August 2012 - Allocations-admins - mailman3.cels.anl.gov

[LCRC Accounts] Yearly Allocation Request from Comp_Soft_Catalysts
by accounts＠lcrc.anl.gov 27 Aug '12

27 Aug '12

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Juan Lopez-Encarnacion Project Name: Comp_Soft_Catalysts Division: CSE Project title: Soft Catalysts for Green Chemistry and Energy applications Associated funding: Strategic Initiative on Materials for Energy (LDRD-2012-060-R1) Other Systems: None Science: The objective of this project is to perform extensive modeling and computational studies that will aid in design and synthesis of new catalytic materials for efficient transformation of abundant C1 sources (carbon dioxide (CO2) and methane (CH4), in particular) into chemical feedstocks and fuels. The planned theoretical/computational work will be performed in close contact with the ongoing experimental effort on the subject at CSE. The goal is to design and synthesize a new type of catalytic materials that will combine the best characteristics of both homogeneous catalysts (high selectivity at low temperature, tunability) and heterogeneous catalysts (stability, ease of separation). Such catalytic systems are not available at present. Project description: In the FY2013, the computational studies will focus on thermal stability of crystalline and amorphous porous organic polymers (POPs) with and without the reaction centers incorporated into it. The dynamics/kinetics and elucidation of the paradigmatic reaction mechanism of the catalytic chemical reactions that will be explored experimentally. Specifically, we will explore the alkane metathesis reaction mechanisms promoted by Ta-based/POP catalysts. One of the targeted processes is conversion of ethane into methane and propane. Based on our preliminary results, we expect the Ta-based reaction centers embedded on POP supports to reduce the relevant reaction barriers as compared to those of the more common supports, e.g., silica or alumina based. The structural and electronic aspects of reactants, intermediates, transition states, and products will be explored and characterized using state-of-the-art density functional theory. In addition, we are planning the development, implementation, and use of new methodologies for generation of 3D amorphous structures for POPs from nodes and/or struts, i.e., building blocks of the POPs, with multiple “heads” and “tails” (the current methodology allows for only one head and tail per node/strut, limiting the generation of POPs to one chain or 1D). Here, the static and random modeling of incorporation of reaction centers into amorphous POPs will be studied as well. The number of atoms treated at a time will vary from a few to a few tens (e.g., in organometallic reaction centers), from tens to about a hundred (e.g., in struts), and to a few hundreds (e.g., in POP networks). The bulk of the planned computations will be performed with the SIESTA code, which is an efficient order-N density functional theory (DFT) algorithm (i.e., the computational time scales linearly with the size of the system). In the case of generated 3D amorphous POP networks, the studies in will require inclusion of thousands of atoms, and they will be performed using efficient and at the same time adequate semiempirical potentials and/or force fields to characterize their low-energy structures and dynamical aspects. Then single-point DFT treatments will be performed on these structures to characterize their electronic features using SIESTA or CP2K which allow to performed calculations for thousands of atoms. The dynamical and thermal behavior will be explored using both first principles based and semiempirical potentials/force fields. The kinetic aspects will be evaluated and characterized using transition state theory. In addition to the SIESTA and CP2K codes we will also use other packages (e.g., LAMMPS, NWChem, and Gaussian) as appropriate. The requested time is based on estimates performed on Fusion (see below). The methods used to study the dynamical/kinetics aspects of our systems require considerably computational power/time than those methods used during the FY2012 and the test show below (e.g., crystal, atomic, and electronic structure computations). The expected number of project members is three (3) or more. Project URL: http://www.cse.anl.gov/catalysis_energy_conversion/homogeneous/index.html Current FY Hours Used: undetermined amount New FY Requested allocation: 980000 Q1: 245000 Q2: 245000 Q3: 245000 Q4: 245000 Justification: The scaling efficiency on Fusion was tested using the code SIESTA in the full optimization of the atomic structure and cell volume of a crystalline porous organic polymer, which contain a total of 584 atoms: 192 atoms of H (5 numerical basis function per each H), 360 atoms of C (13 numerical basis function per each C), and 32 atoms of O (13 numerical basis function per each O) in its unit cell; a total of 6,056 basis functions. Substantial speed-up is achieved with the increase in the number of cores: Cores Average elapsed time per optimization step (min) 16 4.38 32 2.70 64 2.34 128 1.68 Thank You, The LCRC Accounts System

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FW: Soderholm Computer time application
by Bair, Raymond A. 27 Aug '12

