September 2013 - Allocations-admins - mailman3.cels.anl.gov

[LCRC Accounts] Yearly Allocation Request from HNR
by accounts＠lcrc.anl.gov 22 Sep '13

22 Sep '13

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Jiajun Wu Project Name: HNR Division: PHY Project title: Hadron and Nuclear Reaction Associated funding: The U.S. Department of Energy, Office of Nuclear Physics Division, under Contract No. DE-AC02-06CH11357 Other Systems: Science: This project has two parts. In the first part we will study the formation of J/psi-Nucleus bound states in the photon-nucleus and pion-nucleus reactions near the J/psi production threshold. The J/psi-Nucleus bound states are predicted within the Quantum Chromodynamics (QCD). However, it has not been observed so far. These states are directly related to the role of gluon field in the nucleon and nuclei. The clear experimental identifications of J/psi-Nucleus bound states will help us to understand QCD in non-perturbative region. Our goal is to make predictions to facilitate the experimental search of such bound states with hidden charms at JLab with 12 GeV upgrade and the new hadron facility J-PARC in Japan. The second part of this project is to study the three-body final-state interactions on the three-meson decays of heavy and exotic mesons. We will make predictions for analyzing the data of such decay processes from BES, KEK, and JLab. The determinations of the properties of heavy and exotic mesons from the three-meson decay data will provide important information to understand the confinement in QCD. Project description: In both studies, we need to solve coupled-channel scattering equations by inverting a very large (about 200*200) complex matrix, and to perform multi-dimensional integrations. Such calculations need to be repeated many times in performing the chi-sqaure fit the experimental data. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 100000 Q1: 25000 Q2: 25000 Q3: 25000 Q4: 25000 Justification: Thank You, The LCRC Accounts System

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New LCRC report submitted for MDcounterions
by support＠lcrc.anl.gov 19 Sep '13

19 Sep '13

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2013/?project=MDcounterions

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New LCRC report submitted for MDcounterions
by support＠lcrc.anl.gov 19 Sep '13

19 Sep '13

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2013/?project=MDcounterions

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[LCRC Accounts] Yearly Allocation Request from FaddeevSRG
by accounts＠lcrc.anl.gov 19 Sep '13

19 Sep '13

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Lucas Platter Project Name: FaddeevSRG Division: PHY Project title: Few-Body Calculations for Nuclear Physics Associated funding: DOE ONP Other Systems: Science: Few-Body calculations play an important role in nuclear physics. They allow to fix parameters of three-body forces that are relevant in the description of nuclear structure such as the position of the neutron drip line. This project aims at fixing these parameters through different calculations such as scattering and decay calculations for three-nucleon systems. Furthermore, a similarity renormalization group transformation of the three-nucleon Hamiltonian is aspired to soften the interaction which is beneficial for nuclear structure calculations that use discrete bases expansions. Project description: The work will continue with 2 people. We will adjust our (GPU/openmp) code to use MPI/open,p. The code is running with available libraries on fusion (gsl and mkl). The techniques used in the code are standard: matrix inversion diagonalization w/ Arnoldi coupled ordinary differential equations I expect that we will need maximally 10 nodes for a single run when the code has been extended to use mpi. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 40000 Q1: 10000 Q2: 10000 Q3: 10000 Q4: 10000 Justification: Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from MRSA
by accounts＠lcrc.anl.gov 11 Sep '13

11 Sep '13

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Michael North Project Name: MRSA Division: DIS Project title: Agent-based Modeling of Community-Associated Methicillin-Resistant Staphylococcus Aureus Epidemiology Associated funding: NIH Other Systems: Science: This project is developing an agent-based model of the spread of community-associated methicillin-resistant Staphylococcus aureus throughout Cook County. Each agent represents an individual person in a synthetic population. The scientific objective is to better understand the epidemiology of the disease transmission. Current scenarios simulate 2.9 million people and 1.2 locations throughout Cook County for 10 years on an hourly basis. Project description: This project is using Repast for High Performance Computing (HPC (http://repast.sourceforge.net) Repast HPC C++ agent-based modeling system that is designed for use on large computing clusters and supercomputers. Several papers have been produced so far: Macal et al., “Agent-Based Model of Community-Associated MRSA: Implications for Interventions” PLOS Computational Biology (In Preparation). Murphy, J.T., N.T. Collier, and M.J. North, High Performance Agent-based Modeling, Computational Science Series, CRC Press, Boca Raton, FL USA (Accepted for Publication in 2014). Macal et al., et al., “Modeling the Spread of Community-Associated MRSA,” Proceedings of the 2012 Winter Simulation Conference, C. Laroque, J. Himmelspach, R. Pasupathy, O. Rose, and A.M. Uhrmacher, eds., IEEE/ACM, Berlin, FRG (December 2012). Thanks to Fusion, we were able to run the model for the full population of Cook County (2.9 million agents and 1.2 million geographic locations) for the first time. We used this capability to reproduce epidemic curves from a meta-analysis of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infection incidence in Chicago. The model results closely match the observed values. Detailed analysis of the results suggests that commonly held beliefs about high risk transmission locations (e.g., jails) may not be correct. We also used this capability to do early estimates of the potential effectiveness of search-and-destroy decolonization in Cook County. 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] Project Request: metadisolve
by accounts＠lcrc.anl.gov 09 Sep '13

