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

[LCRC Accounts] Yearly Allocation Request from Li_air_battery
by accounts＠lcrc.anl.gov 27 Aug '12

27 Aug '12

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: LDRD Other Systems: CNM Science: Unlocking the true energy capabilities of the lithium metal (negative) electrode in a lithium battery has been mainly limited by the low capacity in intercalation and conversion reaction at the positive electrodes. However, it can be overcome by removing these electrodes and allowing lithium to react directly with oxygen in the amosphere, forming the lithium-air battery as being a hybrid battery-fuel cell system. Compared to other metal-air batteries, Zn-air and Al-air cells have aqueous electrolytes and operate at a relatively low voltage of ~1.4 V and ~1.2 V, respectively, whereas for the non-aqueous Li-air cells, it provides ~3 V and therefore yields a significantly higher specific energy. During the electrochemically reduction of oxygen, the small yet highly reactive Li cations tend to form ionic bonds in terms of lithium (per)oxides (i.e. Li2O2 and Li2O) leading to their precipitation on the electrode surfaces. These surface coverage species by the O2 reduction products passivate the electrode, shut down the reduction, and render the reaction irreversible. The formation of Li2O and Li2O2 are both thermodynamically possible at nearly identical potential (~ 3V), however, the physical and chemical properties of these compounds remain elusive, a systematic theoretical study of these system are therefore critically important. Lithium-air cells can be considered the 'holy grail' of lithium batteries because they offer, in principle, a significantly superior theoretical energy density to conventional lithium-ion systems. While the inherent energy potential of lithium metal approaches that of gasoline, today's battery manufacturers have not yet been able to unlock this potential because of : (1) the non-aqueous electrolytes are unstable at high potentials and are easily oxidized by the oxygen released during charge, thereby seriously limiting cycle life; (2) during discharge, the solid and insoluble Li2O2 and/or Li2O products are deposite d on the surface or within the pores of the carbon cathode, thereby clogging the pores and restricting oxygen flow; (3) poisoning of the lithium electrode due to oxygen crossover destroys the integrity and functioning of the cell; and (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. Thus in the computational studies, these problems will be addressed and explored based on state-of-the-art atomistic modeling techniques. This is a project in its third year that was awarded a Grand Challenge LDRD. Project description: In the coming fiscal year (FY2013), we will complete our current on-going work and explore different systems in Li-air batteries based on experimental input from our colleagues at ANL. To complete the current ongoing study (i.e. ionic transport, ether-based solvents with different Li-salts), our experience indicates that 100, 000 hours is required. For our new study at FY2013, the computational methods will involve largely AIMD (CPMD, VASP) and DFT method (Gaussian09, VASP). For Gaussian09, the DFT calculation scales well up to 8 processors and for 4-6 nodes is the optimal number of nodes for geometry optimization for system size below 100 atoms. We will likely require about 100,000 core hours to study the stability and reaction paths of new longer ether-based (i.e. with spacer and dopants) and DMSO solvents against different Li salts in gas phase and solution phase. To extend our previous DFT study on Li2O2 (crystalline bulk, surfaces and clusters) sys tem, more extensive solid phases of Li2O2/LiO2 and Li2O/Li2O2/LiO2 hetero-interfaces (with and without impurity/dopants), together with the equation of states, mechanical, electronic and thermodynamic properties will be explored using DFT planewave VASP code. The VASP code is well-parallelized for 64-72 cores for 100-200 atoms system for a finite k-point calculation. For a single Γ-point calculation with a total atom ~ 300 atoms, a parallel efficiency of ~ 60% -75% can be achieved using 256 cores. Thus to explore a moderately large systems (~ 100-200 atoms), 200 000 core-hour is needed to perform the tasks. In addition, the larger system of combined electrolyte/electrode (electrolyte/Li2O2/carbon with and without metal catalyst) (~ 400 atoms) interfaces will be computed using CPMD and VASP code. We will explore the chemical reactions (i.e. rare events) based on AIMD method. For system involves metal-catalyst (e.g. Au) that involves d-orbital electrons, the blue-moon approac h based on VASP code will be used. For a system without metal catalyst, the metadynamics approach implemented in CPMD code will be used. In order to have a reliable statistics and long enough simulation time, we will require about 400, 000 core hours to complete these computational intensive simulations. Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 800000 Q1: 200000 Q2: 200000 Q3: 200000 Q4: 200000 Justification: For the details and evidence how to use the hours effectively, please see the project description and project report (FY2012). 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 Thank You, The LCRC Accounts System

