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

[LCRC Accounts] Yearly Allocation Request from qmc_for_nuclei
by accounts＠lcrc.anl.gov 28 Aug '12

28 Aug '12

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 (INCITE 15M hours for 12C studies) ANL Blue Gene/Q (early user time for same) 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. We are also actively engaged in making predictions that can and are being tested at rare isotope beam facilities such as ATLAS, NSCL, and TRIUMF. Project description: A) Electroweak moments and transitions We are studying a variety of electroweak properties and transitions in light p-shell nuclei, including both one- and two-body charge and current operators that include the effect of meson-exchange currents. We are nearing completion of work on magnetic moment and M1 transitions in A=7-9 nuclei. We will extend these calculations to moments and M1 and M3 transitions in A=10 nuclei in FY13. We have also been studying E0 and E2 transitions in A=10 in co-operation with an experimental program at ATLAS, and finding they may provide new constraints on three-nucleon forces. We are just now starting work on longitudinal and transverse response functions, which have not previously been studied for A>7 nuclei. We expect to use 160,000 hours for this work in FY13. B) A=11,12 nuclei Extensive effort has gone into GFMC calculations of 12C using the BlueGene/P system, but only a few exploratory calculations of other A>10 nuclei have been made. We want to explore different possible trial functions for other cases like 11Li, 11B, and 12Be, particularly wave functions that are "clusterized." The VMC codes for these trial functions were made more efficient for large nuclei this year by adding OpenMP commands in addition to the existing MPI structure. We are also continuing studies of unnatural parity and intruder states in A=10 nuclei, where one or two nucleons are promoted from the p-shell to the sd-shell. A particularly interesting case is that of 1- states in 10B which exhibit significant isospin-mixing. We would like 80,000 cpu hours to this work in FY13 C) Asymptotic normalization coefficients and resonance widths for alpha-decay In the last two years we have developed a new method for evaluating asymptotic normalization coefficients (ANCs) that characterize the long-range tails of nuclear bound states and are the key determinant in low-energy astrophysics reaction rates. The calculation uses a short-range integral technique that can make do with relatively simple variational wave functions. A variant of this method allows the calculation of widths of narrow unbound states. The method has been applied to single-nucleon emission up to A=9 nuclei. In FY13 we plan to adapt the method for alpha-particle emission and study ANCs and widths nuclei up to A=10. We will need 40,000 hours for this work in FY13. D) 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. Our earlier n+4He studies were limited to scattering energies of 4 MeV or less. We have made some progress this year in developing better trial wave functions that can be used up to 20 MeV. We would also like to move to some heavier systems like n+8He scattering. We would like 40,000 cpu hours available for this work. Project URL: http://www.phy.anl.gov/theory/research/forces.html Current FY Hours Used: undetermined amount New FY Requested allocation: 320000 Q1: 80000 Q2: 80000 Q3: 80000 Q4: 80000 Justification: Thank You, The LCRC Accounts System

1 0

[LCRC Accounts] Yearly Allocation Request from propylene_epoxidatio
by accounts＠lcrc.anl.gov 28 Aug '12