09 Sep '13

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: John J. Low Applicant's institution: ANL Applicant's division: CLS Project Name: metadisolve Project title: Ab Initio Molecular Dynamics Simulations of Aqueous Reactions of AluminoSilicates Associated funding: Other Systems: Science: The reactions of Aluminosilicates in water are important in nuclear waste storage, zeolite synthesis, hydrothermal stability and mineralogy. These reactions involve changes in the coordination of reactants and products which can be difficult to model with continuum models of solvents often exploited in ab initio simulations of these reactions. We propose to model the kinetics of the polymerization reactions of aluminosilicates in solution and on surface of amorphous aluminosilicates. This study will establish the utility of advanced molecular dynamics with a explicit solvent models over implicit solvent models. Project description: The project will predict the rates of aqueous polymerization reactions of aluminosilicates with ab initio molecular dynamics. We will generate free energy surfaces for dimerization reactions of SiOH4 + SiOH4, Al(OH)3 + SiOH4 and B(OH3) + SiOH4 in water and vacuum. Each of these reactions will carried in pH neutral, acidic (1M HCl) and basic (1M NaOH) solutions to model the effect of pH on these reactions. We will use metadynamics to define the reaction coordinate and estimates of free energies. Umbrella sampling will be use to predict accurate free energies and estimates of rates. CPMD (http://www.cpmd.org) PLUMED (http://www.plumed-code.org) and WHAM (http://membrane.urmc.rochester.edu/content/wham) will be used in this project. CPMD is a plane-wave pseudopotential code which exploits Carr-Parrinello Molecular Dynamics. CPMD is very efficient method for ab initio molecular dynamics. PLUMED is an open source plugin, which works together with CPMD, for free energy calculations in molecular systems. Although CPMD can do metadynamics, PLUMED implements the reaction path collective variable (RPCV). The RPCV should increase the efficiency of metadynamics and umbrella sampling. WHAM is a program which performs a weighted histogram analysis of the trajectory from umbrella sampling to generate the free energy changes along the reaction coordinate. CPMD is a highly scalable parallel code. The hybrid MPI/openMP Version of CPMD 3.15.3 scales very well. CPMD can use 560 cores on either blues or fusion very efficiently for these models considered in this project. Additional scaling can be obtained with multiple walkers and task groups, which is available in CPMD. This will enable additional levels of parallelism could scale efficiently to thousands of cores. PLUMED implements a reaction path collective variable will allow us to simulate this reaction with one dimensional metadynamics. One dimensional metadynamics is at least two to three times more efficient than two or three dimensional sampling. PLUMED will increase the efficiency of our metadynamics and umbrella sampling by a factor of two to three. We expect that there will three members of this project. Project URL: Requested allocation: 900000 Q1: 225000 Q2: 225000 Q3: 225000 Q4: 225000 Justification: CPMD is well known as a program with efficient parallel scaling. I have documented the scaling of CPMD in previous project reports for aimd_catalysis. The table below show the scaling of CPMD for Cellobiose (C12O11H22) dissolved in 1M HCL (6HCl + 256 H2O) for a total on 569 atoms. CPMD scaling on blues on cellobiose in 1M HCl. MPI OMP Task # of elasped time Core cores (seconds) 216 1 1 216 31138 216 4 1 864 9180 432 4 4 1728 5695 432 8 4 3456 4290 The new version of CPMD (3.17.1) is claimed to scale better then 3.15.3. Using the new version will likely increase the efficiency of the code. It is possible that performance profiling of the code will reveal opportunities for vectorization. We study the CPU and communications bottlenecks of the code to determine whether code modifications may improve performance. The requester has used undetermined amount 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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New LCRC report submitted for radix
by support＠lcrc.anl.gov 09 Sep '13

