September 2015 - Allocations-admins - mailman3.cels.anl.gov

Re: [allocations-admins] Yearly Allocation Request for CEES-II-Wolverton
by Bair, Raymond A. 30 Sep '15

30 Sep '15

Dear Chris, While your CEES-II-Wolverton project was started in FY2015, we did not receive a FY16 request before the Allocations Committee meeting on Monday. The Committee assumed you wanted to continue, but did not know how much time you wanted. So they approved 500K core-hours for FY2016. That means that you will have access to 250K core-hours starting October 1, and another 250K April 1. We need to go back to the committee to increase your allocation. How long do you expect the first 250K to last? Regards, Ray ----------------------------------------- Ray Bair Computing, Environment, and Life Sciences Argonne National Laboratory and the University of Chicago TCS Building 240, Room 4122 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751 On 9/29/15, 12:00 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> wrote: >Hello, > >A yearly allocation for the LCRC cluster has been requested with the >following updated information: > >Submitter/PI: Chris Wolverton >Project Name: CEES-II-Wolverton >Division: Computing, Environment, and Life Sciences >Project title: DFT Computation of Hybrid and Li-ion Battery Materials >Associated funding: CEES-II EFRC >Other Systems: >Science: Recent experiments have shown that lithium and oxygen can be >electrochemically removed from Li5FeO4 (5Li2OÂ·Fe2O3) and re-accommodated >during discharge, creating the possibility of its use as a high-capacity >electrode in a hybrid Li-ion/Liâ€“O2 electrochemical cell. Taking this >novel chemistry as a model, we use density functional theory (DFT) within >a high-throughput framework to screen for analogous reactions in other >materials. We also are interested in determining the mass tranport >kinetics of the phase transformations in these materials. >Project description: 1. Thermodynamics studies including electronic >structure calculations, phase transformation calculations for new Li-ion >and hybrid Li-ion/Li-O2 battery chemistries. >2. Kinetics studies including defect formation energy calculations, >ab-initio molecular dynamics, nudged elastic band calculations and >kinetic Monte Carlo simulations for Li/O transport in hybrid materials >including Li-Fe-O and Li-Mn-O. >3. New high-throughput DFT discovery of novel hybrid Metal-ion/Metal-O2 >battery chemistries, novel battery anode/cathode materials. >4. Structure predictions of new phases observed in the >charging/discharging of transition metal oxides. > >Computational methods employed will largely be DFT-based, multiprocessor >jobs. >Industry partnership: >Project URL: >Current FY Hours Used: undetermined amount > >New FY Requested allocation: 2000000 > Q1: 500000 > Q2: 500000 > Q3: 500000 > Q4: 500000 > >Justification: Our group has considerable experience with >high-throughput DFT computation, and have demonstrated this in the Open >Quantum Materials Database (OQMD). OQMD is available online at oqmd.org, >and consists of a database of >300,000 DFT calculations of known and >hypothetical inorganic materials. >Storage requirements: > >Thank You, > >The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request for ACME
by accounts＠lcrc.anl.gov 29 Sep '15

