September 2011 - Allocations-admins - mailman3.cels.anl.gov

[LCRC Accounts] Yearly Allocation Request from HPCC
by accounts＠lcrc.anl.gov 15 Sep '11

15 Sep '11

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Amit Sharma Project Name: HPCC Division: CSE Project title: Ab-initio chemical kinetics study of high pressure combustion: A theoretical study of the radical-complex mechanism. Associated funding: Department of Energy Other Systems: Two small clusters (named: Pople and Linus) in the CSE fundamental interaction theory group. Science: Recent experimental studies of the falloff curve of the radical-radical association reaction show an unexpected additional rise of the rate constants at pressures above 300 bar in the 300 to 400 K temperature range. Contribution from the radical-complex (RC) mechanism, in addition to the usual energy-transfer (ET) mechanism, is believed to be the dominant factor for this phenomena. The radical-complex mechanism, which has not been theoretically studied and quantified, is the formation of the radical-bath gas (R-M) complex and the stabilization/complexation is related to the strength of the R-M bond in the van der Waals complexes. The decomposition of these R-M complex to stabilized reactants yields an increase in the net association rate. We propose to study the radical-complex mechanism using high level ab-initio kinetics approach and first principle electronic structure methods. The theoretical/computational approach involves development of a reduced dimensional, semi-global, potential energy surface (PES). This PES development is a novel approach due to high-dimensionality of the molecular system under study. For example, a simple oxidation reaction of CH3 with O2 in a monoatomic bath gas is a 15 dimensional system. The PES is developed by fitting high-level electronic structure energies for the radical-radical addition channel and R-M molecular system.The rate constant for the association reaction is calculated using variable reaction coordinate-transition state theory (VRC-TST) for different bath gas species. Project description: We extensively use single reference methods and multi reference electronic structure methods for evaluating the electronic structure energies for a given molecular configuration. In order to fit a full dimensional potential energy surface we need to compute thousands of such configuration spanning a multi-dimensional configuration space. These electronic structure methods are available in the software packages like Molpro, Gaussian, CFOUR, NWCHEM and similar quantum chemistry packages. The VRC-TST code for computing the sum of states at the transition states is developed within our group. This code is used for the calculation of reaction rates. The size of electronic structure calculations, typically, is about 40,000 to 50,000 electronic structure calculations for each system. The computational cost of each electronic calculation depend on the size of the basis set, electronic structure methods and other auxiliary routines such as integral calculations and i/o routines. This can vary anywhere between 0.5 hours to couple of hours for a single electronic structure calculation, for the system we propose to study. There will be 1 to 2 people working on this project who will be using the computational resources. About 30-40% of the allocation will use non-parallel computations. This year we would be making use of the MULTIMODE program developed in the group of Joel Bowman from Emory university. Multimode does Vibrational Self Consistent Field (VSCF) and several types of "CI" calculations for the rovibrational energies and wavefunctions of polyatomic molecules, transition states, clusters, etc. The code is based on the Watson Hamiltonian for non-linear molecules. The many-mode wavefunction is expanded in terms of the eigenstates (also known as the virtual states) of a given VSCF Hamiltonian. Usually the ground state VSCF Hamiltonian is used. This basis is orthonormal and results in a standard eigenvalue problem. The resulting eigenvalues and eigenfunctions are true variational upper bound approximations to the exact eigenvalues and eigenfunctions. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 220000 Q1: 55000 Q2: 55000 Q3: 55000 Q4: 55000 Justification: Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from MCSG_MD
by accounts＠lcrc.anl.gov 15 Sep '11

15 Sep '11

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Yao Fan Project Name: MCSG_MD Division: BIO Project title: Molecular dynamics simulations on protein structure determined at MCSG Associated funding: NIH, DOE Other Systems: Surveyor Science: EsxB is an antigenic protein secreted by Bacillus anthracis that plays an important role in host-pathogen interactions. Our group has determined high-resolution crystal structures of this protein and several mutants. Interestingly, this protein exhibits structural polymorphism, being able to adopt different conformations with minor perturbations from the environment, which may have profound biological implications. We want to investigate the free energy change between the different conformers and how different mutations affect the free energy landscape. Project description: Free energy perturbation methods will be used to calculate the free energy of conformational change and ligand binding. The code being used is NAMD, which has been tested and scales very well on Fusion. >From the previous run, we have determined the free energy change involved in the Tyr-->Phe mutant on EsxB, a virulence factor from B. anthracis. We have also performed preliminary calculations on the free energy between its two conformations from a proposed in silico pathway. The newly allocated computing resource will be used to further refine the conformational free energy calculation, and apply the method to other mutants of EsxB for a full understanding of the protein's structural polymorphism. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 300000 Q1: 100000 Q2: 100000 Q3: 50000 Q4: 50000 Justification: Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from MD_solvent_mixtures
by accounts＠lcrc.anl.gov 15 Sep '11