09 Sep '13

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2013/?project=radix

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[LCRC Accounts] Project Request: ALCF_BOEING_BLUES
by accounts＠lcrc.anl.gov 09 Sep '13

09 Sep '13

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: Ramesh Balakrishnan Applicant's institution: ANL Applicant's division: ALCF Project Name: ALCF_BOEING_BLUES Project title: On the assessment of a proprietary unstructured finite volume solver for massive parallelization for hybrid RANS-LES computations Associated funding: Other Systems: Boeing Linux Clusters Science: Motivation: The Boeing BCFD code is an industrial-strength unstructured grid flow solver that is used in both the defense and commercial parts of Boeing to perform aerodynamic and propulsion analysis. It is seeing increased use for high-fidelity unsteady simulations that are compute intensive and additional scaling/performance is desired to facilitate analysis cycle time. The purpose of this proposal is to examine the performance of BCFD on a representative class of problems on its typical hardware to identify potential avenues for improving performance and porting to the Blue Gene/Q. This plan may lead to a follow-up effort to begin the modifications for efficient use of Blue Gene/Q hardware. Project description: Problem Description: An offset diffuser that was used in the first AIAA Propulsion Aerodynamics Workshop will be used as a representative geometry, as illustrated in Figure 1. Current results will be extended to add an additional level of grid refinement and a range of turbulence modeling techniques will be examined ranging from RANS to hybrid RANS-LES and, ultimately, to LES. This configuration provides a representative geometry that will provide accurate representation of industrial efforts and extend the state of the art to which LES has been performed. Computational Challenges: Offset diffusers often lead to local regions of separated flow that decrease engine performance and may lead to significant integration issues that are presently mitigated by increasing the length (and weight) of the diffuser. This often leads to increased size and cost of the overall vehicle. In order to reduce the impact of the separation, improved understanding of the detailed flow situation is desired. To this end, computational fluid dynamics (CFD) with high fidelity turbulence models can provide significant insight. However, these methods require intensive compute resources and lengthy times to obtain statistically meaningful data. This proposal will evaluate the accuracy and computational performance characteristics of a range of turbulence modeling approaches for this problem to provide better insight into both physical models and numerical algorithms. Recent (2013) modifications to the BCFD code have been made to improve its scaling on large -scale problems. A hybrid OpenMP/MPI method has been implemented that has significantly improved scaling as demonstrated in Figure 3. However, additional performance gains through algorithm modifications may still be possible, especially for application on the Blue Gene/Q system. Allocation Request: Meshes for the S-duct case appropriate for hybrid LES schemes are expected to be about 200 million cells (RANS fine grid from PAW was 60M cells). For unsteady simulations with reasonable throughputs, this would be computed on about 85-100 16-core compute nodes. At this level of grid size per processor, each physical time step will require about 150 wall-sec (15 cycles at 10 s/cycle). For a meaningful simulation, approximately 10K time steps will be required (0.50 sec at time steps of 50 microsec), leading to a cost per case of 416 wall-hours or 650K core-hours. With an expected 5 simulations required, this leads to a desired allocation of 1.5M core hours. Job Characterization: Typical cases 80-100 nodes (see above); Scaling cases could go to to approximately 150 nodes. Personnel: Ramesh Balakrishnan (Argonne National Lab): Perform analysis of code performance and develop plan for code modification for improved performance on Blue Gene/Q Mori Mani (Boeing): Develop analysis cases and assess both code scaling and physical modeling performance Mark Fisher (Boeing): Install BCFD on blues and assist in porting current code to Blue Gene. Provide guidance on current process implementation and concerns. Andrew Cary (Boeing): Provide user consulting on BCFD including appropriate case set-up for current practices. Provide insight into code algorithms and options. Project URL: Requested allocation: 1500000 Q1: 375000 Q2: 375000 Q3: 375000 Q4: 375000 Justification: I have a PDF that have this scaling information. I can attach it to an email that is generated by you system upon successful submission of this request. The requester has used undetermined amount 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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New LCRC report submitted for Linr_sclng_catalysis
by support＠lcrc.anl.gov 06 Sep '13

06 Sep '13

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2013/?project=Linr_sclng_ca…

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[LCRC Accounts] Project Request: DFT_NiOxHy_on_Pt3Ni
by accounts＠lcrc.anl.gov 06 Sep '13