28 Aug '12

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Lei Cheng Project Name: propylene_epoxidatio Division: MSD Project title: DFT Calculations of Propylene Epoxidation with Silver Aggregates Associated funding: LDRD Other Systems: EMSL Science: Propylene oxide is an important precursor for production of commodity chemical. However, most production methods of the chemical are energy-intensive and environmentally unfriendly. In a recent study (Science 328, p. 224 (2010)), alumina supported Ag3 cluster and ~3.5nm Ag nanoparticles were found to have high activity and selectivity for direct propylene epoxidation to propylene oxide. Previous density functional theory studies suggest that the spin on the small Ag3 cluster plays an important role in improving the catalytic activity and the interface between the Ag3 cluster and alumina support is the active site toward O2 dissociation. In this study, we plan to further examine these proposed determining factors to catalytic activity by calculating reaction thermodynamics and kinetics of propylene oxidation catalyzed by slightly bigger silver aggregates (15-30 atoms), both in gas phase and on alumina support. Such study will provide valuable information toward ratio nal designs of catalysts with high activity and selectivity. Project description: With allocation of FY2012, we were able to investigate O2 dissociation on various sites of gas phase Ag19 and Ag20 aggregates, as well as propylene epoxidation reaction thermodynamics and kinetics on these two aggregates. Some key intermediate structures and transition states of epoxidation reaction on theta alumina supported Ag19 were also identified. In FY2013, we will continue the activity studies of various sites on the supported aggregates for propylene epoxidation. This can be done by performing structure optimization of reaction intermediate and locating reaction transition state for each elementary step. Results from these calculations can help explaining the reactivity and selectivity differences observed experimentally between supported trimer and slightly larger aggregates. These insights should further hint design and synthesis of more efficient catalysts. In addition, we will validate using theta alumina to represent amorphous alumina and also test the effect of hydroxylation on support. This will be done by calculating O2 dissociation energies and barriers on the aggregate-support interfacial sites using a hydroxylated amorphous alumina support model that we have obtained using molecular dynamics simulation method. Although we don’t except qualitative difference, the comparison of results calculated using unhydroxylated theta alumina with those of hydroxylated amorphous alumina should show quantitatively how different it is to use a simpler and computationally less costing model vs. a more realistic and larger model. The method we will use for this study is DFT/PW91 implemented in the VASP package, consistent with our previous calculations. To locate transition states, the nudged elastic band method (NEB) will be used. Further charge and spin density analysis of some key structures will be carried out to correlate intrinsic properties of the cluster to its catalytic activity. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 996000 Q1: 249000 Q2: 249000 Q3: 249000 Q4: 249000 Justification: Our typical system contains 270 atoms and previous scaling tests have shown that VASP calculations of such size scale really well up to 8 nodes with 8 cores per node on the Fusion cluster. Especially with the parallelization techniques built in for VASP (NAPR and LPLANE switch for parallelization and distribution over band and over plane wave coefficients, respectively), the high efficiency of such parallel calculation can be achieved. Thank You, The LCRC Accounts System

1 0

[LCRC Accounts] Yearly Allocation Request from stoch_prog
by accounts＠lcrc.anl.gov 28 Aug '12

28 Aug '12

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: MCS 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: We have won an INCITE Award of 10 million hours on BG/P. Science: This project is aimed at developing scalable methods and implementations for the solution of stochastic optimization problems on massively parallel computing platforms. On the application side we focus on the optimization of power grid in the presence of uncertainty. Our objective is to illustrate how the use of forecast information, accurate physics and high performance computing reduce the operating costs. Project description: In the previous years, we obtained an unprecedented level of parallelization in solving stochastic optimization problems by exploiting the half-arrow shaped structure these problems have and using Elemental to reduce the computational bottleneck associated with the first stage dense Schur complement system. We also have a hybrid, MPI+SMP implementations. The intranode parallelization is obtained via OpenMP. Our C++ code, PIPS, solved a stochastic economic dispatch problem with close to 2 billion variables using 131072 cores on Intrepid with a strong scaling efficiency of more than 90%. A paper on these findings has been accepted to SC11. The final version can be found here: http://www.mcs.anl.gov/~anitescu/PUBLICATIONS/2011/miles-2011-pips-SC.pdf Currently, we are adding capabilities for integer variables. An example of such variables are the binary (integer) variables representing switches and the “on/off” status of generators (a.k.a unit commitment) present in the power grid optimization models. A first step in the direction of adding capabilities for integer variables was the implementation of PIPS-S, a parallel SIMPLEX implementation for stochastic linear programming problems. To our knowledge, PIPS-S is the first simplex implementation for HPC platforms. The runs on FUSION showed a good strong scaling, up to 50%. A full report on the implementation details and the performance on Fusion and Intrepid was submitted to the Journal of Computational Optimization and Applications. The ANL report can be found at http://www.mcs.anl.gov/~petra/papers/pipss.pdf . Integer optimization problems have a combinatorial nature, and are often solved by recursively exploring the finite but exponentially large binary solution space using an approach called branch and bound. However, parallel branch-and-bound has not previously been used to solve problems so large that the continuous relaxation must be decomposed and solved in parallel. Now we can efficiently solve the relaxations using PIPS-S and we will pursue the implementation of a parallel branch-and-bound code. The requested hours on Fusion will be used in the development phases of the code to run small and medium scale computations. Large scale runs and studies will be done on BG/P or Q platforms Project URL: http://www.mcs.anl.gov/~petra/pips.html Current FY Hours Used: undetermined amount New FY Requested allocation: 140000 Q1: 10000 Q2: 10000 Q3: 40000 Q4: 80000 Justification: Thank You, The LCRC Accounts System