27 Aug '12

FYI... On 8/27/12 4:08 PM, "Soderholm, Lynda" <ls(a)anl.gov> wrote: >Ray: > >Thanks. Yes I will be. > >Lynne > >-----Original Message----- >From: Bair, Raymond A. >Sent: Monday, August 27, 2012 3:25 PM >To: Soderholm, Lynda >Subject: Re: Computer time application > >OK, we will look for the proposal. Will you be the PI? (It requires an >Argonne PI) > >Ray > > > >On 8/27/12 3:18 PM, "Soderholm, Lynda" <ls(a)anl.gov> wrote: > >>Ray: >> >>We have a theorist visiting from France who arrived last week. She is >>interested in getting access to some of your computing facilities. Last >>week she spoke with Al Wagner and the Jeff Hammond, who have both been >>very supportive. Jeff has offered to work with us to guide us through >>the process. She interacted further with Jeff today, trying to put >>together a proposal. Jeff got back to her, informing us that the >>deadline for such a proposal is tomorrow. He also indicated that you >>may be able to grant us a couple of days stay-of-execution. So I am >>writing to ask about the possibility of us submitting a proposal a >>couple of days late (say on >>Friday) for your consideration. >> >>Take care >>Lynne >

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[LCRC Accounts] Yearly Allocation Request from HEIGHTS-3D
by accounts＠lcrc.anl.gov 27 Aug '12

27 Aug '12

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: 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. This is multi-physics multi-phase package that combines state-of-the art models of energy deposition, vapor/plasma formation/evolution and magneto hydrodynamic (MHD) processes, thermal conduction in material and in plasma, atomic physics and resulting opacities, detailed photon radiation transport, and interaction between plasma/radiation and target material in full three dimension configurations. The package has many areas of applications. It is used to simulate the effect of plasma transient instabilities on plasma facing components in magnetic fusion reactors. This is a critical problem and a serious obstacle to the success of tokamak concept as a viable energy producing device. Most plasma instabilities will cause both surface and bulk damage to plasma-facing and structural materials. HEIGHTS is used to study self-consistently and benchmark various plasma interaction processes, to predict particle and heat intensity at chamber components surfaces, and to study the effects of plasma transient events and high power deposition on reactor walls and predicting/simulating components lifetime. Next area of research with HEIGHTS is optimization of sources for the advanced lithography that includes extreme ultraviolet (EUV) and beyond EUV (BEUV) lithography, which are perspective techniques in the development of the next generation computer chips. Numerical simulations will study various processes for photon production at 13.5 nm and 6.7 nm in efficient and optimized sources design that require detail atomic and plasma radiation physics. Project description: 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. We use splitting methods that involve decoupling the full model into separate component for each process, employing specialized numerical methods to solve each component, and coupling the resulting solutions. The MHD equation system is solved using the total variation diminishing scheme in the Lax–Friedrich formulation (TVD-LF). The three-dimensional Monte Carlo algorithm is developed and benchmarked for plasma particles interactions with solid and plasma matter in magnetic field in any geometrical configuration. The heat conduction and vaporization block simulates heat transfer, melting and surface vaporization of target due to various input energy sources. Heat conduction in plasma is developed using an implicit algorithm of the sparse matrix technology. The radiation transport and laser photons interaction with matter are based on the weighted Monte Carlo method. Above models in the frame of HEIGHTS package will be used for the simulation of various plasma physics applications. We will study the following state-of-the art multi-phase multi-physics engineering applications: 1. EUV lithography and beyond using both YAG and CO2 lasers, pre-pulse/main pulse, mass-limited tin targets; output in 13.5 nm range as well as in 6.5-6.7 nm range; 2. Water-Window microscopy: N2 or BN, mixed material and plasma properties, nanosecond laser beams; output in 2.48 nm and 2.88 nm; 3. Femto and nanosecond Laser Ablation mass-spectroscopy in the presence of an ambient gas: several materials, mixed material and plasma properties, the effect of plasma plume evolution on the spectrally integrated signal strength; 4. Colliding plasmas physics for various applications; 5. High-power transient plasma interactions with plasma facing and nearby components and calculation of erosion component lifetime in magnetic fusion application. 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 FY2013. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 300000 Q1: 75000 Q2: 75000 Q3: 75000 Q4: 75000 Justification: Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from Linr_sclng_catalysis
by accounts＠lcrc.anl.gov 27 Aug '12