06 Sep '13

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: Zhenhua Zeng Applicant's institution: ANL Applicant's division: Project Name: DFT_NiOxHy_on_Pt3Ni Project title: First principles studies of stability and reactivity of Ni (hydr)oxide films on Pt3Ni(111) surface in alkaline environments Associated funding: DOE, Office of Basic Energy Science Other Systems: Carbon (CNM-ANL), Carter (Purdue) Science: This project will employ Density Functional Theory (DFT) plus Hubbard U and van der Waals corrections, combined with atomistic thermodynamic models, to optimize the structures of the interfaces between thin (1-2 monolayer, 3-10 nm) Ni oxide/hydr(oxy)oxide films, close-packed Pt3Ni alloy substrates, and vacuum or aqueous bulk phases; additional work will focus on probing the catalytic properties of these interfaces for the hydrogen evolution reaction (HER) in alkaline solution. The relevant films, i.e. Ni (hydr)oxide films on Pt(111) surface, which can be synthesized using standard electrochemical techniques, have been investigated experimentally in the group of Nenad Markovic (ANL-MSD) and have been shown to exhibit bifunctional catalytic properties for hydrogen evolution and other electrocatalytic reactions. Dr. Greeley has previously collaborated with the Markovic group to demonstrated that thin nickel hydroxide nanoislands on Pt(111) exhibit subst antially reduced activation barriers for water dissociation than pure Pt(111). Recently, we have performed an extensive series of studies on the bulk oxide/hydr(oxy)oxide and found that using water reference, van der Waals correction and optimized Hubbard U together, the formation energy can be predicted highly precisely. We have used the approach to develop the electrochemical phase diagrams/pourbaix of Ni oxide/hydr(oxy)oxide films on Pt(111) and the three-phase boundaries at the film edges at different potential. The kinetic studies have shown that water dissociation, a key step in alkaline HER, is significantly accelerated at the three-phase boundary edges. In the present proposal, based on our new developed technique and the insight on Pt(111) systems, We will extend these efforts to probe similar chemistry on Pt3Ni alloy substrates. We anticipate that the alloying effect will have a substantial impact on both the structure and chemistry of the interfaces. Project description: Electrochemical surface studies on well-defined, single crystal metal and oxide surfaces have provided tremendous understanding of the fundamentals of chemistry and catalysis at interfaces in the past 20 years. The applications of such systems are wide-ranging, from fuel cells to solar fuels production. However, very few studies have rigorously probed the fundamentals of electrocatalytic processes at the interface between oxide/hydr(oxy)oxide films, metal or alloy substrates, and bulk solution phases. Metals and oxides have dramatically different structures, properties, and affinities to reactive species, which bring potentially unique properties to electrocatalytic process at interfaces between these disparate classes of materials. Experimental results by Nenad Markovic’s group (ANL/MSD) have demonstrated that certain electrochemically deposited oxides/hydr(oxy)oxides (nickel, cobalt, iron, and manganese-based, deposited as islands with diameters of 5-10 nanometers) on Pt(111) can efficiently catalyze the hydrogen evolution reaction (HER) with activities never before seen on either metal or oxide catalysts in alkaline electrolytes. However, the atomic-scale structures and the underlying fundamentals of the high catalytic activity on these transition metal oxide/Pt(111) interfaces are still not fully understood. In addition, the generalization of previous experimental and theoretical investigations to more complicated metal substrate structures, such as Pt-based alloys, has not been attempted. Indeed, some Pt alloys have shown higher electrocatalytic activity than Pt itself. Investigation of alloy substrates is thus a natural extension of the work on pure Pt substrates and may provide an extra variable to tune the activity of water dissociation and hydrogen evolution reactions at three phase interfaces. As there is still no experiment on these combined systems, the trend predicted from present study could provide a bl ueprint for the future search for and preparation of catalysts with higher activity. Our previous calculations focused on the electrode potential-dependent structures of two dimensional, two ML films of hydroxides (Ni, Co, Fe and Mn) deposited on Pt(111) substrates; this work demonstrated that the Ni and Co-based structures bind hydroxyl groups significantly more weakly than do the Fe and Mn-based structures. Recently, Hubbard U and van der Waals corrections have been added to the calculations due to their importance in describing strongly correlated systems and layered systems with weak interaction between the layers; these results have shown a remarkable level of agreement with experimentally measured bulk oxide/hydr(oxyl)oxide reaction energies. We have tried to use the same approach to study Ni oxide/hydr(oxyl)oxide on Pt(111) surface to generate interface models at relevant potential. The preliminary studies of water dissociation have shown that the barriers at the three-phase boundary edges are much lower than on Pt(111) and step surfaces. In this work, we will try to firstly refine the study on Ni oxide/hydr(oxyl)oxide films. Besides studying the barrier of water dissociation, we will evaluate the barriers for other elementary reaction steps in HER, together with the coverage-dependent thermodynamics of OH and hydrogen adsorption at these