1 0

[LCRC Accounts] Yearly Allocation Request from dynamics
by accounts＠lcrc.anl.gov 28 Aug '12

28 Aug '12

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: James Fonseca Project Name: dynamics Division: MCS Project title: Dynamics of biophysical systems. Associated funding: DOE Other Systems: MCS workstations, Beagle at Computation Institute Science: Determine key characteristics of ion selectivity of the Na channel using a reduced model combined with Monte Carlo simulations. Materials' Science, polymer physics, electrophysiology, molecular biology Project description: List of funding agencies that support this project. DOE Description of the science objective(s) for the project. Determine key characteristics of ion selectivity of the Na channel using a reduced model combined with Monte Carlo simulations. PROJECT SUMMARY This project focuses on a range of computational studies of electrolyte and electrolyte-protein solutions. We investigate the fundamental behavior of *confined* electrolytes outside of equilibrium, which is of paramount importance to the understanding of the functioning of many biological and physical systems. The primary mode of investigation is Monte-Carlo (equilibrium) simulations of protein-electrolyte mixtures (in the primitive or restricted primitive model of the electrolyte). This project scope is twofold. The first project continues work performed on LCRC systems over the last two years. The goal this year is to extend simulations of the reduced model of the sodium channel as described below. A second request is an extension of an existing project and is included with this allocation request. This project is similar to the first in that it focuses on reduced models of ion channels and the software core is the same. But the goal of these simulations will be provide verification of a recently developed method which uses an energetic variational approach applied to the primitive (implicit solvent) model of ionic solutions. This project is called PNP (Poisson-Nernst-Planck) simulations with steric effects and is discussed in a following section. PROJECT TEAM A new team member, Janhavi Giri, PhD, has been brought on to the project to help with manuscript preparation, simulation execution, and project direction. Janhavi performed her doctoral work with Prof. Eisenberg at Rush University and is experienced in both experimental and theoretical research of the Na and related ion channels. Janhavi joins the team with Gary Leaf, Jim Fonseca, and Bob Eisenberg. REDUCED MODEL OF THE SODIUM CHANNEL Overview Sodium vs. Potassium selectivity is one of the most important properties of sodium channels. Any failure in this selectivity means quick death. Small nerve terminals in the brain quickly swell and burst, doing irreversible damage to the nervous system stopping respiration and then a wide range of other functions. Potassium leakage from nerve terminals of the brain is the immediate cause of brain death in almost all cases. Indeed, a substantial fraction of all the ATP used in the body (e.g., some 30 to 50%) is spent pumping out potassium (and sodium) that leaks out of or into cells. There is hardly a more important physiological property than sodium vs. potassium selectivity. The system representative of our investigation is a membrane channel protein operating under a concentration and voltage gradient. The primary function of channel proteins is to pass ionic current in and out of the cell *selectively* (i.e., favoring some types of ions over others). This selectivity mechanism is crucial to the functioning of the cell and the overall organism, but it is still relatively poorly understood. In particular, since a channel can be sensitive to trace amounts of the selected ion, the permeation and selectivity mechanisms are subtly related to the atomic structure of the protein. At the same time, since the ionic current is largely independent of the thermal fluctuations of the protein (in the open configuration), the channel function is rather robust. Thus, there is a need to isolate the relevant features of the channel geometry and, most importantly, permanent charge distribution, that are responsible for this sensitive yet robust selective beha vior. Simple models of channels have been able to account for essentially all the selectivity properties of two types of calcium channels, with distinctly different functions, properties, and structures, and the classical voltage activated sodium channel DEKA (so-named for the amino acid residues implicated in ion selectivity as determined by electrophysiological and biochemical experiments). The DEKA channel selects sodium over calcium in a complex manner not yet understood. The DEKA channel excludes potassium from the channel in a number of conditions and thus does not conduct this dangerous ion at all. Past Work on LCRC systems We have nearly completed a survey of the Na channel model we employ to determine its behavior. The survey has included a wide variety of bath concentrations and model parameters such as pore radius (structural effects) and channel dielectric (polarization effects) constant. So far we have collected selectivity data on a two parameter grid for a variety of common mono and divalent cations at various physiological concentrations. Work thus far has included the following sets of simulations (most of which include dozens of simulations): 1. Size selectivity: Na+ vs. monovalent ions (Li+, K+, Rb+, Cs+) at various concentrations 2. Effect of pore radius on Na+ vs. K+ and Na+ vs. Li+ selectivity 3. Charge selectivity: Na+ vs. divalent ions (Mg2+, Ba2+, Sr2+) at various concentrations 4. Effect of relative difference in bulk ionic concentrations on Na+ vs. K+, Na+ vs. Li+ selectivity 5. Anomalous Mole Fraction Effect in Na channel: Na+ vs. K+, Na+ vs. Li+ Proposed Work This approach has provided several unexpected results that we wish to investigate further. They include a strong dependence of conductance dielectric constant, as well as a possible selectivity mechanism that may help explain the selectivity of Na and Li in the Na channel. Future work will focus on determining the robustness of this phenomenon under different conditions. We will also continue with planned studies to investigate the role of the model’s permanent structural ions. Although the model works robustly, the mechanism by which DEKA selects sodium over potassium is not known. The mechanism by which potassium is excluded is not known. We propose here to study the role of the following aspects of the model. We have estimated the number of simulations we believe will be required for each aspect. Each set of simulations will investigate the model under a set of conditions, such as different bath salt concentrations, including physiological scenarios as well bath concentrations to match to experiment. 