September 2016 - Allocations-admins - mailman3.cels.anl.gov

[LCRC Accounts] Yearly Allocation Request for PETSc-Foam
by accounts＠lcrc.anl.gov 07 Sep '16

07 Sep '16

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Shashi Aithal Project Name: PETSc-Foam Division: CELS Project title: Investigation of robust, scalable solvers for OpenFoam Associated funding: Other Systems: Science: OpenFOAM (OF) is a multi-physics open-source solver code capable of modeling a wide-range of problems of interest to various divisions at ANL. One of the strengths of OpenFOAM is that new solvers and utilities can be created by its users. In this project, we intend to investigate fast, robust, scalable solvers for problems involving moving boundaries and combustion. The goal is to study various methodologies for load-balancing and solvers for large-scale simulations. Project description: OF is parallel, finite-volume CFD code which will be used for this project. Scaling studies on dsmcFoam and dieselFoam have shown good scalability. Small DSMC cases (1 million cells) have shown good scalability up to 192 cores. DieselFoam has shown good scalability up to 512 cores with about 500K cells. We will continue our with using the development branch of OpenFoam as with the previous year. Various algorithms for efficient domain decomposition and solution methods for combusting mixtures will continue to be investigated for optimal performance and robustness. New mesh-motion strategies, turbulence models and higher resolution studies are planned. 1) We will continue work on integrating reactingFoam solver currently capable of premixed/diffusion flow solver with engineFoam (moving mesh). Standard mechanisms such as gasoline (874 species, 3811 reactions) will be tested with the moving mesh problem for simplified engine geometries. 2) VOF modeling of the primary breakup of sprays in next generation injectors including effects of needle valve opening and closing 3) Investigation of improvements in OF solvers for reduction of numerical dissipation. Most of the effort this year will be on code development and testing of enhancing engineFoam. Industry partnership: None Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 100000 Q1: 25000 Q2: 25000 Q3: 25000 Q4: 25000 Justification: Storage requirements: Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Request: ph_dynamics
by accounts＠lcrc.anl.gov 07 Sep '16