1 0

New LCRC report submitted for Chaos
by support＠lcrc.anl.gov 27 Aug '12

27 Aug '12

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2012/?project=Chaos

1 0

Re: [allocations-admins] [LCRC Accounts] Yearly Allocation Request from Chaos
by John Valdes 27 Aug '12

27 Aug '12

Mark, We received your renewal request for the Chaos project. In the description, you indicated that you'd like 450,000 corehours for the coming FY: > Allocation request: > > 150,000 Transport in chaotic convection > 150,000 Covariant Lyapunov vectors and exponents > 150,000 Turbulent thermal convection > > 450,000 Total Request but in the quarterly request fields, it looks like you entered "112" per quarter, which gives only 448 corehours for the year: > New FY Requested allocation: 448 > Q1: 112 > Q2: 112 > Q3: 112 > Q4: 112 I assume you meant for those to be in thousands of corehours, and that you really entered "112.5" so that the total would come to 450K (450,000)? John LCRC Support Team

1 0

New LCRC report submitted for Comp_Nanocatalysis
by support＠lcrc.anl.gov 27 Aug '12

27 Aug '12

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2012/?project=Comp_Nanocata…

1 0

[LCRC Accounts] Yearly Allocation Request from Comp_Nanocatalysis
by accounts＠lcrc.anl.gov 27 Aug '12

27 Aug '12

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Julius Jellinek Project Name: Comp_Nanocatalysis Division: CSE Project title: Theoretical/Computational Studies of the Fundamentals of One-Component and Alloy Metal Based Nanocatalysis Relevant to Alternative Sources of Energy Associated funding: EFRC/IACT funded by BES/DOE Other Systems: NERSC, ~650000 core-hours Science: The central objective of this project is to perform modeling and computational studies that aim at understanding and characterization of the chemical reactivity and catalytic functionality of pure and alloy metal nanoparticles at the microscopic (i.e., atomic and electronic) level. The systems and processes of interest are those defined in the project “Institute for Atom-Efficient Chemical Transformation”, a DOE Energy Frontier Research Center. The overall emphasis is on finding new ways of generating fuels from biomass. Specific examples of transformations of interest include reforming of glycerol and formic acid into H2. The goal of the planned computational studies is to aid the ongoing experimental investigations on synthesis of novel, primarily alloy, nanocatalysts and characterization of their various physico-chemical properties and catalytic characteristics. The aim is not only to explain the experimental findings but also to provide guidance to future ex periments. Project description: The planned computations for the next fiscal year will explore conformational and energetic characteristics of the adsorption and chemical transformations of molecules, which are of relevance to the liquid phase reforming of glycerol (C3O3H8, C3O3H7, C3O3H6, H2O, CO and others), on pure Pt and mixed bimetallic nanoparticles. Among the issues that will be addressed is usage of size, structure and composition of the nanocatalysts as knobs for maximizing their activity and selectivity in hydrogen production. Computational results of last year revealed that doping with Mo decreases the energy barriers for both the dehydrogenation and the dehydroxylation of glycerol and its derivatives on Pt nanocatalysts and the degree of this decrease is proportional to the Mo composition in the particle. The decrease in the energy barriers of the decomposition reactions matches with the experimentally observed increase in the catalytic activity of Pt after the doping. The computations will be continued this year in a similar fashion and will be expanded to include other bimetallic systems, mainly alloys of Pt, i.e. Pt/Mo, Pt/Co, Pt/Ni (work on Pt/Co is already ongoing) at various compositions and structural, including both geometric and homotopic (different placement of atoms of different elements between the sites of a given geometric conformation), forms. The overall aim is to provide guidance for the optimum bimetallic system to be used in future experiments. The studies will include, apart from the characteristics of gas phase nanoparticles, the supports of the nanocatalysts. The supports of relevance are oxides such as SiO2, TiO2, Al2O3, etc. We will continue to use the parallelized version of the NWChem code, which proved to be very efficient in our studies performed last year. In addition we will also use the Crystal and VASP packages, for both of which we have the necessary licenses and are available on Fusion. Project URL: http://www.anl.gov/catalysis-science/index.html Current FY Hours Used: undetermined amount New FY Requested allocation: 920000 Q1: 230000 Q2: 230000 Q3: 230000 Q4: 230000 Justification: The scaling efficiency of the NWChem, Crystal, and VASP codes with an increase in the number of cores is well documented for the types of computations that are being and will be performed within the scope of this project. Examples include: 1) Scalability of NWChem on Fusion as evaluated by us for the Pt12Mo-CO system (total of 554 basis functions): Cores Average SCF cycle (s) 64 9 128 6 192 5 2) Scalability of MPP_Crystal on Hector (UK) as evaluated for TiO2(3x3x3) supercell (648 atoms, 13608 basis functions) [1]: Cores Average SCF cycle (s) 256 739 512 398 1024 213 2048 135 4096 85 [1]I. J. Bush et al., Proc. Royal. Soc. 467, 2112 (2011). 3) Scalability of VASP on Fusion as evaluated for the C10H16O supported on Pt(111) surface: Cores Average SCF cycle (s) 32 131.77 64 63.21 80 58.28 96 48.51 128 38.02 256 20.09 Thank You, The LCRC Accounts System