1. Entropy and energy of the side chains DEKA (20 simulations) 2. The entropy and energy of the sodium ion (30 simulations) 3. The entropy and energy of the calcium ion (30 simulations) 4. The entropy and energy of the potassium ion (30 simulations) 5. Explore the selectivity of DEKA to lithium, rubidium and cesium, investigating the entropy and energy in interesting cases (30 simulations) 6. Study the effect of dielectric coefficient and diameter in cases (1)- (5) seeking the biological adaptation. (~200 simulations) It is clear from earlier work that dielectric coefficient and diameter have orthogonal actions on Na vs. K selectivity in DEKA. Diameter determines the RATIO of occupancy, i.e., selectivity, with virtually no effect on the amount of ions (which determines conductance) in the channel. Dielectric coefficient determines the actual OCCUPANCY with virtually no effect on the ratios. We are eager to see how the components of free energy of the system, listed above manage to make this happen. We are eager to see if other control systems are at play for other important ions listed above. PNP (POISSON-NERNST-PLANCK) SIMULATIONS WITH STERIC EFFECTS Overview The flow of current through an ionic channel is studied using the energetic variational approach, applied to the primitive (implicit solvent) model of ionic solutions. This approach allows the derivation of self-consistent (Euler Lagrange) equations to describe the flow of spheres through channels. The partial differential equations derived involve the global interactions of the spheres and are replaced here with a local approximation1, we call steric PNP (Poisson-Nernst-Planck). Kong combining rules are used and a range of values of steric interaction parameters are studied. These parameters change the energetics of steric interaction but have no effect on diffusion coefficients in model and simulations. Calculations are done for the calcium (EEEE, EEEA) and sodium channel (DEKA) previously studied in Monte Carlo simulations with comparable results. Biological function is quite sensitive to the steric interaction parameters and we speculate that a wide range of the function of channels and transporters, even enzymes, might depend on such terms. We point out that classical theories of channels, transporters, and enzymes depend on ideal representations of ionic solutions in which nothing interacts with nothing, even in the enormous concentrations found near and in these proteins, or near electrodes in electrochemical cells, for that matter. We suggest that a theory designed to handle interactions might be more appropriate. We show that one such theory is feasible and computable: steric PNP allows direct comparison with experiments measuring flows as well as equilibrium properties. Steric PNP combines atomic and macroscales in a computable formulation that allows calculation of the macroscopic effects of changes in atomic scale structures (size ≅ 10-10 meters) studied so extensively in channelology and molecular biology. Proposed Work Since the work is essentially a verification of an analytic approach (the results of which will be performed by other collaborators), there are many short simulations that will need to be performed. This parameter matrix will include filter radius, filter length, dielectric constants of the protein and the channel regions, boundary conditions in the form of applied voltages, and finally, bath concentration for various physiologically relevant salts. REQUEST FOR REDUCED MODEL OF THE SODIUM CHANNEL These calculations and similar less-intensive published results fit a large amount of important experimental data which is not fit by any other model. It should be noted that at these very low physiological concentrations, such computations, if based on molecular dynamics, would not be feasible. Nevertheless, even with this primitive model, the computations are extremely CPU intensive. The desired allocation of the Reduced Model of the Sodium Channel project is 90,000 core-hours per quarter. This allocation is slightly more than our current allocation. With a new team member and more experience running simulations, we feel we will be able to productively use the additional hours. Each simulation under a particular set of conditions requires in the neighborhood of 1,000 core-hours of computational time. We have found that the code and simulation setup and analysis is most efficient simulations are performed in parallel on 24 cores. With 340 proposed simulations, this request provides some leeway for issues like testing and post processing. Longer walltimes are required for advanced analysis and publication figures. A particular set of conditions means, for example, a particular concentration of NaCl and particular concentration of LiCl with given pore geometry and dielectric constant. REQUEST FOR PNP (POISSON-NERNST-PLANCK) SIMULATIONS WITH STERIC EFFECTS The desired allocation of the PNP (Poisson-Nernst-Planck) Simulations with Steric Effects project is 5,000 core-hours per quarter. Each simulation requires between 5 and 100 core-hours to perform. These jobs will run on single-cores and therefore will make up less than 6% of the total request. Related, previous, simulations have been performed on the Ohio Supercomputer Center and we would like to consolidate our work a single system for efficiency and ease of use. Project URL: http://www.phys.rush.edu/RSEisenberg/physioeis.html Current FY Hours Used: undetermined amount New FY Requested allocation: 380000 Q1: 95000 Q2: 95000 Q3: 95000 Q4: 95000 Justification: Thank You, The LCRC Accounts System

