 + 2* Carboxyl CO + * ↔ CO* H2O + * ↔ H2O* H2O* + * ↔ OH* + H* OH* + CO* ↔ COOH* COOH* + OH* ↔ H2O* + CO2* COOH* ↔ CO2* + H* CO2* ↔ CO2 + * H* + H* ↔ H2 + 2* The first three steps and last two steps are the same in both mechanisms. Previously we have shown that a competition exists between CO oxidation and water activation as the rate limiting step regardless of the mechanism11. On both surfaces, the carboxyl mechanism is preferred over the redox mechanism. However, the rate limiting step in the carboxyl mechanism varies between the two surfaces. Over NiZn(111), the rate limiting step is the reaction between CO and OH to form carboxyl (COOH) whereas over PdZn(111) the dissociation of COOH to CO2 and H has the highest barrier. In both cases, the highest barrier was about 1.00 eV so the overall rate of the reaction may be similar. Over Cu(111), Mavrikakis and co-workers has determined that H2O dissociation is the slow step with a barrier of 1.15 eV12 whereas the barriers for water dissociation over PdZn(111) and NiZn(111) are 0.95 and 0.82 eV respectively. It is interesting to note that the reaction enthalpy over Cu(111) is 0.37 eV whereas it reduces to 0.20 eV over PdZn(111) and is actually exothermic over NiZn(111) (ΔE=−0.26 eV). This work will be submitted for publication in the coming weeks. Second we have performed PDOS calculations on Pt clusters in an effort to understand how the PDOS of Pt is related to the XANES spectra. We have examined both size effects as well as the effect of simple adsorbates such as CO and H2. Our calculations indicate Recent work from Schweitzer et al. suggests that the position of the edge is directly related to the density of states at the Fermi level (and not due to the charge transfer effects). For CO, the d-electron density is significantly depleted and the center of the d-band is shifted away from the Fermi level from −2.61 eV for Pt(111) to −4.17 eV for CO/Pt(111). We hypothesize that the shift in the edge is related to the depletion of states at the Fermi level and that the increase in edge intensity is related to the presence of empty (presumably anti-bonding) states above the Fermi level that are created from hybridization of d-states of the metal with adsorbate states as proposed by Hoffmann. Conversely, in the case of OH, antibonding states are partially filled leading to an increase in electron density near the edge and a shift to lower energy in the simulated XANES. In addition to adsorbate effects, we have also probed size effects. Experimentally we observe a decrease in intensity at the edge as the particle size falls below 3 nm but an increase in intensity slightly beyond the edge. In our preliminary investigation, we have found that simulations of the XANES for a Pt6 cluster as a model of an extremely small cluster, reasonable agreement exists with experiment. However, two competing effects emerge. First, as the particle size shrinks, the average metal-metal coordination number shrinks. This leads to a localization of the DOS and increases the DOS near the edge. However, metal particles are also known to undergo lattice contraction as the particle size shrinks to the nanometer scale. The lattice contraction has been linked to changes in the hybridization of metal bonds as the particle seeks to minimize its undercoordination. Compressing the Pt lattice, moves the d-band center away from the Fermi edge and results in an increase in sta tes 2 eV above the edge as the d-band is smeared over a larger energy range. In our simulations, we find that the loss of intensity at the edge is related to undercoordination while the increase in intensity beyond the edge is related to the diffuse states above the edge arising from lattice contraction. Calculations will continue on two fronts. First, we will move our studies of intermetallics to acrolein hydrogenation. . In this case, four possible intermediates have been suggested which give rise to the two products. Hydroxyallyl and allyloxy could be formed if the aldehyde functionality is hydrogenated as intermediates to the unsaturated alcohol. However, if the double bond is hydrogenated, either 1-formylethyl or 2-formylethyl will serve as an intermediate for hydrogenation to the saturated aldehyde. Density functional theory (DFT) calculations from Rosch and co-workers suggest that over silver surfaces, 1-formyl ethyl is the favored intermediate to the dominant (but undesired) product. We will compare our results over Pd alloys with Pd and Ag monometallic surfaces. Second, we will continue our examination of XANES of supported clusters, focusing on PtMo alloys for which interesting results of WGS exist. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 300000 Justification: Thank You, The LCRC Accounts System

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