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[LCRC Accounts] Project Request: VegClimGeo
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: Robert Jacob Applicant's institution: ANL Applicant's division: MCS Project Name: VegClimGeo Project title: Vegetation-climate feedback over geologic time. Associated funding: NFS Other Systems: Science: Before the Late Cretaceous, the tropics were drier and without an "everwet" rainforest biome. We have hypothesized that the Cretaceous/Cenozoic spread of tropical rainforests was enhanced by the evolution of the unique hydraulic properties of the flowering plants, or angiosperms. Our preliminary results using present-day climatic conditions imply that the high transpirational capacity of angiospermous plants increases moisture recycling by the land surface and thus increases the area of everwet rainforest. However, the impact of angiosperms on the hydrological cycle could be different in magnitude during Late Cretaceous/Early Cenozoic since the land-ocean configuration and atmospheric concentration of CO2 are also different. Here we propose quantifying the impact of plant physiology, land-ocean configuration, and atmospheric CO2 concentration on the seasonal distribution of tropical land precipitation and the size of the tropical rainforest. Project description: We plan to use the NCAR CAM3 (Community Atmosphere Model) coupled with CLM3.5 (Community Land Model) for this work. To explore the role of plant physiology, land-ocean configuration, and atmospheric CO2 concentration, CAM will be run at T42 resolution (~3ox3o) with a Slab Ocean Model and a Dynamic Vegetation Model. Since the Dynamic Vegetation Model describes the allocation, competition, and establishment of present-day ecosystems, we need to test and improve the model to be able to run it for our target period. CAM3/CLM3.5 has been parallelized with MPI and uses Fortran90 and C languages. A NetCDF library is also required for input/output. The dynamic vegetation model ~100 years to reach an equilibrium. We request fusion time to run 4 (CO2) * 4 (land-ocean configuration) * 4 (plant physiology) * 100 years for a scenario * 10 (testing) = 64000 years. We have measure the cost of this configuration on Hopper (an XT5) at NERSC with 2.4GHz AMD cores (similar to those on Fusion) and found it takes about 7 core-hours per year. We thus request 450000 core-hours Project URL: Requested allocation: 450000 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 foam
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 Jacob Project Name: foam Division: MCS Project title: Global Climate Modeling with the Fast Ocean Atmosphere Model Associated funding: Department of Energy, Office of Science National Science Foundation Other Systems: external: NERSC, NCAR Science: Climate models treat the atmosphere and ocean as interacting fluids. They contain numerical methods to solve the basic partial differential equations which are in turn derived from the Navier-Stokes equations for a fluid on a rotating sphere. They also contain detailed parameterizations to compute the internal and external forcing terms that come from such diverse phenomena as the passage of radiation through the atmosphere, the release of latent heat by phase changes of water and the effects of friction and unresolved turbulent scales. In general, climate model development is focused on increasing the fidelity of the simulation compared to the observations. On long time scales, the climate is controlled mostly by the ocean because it is a slower, more dense fluid then the atmosphere and has a higher heat capacity. For some problems in climate science, such as understanding the different climates of the geologic past and the internal variability of the climate, it may not be necessary to have the most accurate representation of the atmosphere in the climate model being used. Project description: The goal of the FOAM project is to maintain a fully coupled climate model that puts an emphasis on high throughput as measured in simulated years per day. Like most climate models, FOAM is composed of separately developed pieces, many developed by other groups. The atmosphere model is called PCCM3. PCCM3 contains two numerical methods, a spectral transform scheme for the dry dynamics and a Semi-Lagranian transport scheme for moisture. Both methods have been parallelized with a two-dimensional decomposition of the horizontal dimension. The physics, which refers to all the parameterizations of things like radiation and convection, is done entirely within a vertical column and so parallelizes trivially with the dynamics. The ocean model is Om3. Om3 uses a finite-difference method with explicit sub-cycled time stepping. It also has a 2D parallel data decomposition and does the small amount of ocean physics in columns. The other pieces of FOAM inclu de a land model (which contains no dynamics and can be thought of as an extension of the atmosphere column physics) and a sea ice model. The pieces are integrated into a single system with a special purpose coupler. See www.mcs.anl.gov/foam for more information. FOAM can simulate 360 years of integration in a single day using 32 cores on fusion. FOAM gets its speed from both the efficiency of the individual models and by keeping the resolution of the atmosphere model as low as possible. FOAM scales nearly linearly on a wide range for platforms for processors counts between 4 and 64. Because FOAM stays at a relatively low resolution, there isn't enough work per processor to scale to higher processors counts. FOAM requires a Fortran90 and C compiler and the MPI library to run. For FY11, we will be testing the application of the Ensemble Kalman Filter to FOAM for tuning its parameters in a coupled mode. In spite of decades of effort, coupled ocean-atmosphere general circulation models (OAGCM) like FOAM still suffer from significant model biases, notably in the tropics. A significant part of these biases is caused by uncertainties in the model parameters. So far, however, parameter tuning in OAGCMs remains rudimentary. We will use our time to develop a strategy of systematic parameter optimization in an OAGCM. Building on the GFDL coupled EnKF data assimilation system, we will develop an adaptive coupled ensemble Kalman Filter system (AcEnKF) for a simultaneous estimation of model parameter and state using FOAM. We will explore different assimilation techniques to search for an effective method of parameter optimization in OAGCMs. We will also study coupled dynamics relevant to parameter optimization in the tropical climate system for both the c limatology and climate variability. Our work is expected to give the first comprehensive evaluation of a novel strategy for parameter optimization in OAGCMs. Project URL: http://www.mcs.anl.gov/foam Current FY Hours Used: undetermined amount New FY Requested allocation: 700000 Justification: We have to do a great deal of testing to develop the ENKF system. The ENKF use an ensemble to represent the forecasting PDF. We plan to test different ensemble sizes to find the right one for the EnKF for FOAM. For this request, we'll assume 50 members. Based on the this ensemble size. we will run some "perfect model experiment" EnKF simulation which assume the model core is perfect, only parameters and initial condition have uncertainty. We expect about 200 different sets of parameters and initial conditions. Each integration should be for 30 years. 50x30x200 = 300000 years. We have measured a cost of 2.133 core-hours/simulated year leading to a request of 640000 core-hours. Additional time is added for testing of the EnKF system. Thank You, The LCRC Accounts System