1 0

[LCRC Accounts] Yearly Allocation Request from glassforms
by accounts＠lcrc.anl.gov 28 Aug '12

28 Aug '12

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Xin Tan Project Name: glassforms Division: MSD Project title: First-principles Calculations of Mineral and Glass Dissolution under Various pH Conditions Associated funding: DOE-NE Other Systems: Science: The dissolution of glass forms in nuclear waste disposal determines their long term stability, which is critical for evaluating disposal scenarios. 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-borosilicate 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 and kinetic Monte Carlo simulations. The calculated reaction barriers by using DFT calculations can then be used as input in kinetic Monte Carlo simulations to estimate the over all dissolution rates and compare with experimental values. These investigations will be very important to better understanding of the dissolution behavior and prediction of dissolution rates. Project description: Task I: The first task for this year is to extend our study from pure orthoclase feldspar (KalSi3O8) to a model crystalline material with other constituting elements. In the past two years, we have calculated hydrolysis reaction barriers of the Si-O-Si bridges and the Si-O-Al bridges at surface sites of KAlSi3O8 as a model system in different protonation states – neutral (≡SiOH), protonated (≡SiOH2+) and deprotonated (≡SiO-) using the Nudged Elastic Band (NEB) method. As there are other constituting elements, e.g. B, in borosilicate glasses, we will calculate the reaction barriers of Si-O-B bridges and the B-O-Al bridges at surface sites in different protonation states – neutral (≡SiOH), protonated (≡SiOH2+) and deprotonated (≡SiO-) using the Nudged Elastic Band (NEB) method by using VASP code. Task II: The second task of our research is to simulate the process of glass and mineral dissolution. In the past year, we use constrained molecular dynamics (MD) simulations to study single H2O attack on the Si-O-Si or Al-O-Si bridge that causes bond rupture with the simultaneous H2O dissociation. Studies of the bulk water effect will determine the role of proton shuttle in aqueous solution and the entropic effect of water. Both effects contribute to the free energy reaction barriers. In this year, we will perform MD simulations to study the dissolution process of glass with Si, Al and other constituting elements under acidic, neutral and basic conditions by using VASP code. Task III: The third task for this year is to use DFT calculated reaction barriers as input in kinetic Monte Carlo simulations to simulate the dissolution process both of mineral and the glass. In the past year, we developed a kMC model for dissolution process of a model crystalline KalSi3O8. We are currently expanding our kMC simulation study from a model crystalline material to glasses to simulate the dissolution process of borosilicate glass. This project will primarily use the density functional theory (DFT) implemented in electronic structure code VASP. The system sizes of our calculations ranges from 100 to 300 atoms. VASP has been tested to scale very well in parallel processing on Fusion. The optimum number of processors used for these systems is 16-64 processors per calculation. The kMC simulation code is written in Fortran. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 800000 Q1: 200000 Q2: 200000 Q3: 200000 Q4: 200000 Justification: The first-principles calculations will be carried out using the electronic-structure code VASP. In Task I, NEB calculations will be performed to calculate the reaction pathways for a variety of composing elements under acidic, neutral and basic conditions. A single optimization calculation takes 48 hours on 32 processors. We are considering 30 supercell samplings of silicate glasses including multiple components (Si, Al, B, Na, K). The calculation for possible reactants, intermediates, products will take about 138,240 core hours. It takes about 50 hours on 160 processors (5 images) to calculate a reaction barrier along the reaction pathway. The total estimated computer time for barrier calculation is 240,000 core hours. In Task II, ab initio MD simulations will be performed, where each trajectory runs for 30-50 ps and it takes 16 processors to run for 96-160 hours (average 2048 core hours per trajectory). We will need to run 100 trajectories for five sets of calculations. That requires 200,048 core hours. In task III, kMC simulation will be performed to simulate the dissolution process of glass for 10 different temperatures and 6 different pH values for 72 hours (each simulation should run 50 times in order to get the statistical results). That requires 216,000 core hours. In sum, the total requested allocation for this project is 800,000 core hours. Thank You, The LCRC Accounts System