29 Sep '15

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Robert Jacob Project Name: ACME Division: MCS, EVS Project title: Accelerated Climate Modeling for Energy Associated funding: DOE BER Other Systems: ALCF (100M) OLCF (50M) Science: This project is designed to accelerate the development and application of a fully coupled, state-of-the-science Earth system model (ESM) for scientific and energy mission applications. While the goal is to build a state-of-the-science Earth modeling system for the full complement of DOE’s mission-related goals and needs, initial scientific development of the system will be dictated by the team’s focus on three climate change thematic areas (called “science drivers” hereafter). These science drivers cover broad, important areas of science requiring an accurate treatment of climate system processes for more accurate simulation and prediction of climate change. The three drivers are: 1. How do the hydrological cycle and water resources interact with the climate system on local to global scales? 2. How do biogeochemical cycles interact with global climate change? 3. How do rapid changes in cryospheric systems interact with the climate system? The three questions are characterized by their centrality to major open issues in climate science, their relevance to DOE’s mission objectives, and their potential to advance the state of Earth system simulation using ACME capabilities. Project description: ACME is starting with a branch of the Community Earth System Model (CESM). CESM is a fully-coupled, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states. ACME's atmosphere component is the Community Atmosphere Model. The CAM model has flexible formulations for atmospheric dynamics and has recently transitioned to the spectral finite element method coupled to an extensive suite of sub-grid physical parameterizations in its standard configuration. It runs on unstructured quadrilateral grids. The land model, CLM, contains a suite of column process parameterizations running at each grid point with no communication between grid points. The ice sheet model, CISM, is based upon the Glimmer model, an open source (GPL) three-dimensional thermomechanical ice sheet model designed to be interfaced to a range of global climate models. CLM represents surface and subsurface water, energy, carbon, and nitrogen dynamics, with a nested hierarchical sub-grid parameterization that allows glaciers, lakes, urban areas, agricultural fields, managed forest, and natural (unmanaged) vegetation types to share space on each grid-cell. Incident radiatio n is intercepted in a two-layer canopy, with vegetation, soil, snow aging, and black carbon impacts on albedo. Subsurface processes include vertically resolved biogeochemistry, options for carbon and nutrient cycle parameterization, and recently improved treatment of wetlands and permafrost dynamics. In the fully-coupled configuration, the sea-ice and ocean (CICE and POP) component models run with a nominal grid spacing of 1/10° (approximately 11km at the equator and 3km in polar regions) and, for POP, 42 levels in the vertical. CAM grids have both uniform and variable resolution configurations. The uniform grid with an average grid point spacing at the equator of 1/4° contains 86,400 elements, each with 30 vertical levels. Doubling the resolution to an average grid spacing of 1/8° requires 345,600 elements. The variable resolution configuration allows a small region of 1/8° grid spacing transitioning to an average global resolution of 1°. The CLM is run on the same g rid as CAM. The team expects to replace POP with a new, variable-resolution grid model based on the Model Prediction Across Scales (MPAS) dynamical and numerical framework that has been recently released. The output of the CESM consists of monthly means of several hundred quantities, plus daily averages of a subset of these quantities and hourly output of some key variables. ACME requires Fortran90 and C compilers and the MPI library to run. We will be using time on Blues to perform regular testing of ACME. ACME contains a large set of system tests that perform runs of the full model to test various functions. The runs sizes range from a few nodes to a few dozen nodes. The output sizes are relatively small and we will have modest storage needs. In FY16, we will begin regular testing with the NAG compiler now that pnetcdf is available. We also port the "acme integration" suite to join the "acme developer" suite in regular nightly testing. Industry partnership: Project URL: http://climatemodeling.science.energy.gov/projects/accelerated-climate-mode… Current FY Hours Used: undetermined amount New FY Requested allocation: 300000 Q1: 50000 Q2: 50000 Q3: 100000 Q4: 100000 Justification: Storage requirements: Thank You, The LCRC Accounts System

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New LCRC report submitted for ACME
by support＠lcrc.anl.gov 29 Sep '15

29 Sep '15

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2015/?project=ACME

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New LCRC report submitted for foam
by support＠lcrc.anl.gov 29 Sep '15

29 Sep '15

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2015/?project=foam

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[LCRC Accounts] Yearly Allocation Request for CEES-II-Wolverton
by accounts＠lcrc.anl.gov 29 Sep '15