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New LCRC report submitted for SepCFD
by support＠lcrc.anl.gov 17 Sep '10

17 Sep '10

Full project report at https://accounts.lcrc.anl.gov/reporting/project/index.pl?project=SepCFD

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New LCRC report submitted for SepCFD
by support＠lcrc.anl.gov 17 Sep '10

17 Sep '10

Full project report at https://accounts.lcrc.anl.gov/reporting/project/index.pl?project=SepCFD

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New LCRC report submitted for SepCFD
by support＠lcrc.anl.gov 17 Sep '10

17 Sep '10

Full project report at https://accounts.lcrc.anl.gov/reporting/project/index.pl?project=SepCFD

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[LCRC Accounts] Yearly Allocation Request from DFT_TM_Catal_Screen
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: Rees Rankin Project Name: DFT_TM_Catal_Screen Division: CNM Project title: DFT Screening Investigation on Catalytic and Electrocatalytic Phenomena of Transition Metals Associated funding: LDRD-$ and Basic Sciences Other Systems: Carbon compute cluster @ CNM here at ANL Science: In this project, we will expand on successful previous efforts (FY2009,FY2010) to utilize the Density Functional Theory (DFT) framework to determine the geometry and associated energy(ies) of molecular reactants, intermediate moieties (e.g. reaction intermediates, and products) on the exposed surfaces of transition metals (TM ). By obtaining such properties, we can derive understanding that serves dual purposes. First, we can directly calculate the potential energy, and hence the free energy of reaction mechanisms of interest on these TM surfaces- whether they be ideal defect free surfaces (flat 111 type surfaces) or step type surfaces which represent the more reactive sites on realistic nanoparticles. Second, we can further populate our database of computational catalytic properties which will be used for predictive screening of additional reactions, catalysts, and products via interpolative schemes and Sabatier Volcano type analysis through previously determine d (and calculated) descriptors. This is particularly relevant when considering catalyst design involving multiple atomic species, such as in the case of binary or ternary alloys. These materials are of great interest for future catalytic needs for reasons of improved catalytic efficiency, product (de)selectivity, and economic viability. Project description: In the previous work in FY2009 and 2010 we performed DFT calculations to begin to study an important reaction in the context of fundamental heterogeneous catalytic as well as electrocatalytic applications, as well as build our computational database and Sabatier Volcano analytical methods. Specifically, this reaction involved the selective reduction of molecular oxygen (O2) by TM catalysts to hydrogen peroxide (H2O2). The applications of studying this reaction were numerous. It is well known that H2O2 historically has not been synthesized efficiently via direct conversion of H2 and O2. Recent work in the literature suggests metallic alloy nanoparticles can create new chemistry in the selective synthesis of H2O2 from H2 and O2. After completing our initial work (flat, and stepped surfaces of 'pure' single component TM species) on this reaction in FY2009/FY2010, we have begun initial work towards similar studies using the same methods to characterize selective product reactions in the electrochemical reduction of CO2 (CDR) towards more economically and environmentally beneficial target species. Compared to the previous work on H2O2 this is a much more complex reaction network to study (with more paths and branchpoints) that requires significantly more calculations of potential descriptors and transition states to determine the appropriate Sabatier Volcano relations. However, by building on the knowledge generated from such studying such critical, and fundamental reactions, it will be much more feasible to predict the performance of novel catalysts in other reactions which involve the same or similar reactants and intermediates but different products, or conversely, differing reactants with similar intermediates and products. Our work will continue to supplement the computational materials-by-design and Materials Design Workbench database being developed. The results of populating the MDW database will allow far great er amounts of materials and catalyst reactions to be quickly predictively screened in the future. Calculations will be expected to be performed using the Vienna ab initio Simulation Program (VASP). This program , currently deployed on Fusion, uses a periodic plane-wave representation of the electronic wavefunctions of materials with a self-consistent minimization/solution under the Density Functional Theory (DFT) formalism. Recent improvements in the parallelization of VASP combined with the excellent parallel hardware capabilities in the LCRC Fusion system allow for reasonably efficient near-linear scaling for jobs running on up to ~ 80 cores (10 nodes). Superlinear scaling can occasionally now even be seemingly witnessed for small jobs in a single compute