1 0

[LCRC Accounts] Yearly Allocation Request from NuclearStructure
by accounts＠lcrc.anl.gov 28 Aug '12

28 Aug '12

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Richard Chasman Project Name: NuclearStructure Division: PHY Project title: Optimization of many-body wavefunctions Associated funding: DOE/Office of Nuclear Physics Other Systems: desktop Science: The purpose of this work is to obtain a good description of low-lying nuclear states, going beyond a mean-field description. It becomes necessary to go beyond the mean-field approximation when the nucleus of interest is transitional in some sense, e.g. transitional between a spherical shape and a deformed shape. The need to go beyond a mean-field description is particularly important for excited states. Project description: We are studying medium mass nuclei using an interaction that includes n-p pairing together with deformation. At present, we are investigating several interactions that give rise to deformation in order to determine which ones provide a good description of nuclei having almost equal numbers of protons and neutrons. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 6000 Q1: 1500 Q2: 1500 Q3: 1500 Q4: 1500 Justification: Thank You, The LCRC Accounts System

1 0

[LCRC Accounts] Yearly Allocation Request from aimd_catalysis
by accounts＠lcrc.anl.gov 28 Aug '12

28 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: aimd_catalysis Division: MCS Project title: Ab Initio Molecular Dynamics for Catalysis of Biomass to Fuels Associated funding: Department of Energy, Office of Science, and Office of Basic Energy Sciences Other Systems: None Science: Since the catalytic conversion of biomass occurs in the aqueous phases, water will be intimately involved with the reaction mechanisms. Ab Initio Molecular Dynamics allows for the quantum mechanical simulation of reaction mechanisms in aqueous phases under reaction conditions such as low pH and high temperature (~500K). Metadynamics accelerates the molecular dynamics along collective variables and enables the mapping of the free energy surfaces from reactants to products with trajectories covering several picoseconds. These trajectories reveal the reaction mechanism and estimate the free energies of activation for competing pathways. This project will model the acid catalyzed decomposition of glucose to hydroxy-methyl furfural (HMF) in water. HMF is precursor to transportation fuels and industrial chemicals. The AIMD of reactions with explicit water molecules is more realistic than the self consistent reaction fields used to predict thermodynamics in solutions with quantum chemistry because clusters of water hydrogen bond strongly to glucose and mediates hydrogen transfer reactions in aqueous phases. The results of the AIMD will be used to model the effects of mixed solvents on the glucose decomposition reaction and improved yields of fuel from glucose. Project description: We will use CPMD to model reactions in aqueous phases. This program has the very efficient Carr-Parinello algorithm for AIMD and several different methods for thermodynamics sampling including metadynamics, umbrella sampling and the Blue-Moon ensemble. CPMD is an excellent tool for modeling reactions in liquids and sampling phase space. CPMD has been installed on Fusion for general use. Several Argonne researchers have been trained to use this software in their research. A workshop will further promote the use of CPMD to model reactions. The parallel performance of CPMD is fair. The unit cell for our model of glucose in sulfuric acid contains 230 atoms and a unit cell volume of 2500 Å3. The MPI version of CPMD had a parallel efficiency of 70% on 160 processors for this model. The number of planes in the real space grid limits the number of processors which can be used efficiently by CPMD. The new version of CPMD has implemented multiple walker dynamics. This will increase the scalability of metadynamics, umbrella sampling and the Blue-Moon ensemble by an order of magnitude. A metadynamics run of 10ps is adequate to model a step in the glucose decomposition reaction. Ten picoseconds require 7.3 kilocore-hours. We plan to model ten reaction pathways in the glucose to HMF reaction mechanism in three different solvent mixtures. This work will require approximately 200 kilocore-hours. 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