15 Sep '11

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Sanket Deshmukh Project Name: MD_solvent_mixtures Division: CNM Project title: Atomistic simulations to understand the effect of Water/Methanol Solvent Mixtures on the Lower Critical Solution Temperature of poly(N-isopropylacrylamide) Associated funding: Other Systems: Carbon (CNM) Science: PNIPAM is a thermo-sensitive polymer that has a lower critical solution temperature (LCST) around 305K in aqueous solution.1 As the LCST of PNIPAM is close to human body temperature, it is a serious contender for a controlled drug delivery system.2,3 Coil-to-globule transition occurs in PNIPAM when temperature is raised above the LCST. It is believed that this occurs due to the change in hydrophilic interaction to the hydrophobic interaction.1 Concentration and molecular weight of PNIPAM affects the LCST by less than 1K (304–306K). Lower molecular weight samples appear to have slightly higher LCST. On the other hand, the presence of salts ions in the solution lowers the LCST significantly.1,4 It is believed that, when PNIPAM is dissolved in solvent such as water, PNIPAM has to arrange itself in a specific orientation to form hydrogen bond with the already somewhat arranged water molecules.1 In the case of water molecules, which are near to hydrophobic group of polymer, -CH3 of the PNIPAM side chains, these water molecules must reorient being unable to form hydrogen bond with the non-polar groups in PNIPAM. This reorientation leads to formation of clathrate-like structures, this phenomenon is known as hydrophobic effect, results in decreased entropy upon mixing (negative ΔS).1 When temperature is raised, the entropy term dominates the otherwise exothermic enthalpy of the hydrogen bonds formed between the polymer polar groups and water molecules that is the initial driving force for dissolution. Once the free energy change (ΔG) becomes positive upon mixing, the consequence is phase separation above a LCST as seen in the case of PNIPAM.1 If the concentration of th e PNIPAM is high enough, this replacement of PNIPAM-water contacts with PNIPAM-PNIPAM and water-water contacts is manifested by precipitation.1 In addition to the temperature’s inducing the collapse of the polymer chain, PNIPAM is insoluble in a proper mixture of water and methanol, despite both water and methanol being good solvents for PNIPAM at low temperature.1 The reentrant coil-to-globule-to-coil transition of PNIPAM takes place in a water/methanol mixture with an increase in the methanol content at room temperature. However, the mechanism of this transition is still not well established. It is believed that the transition is implicative to the solvation effect. Two potential mechanisms have been proposed. One suggested that the transition should be induced by the preferential adsorption of methanol molecules on PNIPAM. However, Theoretical calculations done by Pang et. al. demonstrate that water is as stable as methanol for staying in the vicinity of PNIPAM.5 The others ascribed it to the formation of water/methanol clusters. In addition to water/methanol clusters, pure water/water and methanol/methanol clu sters can also be formed in their mixtures and may affect the conformational change of polymer chain. MD simulation techniques can be used to evaluate the various hydrogen bonding interactions between methanol-water and methanol-polymer and methanol-methanol and understand the lowering of LCST at atomistic level. We plan to use MD simulation techniques to understand the role of methanol in influencing the LCST of PNIPAM at atomistic level. To carry out these MD simulations, a simulation cell with ~30-mer of PNIPAM will be solvated with a mixture of water and methanol with different molar ratios. Simulations will be carried out at 260, 278, and 310K for 40ns. The simulated MD trajectories will be used to evaluate the various structural (e.g. radius of gyration (Rg), radial distribution functions (rdf)), and transport properties of water molecules. Project description: Accuracy of the model and MD simulation results mainly depends upon the