07 Sep '16

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: Sridhar Sadasivam Applicant's institution: ANL Applicant's division: NST Project Name: ph_dynamics Project title: Hot phonon dynamics in III-V semiconductors Associated funding: Department of Energy (LDRD) Other Systems: Carbon cluster, Center for Nanoscale Materials (560,000 hours) Science: The need for improved thermal management of devices is ubiquitous in present day technologies, impacting fields as diverse as the miniaturization of electronic components [1], the durability of new-generation solar cells [2], and the efficiency of thermoelectrics and thermophotovoltaics [3]. In this work, we propose to compute the phonon thermalization/equilibration time in III-V semiconductors using a combination of first-principles calculations and transient solutions of phonon distribution under the Boltzmann transport equation (BTE) framework. The objectives of the present work include the need for development of design rules that can be used to provide quantitatively accurate estimates of phonon thermalization time. Also, the proposed work is expected to contribute towards the development of quantum corrections to classical molecular dynamics simulations at short time scales during which non-equilibrium effects between the different phonon modes is prominent. We choose to work with III-V semiconductors due to their applications in electronics and photovoltaic applications where hot electrons and phonons are expected to prevail over picosecond timescales. Also, the wide range of III-V semiconductors with variations in atomic masses and bond polarity can provide interesting insights on tuning of electronic and vibrational properties to engineer the phonon thermalization time in such materials [4]. The proposed work involves the calculation of electron-phonon scattering matrix elements on a fine wavevector grid using a combination of density functional perturbation theory on a coarse grid along with Wannier interpolation to dense electron and phonon wavevector grids [5]. Phonon-phonon interactions require the computation of third-order force constants using a real-space supercell approach [6]. The electron-phonon and phonon-phonon scattering matrix elements will then be used in Fermi’s Golden Rule to compute the scattering rates for each phonon state. The calculated scattering rates will be used as input to the BTE to evaluate the time evolution of phonon occupation and the equilibration time between the various (acoustic, optical) phonon modes. References: 1. D. G. Cahill, et al. J. Appl. Phys., 93, 793 (2003); J.E. Turney et al., Phys. Rev. B, 79, 224305 (2009)  2. S. Zhang et al., J. Mater. Chem., 21, 466–474 (2011)  3. C. Ungaro, S.K. Gray, and M. C. Gupta, Applied Phys. Lett. 103, 071105 (2013)  4. Y. Yao & D. Konig, Solar Energy Materials & Solar Cells, 140, 422-427 (2015) 5. F. Giustino, et al., Phys. Rev. B, 76, 165108 (2007); J. Noffsinger et al, Comput. Phys. Comm., 181, 2140 (2010); URL: http://epw.org.uk/ 6. L. Lindsay and D. Broido, Phys. Rev. B, 81, 205441 (2010) Project description: We propose to perform phonon dynamics calculations on a wide range of III-V semiconductors (e.g., BN, BAs, BSb, GaN, GaAs, AlN, InN) in order to understand the effects of changes in atomic mass, bond polarity and electronegativity of constituent atoms on the dynamics of hot phonons. Hence, the following steps need to be performed for each III-V semiconductor: 1. Computation of phonon bandstructure using density functional perturbation theory (DFPT): Since we are primarily interested in III-V semiconductors with a two atom unit cell in the zinc-blende structure, the phonon bandstructure calculations can be performed in serial mode. For a typical 5 x 5 x 5 phonon wavevector grid, the phonon dispersion can be obtained in about 5 hours based on preliminary calculations using the phonon module of Quantum Espresso in the Carbon Cluster at the Center for Nanoscale Materials. 2. Computation of electron-phonon scattering rates: The electron-phonon scattering rates for each phonon mode in a dense grid (e.g., 50 x 50 x 50) needs to be computed. For each point on the phonon grid, the corresponding electronic wavevector grid also needs to be of the order of 50 x 50 x 50 in order to obtain convergence of energy conservation delta functions around the Fermi surface. These calculations will be performed using the Electron-Phonon Wannier (EPW) code that is available as a module in Quantum Espresso. The Wannier interpolation procedure will be parallelized over at least 4 nodes (64 cores) and this calculation is expected to require about 100 hours based on preliminary calculations on coarser wavevector grids. Hence the total time required for electron-phonon scattering calculations is about 64 x 100 = 6400 hours. 