1 0

[LCRC Accounts] Yearly Allocation Request from spray-modeling
by accounts＠lcrc.anl.gov 28 Aug '12

28 Aug '12

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Sibendu Som Project Name: spray-modeling Division: Energy Systems Project title: Development of a near nozzle spray modeling approach Associated funding: DOE - Office of Vehicle Technologies Other Systems: Convergent Science Inc., Cummins Engine Company Science: The flow inside the nozzle is critical to the near nozzle flow development which in turn influences engine performance and emission characteristics. In the past decade, there has been significant increase in interest for improving the performance and emission characteristics of compression ignition (CI) engines using different nozzle orifice geometries and alternative fuels. However, the lack of modeling tools to accurately predict the influence of in-nozzle flow on spray and combustion development has partly decelerated its (combination of nozzle geometries and alternative fuels) large-scale implementation into the existing infrastructure. The proposed objectives of this project are aimed at further enhancing the predictive capabilities of the near nozzle spray model. The nozzle flow, spray, and combustion model developments will be performed using the commercial code called CONVERGE. This tool is being used by several transportation OEMs such as Caterpillar Inc., Chrysler LLC., Cummins Inc., Ford Motor Company, etc. Hence, these developments will readily facilitate improvements in nozzle orifice design and choice of fuel blends. Project description: The project is divided into 5 major tasks to be performed in 3 years in collaboration with Convergent Science Inc., and Cummins Engine Company: Task 1: Development and validation of a nozzle flow model to account of transient effects such as needle movement, needle off-axis motion, rail pressure fluctuations etc. Task 2: Further advancement of KH-ACT (Kelvin Helmholtz – Aerodynamic Cavitation Turbulence) primary breakup model to calculate more accurately relevant length and time-scales for the cavitation, turbulence, and aerodynamically induced breakup processes. Task 3: In the past nozzle flow and spray simulations have been statically coupled. A dynamic coupling approach will be developed so that the nozzle flow simulations can influence the spray development and vice versa. This is quite complicated since the length and time scales associated with nozzle flow processes are significantly different from spray processes. Task 4: An one equation non-viscosity dynamic structure model large eddy simulation (LES) based turbulence modeling approach will be implemented in CONVERGE. Grid-convergence on critical spray parameters will be evaluated with the implemented LES models. Task 5: Implementation of an Eulerian-Lagrangian spray model: While dynamic coupling of the nozzle flow and KH-ACT models will enhance the accuracy of spray simulations, a transition between the Eulerian and Lagrangian phases must take place at the nozzle exit with this approach. Moving the transition point downstream allows for a more natural bridge between the coupled simulations as the liquid fuel is modeled in an Eulerian framework on both sides of the nozzle exit. A specific challenge of this task is developing an algorithm to convert the Eulerian liquid to Lagrangian parcels outside of the dense spray region. Project URL: http://www.transportation.anl.gov/engines/multi_dim_model_home.html Current FY Hours Used: undetermined amount New FY Requested allocation: 495000 Q1: 125000 Q2: 125000 Q3: 125000 Q4: 120000 Justification: Thank You, The LCRC Accounts System