method of structure generation and force-field used for MD simulations.6 In this work we propose to use the Polymer consistent force field (PCFF) and Amber force field to understand the atomic scale role of methanol on the LCST of PNIPAM.7 The preliminary studies we carried out with PCFF on the PNIPAM-pure water systems predicted the LCST close to 305K, which is in good agreement with the experimentally observed value. A fully atomistic level polymer chain of PNIPMA with ~30 monomer units will be placed in a simulation cell with water/methanol mixtures. Solvated polymer chains will then be equilibrated using MD simulations technique. Methanol concentration will be varied from 1M to 80M. In the case of PNIPAM, our preliminary studies and results from the literature show that to observe any phase transition in these systems, simulation time length must be in the range of 30-50ns. Simul ations will be conducted at 260, 278, and 310K for 40ns. Structural and dynamical properties will be studied for both polymer and water/methanol mixtures by analyzing trajectories of MD simulations. Transport properties of water and methanol will be studied using Einstein relation.6 The structural evolution in all the polymer and water/methanol systems will be studied and compared with each other to study the structure of water, methanol and PNIPAM 30-mer at different temperatures. The computational requirements for the proposed study will be substantial. For the proposed calculations, to study the phase transition across the LCST simulations should be run for ~40ns. From preliminary results of the simulations, we carried out on the CNM’s cluster Carbon and observed a clear phase transition across the LCST, for polymer chains with 30 monomer units (572 atoms) in presence of 9,000 water molecules. This system with ~30,000 atoms required ~145 hrs of simulation time for 10ns on 96 cores. In the proposed work we plan to study, PNIPAM 30-mer polymer chains in presence of different molar ratios of water/methanol mixtures. Total number of atoms in the systems we plan to study can vary from ~66,000 to ~42,000. Table 1 lists the systems we plan to study in detail. Table 1: System details that are planned to study # of PNIPAM #of water #of methanol methanol mole monomer units molecules molecules fractions 30 200 11000 0.018 30 1000 10000 0.09 30 2000 9000 0.18 30 3000 8000 0.27 30 5500 5500 0.5 30 8000 3000 0.73 We plan to study 6 different concentrations of water/methanol system as listed in Table 1. All the systems will be studied at 260, 278 and 310K (Total number of simulations = 6 x 3 = 18). Each simulation will be run for ~40ns (total simulation time = 18 x 40 = 720ns). The estimated time for this particular work to carry out the mentioned calculations would be ~800,000 core hours. References: 1.H. G. Schild, Prog. Polym. Sci. 1992, 17,163-249. 2. D. Schmaljohann, Adv. Drug Del. Rev. 2006, 58(15), 1655-1670. 3. A.S. Hoffman, J. of Cont. Rel. 1987, 6(1), 297-305. 4. H. Du, R. Wickramasinghe, and X. Qian, J. Phys. Chem. B 2010, 114, 16594-16604. 5. H. Y. J. Pang and R. Cheng, Journal of Physical Chemistry B, 2010, 114, 7429 - 7438. 6. M.P. Allen, D. J. Tildesley, Computer Simulations of Liquid, Clarendon Press, Oxford, 1987. 7. Accelrys, Inc. Cerius2 and Discover (programs) and Discover User Guide, version 96.0/4.0.0; Molecular Simulations, Inc.: San Diego, CA, 1996. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 800000 Q1: 400000 Q2: 200000 Q3: 200000 Q4: 000000 Justification: To study the phase transition across the LCST in the case of single PNIPAM chain, simulations should be carried out for ~50ns. From preliminary results of the simulations we carried out on the CNM’s cluster Carbon, we observed a clear phase transition across the LCST, for polymer chains with 30 monomer units (572 atoms) in presence of 9,000 water molecules. This system with ~30,000 atoms required ~145 hrs of simulation time for 10ns on 96 cores. On the Fusion cluster same calculations took ~135 hrs. Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from Neocortex_sim
by accounts＠lcrc.anl.gov 15 Sep '11