29 Sep '15

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Chris Wolverton Project Name: CEES-II-Wolverton Division: Computing, Environment, and Life Sciences Project title: DFT Computation of Hybrid and Li-ion Battery Materials Associated funding: CEES-II EFRC Other Systems: Science: Recent experiments have shown that lithium and oxygen can be electrochemically removed from Li5FeO4 (5Li2O·Fe2O3) and re-accommodated during discharge, creating the possibility of its use as a high-capacity electrode in a hybrid Li-ion/Li–O2 electrochemical cell. Taking this novel chemistry as a model, we use density functional theory (DFT) within a high-throughput framework to screen for analogous reactions in other materials. We also are interested in determining the mass tranport kinetics of the phase transformations in these materials. Project description: 1. Thermodynamics studies including electronic structure calculations, phase transformation calculations for new Li-ion and hybrid Li-ion/Li-O2 battery chemistries. 2. Kinetics studies including defect formation energy calculations, ab-initio molecular dynamics, nudged elastic band calculations and kinetic Monte Carlo simulations for Li/O transport in hybrid materials including Li-Fe-O and Li-Mn-O. 3. New high-throughput DFT discovery of novel hybrid Metal-ion/Metal-O2 battery chemistries, novel battery anode/cathode materials. 4. Structure predictions of new phases observed in the charging/discharging of transition metal oxides. Computational methods employed will largely be DFT-based, multiprocessor jobs. Industry partnership: Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 2000000 Q1: 500000 Q2: 500000 Q3: 500000 Q4: 500000 Justification: Our group has considerable experience with high-throughput DFT computation, and have demonstrated this in the Open Quantum Materials Database (OQMD). OQMD is available online at oqmd.org, and consists of a database of >300,000 DFT calculations of known and hypothetical inorganic materials. Storage requirements: Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request for ds_ime
by accounts＠lcrc.anl.gov 28 Sep '15

28 Sep '15

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Emmanouil Doxastakis Project Name: ds_ime Division: IME/MSD Project title: Modeling of Scattering from Block Copolymer Films Associated funding: IME/ANL FWP Solvent-Assisted Assembly Other Systems: Science: Grazing-Incidence Small Angle X-ray Scattering (GISAXS) is emerging as an efficient and accurate structural characterization technique at the nanoscale. GISAXS offers the ability to probe large sample areas, offering three-dimensional information at high detail in a thin film geometry. Furthermore, the potential to probe samples in different environments provides for an attractive technique with unique advantages. This departs significantly from other available methods which are often limited to small areas and/or two-dimensions. In this study we exploit the application of GISAXS to determine the structures formed at each step of LiNe (Liu-Nealey) flow using chemical patterns for directed self-assembly (DSA) of block copolymer (BCP) films. Experiments conducted at the Advanced Photon Source, Argonne National Laboratory provided characteristic scattering patterns at low incident angles that probed film characteristics at both parallel and normal directions to the surface. Project description: The primary goal of the project is to build models of materials that would provide scattering patterns in agreement to current ongoing experiments at APS. Modeling of GISAXS data requires an accurate and precise description of scattering emanating both from a mean structure dominating the sample as well as variances around this shape. To recreate the scattering patterns we employ a hybrid computational model. Fist images generated at APS are loaded through a Python interface. Subsequently we construct a statistical model of the structure. Scattering is built employing an efficient Fortran subroutine, parallelized with OpenMP. Current efforts (depending on time allocated) will translate the form factor calculations to MPI. It is emphasized that there is minimal scalability issues since the main computational load is during the calculation of averages of scattering from i.e. 1000 structures representing individual fluctuations in the sample. This is performed with a simple reduction operation after which the predicted scattering pattern is available to compare to experiments. We also emphasize that this effort would advance significantly the current state-of-the art modeling of GISAXS data which focuses on extracting only the best average structure. Currently the whole modeling process is coupled to an optimization library (Nlopt) to reach beyond simple modeling and fit experimental spectra. We are also exploring other libraries (genetic algorithms) that will also scale well in high performance systems. Finally we are uniquely equipped with predictions of film structures from molecular simulations (de Pablo group). In a parallel effort we will recreate (rather than fit experimental data) scattering from structures predicted by simulations. This will allow for direct comparison to experimental data. Industry partnership: Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 320000 Q1: 80000 Q2: 80000 Q3: 80000 Q4: 80000 Justification: Storage requirements: Thank You, The LCRC Accounts System

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New LCRC report submitted for chemexp
by support＠lcrc.anl.gov 28 Sep '15

28 Sep '15

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2015/?project=chemexp

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[LCRC Accounts] Project Request: protein_e-wire2
by accounts＠lcrc.anl.gov 28 Sep '15