1 0

[LCRC Accounts] Project Request: OSCon
by accounts＠lcrc.anl.gov 28 Aug '12

28 Aug '12

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: Dmitry Karpeyev Applicant's institution: ANL Applicant's division: MCS,MSD Project Name: OSCon Project title: Optimizing Superconductor Transport Properties Through Large-scale Simulation Associated funding: DOE ASCR/BES SciDAC-3 project OSCon Other Systems: N/A Science: Most energy applications of superconductivity, such as power transmission over superconducting cables, are based on achieving low energy dissipation in high-temperature superconductors. Dissipation is minimized by restricting the mobility of the vortices carrying magnetic field in the superconducting material by pinning them with admixed inclusions. Understanding the interaction of vortices with general configurations of inclusions is a major outstanding challenge both for fundamental science and energy applications. The task is complicated by the high density of the vortices, their mutual long-range interaction, and the dependence of their behavior on external parameters, such as temperature and the applied magnetic field. These features in general preclude analytical description of vortex dynamics and, until recently, made numerical simulation prohibitively expensive. The new capabilities of DOE's leadership-‐class computing hardware and the development of scalable algorithms and software now put detailed numerical investigation of vortex pinning within reach. Capitalizing on these developments, this project aims to advance the fundamental understanding of vortex dynamics in superconductors and to determine the optimal size, shape and concentration of the admixed particles required to achieve optimal power transmission properties. Project description: Computational modeling of superconductor properties is done via Time-dependent Ginzburg-Landau equation. This is a system of coupled nonlinear PDEs of largely parabolic character that have to be run for long times out to a stationary state where the supercurrent statistics can be collected. Resolving the inclusions as well as the evolving structure of magnetic vortices requires both unstructured and time-varying adaptive meshing. Sufficient mesh resolution pushes the mesh and convergence time requirements well past the capabilities of multicore workstations, so we plan to develop our codes in the MPI-based programming model based on PETSc. Later in the project TAO, a PETSc-based scalable optimization package will be used to optimize pinning site configurations. Scalability issues arise primarily from the need to optimize the performance of implicit time integration schemes involving coupled systems, which in turn requires fine-tuning the preconditioner. Main issues encountered here are the non-positive-definite nature of the coupled system and nonstandard nullspaces of the curl-curl operator challenging the standard multigrid techniques. In FY13 we expect to focus on our simulation, meshing, and time-stepping capabilities. We will develop our own code in C and fortran and our typical scaling runs will require up to 800 cores for 2 hours. We expect to do on the order of 100 runs in FY13 and will request additional resources as needed. We expect to have 8 users for this project: 4 in MSD (Aronson, Glatz, Koshelev, new postdoc hire) and 4 in MCS (Karpeev, Munson, Sarich, Wild). Project URL: Requested allocation: 160000 Q1: 40000 Q2: 40000 Q3: 40000 Q4: 40000 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

1 0

[LCRC Accounts] Project Request: lith_ox_md
by accounts＠lcrc.anl.gov 27 Aug '12

27 Aug '12

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 Russell Applicant's institution: ANL Applicant's division: MSD Project Name: lith_ox_md Project title: Molecular Dynamics Calculations of Lithium Oxides Associated funding: Strategic LDRD project entitled Multiscale Modeling of Advanced Electrical Energy Storage Systems Other Systems: Carbon, CNM Science: We will perform molecular dynamics (MD) simulations on nanocrystalline lithium-oxide compounds (including Li2O and Li2O2) of relevance to lithium-air batteries. These simulations include determination of the structures, energies and some properties (such as the diffusivities) of the free surfaces and grain boundaries in these microstructures. A key feature of the simulation approach involves the use of a method to evaluate the Coulomb energy, forces and stresses by direct 1/r summation with spherical truncation (Wolf et al. 1999). This order-N method, which has recently been incorporated into the LAMMPS code that will be used for this work, is computationally superior to both the widely used Ewald method and fast-multipole methods while at the same time producing numerically identical and physically more transparent results. Using this approach, we are able to consider ionic systems consisting of a very large number of ions, thus enabling elucidation of microstructural phenomena and physical behavior that can subsequently be used as input to parameterize a physically realistic mesoscale battery model of microstructure evolution during the charge/discharge cycle. Project description: The goal of this project is calculate structural and thermodynamic properties of lithium-oxide materials and to develop parameters for collaborators studying mesoscale models where experimental values may be unavailable. Our approach will be to use a Buckingham potential to model covalent interactions and a Wolf summation potential for elecrostatic interactions in a fixed charge Li2O model as implemented in the LAMMPS molecular dynamics package. Our model systems will include free particles, surfaces and nanocrystalline materials. This modeling approach is well suited for large systems due to the favorable scaling of the potentials and software. LAMMPS is massively parallel with nearly linear scaling with system size which can allow for 100k+ atom models for tens of nanoseconds. Project URL: Requested allocation: 900000 Q1: 225000 Q2: 225000 Q3: 225000 Q4: 225000 Justification: Both the Buckingham potential and the Wolf summation method scale as pair potentials. LAMMPS benchmarks are available for 1-billion atom LJ models and also scaling for LJ systems with up to 64k processors. http://lammps.sandia.gov/bench.html 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

1 0