15 Sep '11

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Mark Hereld Project Name: Neocortex_sim Division: MCS Project title: Neocortical Seizure Simulation Associated funding: LDRD, NSF and UChicago Development Funds Other Systems: Science: Epilepsy remains a difficult disease to treat. Its causes are likely many and its genesis and development is not well understood. We are applying computational techniques to the study of models of neocortex tissue to extend our understanding of root causes and effects that compliment ongoing clinical and laboratory work at the University of Chicago Hospitals. Project description: Improved scaling that has enabled 1M+ neuron simulations on another large platform. New scale makes simulating realistic tissue slices feasible. Need to develop methods to compare simulation to optical areal measurements of samples in lab. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 5000 Q1: 500 Q2: 1500 Q3: 1500 Q4: 1500 Justification: Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Request: bragg_ptychography
by accounts＠lcrc.anl.gov 15 Sep '11

15 Sep '11

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: Stephan Hruszkewycz Applicant's institution: ANL Applicant's division: MSD Project Name: bragg_ptychography Project title: Development of algorithmic approaches to simulated and experimental x-ray Bragg ptychography imaging. Associated funding: DOE-Basic Energy Sciences Other Systems: CNM Carbon cluster, ~20k cpu-hrs Science: The push towards nanoscale materials design and functionality creates new and difficult challenges in effectively characterizing structural features in materials at these target length scales. Recently developed coherent x-ray characterization techniques can non-destructively image nanoscale diffracting volumes, thus providing a means of studying the internal structure of nanocrystals. Lensless coherent x-ray diffraction imaging (CXDI) techniques have been developed that generate two-dimensional complex image reconstructions of diffracting planar samples and that yield 3D internal strain fields of isolated nanocrystals from volumetric Bragg diffraction. However, the sample requirements of these CXDI methods make studying three dimensional "as grown" or "as designed" nanomaterials difficult. Nanofocused x-ray Bragg ptychography uses the underlying principles of these CXDI techniques, but overcomes their experimental limitations, making it potentially a very powerful tool for nanoscale characterization in materials. This new technique, which we are developing at the CNM/APS Hard X-ray Nanoprobe, is in its infancy and will benefit greatly from simulations of nanofocused diffraction patterns and image reconstruction strategies in order to optimally design and execute experiments on real materials. Project description: We have developed in-house parallel computing software (C++/MPI) specifically to address issues of experimental design and image reconstruction for ptychographic coherent x-ray imaging. The kinematic x-ray scattering summations at the heart of the simulation scale linearly with the number of processors and incorporate realistic x-ray optic models, simulated materials defects, and real-world detector parameters in order to best recreate experimental conditions at the CNM/APS Hard X-ray Nanoprobe. We plan to explore two outstanding issues in this proposal: 1) to understand the limits of 3D Bragg ptychographic imaging of single dislocations in bulk materials, and 2) to develop strategies for imaging 2D Bragg ptychography imaging first from simulated, then from experimental data of nanoscale twin domains in ferroelectric thin films. Both of these thrusts have never before been explored and, if successful, will lead to high profile publications in the field of coherent x-ray diffraction imaging. The ptychography software package we developed requires standard OpenMPI C++ compiling packages, and is controlled through Bash scripting. No special or proprietary libraries or programs are needed. A typical calculation uses 8-40 cpu's simultaneously using >1Gb of memory to store the atomic structure of the simulated sample in question. The code is efficient in that it is based on an "embarrassingly parallel" algorithm and has been tested and used on the CNM Carbon cluster successfully. The computations proposed here will be performed by the PI, and does not cover any other users. Project URL: Requested allocation: 28000 Q1: 7000 Q2: 7000 Q3: 7000 Q4: 7000 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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[LCRC Accounts] Yearly Allocation Request from Atmos_Chem
by accounts＠lcrc.anl.gov 15 Sep '11