3. Computation of phonon–phonon scattering rates: The phonon-phonon scattering rates will be computed using a real-space supercell approach. From our initial calculations on BN using a 6 x 6 x 6 supercell with 432 atoms, the time required for each supercell DFT calculation is about 1 hour with 16 cores. The total number of supercells that need to be considered is 136 assuming a third-nearest neighbor cutoff for third-order force constants. Further convergence studies will need to be performed to ensure convergence of phonon-phonon interactions with respect to the cutoff distance. Assuming that phonon-phonon interactions are computed for three different cutoff distances and 150 supercell DFT runs for each cutoff distance, the total time required for these calculations is approximately 150 x 3 x 16 x 1 = 7200 hours. 4. Computation of phonon thermalization time: The electron-phonon and phonon-phonon scattering matrix elements computed in the previous steps will be used to obtain the transient evolution of phonon occupation function over a time scale of approximately 100 ps. This will involve the use of Fermi Golden rule to compute transition rates between the different phonon states due to electron-phonon and phonon-phonon scattering. Since we will be using an explicit time-stepping scheme, the calculation of transition rates is readily parallelizable. We have performed preliminary calculations using the opensource code ShengBTE and the calculation of phonon-phonon scattering rate for all wavevectors in a 20 x 20 x 20 grid requires about 5 minutes over 16 processors. Assuming 1000 time steps for transient solution of the BTE, the total time needed for phonon-phonon scattering rate alone is expected to be about 1300 hours. However finer grids such as 40 x 40 x 40 (8x more wavevectors) will also need to be tested and electron-phonon scattering rates will have to be computed in conjunction with the phonon-phonon scattering rates. Hence the total time required for this part of the calculation is approximately 20,000 hours. The estimated time required for each of the above steps is summarized below: 1. Computation of phonon dispersion in serial mode: 5 hours 2. Wannier interpolation of electron-phonon matrix elements: 6400 hours 3. Computation of third-order force constants: 7200 hours 4. Transient solution of BTE: 20,000 hours The time needed for the above calculations is about 35000 hours. However, the foregoing steps need to be repeated for a wide range of III-V semiconductors (~10) to obtain the dependence of phonon thermalization time on atomic masses and electronegativity of atoms. Hence, the total requested time is 350,000 core-hours. Less than 1% of these calculations will be performed in serial mode. Dr. Sridhar Sadasivam and Dr. Pierre Darancet will be responsible for carrying out the simulations. Industry partnership: Project URL: Requested allocation: 350000 Q1: 100000 Q2: 100000 Q3: 100000 Q4: 50000 Justification: Storage requirements: 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 for copolymer_dsa
by accounts＠lcrc.anl.gov 07 Sep '16

07 Sep '16

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Abelardo Ramirez-Hernandez Project Name: copolymer_dsa Division: MSD Project title: Directed Self-Assembly of Block Copolymers Associated funding: Other Systems: Science: The morphology of a block copolymer thin film is particularly sensitive to its boundary conditions. Lithographic applications of block polymers in the microelectronics and memory device industries require formation of particular complex morphologies. Current fabrication targets envisage the creation of dense arrays of structures with domain sizes in the sub-10 nm regime. In this project, a coarse grained approach will be used to perform a systematic study of a wide range of polymeric material combinations and conditions, leading to optimal assembly. We will consider the effect of molecular weight, block copolymer film thickness and chain architecture, and degree of incompatibility, etc. Our results will be summarized in the form of generic phase diagrams that should serve as a guide for experiments. Project description: Our efforts in this project will be focused on the self-assembly of block copolymer thin films directed by patterned surfaces. Given the relatively large number of parameters involved, a combinatorial search of optimal conditions is necessary. Multiple simulations will be bundled together as ensemble jobs using a coarse grained simulation approach. Ensemble runs performing parameter sweep (chain architecture, polymer-substrate interactions, etc.) will be structured as 24-hour ensemble runs. This project is a collaborative effort between Brewer Science and our group at IME/MSD. It was recently approved and we are in the process of getting simulations ready for production runs. Industry partnership: Brewer Science Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 96000 Q1: 48000 Q2: 48000 Q3: 0 Q4: 0 Justification: Storage requirements: 1TB Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request for ESMF
by accounts＠lcrc.anl.gov 07 Sep '16