node with appropriate cache sizes. Additional calculations in the future may utilize the Dacapo DFT code, which performs similarly to VASP in the above regards Ongoing and previous calculations for this work have already been performed on the HPC Carbon cluster available at the CNM (ANL), and the Fusion system at LCRC (ANL) in FY2009/FY2010, and are continuing into FY2011. However, the resources available at CNM-ANL Carbon cluster are currently significantly overloaded even after the recent hardware expansion; small scale jobs can actually sit in the submission queue for time intervals longer than their execution related wall time. An allocation of 750k core hours on LCRC-Fusion would ostensibly allow for approximately 1800 calculation-sets (1 calculation-set here can be envisioned as scanning several related materials (such as differently structured surface alloys of the same stoichiometry) + adsorbate over many adsorption sites, or scanning a single material surface +adsorption site over many adsorbates, or as a series of coupled calculations to determine the transition state/activation energy between two local minima). The abil ity to augment our knowledge base with the incorporation of this many additional calculation-sets would be paramount in developing the detailed understanding necessary to move forward in a purely computational catalysis by design (or broader materials by design) project. As a note, we used essentially all of our FY2010 Allocation of 650k hours effectively in ~8-9 months, and we propose to do effectively the same the number of total calculations in FY2011 now that we have a detailed initial understanding of our methods and some basic insights into fundamental reaction mechanisms/TM species we wish to study in vastly greater detail. The availability of high performing computing resources such as Fusion will greatly augment our calculation possibilities and accelerate understanding of our Sabatier relations for the CDR reaction and simultaneously help us continue populating our computational catalysis database. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 750000 Justification: As a brief summary of typical results, Vasp 4.6 or Vasp 5.x+ with appropriate compilation, Infiniband, and modern processor cores scales well (near linear) out to approximately 80 cores or 10 (Fusion) nodes for most typical calculations on these similar HPC systems. VASP scaling does fall significantly in the regime of calculations with severely large file I/O overhead--however, this is not expected to apply to the jobs performed in the proposed work. We can provide sample benchmarks representative of the type of scaling efficiency our typical calculations have achieved to date on Fusion nodes if necessary. Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from nanocatalysis
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: Peter Zapol Project Name: nanocatalysis Division: CHM/MSD/CNM Project title: Catalysis in nanostructured materials Associated funding: Strategic LDRD in Materials Design;BES-Chemical Sciences; Other Systems: Science: Our recent theoretical work on Pt nanoparticles and subnanometer clusters coupled to experiments at Argonne have resulted in several intriguing results on size and shape dependence of rectivity. The indications of modified selective catalytic activity in these systems require computational studies to understand catalytic reaction mechanisms and their dependence on the size and structure. This will involve large-scale calculations using molecular dynamics and electronic structure methods to find out optimized structures , reaction energies and barriers of catalytic reactions, diffusion barriers along the surfaces. Project description: Molecular dynamics studies using many-body potentials as implemented in DL_POLY computer code and DFT studies in VASP will be used to simulate support structures covered by hydroxyl groups. Radial distribution functions will be compared to available experiments. The code uses 32 to 48 PEs for about 50,000 atom calculations. The geometries from molecular dynamics simulations will be used in studies of catalytic activity. We will study reactions on supported metal subnanometer clusters. We will also continue investigations on using thermodynamics to modify shape of catalytic particles, in particular in electroche4mical environment. Density functional studies will be performed using VASP, NWChem and GAUSSIAN codes to determine reaction energies and barriers. The VASP calculations typically use 24-64 processors for 24 hours to 48 hours. Expected number of members in the project is three to six. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 800000 Justification: We have used our allocation very effectively in the previous year. Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from compnano