15 Sep '11

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Rao Kotamarthi Project Name: Atmos_Chem Division: EVS Project title: Process Scale Modeling of Atmospheric Chemistry and Transport Associated funding: DOE,BLM,NASA Other Systems: NERSC Science: The scientific aim of the proposed modeling activity is to further the understanding of the chemistry and distribution of aerosols over certain regional domains and calculate the heating rates as a result of increased aerosol loading primarily over India. This modeling effort supports the Ganges Valley Aerosol Project (GVAX) a one-year field study funded by DOE BER for the years 2011-2012. Project description: 1. What are the sources and sinks of the aerosols comprising the “Asian brown cloud,” and what effects does it have on clear-sky radiation fields, as well as on cloud micro- and macrophysical properties? What effect does the diurnal PBL cycle in the Ganges valley have on the atmospheric distribution of aerosols? Recent studies indicate that nearly 50 90% of the measured black carbon aerosols that give rise to brown clouds over the Indian Ocean are from biomass burning (residential cooking and agricultural burning), but little quantitative information is available regarding how properties of these aerosols — such as light scattering and absorption and droplet nucleating properties — evolve as a function of time near the source Ganges valley region. Very little is also known about the vertical structure of the distribution of aerosols and the fraction of the aerosols that are available for regional- and global-scale transport from the source region in the Ganges valley. The one-year long AMF deployment is uniquely positioned to make continuous, high frequency measurements through the atmospheric column of aerosol optical properties, radiative transfer and cloud properties. In addition, to bring additional focus on resolving some of the more regional and chemical composition relate d questions inherent in this objective, we propose to conduct a winter intensive field operation starting from January 15th 2012 to March 15th 2012, at a time where aerosol loading over this part of India is known to be the highest. During this intensive, the G 1 will add the additional capability of generating in situ measurements and vertical profiles within the PBL and above to generate estimates of the amounts of aerosols that are transported into the mid troposphere and to regional scales. Additional resources such as MAOS, a surface site below in the valley from the location of AMF and a number of supporting surface sites operated by ISRO/IISc will be available. A more detailed description of this intensive is provided below. 2. What effect do increasing aerosols in the Ganges Valley have on the ISM? What effect do aerosols have on shortwave radiative forcing, mid-tropospheric heating and convective activity over continental India? With the AMF, we will be in a position to make continuous, extended estimates of heating rates within cloud over continental India by measuring cloud properties, drop sizes, and LWC and making complete radiative balance measurements of clouds. The uncertainty in parameterization of deep convective activity in climate models has a profound impact on the calculated climate sensitivity to rising CO2. Deep convective activity is common during much of the summer and pre-monsoon period; the initial onset of monsoon over the southern tip of India is initiated by land-sea circulation and then enhanced and driven by deep convective activity over the northern Indian plains. Specific to this study would be an opportunity to measure the influence of aerosols on deep convection. This highly complex, little understood problem in modeling deep convection is complementary to the elevated heat pump hypothesis. Measurement of aerosols from surface supersites to identify their chemical and phys ical characteristics will provide key constraints to the estimates of radiative forcing heating rates from these aerosols in the PBL during the winter and early spring intensive as discussed above. A second intensive operating period, during the pre-monsoon, is planned for the period extending from February 1, 2012 to April 1st, 2012 for the purpose of coupling the surface measurements made by the AMF with measurements of in situ cloud properties and aerosol measurements made the IISc/ISRO Beechcraft-20, as well as ongoing Indian activities (Aerosol Radiative Forcing over India; ARFI) to obtain a regional footprint. This would be the first ever such effort to synthesize the various measurements into a combined data product over this region that would be available for model validation and evaluating current cloud level aerosol heating hypotheses. We plan to use a combination of models for the project, including the CCSM4.0, GEOS-CHEM for aerosol transport and IMAGE model for aerosol cloud interactions. 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 HEIGHTS-3D
by accounts＠lcrc.anl.gov 15 Sep '11