07 Sep '16

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Silverio Vasquez Project Name: ESMF Division: MCS Project title: Earth System Modeling Framework Associated funding: DOD, NASA, NSF, NOAA Other Systems: external: NERSC, NCAR, ORNL, NCSA, NASA, NOAA Science: The Earth System Modeling Framework (ESMF) enables the coupling of model components in high performance Earth system modeling codes. ESMF component interfaces have been implemented in most of the prominent climate and weather codes in the U.S.: CESM, NASA GEOS-5 and ModelE, NOAA NEMS, NRL COAMPS and NavGEM, and the GFDL MOM5 ocean. In general, componentization with ESMF has been implemented at the level of major physical domains, where simulated interactions require inter-component data communications (e.g. atmosphere, ocean). Over the years ESMF has evolved and now can be used in multiple ways: 1) to create interoperable component-based modeling systems; 2) as a source of remapping, time management, metadata handling, and other functions; and 3) as a file-based offline generator of interpolation weights for many different kinds of grids. ESMF grid remapping is also available through a Python interface (ESMPy). New capabilities were added this year as a consequence of feedback we received from the modeling and data communities. Activity continued in areas of the NUOPC Layer, ESMF regridding, and ESMPy, the ESMF Python interface. Project description: The previously released NUOPC Layer reference API was refined to provide a more object-oriented interface that better reflects the NUOPC Driver, Model, Connector, and Mediator concepts. The NUOPC Driver now allows child components to be added dynamically, supporting the implementation of more flexible applications. String labels are consistently used to identify component instances and initialize/run/finalize phases. The introduction of namespaces allows for more control over automatic field pairing, and LocStreams (a geometric type that can be used to represent a set of disconnected points) can now be transferred between components during initialize. The compliance checker has become aware of the component context and produces more useful output. Finally, some of the utility routines previously contained in the NUOPC Layer have moved into ESMF. In the area of ESMF regridding, a new application, ESMF_Regrid, was added. This command-line tool can be used to regrid a data field defined in a UGRID or GRIDSPEC format file to another field defined in a different file. The ESMF_RegridWeightGen application, which precomputes regridding weights, now supports additional options to i) allow non-conservative regridding on cell center locations in the unstructured case, ii) ignore degenerate cells, and iii) choose between different line options when regridding on a sphere. The ESMF regridding implementation now supports an option for using a first order conservative method for unstructured Meshes built on DOE's MOAB mesh library (the version built on ESMF's native mesh library is still available). ESMF unstructured Meshes have been extended to handle elements that consist of more than one polygon to allow the representation of geographically disconnected areas (e.g. the Hawaiian Islands) as a single element. The ESMF regridding capability was further extended to cover i) ESMF LocStreams, ii) first-order conservative regridding of concave quadrilateral cells, iii) non conservative regridding on Mesh elements with more than four sides, and iv) the use of great circle lines when computing 3D bilinear interpolation weights on a sphere. The ESMF Python interface ESMPy has matured and offers more complete coverage of the ESMF Grid, Mesh, and LocStream classes. It also now offers read methods that allow a Field to be filled with data from a NetCDF file. Anaconda packages are now available for easy installation of ESMPy on Linux and Darwin systems. Currently ESMF is regression tested daily on Blues with: -- gfortran with mvapich2, and mpich3 -- intel with mvapich2 and mpich2 -- nag with mpich2, mpich3, and openmpi -- pgi with mvapich2 and mpich3 On the Blues gfortran, benchmark testing is included to detect any unexpected change in the performance of the software. ESMPy is also tested on Blues with mvapich2. ESMPy is the ESMF Python Regridding inteface. ESMPy testing includes building and installing ESMF with NetCDF, building python, running unit tests, examples and regridding from files tests. On Fusion, ESMF is regression tested with: -- g95 with mvapich2 -- gfortran with mvapich2 and mpich2 -- intel mvapich2 mpich2 . The regression test includes: - building the ESMF software and installing it, - building and testing 6 applications, - building and running system tests, examples and unit tests bundled with the software. The entire test suite is run with debug and optimized settings. In addition, two versions of ESMF are regression tested, the head of the development, and a branch based on the last public release where limited development has continued. Industry partnership: Project URL: http://www.earthsystemmodeling.org Current FY Hours Used: undetermined amount New FY Requested allocation: 24000 Q1: 6000 Q2: 6000 Q3: 6000 Q4: 6000 Justification: Storage requirements: Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request for IntensitySim
by accounts＠lcrc.anl.gov 07 Sep '16