28 Sep '15

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: David Tiede Applicant's institution: ANL Applicant's division: CSE Project Name: protein_e-wire2 Project title: Solar energy conversion in biomimetic molecular architectures Associated funding: This project is supported by three funding programs within the DOE-BES Division of Chemical Sciences, Geosciences, and Biosciences: i) Solar Photochemistry; ii) Photosynthetic Systems; iii) Energy Frontier Research Center: Argonne Northwestern Solar Energy Research (ANSER) Center Other Systems: N/A Science: This computational project will supplement our experimental work on construction and characterization of water-splitting catalysts and biomimetic molecular architectures for solar energy conversion. The first aim is to explore replica-exchange all-atom Molecular Dynamics (MD) simulations as a tool to achieve a better sampling and to predict impact of protein mutations and chemical modifications on conformational dynamics and structural stability with various photosensitizers and photosensitizer-catalyst dyads covalently linked to PpcA, a multi-heme c-type cytochrome from Geobacter sulfurreducens. These results will facilitate interpretation of kinetic electron transfer rates as well as Small- and Wide-Angle X-ray Scattering (SAXS, WAXS) as well as NMR data to provide an insight into strategies for optimization of electron transfer rates within biomimetic hybrids. The second aim is to use replica-exchange MD to simulate equilibrium positions and dyna mics of mutations needed in order to tune redox potentials of PpcA hemes. Our third goal is to use several types of ligand docking simulations to screen and optimize ligand binding sites on PpcA protein surface. Project description: We are developing biomimetic molecular architectures for efficient solar energy conversion using artificial and natural photosensitizers combined with natural and genetically engineered host systems capable to support long-lived charge-separated states and conduct charges away from the photosensitizers. We recently significantly expanded a series of cysteine mutants of PpcA, a multiheme redox protein from Geobacter sulfurreducens, and synthesized a number of photosensitizers which can be selectively attached to the engineered residues. These bio-hybrids demonstrate an unexpectedly wide range (2x107-5x1011 s-1) of light-induced electron transfer (ET) rates. However, the precise targeted control of charge transfer rates and quantum yields remain elusive. Furthermore, there is no agreement in scientific community on whether the donor-acceptor distance, driving and re-organization energies are the only factors responsible for control of ET rates (Moser e t al. Nature, 355:796; Page et al. Nature, 402:47) or frameworks of internal bonds and protein dynamics can also have a significant impact on the ET in protein systems (Balabin and Onuchic, Science, 290:114; Lin et al. Science, 310, 1311). In the past we have developed CHARMM force field parameters for several photosensitizers and obtained promising preliminary results for some of PpcA mutants in their oxidized form linked to Ru(bpy)3 which closely matched X-ray scattering data. However, in some instances the complete equilibration of photosensitizer-cytochrome complexes required 50-75 ns trajectories and a lingering question remained whether 200-300ns simulations were sufficient. In FY2016 our main focus will be on obtaining a better sampling of possible conformers with replica-exchange molecular dynamics. We expect that MD simulations will provide a sufficient sampling of protein conformational space and help us to better rationalize the collected kinetic data on charge transfer rates and SAXS/WAXS scattering profiles as well as the observed perturbations in NMR data. To achieve this goal we plan to run a series of 100-500 ns MD simulations on selected PpcA mutants. At the initial stages of the project we wil l focus on the systems with all three PpcA hemes either oxidized or reduced. The latter is particularly interesting as it results in a significant change of the total protein change from +4 to +1. All MD simulations will be performed with NAMD 2.8 and CHARMM force field. We will use standard for protein MD conditions: nPT, PME electrostatics, explicit TIP3 water boxes sufficiently large to keep interaction energy negligible between protein mirror images. The analysis of MD trajectories, computational docking and calculation of X-ray scattering profiles will be carried out on our lab computers. The second goal is to use several rigid and flexible ligand docking approaches in order to predict and optimize binding sites for a new generation of photosensitizers and photosensitizer-catalyst dyads. We will continue to use an MPI version of DOCK6. We previously successful used this code on Blue and it already resulted in one peer-reviewed publication. NAMD is a highly scalable molecular dynamics simulations code. Our past benchmarks on Blues with PpcA in a water box (~13,000 atoms) showed more than 99% speed-up efficiency with ~1,600 atoms/CPU core and ~80% efficiency with ~400 atoms/core and yielded 5.1 and 15.7 ns/day on 8 and 32 cores, respectively. DOCK 6 typically had more than 95% scaling efficiency on 32-128 cores used in our previous work and we expect to get similar scaling figures with new simulations Industry partnership: Project URL: Requested allocation: 950000 Q1: 250000 Q2: 250000 Q3: 250000 Q4: 200000 Justification: NAMD is a highly scalable molecular dynamics simulations code. Our past benchmarks on Blues with PpcA in a water box (~13,000 atoms) showed more than 99% speed-up efficiency with ~1,600 atoms/CPU core and ~80% efficiency with ~400 atoms/core and yielded 5.1 and 15.7 ns/day on 8 and 32 cores, respectively. DOCK 6 typically had more than 95% scaling efficiency on 32-128 cores used in our previous work and we expect to get similar scaling figures with new simulations. 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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New LCRC report submitted for udmh_pyrolysis
by support＠lcrc.anl.gov 28 Sep '15