15 Sep '11

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Tatyana Sizyuk Project Name: HEIGHTS-3D Division: NE Project title: HEIGHTS-3D modeling of plasma material interaction during edge-localized modes (ELM) and disruptions in fusion devices. Advanced 2D and 3D Laser-Produced Plasma Processes modeling for EUV Lithography and other advanced plasma applications. Associated funding: SEMATECH Other Systems: BG/P Science: HEIGHTS package is being developed as a comprehensive tool for simulation and optimization of various interaction processes during intense power deposition of various energy sources such as plasma, laser, and particle beams incident on target materials. This is multi-physics multi-phase package that combines state-of-the art models of energy deposition, vapor/plasma formation/evolution and magneto hydrodynamic (MHD) processes, thermal conduction in material and in plasma, atomic physics and resulting opacities, detailed photon radiation transport, and interaction between plasma/radiation and target material in full three dimension configurations. The package has many areas of applications. It is used to simulate the effect of plasma transient instabilities on plasma facing components in magnetic fusion reactors. This is a critical problem and a serious obstacle to the success of tokamak concept as a viable energy producing device. Most plasma instabilities will cause both surface and bulk damage to plasma-facing and structural materials. HEIGHTS is used to study self-consistently and benchmark various plasma interaction processes, to predict particle and heat intensity at chamber components surfaces, and to study the effects of plasma transient events and high power deposition on reactor walls and predicting/simulating components lifetime. Next area of research with HEIGHTS is optimization of sources for the advanced lithography that includes extreme ultraviolet (EUV) and beyond EUV (BEUV) lithography, which are perspective techniques in the development of the next generation computer chips. Numerical simulations will study various processes for photon production at 13.5 nm and 6.7 nm in efficient and optimized sources design that require detail atomic and plasma radiation physics. Project description: HEIGHTS package is being updated on continuing basis with frequent add-on of new modules, improving of developed physical models and mathematics, and revising of parallel computing methods. With the upgraded HEIGHTS, we will study the following state-of-the art multi-phase multi-physics engineering applications: 1. EUV and BEUV Lithography applications - the next generation lithography of 13.5 and 6-7 nm wavelength photons using 3D laser produced plasmas and multiple laser beams on targets. 2. Colliding plasmas physics for various applications 3. High-power transient plasma interactions with plasma facing and nearby components and calculation of erosion component lifetime in magnetic and inertial fusion applications We would like to request 300,000 allocation hours to conduct various optimizations, benchmarking, and parametric studies of the HEIGHTS 3D packages for several projects during FY2012. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 300000 Q1: 40000 Q2: 80000 Q3: 80000 Q4: 100000 Justification: Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from foam-EngineProcesses
by accounts＠lcrc.anl.gov 15 Sep '11

15 Sep '11

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Sibendu Som Project Name: foam-EngineProcesses Division: ES Project title: Assessment of OpenFOAM for different Engine-Process Applications Associated funding: DCG-LDRD, DOE-Vehicle Technologies Office Other Systems: Science: This project will use an Eulerian-Lagrangian Computation Fluid Dynamics (CFD) open source code called OpenFOAM to model various internal combustion engine processes like engine full-cycle and gas-exchange, sprays and gaseous jets behavior, nozzle internal flow, mixture formation, combustion and exhaust emissions. The goal is to assess the performance of OpenFOAM for varied engine-process applications. Scalability of OpenFOAM for different applications will also be tested. Project description: CFD problems in general are not linearly scalable because of the need for high inter-processor communication. This results in loss of computational efficiency. Performance monitoring tools will be used extensively to understand computation and communication patterns for various physical models (turbulence, transport properties), chemistry mechanisms (varying number of species and reactions) and grid-sizes. Based on these studies, different domain decomposition approaches will be assessed for optimum load-balancing among different processors. Strong and weak scalability for various problem-sizes will thus be assessed. Some key features of the simulations include: 1) Finite volume schemes 2) LES and RANS turbulence models used 3) Detailed chemical kinetic models for diesel and biodiesel fuels 4) Detailed spray models used for different spray processes 5) Full cycle engine simulations Project URL: http://www.transportation.anl.gov/ Current FY Hours Used: undetermined amount New FY Requested allocation: 250000 Q1: 62500 Q2: 62500 Q3: 62500 Q4: 62500 Justification: Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from LiAirLDRD-TMOxides
by accounts＠lcrc.anl.gov 15 Sep '11