07 Sep '16

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Justin M Wozniak Project Name: IntensitySim Division: MSD Project title: Simulation Support for APS Data with ab initio Hybrid Reverse Monte Carlo Associated funding: LDRD Other Systems: Science: Our high-level goal is to improve the methods for determining large-scale structure for materials imaged at the APS by using Hybrid Reverse Monte Carlo, a combination of DFT, energy, and X-ray intensity calculations. Project description: Development history: The Calculate_I software came out of the Discovery Engines LDRD for combining experimental science with simulation. The program is written in Fortran with MPI for parallelism. OpenMP integration is planned. The code is compute-intensive: it reads a small amount of data produced by experiment and writes out a ~1 MB atomic structure dataset at the end. The computational method used models and improves a simulated atomic struction. A Monte Carlo iteration process then proposes improvements. The potential improvements are evaluated based on an energy calculation and an X-ray scattering intensity comparison to experimental data. The programming model used is Fortran + MPI. The code has been tested on LCRC scales and is expected to scale beyond that. We think that the analysis of data recently produced at CHESS by Ray Osborn will produce a Nature Materials paper. This project will use our software, Calculate_I, supported by 2000 VASP calculations. The plan to run VASP 2000 times and Calculate_I once for each experimental data set. The project initially contains the developers: Anh Ngo and Justin Wozniak. We will perform structure optimizations based on APS experiments of mullite and NaXV2O5 with different magnetic configurations will be carried out using (2 x 1 x 2) bulk unit cells. By comparing different magnetic ordering energies we will conclude which configuration corresponding to the ground state energy. We will determine the ground state structure as a result of the density functional theory (DFT) calculations using the VASP package. Periodic boundary condition (PBC) will be imposed in order to maintain periodicity of the solid support. Gradient corrected PBE density functional will be used for these calculations. From there, we can run Calculate_I to optimize the large scale structure. Those programs are currently available on Blues cluster and scale very well. Our total request is 1,000,000 core hours divided over the 4 quarters. Recent research products include: “The Incommensurate Modulation in Mullite: An ab initio Approach” Anh T. Ngo, Raymond Osborn, Stephan Rosenkranz, Justin Wozniak, and Peter Zapol "Mechanical Flexure and Vibrational Maps of Individual Sexiphenyl Molecules on Ag(111)" Anh T. Ngo, Raymond Osborn, Justin Wozniak, and Peter Zapol Industry partnership: Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 1000000 Q1: 250000 Q2: 250000 Q3: 250000 Q4: 250000 Justification: We plan to use two codes: VASP and Calculate_I. The current version of Calculate_I scales well to 200 cores, which is the level at which we plan to run it. Storage requirements: 100GB Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request for uo2_md
by accounts＠lcrc.anl.gov 07 Sep '16

07 Sep '16

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: John Russell Project Name: uo2_md Division: MSD Project title: Thermal conductivity of uranium oxide with embedded carbon nanotubes Associated funding: Other Systems: Science: Heat dissipation is an important factor in safely using and storing nuclear fuels. Uranium oxide has a low thermal conductivity which can allow temperatures to rise quickly. One strategy to improve heat flow in uranium oxide is to embed carbon nanomaterials in the oxide. We investigate by molecular dynamics the phonon thermal conductivity of uranium dioxide with embedded carbon nanotubes. In initial calculations, we find a three fold increase in thermal conductivity of a 50 nm uranium oxide model system with an embedded (10,0) CNT. Real values will likely be higher since phonon confinement effects in the relatively small model system result in systematically lower values. Project description: Uranium and uranium oxide spent fuels are stored in water to safely maintain temperatures well below the melting point. Power disruptions from a tsunami interupted cooling of fuel rods at the Fukushima Daichi power plant resulting in a meltdown [1, 2]. Increasing thermal conductivity of fuels will result in a faster cooling rate, which could improve safety. Embedded carbon nanotubes (CNTs) or nanofibers might be a strategy to improve thermal conductivity in bulk UO2. CNTs have large surface areas, high mechanical strength, chemical stability, and thermal conductivity which makes them an intriguing candidate for design of a hybrid material. The goal of this project is calculate structural and thermodynamic properties of UO2 and hybrid materials where experimental values may be unavailable. Our initial approach will be to use a partially ionic model (PIM) of the Born-Mayer-Huggins (BMH) potential to model the UO2 material [3, 4]. The PIM features a reduced ionicity with less than full ionic charge on U and O atoms, and it matches the UO2 lattice constant at temperatures over 1000K, which a full ionic model gets wrong. Likewise, electrostatics will be calculated with a linear-scaling Wolf summation. For coupling terms, C-C interactions will be handled by means of a Tersoff potential [5], and the remaining U-O and U-C interactions will be handled with Morse potentials fit to density functional theory (DFT) reference calculations. With respect to thermodynamic proprerties, we will calculate the thermal conductivity by means of the Muller-Plathe [6] method and the Green-Kubo method. In this way, our approach will capture the salient features of the problem, including ionicity of the UO2 and covalency of the CNTs. Our model systems will include free particles, surfaces and nanocrystalline materials. To calculate properties of our model system, we will conduct molecular dynamics simulations using LAMMPS and DFT calculations will be using CP2K and/or VASP. 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 [7]. CP2K is an electronic structure package with good efficiency for serial and parallel systems and excellent accuracy. [8,9] Depending on the size of the model system, it may make more sense to use VASP with a larger number of K-Points. For this reason, we also include VASP, which is a standard electronic structure package with reasonable parallel scaling up to hundreds of cores. Our team has 5 members: John Russell (MD calculations), John Low (DFT calculations), Peter Zapol, Petr Kral, and Larry Curtiss providing scientific leadership and oversight. [1] D. Cyranoski, G. Brumfiel Nature 477, 139-140 (2011). [2] J. Medalia Congressional Research Service, R41728 (2011). [3] T. Arima, S. Yamasaki, Y. Inagaki, K. Idemitsu J. Alloys Compd. 400, 43-50 (2005). [4] T. Arima, S. Yamasaki, K. Idemitsu, Y. Inagaki J. Nucl. Mater. 376, 139-145 (2008). [5] P. Erhart and K. Albe Phys. Rev. B 71 035211 (2005). [6] F. Muller-Plathe J. Chem. Phys. 106 6082-6085 (1997). [7] S. Plimpton J. Comp. Phys. 117, 1-19 (1995). [8] J. VandeVondele, M. Krack, F. Mohamed, M. Parrinello, T. Chassaing and J. Hutter, Comp. Phys. Comm. 167, 103 (2005). Industry partnership: Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 100000 Q1: 25000 Q2: 25000 Q3: 25000 Q4: 25000 Justification: The total request is for 100k hours, with the bulk of the time spent on DFT calculations of UO2 surfaces and interfaces, which are extremely challenging. Storage requirements: Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request for Li_air_battery
by accounts＠lcrc.anl.gov 07 Sep '16