28 Sep '15

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2015/?project=udmh_pyrolysis

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[LCRC Accounts] Yearly Allocation Request for chemexp
by accounts＠lcrc.anl.gov 28 Sep '15

28 Sep '15

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Peter Zapol Project Name: chemexp Division: MSD Project title: Chemical Expansion in Perovskites Associated funding: DOE BES Other Systems: none Science: The solid oxide fuel cell (SOFC) presents a highly attractive energy conversion option besides the conventional energies as a clean and efficient energy conversion technology. However, the high operating temperature limits its commercial applications. The LaxSr1-xCoyFe1-yO3-delta (LSCF) displaying mixed ionic electronic conductivity serves as a promising cathode material for intermediate-temperature SOFCs. For the LSCF perovskite materials, the oxygen stoichiometry plays a critical role in the materials performance characteristics. Recently experiments showed that the oxygen stoichiometry can be tuned by applying electrical potentials across the LSCF/YSZ (yttria-stabilized zirconia) heterostructures. However, the large change in the oxygen vacancies leads to a significant dilation or contraction of the lattice known as chemical expansion. This phenomenon of lattice change with the applied voltage is also reported in La0.8Sr0.2CoO3-delta (LSCO) materials. Understand ing the lattice changes with the bias voltage is critical because the large stresses induced by the changing lattice may lead to failure operation of the SOFC. To the best of our knowledge, there is no good explanation on the lattice changes with the applied voltage yet. Collaborating with the experimentalists at Argonne, we will carry out a series of researches to compare and explain the experiment results. Project description: The project started in the middle of FY15 and we have performed calculations using density functional theory to explore the lattice changes with the oxygen stoichiometry in the bulk LSCF. Next, we will explore thin films and the oxygen vacancy migration across the LSCF/YSZ interface and in the thin film LSCF. The projector augmented plane-wave method as implemented in the Vienna ab initio simulation package (VASP) will be employed to find the optimized structure of each oxygen vacancy configuration. VASP is a well validated code which is installed at LCRC and is widely used for this type of calculations with good performance. We will use the climbing image nudged elastic band method (NEB)to do research on the oxygen vacancy migration. Our bulk calculations on system with 40 atoms to find the optimized structures using 32 cores worked very well, as expected. We plan to do calculations of different oxygen vacancy concentrations corresponding to deviation from formal oxygen stoichiometry of 3 by 0.075, 0.125, 0.25, 0.375, 0.5. For each configuration, we need several calculations to find the optimized ionic positions at fixed in-plane lattice constant. In each calculation, we need about 15 hours of run time when using 32 cores. For the oxygen vacancy migration, each NEB calculation is about 20 hours using 32 cores. We need to calculate about 5 NEB points, 10 pathways for the different 5 oxygen vacancy concentrations. Therefore, expected time estimate for structural optimizations is (8 cores/node * 4 nodes * 15 hours of run time * 100 different runs) 48,000 core-hours and for NEB calculations is (8 cores/node * 4 nodes * 20 hours of run time * 250 different runs)=160,000 core-hours.We also want to do some tests on larger system sizes, which adds about 30,000 core hours. The total time requested is 240,000 core hours. There will be two to three members in the project. Industry partnership: none Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 240000 Q1: 60000 Q2: 60000 Q3: 60000 Q4: 60000 Justification: Storage requirements: default storage allocation is sufficient Thank You, The LCRC Accounts System

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