1 0

[LCRC Accounts] Yearly Allocation Request from Multicomp_Nanopart
by accounts＠lcrc.anl.gov 27 Aug '12

27 Aug '12

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Sanjubala Sahoo Project Name: Multicomp_Nanopart Division: CSE Project title: Next Generation of Multicomponent Nanocatalysts: Computational Studies Associated funding: Strategic Initiative on Material for Energy (LDRD 2012-123-R1) Other Systems: None Science: The goal of this project is to explore, understand, and characterize, through modeling and simulations, the complex correlations between the size, composition, structure, thermal properties, electronic features, and chemical reactivity of multicomponent nanoparticles. The central aim is to aid the ongoing experimental effort currently underway at CNM and CSE on synthesis of novel heterogeneous - primarily binary and ternary metallic - nanocatalysts with superior activity and selectivity. Among the targeted catalytic transformations are selective hydrogenation of unsaturated hydrocarbons and aldehydes, which are the processes of importance in various chemical technologies including those relevant to novel sources of energy. Project description: The planned computations will explore the structural, energetic, electronic, and chemical or catalytic properties and characteristics of single and multicomponent (mixed, core-shell, dumbbell-like, and other) transition metal nanoparticles. The work is planned for nanoparticles, both in gas phase and supported on substrates. Among the targeted nanocatalysts are Pt with deposits of Co, Ni, Fe, Pd cations (the work on this system has been initiated already). Our studies will be extended to different transition metal surfaces such as Pt, CoPt3, FePt, FePt3, and others. The candidates for catalytic transformations (these systems will be tested) are the selective hydrogenation of unsaturated hydrocarbons and aldehydes with and without the vicinity of modifying ligands, such as amines, phosphines, acids and others as an additional means of affecting the catalytic functionality. The computations carried out last year revealed the competition for adsorption sites between alkenes and amines, and thus explained the underlying mechanism for the experimentally observed improvement in the selectivity of partial hydrogenation of alkynes to alkenes. The choices for the transition metal nanocatalysts and catalytic transformations are made based on the planned experimental investigations, some of which are currently undergoing. Within the planned studies, the issues that will be addressed are: 1) Use of size, structure and composition of the nanocatalysts as "knobs" for tuning their activity and selectivity. For such purpose, computations are in progress for both finite size systems (55-atom cuboctahedral clusters and on the (001) and (111) surfaces of bulk crystal) and 2) Use of functionalized ligands such as amines with of different lengths of the carbon chains as an additional means of controlling the catalytic functionality. Our previous research have satisfactorily explained the experimentally measured differences in the effects of various modifiers on the selectivity of partial hydrogenation reaction of unsaturated hydrocarbons. We plan to expand the studies to include the hydrogenation selectivity of organic compounds with different functional groups. The task will be undertaken in parallel with the ongoing experiments. The computational studies of the structural, energetic, and electronic s tructure aspects will be performed using density functional theory. The packages that will be utilized include VASP, NWChem, CP2k and Crystal. Naturally, we will benefit from the efficient scaling of the codes