15 Sep '11

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Maria Chan Project Name: LiAirLDRD-TMOxides Division: CNM Project title: Investigations of transition-metal oxides as electrocatalysts for Li-air batteries Associated funding: Argonne LDRD Other Systems: CNM Carbon Science: Argonne has funded a Grand Challenge LDRD project in the development of Li-air batteries [1]. Li-air batteries offer significantly higher capacities than their Li-ion counterparts, but there are significant technological challenges before widespread applications are feasible. Among the challenges are large polarizations between charge and discharge and limited cycleability. Recently, our experimental collaborators at Argonne, Lynn Trahey and Mike Thackeray, have found [2] that the use of Li-Fe/Mn-oxides as electrocatalysts useful both in reducing polarization and improving cycleability, when compared with carbon. The mechanism of this significant improvement remains unknown, and first principles computation is important in unraveling this mystery. The electrocatalysts considered are Fe and Mn oxides that incorporate or can accommodate both Li and LixOy species in their structures. Using Fusion allocation from the previous FY, we have sampled configurations of Li and LixOy insertion into MnO2. The results indicate that the equilibrium voltages of Li and LixOy insertion into MnO2 are comparable, which implies the possibility of MnO2 acting as a LixOy-storage material during cycling in Li-O2 cells [3, 4]. But comparison of computed structural parameters with radial distribution functions obtained from EXAFS data taken at the Advanced Photon Source shows that insertion of Li rather than Li2O is more likely [5]. This indicates possible significant kinetic factors related to the reduction of O2 or transport of LixOy which requires further investigation. Moreover, XANES data indicates the partial reduction of Mn prior to the beginning of battery cycling and the nature of the reduced sample is unknown. Since experimental data on Mn oxidation and bond distances are available, computational investigation of various scenarios such as proton and CO acting as reduction agents can be helpful for explaining the observations. Finally, the fundamental question of “What are the stable configurations of (Li2O)x.MnO2 at the experimentally-observed value of x=0.15?” has yet to be unanswered. Understanding these configurations and their effects on Li and LixOy insertion may have significant implications for optimal electrocatalyst sample treatment. Preliminary results on Li2O removal from Li5FeO4 have also been obtained from previous year’s Fusion allocation, showing a reasonable range of voltages compared to experiment. The insertion of LixOy into the subsequent amorphous Fe-oxide structures is important to complete the understanding of how Li5FeO4, after Li2O removal by acid treatment, can act as an effective electrocatalyst. Finally, looking towards further integration of first principles computation and x-ray absorption and scattering data from the APS, we have studied the structure of a key Li-air battery discharge product, Li2O2, using a combination of first principles spectra computed using the Bethe-Salpeter Equation, measured inelastic x-ray scattering data, and DFT total energy using hybrid functionals [6]. Further extension of this approach to compute the XANES of Mn and Fe-oxides is planned in order to make more robust comparisons between experiment and theory. [1] http://www.anl.gov/Media_Center/News/2009/batteries090915.html [2] L. Trahey, C. S. Johnson, J. T. Vaughey, S.-H. Kang, L. J. Hardwick, S. A. Freunberger, P. G. Bruce, and M. M. Thackeray, “Activated Lithium-Metal-Oxides as Catalytic Electrodes for Li–O2 Cells” Electrochemical and Solid-State Letters, 14 (5) A64-A66 (2011). [3] M. K. Y. Chan, L. Trahey, N. Karan, M. M. Thackeray, M. Balasubramanian, Y. Ren, L. Curtiss, and J. Greeley, “First principles studies of MnO2 as electrocatalyst for Li-O2 cells,” in preparation. [4] L. Trahey, N. Karan, M. K. Y. Chan, Y. Ren, J. Greeley, L. Curtiss, M. Balasubramanian, and M. M. Thackeray, “MnO2 as electrocatalyst for Li-O2 cells,” in preparation. [5] N. Karan, M. K. Y. Chan, L. Trahey, M. M. Thackeray, J. Greeley, and M. Balasubramanian, “Structural characterization of acid-treated Li2MnO3 as an electrocatalyst in operating Li-air battery using x ray absorption spectroscopy,” in preparation. [6] M. K. Y. Chan, E. L. Shirley, N. K. Karan, M. Balasubramanian, J. P. Greeley, and T. Fister “Structure of lithium peroxide,” Journal of Physical Chemistry Letters, doi: 10.1021/jz201072b, (2011). Project description: We will use density functional theory (DFT) with the Hubbard U (+U) correction and hybrid functionals which we have benchmarked to show accurate energetics in the Mn-oxide system [3] and which have previously been shown to show reasonably accurate electronic structures in correlated systems such as TM oxides. (1) Kinetic studies of O2 reduction/oxidation, and LixOy transport The nudged-elastic band (NEB) method will be used to study the barriers for O2 absorption, reduction and dissociation, as well as LixOy transport, inside the MnO2 structure. These processes at various Li concentration will be investigated. Each NEB calculation takes 1000-2000 core-hours, and 30-50 such calculations are planned. Ab initio molecular dynamics (AIMD) calculations will also be used to study transport in high-Li concentration regime where stable configurations are numerous. Each AIMD calculation takes 1000-3000 core-hours, and 40 such calculations are planned. Total requested: 140,000 core-hours. (2) Reduction of MnO2 by various species prior to battery cycling The insertion into MnO2 of CO, H, and other possible reducing agents from the electrolyte will be studied by total-energy DFT calculations. Some configurational sampling is required. Approximately 100 such calculations requiring 100-500 core-hours each are planned. Total requested: 30,000 core-hours. (3) Stable configurations of (Li2O)x.Li2O for x=0.15 The large configurational space of a dilute concentration of Li2O within the MnO2 tunnel structure requires the use of the cluster expansion technique. We will perform total-energy DFT calculations on 100-300 sample configurations requiring 100-500 core-hours each, and use the resultant energies to construct a cluster expansion model, which is then used in monte carlo simulations to obtain stable configurations. Total requested: 60,000 core-hours. (4) Insertion of LixOy into amorphous Fe-oxides We have obtained configurations of amorphous Fe2O3 from the Li2O-removal of Li5FeO4. To complete the study of this electrocatalyst, we will perform Li and Li2O insertion sampling of the amorphous structure. A configurational sampling/lithiation simulation algorithm developed with our work on Si will be used. Approximately 2000 calculations of 20-60 core-hours each will be required. Total requested: 80,000 core-hours. (5) XANES and NIXS spectra for TM oxides The x-ray absorption and inelastic scattering spectra of TM oxides with Li and LixOy inserted, obtained from the DFT studies, will be calculated by solving the Bethe-Salpeter equaiton. The use of high-memory nodes will be necessary for such calculations. Total requested: 10,000 core-hours. For items (1)-(4), we will use the well-established DFT code VASP, which uses a plane wave basis set. Using the projector-augmented wave method, only valence electrons will be included which reduces computational costs. For routine calculations, hard scaling efficiency of 70%-80% has been demonstrated for 64 to 128 cores compared to 8 cores, thus enabling efficient calculations of large numbers of configurations. For (5), we will be using the code OCEAN developed at the University of Washington. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 320000 Q1: 100000 Q2: 60000 Q3: 80000 Q4: 80000 Justification: Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request from cfd_enginemodeling
by accounts＠lcrc.anl.gov 15 Sep '11