27 Aug '12

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: John J. Low Project Name: Linr_sclng_catalysis Division: MCS Project title: Linear Scaling Electronic Structure for Catalysis in nanobowls. Associated funding: of Energy, Office of Science, and Office of Basic Energy Sciences Other Systems: None Science: Metal clusters supported in metal oxide nanobowls are being synthesized by the Institute for Atom-efficient Chemical Transformations (IACT). These nanobowls are synthesized by depositing several layers of an oxide (i.e. Al2O3) with atomic layer deposition [i.e. Al(CH3)3] on another a substrate oxide (i.e. SrTiO3). Complexes (i.e. Fe-calixarene) on the substrate oxide form nanobowls in the deposited oxide. These nanobowls have diameters of about 1-2 nm. Modeling the chemistry in 1 nm nanobowls will require cells with a volume of 10 cubic nanometers containing thousands of atoms. The computational effort for VASP, GPAW and other plane wave code scales like the number of electrons to the third power. Although simulations of this magnitude are possible with VASP or GPAW on high performance supercomputers, programs like CP2K implement linear scaling methods of electronic structure require an order of magnitude less computer time than conventional electronic stru cture codes for models containing a thousand atoms. CP2K will allow the efficient modeling of the catalytic chemistry in nanobowls at the atomic level. Project description: Cp2k has been built, tested and put into production on fusion. We have completed a metadynamics and NEB study of surface segregation in Pt/Mo bimetallic clusters to demonstrate the efficiency of cp2k in modeling metal clusters. We are currently working on modeling systems containing 1000s of atoms required to model nanobowls. Variously workarounds were required to get CP2K to fit into the 32 Gigabytes of memory available on each node of fusion. The linear scaling program CP2K can handle models containing 1000s of atoms efficiently. CP2K has been shown to scale well to 256 processors for a model containing 1028 water molecules. The elapsed time required for a calculation containing a thousand atoms is approximately 28 hours on 256 processors (7,000 hours) to optimize the geometry for a metal cluster in a nanobowl. We plan to run geometry optimizations for models of nanobowls, metal clusters in nanobowls and chemisorption of H, O and CHx species on metal clusters in nanobowls. Performing these calculations on three different combinations of metal oxides will demonstrate whether metal-support interactions alters the chemistry of a metal cluster in a nanobowl and the utility of this approach to modeling chemistry in nanobowls. The twenty-four calculations described here will require 200,000 hours of CPU. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 200000 Q1: 50000 Q2: 50000 Q3: 50000 Q4: 50000 Justification: Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from ScalaGAUSS
by accounts＠lcrc.anl.gov 27 Aug '12

27 Aug '12

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Jie Chen Project Name: ScalaGAUSS Division: MCS Project title: Scalable Gaussian Process Data Analysis Associated funding: Scalable Gaussian Process Analysis of Spatio-Temporal Data (PI: Mihai Anitescu) Other Systems: MCS workstations Science: This project uses a maximum likelihood approach to perform Gaussian process analysis on both synthetic and real data. The observations considered for analysis are simulation and data from nuclear engineering and climate science. The resulting analysis is used to describe the spatial correlation of the sampled data, to predict and to understand uncertainty in very high fidelity phenomena. Project description: ScalaGAUSS is a statistical software for analyzing spatialtemporal data arising from various applications (chemistry, power grids, material science) and modeled as a Gaussian process. The goal of ScalaGAUSS is to handle both gridded and scattered data at the scale of 10^9 to 10^12 points and beyond. Following the framework of a reformulation of the maximum likelihood estimation using sample average approximation, the core of the computations is to solve several linear systems with respect to the fully dense covariance matrix (having the number of rows/columns the same the data size). For gridded data, we implemented a multilevel Toeplitz linear solver and tested it with up to 1024 cores last year; see the FY2012 report. This year’s work will be built on that of the last year. In particular, we will be focusing on 1. Improving the scaling of the solver; 2. Incorporating the solver into ScalaGAUSS. The objective is to finish a working version of ScalaGAUSS that can be applied to real applications, such as for analyzing ozone data. On the other hand, for scatted data, a linear solver requires efficient matrix-vector multiplications. For this, we have developed a fast summation program for a specific covariance kernel, based on the treecode methodology. This program will be the essential building block of the linear solver. We will be investigating its performance for solving linear systems. The goal is to add to ScalaGAUSS a component that handles scattered data as efficiently as for gridded data. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 400000 Q1: 100000 Q2: 100000 Q3: 100000 Q4: 100000 Justification: Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from Chaos
by accounts＠lcrc.anl.gov 27 Aug '12