07 Sep '16

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Kah Chun Lau Project Name: Li_air_battery Division: MSD Project title: Computational studies of Li-Air battery components Associated funding: DOE-EERE Other Systems: Science: Today's battery researchers and developers have not yet been able to unlock the theoretical potential of Li-Air battery into practical application due to : (1) the unstable non-aqueous electrolytes that easily oxidized and decomposed during discharge/charge, thereby seriously limiting cycle life; (2) during discharge, the insulating solid LixOy products are deposited on the surface or within the pores of the cathode, thereby clogging the pores, restricting oxygen flow and shut down the electrical conductivity; (3) poisoning of the lithium electrode due to oxygen crossover destroys the integrity and functioning of the cell; (4) commonly used cathode catalysts, such as metals, metal complexes, and metal oxides, do not access the full capacity of the oxygen electrode or enable sufficiently high rates; and (5) the possible parasitic effects due to unavoidable impurities (e.g. CO2, H2O) for practical applications. Thus in the computational studies, these problems will c ontinue be addressed and explored based on state-of-the-art ab initio atomistic modeling techniques that work closely with experimental colleagues at ANL and our collaborators from Ohio State University (OSU) and Tsinghua University at China. This project will also be in its 2nd year that was awarded under the DOE-EERE program on year 2015 that led by Argonne to proceed a fundamental study towards the newly proposed Li-O2 battery that based on lithium superoxide (LiO2) system [1]. Project description: In the coming fiscal year (FY2017), we need 1200 000 core-hour to complete our proposed tasks. We will complete our current on-going work and continue to explore different problems in lithium superoxide based Li-O2 batteries based on experimental input from our colleagues at ANL. To complete the current ongoing study (i.e. the thermodynamic of LiO2/substrates several thermodynamic stable LiO2 surfaces grow on the metal alloy substrate surface based on VASP calculations), our experience indicates that 100, 000 hours is required to complete the investigation. For our new study at FY2017, the computational methods will involve largely AIMD (CPMD, VASP, CP2K) and DFT method (Gaussian09, VASP, Quantum Espresso). For Gaussian09, the DFT calculation scales well up to 8-16 processors and for 4-6 nodes is the optimal number of nodes for geometry optimization for system size below 100 atoms. We will require about 200,000 core hours to study the underlying chemical reaction pathways and vibrational spectroscopic (IR/Raman) properties of solvated complexes (i.e. MxOy@electrolyte molecules or M+@electrolytes molecules with M = Li, Na, K) at different electrolytes in solution phases. To extend our previous enhanced thermodynamic stability of LiO2 towards electrolyte/LiO2 interface [2], we will continue extend our focus study on the thermodynamic stability towards disproportionation of LiO2 in close collaboration with experimental investigations. One of the future research direction is focus on the enhanced stability of crystalline LiO2 growth through potassium doping [3] and potassium oxide substrate. Our preliminary results suggested that a small amount of potassium impurities might be useful to stabilize superoxide radical on cathode [3]. To extend our investigation, a systematic DFT investigation of LiO2 crystalline growth on potassium oxide/superoxide substrate will be carried out. To complete this study, we will need 300,000 core hours for the simulation to cover 3-4 different low energy crystalline surfaces with different surfaces or substrates thickness. In addition, we will explore our investigation into the roles of mixed electrolytes into the performance of Li-O2 battery with the supporting efforts in experiments from Argonne and OSU colleagues. For the preliminary focus study, we will investigate the effects of mixed potassium (K) and lithium (Li) salts and mixed sodium (Na) and lithium (Li) salts in electrolytes for Li-O2 battery performances. In this focus study, we will need 600,000 core hours (i.e. 300,000 core hours for each mixed K+/Li+ and Na+/Li+-electrolytes) for large scale AIMD simulation based on CPMD, CP2K or VASP calculations to locate the thermodynamic favorable solvation structures in bulk electrolytes based on experimental pre-determined electrolytes. In conclusion, this will need 1200 000 core-hour (1.2 Million core-hour) to complete all these proposed problems in FY2017. References: (1) J. Lu, Y-J. Lee, X. Luo, K.C. Lau, M. Asadi et. al. Nature 529, 377-382 (2016). doi:10.1038/nature16484 (2) D. Zhai, K.C. Lau, H. Wang, J. Wen, D.J. Miller, J. Lu, F. Kang, B. Li, W. Yang, J. Gao, E. Indacochea, L.A. Curtiss, K. Amine, Nano Lett. 15 (2), 1041-1046 (2015). (3) D. Zhai, K.C. Lau, H.H. Wang, J. Wen, D.J. Miller, F. Kang, B. Li, K. Zavadil, L.A. Curtiss, ChemSusChem. 8 (24), 4235-4241 (2016). Industry partnership: Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 1200000 Q1: 300000 Q2: 300000 Q3: 300000 Q4: 300000 Justification: For the details and evidence how to use the hours effectively, please see the project description and project report (FY2015 and FY2016). Further details of the scaling and the performance of the codes can be found as follows: (1) VASP: http://cms.mpi.univie.ac.at/vasp/vasp/Performance_parallel_code_on_various_… (2) CPMD: http://cpmd.org/documentation (3) Gaussian09: http://www.gaussian.com/g_prod/g09_glance.htm Storage requirements: Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Request: GATEM
by accounts＠lcrc.anl.gov 07 Sep '16