15 Sep '11

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Sibendu Som Project Name: cfd_enginemodeling Division: ES Project title: Computational Fluid Dynamics Modeling of Petrodiesel and Biodiesel for Compression Ignition engine applications Associated funding: LDRD Project Other Systems: Science: This project will use an Eulerian-Lagrangian Computation Fluid Dynamics (CFD) software called CONVERGE to model various diesel engine processes like internal nozzle flow, spray behavior, combustion and emission processes. The goal is to capture the differences between diesel and biodiesel fuels from a CFD standpoint since computer based modeling is more cost effective than performing full scale laboratory experiments. Project description: The project is dived in two parts: In the first part, engine processes will be modeled using petrodiesel. The spray data obtained from Advanced Photo Source at Argonne and single-cylinder engine performance and emission data from CAT cell will be used to further develop and validate spray and combustion models in CONVERGE and perform parametric studies. The major motivation is to develop more predictive and robust sub-models for capturing diesel engine processes. In the second part, fundamental studies will be performed to establish flame stabilization and lift-off characteristics of biodiesel using CONVERGE. A new surrogate (methyl decanoate) fuel will be used for modeling the combustion characteristics of biodiesel. Comparison will be performed between inner nozzle flow, nonevaporating and evaporating spray, combustion characteristics, engine performance and emission characteristics of biodiesel and petrodiesel. Some key simulation features are listed below: 1) Finite volume schemes 2) LES and RANS turbulence models used 3) Detailed chemical kinetic models for diesel and biodiesel fuels 4) CONVERGE software is being used - 48 licenses available 5) Scales well up-to 48 processors 6) Detailed spray models used for different spray processes 7) Full-cycle engine simulations Project URL: http://www.transportation.anl.gov/ Current FY Hours Used: undetermined amount New FY Requested allocation: 495000 Q1: 123750 Q2: 123750 Q3: 123750 Q4: 123750 Justification: Thank You, The LCRC Accounts System

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