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: Peter Zapol Project Name: compnano Division: CHM/MSD/CNM Project title: Computational Nanoscience Associated funding: BES-DOE Other Systems: CNM 'Carbon' Science: Electronic structure calculations of chemical reactivity of nanomaterials is a complex problem involving large scale computations. It is important in catalysis, nanocrystalline materials, bio-inorganic interfaces, energy transfer and conversion, etc. Typically, explicit treatment of hundreds to thousands of atoms is required for accurate results on reaction energetics, structures of transition states and reaction mechanisms. Project description: Computational studies aimed at materials by design will be performed using molecular orbital theory, density functional and molecular dynamics methods as implemented in Gaussian09, VASP, and NWChem computer codes. We have successfully performed NWChem, G09 and VASP calculations on Fusion last year. G09 scales well up to 16 processors. VASP shows good scalability from 16 to 256 PEs as well as NWChem which is highly suitable for massively parallel computations. We will also investigate how other codes scale on Fusion and benchmark performance. We will continue our studies of chemical reactivity on the surfaces and interfaces of nanomaterials in FY11. In particular, we will perform DFT calculations coupled to thermodynatic treatments to investigate properties of nanoparticles as a function of their size and shape for metals and metal oxides. We have performed work on computational screening of oxide-based materials for light to energy conversion that resulted in useful predictions for surface modification. We plan to extend these studies to doping with light elements for oxide band gap engineering and transition metals for modifications of catalytic properties. We will extend these studies to different size and shape of oxide particles. In addition, we will work on carbon nanomaterials using them both as support for heterophase nanostructures with novel chemical properties to investigate their potential for electrochemical applications in energy conversion and storage. A typical Gaussian calculation will take for 4 to 16 nodes anywhere from 1-2 hours to several days. VASP and NWChem calculations may involve 16 to 256 nodes and up to several days depending upon the size of the problem. This project will involve 5-7 members of the Molecular Materials Group. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 800000 Justification: The allocation is used by several postdoctoral and staff scientists to perform calculations on DOE-funded projects. From previous year's experience, we have used efficiently a large allocation, about a third of time for Gaussian and NWChem, and the rest for VASP calculations. Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from compnano
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: Peter Zapol Project Name: compnano Division: CHM/MSD/CNM Project title: Computational Nanoscience Associated funding: BES-DOE Other Systems: CNM 'Carbon' Science: Electronic structure calculations of chemical reactivity of nanomaterials is a complex problem involving large scale computations. It is important in catalysis, nanocrystalline materials, bio-inorganic interfaces, energy transfer and conversion, etc. Typically, explicit treatment of hundreds to thousands of atoms is required for accurate results on reaction energetics, structures of transition states and reaction mechanisms. Project description: Computational studies aimed at materials by design will be performed using molecular orbital theory, density functional and molecular dynamics methods as implemented in Gaussian09, VASP, and NWChem computer codes. We have successfully performed NWChem, G09 and VASP calculations on Fusion last year. G09 scales well up to 16 processors. VASP shows good scalability from 16 to 256 PEs as well as NWChem which is highly suitable for massively parallel computations. We will also investigate how other codes scale on Fusion and benchmark performance. We will continue our studies of chemical reactivity on the surfaces and interfaces of nanomaterials in FY11. In particular, we will perform DFT calculations coupled to thermodynatic treatments to investigate properties of nanoparticles as a function of their size and shape for metals and metal oxides. We have performed work on computational screening of oxide-based materials for light to energy conversion that resulted in useful predictions for surface modification. We plan to extend these studies to doping with light elements for oxide band gap engineering and transition metals for modifications of catalytic properties. We will extend these studies to different size and shape of oxide particles. In addition, we will work on carbon nanomaterials using them both as support for heterophase nanostructures with novel chemical properties to investigate their potential for electrochemical applications in energy conversion and storage. A typical Gaussian calculation will take for 4 to 16 nodes anywhere from 1-2 hours to several days. VASP and NWChem calculations may involve 16 to 256 nodes and up to several days depending upon the size of the problem. This project will involve 5-7 members of the Molecular Materials Group. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 800000 Justification: The allocation is used by several postdoctoral and staff scientists to perform calculations on DOE-funded projects. From previous year's experience, we have used efficiently a large allocation, about a third of time for Gaussian and NWChem, and the rest for VASP calculations. Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from TIES