07 Sep '16

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: Maria Chan Applicant's institution: ANL Applicant's division: NST Project Name: GATEM Project title: Genetic Algorithm Optimization of Interfacial Structures from Electron Microscopy Associated funding: LDRD Other Systems: None Science: Electronic, optical, mechanical, electrochemical, and piezoelectric properties are significantly influenced by the presence and characteristics of solid-solid interfaces such as grain boundaries. Atomic structure of materials can be characterized by transmission electron microscopy (TEM) and scanning TEM (STEM). However, it is very challenging to characterize interfaces and surfaces due to imperfections and defects at these regions. The goal of this project is to establish a quantitative method for comparing simulated S/TEM images with experimental S/TEM images, so that comparative decisions about image similarity rely on a quantitative algorithm, rather than expert judgment. Successful automation of a similarity decision, along with energetic information from empirical potential or DFT, is a crucial step in developing a multi-objective genetic algorithm optimization loop for determining 3D structures at a disordered interface. Due to the iterative n ature of the overall optimization process, emphasis must be placed on making each step computationally efficient. Current image simulation techniques based on an FFT multislice algorithm are used to qualitatively confirm the interpretation of conventional TEM images formed from coherently scattered electrons, and are relatively efficient, as they assume a periodic input structure and operate within the constraints of the weak phase object approximation. We will extend the current image simulation capabilities to non-periodic specimens in a computationally efficient manner and include signals from high angle annular dark field (HAADF) region to achieve high lateral resolution, Z-contrast imaging. Project description: A crucial component of most recognition-based tasks in the field of computer vision (CV) is the definition of “image similarity” relative to a target image. This work adapts a popular CV framework, scale invariant feature transform (SIFT), for the purposed of measuring the similarity between real and simulated atomic resolution microscopy images. The similarity metric (SIFT descriptor) will be developed offline, but requires several simulated/experimental image matches to use as a test set for training a machine learning model and/or algorithm refinement. Once the similarity metric is proven adequate, the effort will then shift to parallelizing the current multi-slice code for use in a multi-objective genetic algorithm optimization method, aimed at determining the full three-dimensional structure of materials at solid-solid interfaces. The multi-objective genetic algorithm will be used to optimize the atomic structure to obtain optimum image simi larity from the constructed SIFT descriptor, and the energy of interfaces, simultaneously. The energy evaluations of interfaces can be accurately computed with DFT methods, whereas empirical potentials provide also a reasonably accurate thermodynamics with significant reduction in computational cost. We will start with computing the interface energies using the available empirical potentials for CdTe, namely Stillinger-Weber (Z. Q. Wang, D. Stroud, and A. J. Markworth, Physical Review B 40, 3129 (1989).) and Bond Order potential (D. K. Ward, X. W. Zhou, B. M. Wong, F. P. Doty, and J. A. Zimmerman, Physical Review B 85, 115206 (2012).) from molecular dynamics (MD) simulations in LAMMPS (http://lammps.sandia.gov/) All image simulations will be carried out using the Kirkland TEMSIM code (C++), available as open source from https://sourceforge.net/projects/computem/. The breakdown of the required calculations is as follows: (i) Descriptor development: A single simulated image requires about 500 core hours of computation. At this stage, we require 10 fully-converged simulated images for a total of 10*500 = 5,000 core hours to refine the current SIFT adaptation. Convergence is achieved when the total integrated intensity of the detector region is nearly unity, which is a function of pixel size. For imaging areas in 40‎Å x 40‎Å window, a 1024x1024 sampling size is typical. We will run quick 1D line scans on a few of the images before proceeding with constructing the set for the descriptor development. This convergence checking procedure will only need to be carried out once and will apply to the remaining calculations. It is estimated that this will require 5,000 core hours. (ii) TEMSIM parallelization: Efforts are in order to adapt the Kirkland code (E. J. Kirkland. Advanced Computing in Electron Microscopy. Plenum, New York, (1998)) to a parallel computing environment by propagating several probes at the same time on different processors, and/or by parsing the input structure and distributing each unique structure division to its own core. With two parallelization schemes to test, this overall effort is estimated to require 25,000 core hours. (iii) Multi-objective GA optimization: For the image simulation component of the initial GA testing, we anticipate iterating through 100 generations with 6 images per generation. This calculation requires 100*6*500 = 300,000 core hours for the image simulation component. The time estimated for each MD simulation is 250 core hours. In total, 100 generations * 6 images/structures * 250 core hours/structure = 150,000 core hours. Total computation time requested: 5,000 + 5,000 + 25,000 + 300,000 + 150,000 = 485,000 core hours. Industry partnership: Project URL: Requested allocation: 485000 Q1: 125000 Q2: 120000 Q3: 120000 Q4: 120000 Justification: Storage requirements: 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] Project Request: Cat_LIO
by accounts＠lcrc.anl.gov 07 Sep '16