27 Aug '12

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, NSF CDI-1125302. Other Systems: NERSC, 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 with this year's allocation request building upon last year's progress. 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. We continue to make 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 continue exploring the following problems. 1) Transport in chaotic flow fields In this project we are interested in exploring the transport dynamics 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 apability and our proposed work does not involve significant additional code development. 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. We have computed the transport of a passive scalar quantity in a large shallow fluid layer that is undergoing spiral defect chaos. This allowed us to connect our work with previous calculations in the literature (Chiam et al, Physical Review E, 036205, 2005). This has also provided a baseline computation of the passive transport of a scalar quantity. This baseline computation allows for an important for comparison with the cases where the scalar quantity is not passive but active which we will continue to explore in this allocation. A specific case of interest is the combustion of a scalar quantity in a chaotic flow field. We have begun these calculations and validated the basic approach. With this allocation we will explore the parameter space to quantify the transport of an active scalar. In particular we are interested i n cases of small Lewis and large Damkohler numbers that are most closely related to experiment. 2) Quantifying spatiotemporal chaos In this effort we will perform large scale numerical simulations of chaotic fluid convection for the precise conditions of experiment. We will explore large cylindrical domains with aspect ratios of 30 and larger for very long times (several horizontal diffusion times). We are particularly interested in using and developing diagnostics that shed physical insight upon fundamental features of the underlying high-dimensional chaos. We will use our current capability to compute the Lyapunov exponents, Lyapunov vectors, and the fractal dimension (all using the Gram-Schmidt approach) for a range of conditions of current experimental interest in the convection community. One aspect we will focus upon is using the temporal and spatial averages of the leading order Lyapunov vector to quantify regions and dynamics of interest. We are interested in searching for a connection between these Lyapunov based diagnostics, which can only be computed and are not accessible to experiment, with quantities and diagnostics that can be measured in experiment. We will also develop and explore new diagnostics such as covariant Lyapunov vectors to quantify the spatial disorder in the patterns. The covariant Lyapunov vectors are much more difficult to calculate than the Gram-Schmidt based Lyapunov vectors but have the benefit of providing all of the directions of perturbation growth in the high dimensional phase space (called Oseledec's splitting). The covariant Lyapunov vectors have not been calculated for an experimentally accessible fluid system and have the potential to provide new and important insights into the regions and directions that contribute most to the chaos. In order to connect with experiment we are also going to explore the use of realistic boundary conditions such as walls of finite thermal conductivity and varying fluid properties. 3) Turbulent thermal convection. We would like to continue our three-dimensional numerical simulations of fully turbulent Rayleigh-Benard convection cells for higher Rayleigh numbers (10E10) and lower Prandtl number (0.02-0.7). Simulations have never been performed at such high Rayleigh numbers, system size and Prandtl number. This is exactly the region where there is disagreement between theory and experiments, and there is evidence of a trend towards disagreement by our simulation results at lower Rayleigh number. By going to higher Rayleigh number, we will be able to resolve the disagreements and develop a fuller understanding of turbulence. Many experiments are currently being performed in the proposed regime (and even higher Rayleigh number), but this system is not well understood theoretically. Thermal plumes are present in turbulent convection as a means of heat transport. In addition, a large-scale circulation (LSC) has been found, which sweeps the thermal plumes along like leaves in a wind. This LSC is not steady and 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 present, and we can perform 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. URL: 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 Covariant Lyapunov vectors and exponents 150,000 Turbulent thermal convection 450,000 Total Request Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 448 Q1: 112 Q2: 112 Q3: 112 Q4: 112 Justification: N/A Thank You, The LCRC Accounts System

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New LCRC report submitted for SHARP-IF
by support＠lcrc.anl.gov 27 Aug '12

27 Aug '12

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2012/?project=SHARP-IF

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New LCRC report submitted for TMix
by support＠lcrc.anl.gov 27 Aug '12

27 Aug '12

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2012/?project=TMix

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New LCRC report submitted for SHARP-IF
by support＠lcrc.anl.gov 27 Aug '12

27 Aug '12

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2012/?project=SHARP-IF

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New LCRC report submitted for SHARP-IF
by support＠lcrc.anl.gov 27 Aug '12

27 Aug '12

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2012/?project=SHARP-IF

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