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: hakim iddir Project Name: TIES Division: MSD, CNM Project title: Tailored Interfaces for Energy Storage (TIES) Associated funding: EFRC, EERE Other Systems: EMSL-PNNL, CNM-ANL Science: Lithium-ion batteries have become widely used in various portable electronic devices and are also considered as the most promising power source for plug-in hybrid electric vehicles[1]. However, their use has not yet reached its apogee, primarily owing to their stability and safety problems [2, 3]. One of the possible ways to improve upon the stability and safety performance of Lithium-ion batteries without negatively affecting the physical properties of the electrolyte is through addition of additives in small quantities that will enhance the desired properties of the electrolyte, such as solid-electrolyte interface (SEI) formation, cell voltage, and stability. Li2CO3 is one the components of the film that forms on the surface of the anode (SEI). It was shown to play a protective role for the anode, by limiting the diffusion of large molecules that trigger the exfoliation process, and hence the anode degradation. However, beyond a certain thickness this film reduces the mobility and the diffusion of Li-ion across. To improve the stability and overall performance of Lithium-ion batteries, a detailed study of the SEI formation, structure and properties is necessary. This work will be closely coupled with extensive experimental efforts conducted by two groups from the Chemical Sciences and Engineering (CSE) division. This project is being done as part of the ANL EFRC on energy storage and an EERE funded program. 1. Sun, Y.-K., et al., High-energy cathode material for long-life and safe lithium batteries. Nat Mater, 2009. 8(4): p. 320-324. 2. Chen, Z., J. Liu, and K. Amine, Impact of tripropyl borate on life and impedance of lithium-ion cells. Electrochimica Acta, 2008. 53(8): p. 3267-3270. 3. MacNeil, D.D. and J.R. Dahn, The Reactions of Li[sub 0.5]CoO[sub 2] with Nonaqueous Solvents at Elevated Temperatures. Journal of the Electrochemical Society, 2002. 149(7): p. A912-A919. Project description: We propose to investigate the above mentioned properties (SEI formation, structure, Li transport, and reactions at the interface) on model systems using density functional theory (DFT) as implemented in the Vienna Ab Initio Simulation Package (VASP) currently available on FUSION. We have successfully investigated the growth of Li2CO3 films on the edge sites of graphite, as well as the diffusion of Li in Li2CO3 bulk material. We have started to investigate the growth of Li2CO3 films on the basal planes (clean and defective), and the interaction of solvent molecules (EC) with both edge and basal planes of graphite. During this next period we would like to continue the study of Li2CO3 growth on basal planes as well as the interaction of these films with solvent molecules. The growth of Li2CO3 on edge sites of LiC6 will also be investigated, to get insight on the effect of intercalation on SEI growth and stability. We will also investigate the difference i n structures and transport properties between the films grown on the surfaces of graphite and the structures that could result from deposition of already preformed materials in solution. This study will require the investigation of L2CO3/basal plane interfaces. Vibrational studies will be used to compare with experimental efforts using X-ray spectroscopy techniques being conducted here at Argonne. Similar studies will be performed on Al2O3/graphite interfaces. In this case, separate MD studies will provide us with the starting structures of the interfaces that will be further optimized using VASP. The calculations performed on FUSION during the first part of this project, required (TIES + extension; 750000+77000) 827000 hours. A total amount of 800000 hours would be necessary to complete the proposed work. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 800000 Justification: The study of Li2CO3 growth will require the investigation of about 40 different configurations [(Li2CO3)x, x=1,2,3,4]. For each value of x about 50000 hours would be needed, hence 200000 hours would be necessary to complete this part of the project. Calculations on one specific Li2CO3/graphite interface structure having 406 atoms (largest system that will be investigated using VASP), will require 80000 core hours. The structure optimization for other similar interfaces with different configurations, stoichiometry and relaxation constraints, including Li2CO3 interaction with LiC6 edge sites, would require 350000 hours. Frequency calculations of several adsorbents on graphite (basal planes) support will require at least another 100000 hours, and the NEB calculations will require at least 150000 to study the diffusion of Li+ in Al2O3. A total of 800000 core hours would be needed to perform these calculations. Thank You, The LCRC Accounts System

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