07 Sep '16

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: Liang Li Applicant's institution: ANL Applicant's division: NST Project Name: Cat_LIO Project title: First-Principles Investigations of the Delithiation Mechanisms and Surface Stabilities of Li-rich, Ir Oxide-Based Cathode Materials Associated funding: Center for Electrochemical Energy Science, Energy Frontier Research Center, DOE Other Systems: Internal: 370,000 core-hours, Carbon cluster at Center for Nanoscale Materials Science: Over the past few decades, lithium-ion batteries (LIBs) have seen substantial advances that enable the widespread use of portable electronic devices including mobile phones and laptop computers. LIBs have also emerged as a viable technique in powering electric vehicles; however, considerably higher energy density and longer cyclic stability are required for LIBs application in larger scale energy storage (e.g. grid electric energy storage). Various routes have been explored in the pursuit of improved energy density and enhanced cyclability, and the next-generation Li-rich cathode materials have the potential to meet the above-stated needs. Among these Li-rich materials, layered oxides have been studied extensively due to their high theoretical capacity. Using Ir oxide-based cathode material as a model system, our experimental collaborators at Argonne have studied the electrochemical behavior of layered Li2IrO3, which delivers relatively high capacity (~210 mAh/g) and good cyclability. Recently, a novel type of cathode material used in the so-called “hybrid” Li-ion/Li-O2 battery, has been suggested, whose energy density is predicted to be comparable to that of Li-O2 batteries. Another Li-rich, Ir oxide-based cathode, namely Li8IrO6, is subsequently identified as a candidate hybrid cathode material in a high-throughput computational study. Therefore, these two types of Ir oxide-based cathode materials, i.e. Li2IrO3 and Li8IrO6, can be used as ideal model systems to study the electrochemical properties of layered and hybrid Li-ion/Li-O2 cathodes. We herein propose a comprehensive computational study, performed in conjunction with experimental work by our collaborators, to investigate the electrochemical and thermodynamic properties of Li2IrO3 and Li8IrO6. The proposed work involves primarily density functional theory (DFT) calculations of electronic and thermodynamic properties of bulk Li2IrO3 and Li8IrO6 with various Li concentrations, as well as surface structures with different terminations, with the goals of (a) understanding the structural evolution and charge compensation mechanisms of Li2IrO3 and Li8IrO6 during Li extraction, (b) identifying the thermodynamically most favorable surface structures and oxygen stabilities on these surfaces and (c) performing x-ray absorption near edge structure (XANES) simulations and compare with experimental results. Project description: The structure and energetics calculations of Li2IrO3 and Li8IrO6 will be performed using the plane wave DFT code VASP, with supplied projector augmented wave (PAW) atomic potentials and Perdew-Becke-Ernzerhof (PBE) exchange-correlation functionals. On-site coulomb interactionis accounted for by Hubbard U correction. Dispersion interaction may play an important role in layered Li2IrO3, so several types of optimized functionals that incorporate nonlocal dispersion corrections will be tested and compared with experimental X-ray diffraction (XRD) data to ensure that our calculations yield reasonable geometric properties. XANES spectra simulation will be carried out using OCEAN code5 that utilizes a GW and Bethe-Salpeter equation (BSE) formalism. The following calculations are specifically proposed in this study, and detailed accounting of the computational time requested for each calculation is also presented: Structural variation and electronic properties of Li2IrO3 and Li8IrO6 during Li extraction will first be examined exhaustively, and the DFT energies obtained in this process will be used to determine the most stable configuration at various Li concentration. Bader charge analysis of transition metals and oxygen atoms will also be performed to understand the charge compensation mechanism. The Li atoms will be removed from the material in a sequential manner, i.e. the most energetically favorable structure at a particular Li concentration is used as the starting configuration in the following Li removal step. Li2IrO3 supercell contains 16 Li and 24 O atoms, whereas Li8IrO6 supercell contains 24 Li and 18 O atoms, so to sample the energies along the complete delithiation paths, taking into account of the structural symmetry, 136 and 200 calculations are needed for Li2IrO3 and Li8IrO6, respectively. In addition, to evaluate the possibility of oxygen loss at various Li concentrati ons, the oxygen vacancy formation energy will also be calculated at each of the Li concentrations, which results in 24×16+18×24=816 calculations. Each of the abovementioned structural relaxations requires approximately 8 hours on 32 cores, therefore, all together we expect to need (136+200+816)×32×8~295,000 core hours. The thermodynamic stabilities of low-index surfaces with all possible terminations will be examined, and the oxygen vacancy formation energies of each surface will also be calculate in order to understand the surface stability toward oxygen release. Due to the anisotropy of Li2IrO3 and Li8IrO6 structures, 7 types of surfaces need to be considered: 3 in {100} family of lattice planes, 3 in {110} and 1 in {111}. The complexity of atom arrangements lead to at least 2 possible terminations for each surface types. 10 atomic layers will be used to construct the surface slabs, and the structural relaxation needs roughly 12 hours on 96 cores. Thus, to obtain the energies of relaxed surface structures, 2×7×2×12×96~32,000 core hours are needed. After the favorable terminations of all 7 types of surfaces are identified, the oxygen vacancy formation energies at various local Li concentrations will be calculated. 5 different Li concentrations will be tested, which requires 2×7×5×12 ×96~80,000. Therefore, total core hours of ~112,000 will be a reasonable estimation. The XANES spectra of Li2IrO3 and Li8IrO6 with different Li and O vacancy concentrations will be simulated. Accurate treatment of the BSE formalism is computationally demanding and typically requires 15 hours on 96 cores for the systems under study. Considering there are 16 and 24 structures with various Li contents for Li2IrO3 and Li8IrO6, respectively, and 10 representative structures with O vacancies will also be calculated for Li2IrO3 and Li8IrO6, we therefore request (16+24+10+10)*15*96~86,000. The total time requested for this project is approximately 295,000+112,000+86,000~493,000 core hours. Industry partnership: Project URL: http://www.anl.gov/cees/center-electrochemical-energy-science Requested allocation: 493000 Q1: 125000 Q2: 125000 Q3: 125000 Q4: 118000 Justification: Storage requirements: 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] Project Request: BDF
by accounts＠lcrc.anl.gov 07 Sep '16

07 Sep '16

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: Brewer Propriety Project Project Name: BDF Project title: Brewer Science Defect Formation Project Associated funding: Brewer Sci Other Systems: Science: Continuing this project, density functional theory and ab initio-based methods will be used to analyze the formation of defects in BSI materials. By modeling the polymerization reaction, we can determine the mechanisms leading to varying types of defects for a specified material and develop methods of predicting the formation of such defects. We will use GAMESS to investigate bonding along the reaction pathway and any mechanisms that could lead to side products. These results may be used to predict novel polymer materials and address customer requests for polymers with specific physical and chemical characteristics Project description: First principles methods will be used to analyze the formation of defects in BSI materials. By modeling polymer bonding interactions and determining bond energies, we can determine the types of defects that may form in a specific material and the bonding interactions that are significant for the stability of the polymer. We will use GAMESS to investigate the bonding at these sites and any mechanisms that could lead to side products. The details of this project are further outlined in the Milestones as follows: M1: Model the polymer, systematically determine bond dissociation energies M2: Determine the reaction pathway for successful polymer synthesis and formation of possible side products M3: Model the reaction pathway for a proposed polymer M4: Simulate polymer for a novel material and predict defect behavior GAMESS will be used to conduct calculation of bond dissociation energies and molecular interactions. If successful, these results may be used to predict novel polymer materials and address customer requests for polymers with specific chemical characteristics. Industry partnership: Brewer Science Proprietary Project, Spoke with Ray Bair and David Martin of ALCF Project URL: Requested allocation: 8000 Q1: 2000 Q2: 2000 Q3: 2000 Q4: 2000 Justification: Storage requirements: 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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