interfaces. We will further extend the work beyond Pt(111) to Pt3Ni(111) alloy substrates, with an ultimate goal of comparing not only the structural and catalytic properties of different oxide/hydr(oxy)oxide films, but also to probe the impact of the substrates on this bifunctional chemistry. We will initially focus on extending the two dimensional hydroxide thin-film models to accurately describe three phase interfaces of Ni oxides/hydr(oxy)oxides with Pt3Ni(111) substrates and the surrounding bulk medium. The structure and termination of the edges could deviate from the corresponding structures of the two dimensional films, and we will thus need to consider numerous edge structures with different oxidation states. Then, we will test the chemistry of water dissociation at the edges. This will permit us to more thoroughly understand the impact of the nature of the substrate on the structure and chemistry of the three phase boundary, and we fully anticipate that very different physics and chemistry will be observed for films on the Pt3Ni(111) alloy surface in comparing with Pt(111) surface. Firstly, We will build upon some of our recent work, which has focused on the development of higher computational accuracy and the models of the two dimensional oxide/hydr(oxy)oxide films on Pt(111) and on water dissociation at Ni(OH)2/Pt(111) three-phase interfaces, to extend this work to Pt3Ni alloy substrate . We will follow an analogous procedure to that described for Pt(111) to develop both the two dimensional and three phase interface models on alloys. While it is entirely possible that the structures on alloys will differ substantially from those on Pt(111), we fully anticipate that the experience that we have gained from the Pt work will significantly accelerate our efforts on alloys. Our initial investigations will be on the well-known Pt-skin alloy structures, which should preserve the same qualitative features as the pure Pt(111) substrates, following which we will move to alloys with mixed surface layers, where deviations from the Pt(111) behavior will be more significant. Ultimately, we would like to compare the water dissociation properties for different oxide/hydr(oxy)oxide films on both pure Pt and alloy substrates. If the hypothesis that H produced from water dissociation moves to metal sites is correct, then the thermodynamics and kinetics of water splitting will be substantially different on the different metal substrates. In combining with the influence of substrates to the thermodynamics and kinetic of hydrogen evolution (2HH2), this could provide significant additional information that would be of use in further searching for and optimizing bifunctional catalysts, by tuning the films and substrates. Calculations with the VASP code have shown that full convergence of model hydr(oxy)oxide/Pt(111) spin-polarized calculations on the 2×2 super cells require approximately 48 hours per total geometric optimization on 32 cores Intel Xeon-E5. For the Pt3Ni(111) substrate, we will firstly consider well-known Pt skin structure. From low potential (hydrogen evolution potential region) to high potential (oxygen evolution region), we will need to consider a significant number of different stoichiometries and configurations to find optimized potential-dependent interface structures from monolayer up to four layer films; we tentatively estimate that the total number of resulting optimizations will be around 60 (including many possible permutations of O, OH, and vacancy groups), yielding a requirement of ~90,000 core hours. The edge models do not need to consider so many stoichiometries and configurations, but require bigger super cell, such as 6×2 super cells, which may be at least 4- fold more time consuming than 2×2 super cells on a single geometric optimization. We estimate that there are 10 edge models need to be tested, which may require another 60,000 core hours. To study the kinetics, we need to determine barriers for water dissociation (Volmer step), hydrogen evolution through Heyrovsky mechanism and Tafel mechanism at the three phase boundary edges. We anticipate needing to run approximately six Nudged Elastic Band (NEB) calculations. Due to a single NEB calculation may be 10 fold more time consuming than geometry optimization, we need another 90,000 core hours. Assuming the process could be accelerated through the information accumulated on Pt3Ni Pt skin substrate, the calculations on all alloy substrates with mixed surface layers could be done with comparable core hours. Then our total request comes to 480,000 core hours. The models of fully two dimensional hydroxide films on Pt(111), which were developed in previous proposal cycles, have been published in Nature Materials. We have also developed a new technique to highly accurately describe the stability of oxides/hydr(oxy)oxides, and have found that using water reference, van der Waals correction and optimized Hubbard U together, the formation energy of oxides and hydr(oxy)oxides can be predicted highly accurately, i.e. the standard deviation with respect the experiment values could be around 0.04 eV. This accuracy has never been reached by standard DFT calculations in previous study, and has strong implication for the application on the extended systems, e.g. thin/nano films listed in the present proposal. It also could be the interest of the broad community and the paper is in preparation. Project URL: Requested allocation: 480000 Q1: 120000 Q2: 120000 Q3: 120000 Q4: 120000 Justification: The requester has used undetermined amount 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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