and take advantage of it in order to explore systems with still increasing number of atoms. Thus in our project: 1) The study of the properties of the nanocatalysts for different size of nanoclusters, ranging from a few tens to a few hundreds of atoms, and 2) the effect of different surfaces and composition of the supporting substrates is a priority research program which suits well with the high-performance infrastructure of the Fusion computational resources. Project URL: http://blogs.anl.gov/major_initiatives/materials-for-energy/ Current FY Hours Used: undetermined amount New FY Requested allocation: 920000 Q1: 230000 Q2: 230000 Q3: 230000 Q4: 230000 Justification: The CPU-hours requested is based on the estimates made with VASP on Fusion. It shows that the scaling of VASP was more consistent over large number of processors as (listed below). The test for citral (C10H16O) molecule adsorbed on Pt(111) surface (C10H16O@Pt252) which contains total number of atoms N = 279 have been performed with 32, 64, 80, 96, 128 and 256 processors show a substantial increase in performance with the increase in the number of processors up to about 128 processors. A similar trend is also observed for the scaling trend of NWchem, which is also reported in the following. 1) Scalability of VASP on Fusion as evaluated for the C10H16O supported on Pt(111) surface: Cores Average SCF cycle (s) 32 131.77 64 63.21 80 58.28 96 48.51 128 38.02 256 20.09 2) Scalability of NWChem on Fusion as evaluated by us for the C4H6-Pt14 system (total of 736 basis functions and with charge density fitting): Cores Average SCF cycle (s) 64 19.4 128 12.5 192 10.8 Thank You, The LCRC Accounts System

1 0

New LCRC report submitted for ScalaGAUSS
by support＠lcrc.anl.gov 27 Aug '12

27 Aug '12

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2012/?project=ScalaGAUSS

1 0

[LCRC Accounts] Yearly Allocation Request from biomimetic_systems
by accounts＠lcrc.anl.gov 27 Aug '12

27 Aug '12

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Oleksandr Kokhan Project Name: biomimetic_systems Division: CSE Project title: Solar energy conversion in biomimetic molecular architectures Associated funding: DOE Division of Chemical Sciences, Geosciences, and Biosciences 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 use all-atom Molecular Dynamics (MD) simulations to better understand conformational dynamics and structural impact of 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) data to provide an insight into strategies for optimization of electron transfer rates within biomimetic hybrids. The second aim is to continue our work on understanding of shortcomings of popular all-atom force fields for protein simulations (CHARMM, AMBER) and develop tools facilitating interpretation of protein SAXS/WAXS data. Finally, we plan to explore a possibility of using ab initio molecular dynamics for refinement and getting better fits of structural and hydration models of water splitting catalysts derived for our High Energy X-ray Scattering data. 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 developed 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 light-induced electron transfer (ET) but the observed rates and quantum yields are far from optimal. 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 et 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). During FY2012 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. In FY2013 our main focus will be on significantly extending those simulations as well as adding other types of photosensitizers. 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 electron transfer rates and SAXS/WAXS scattering profiles. To achieve this goal we plan to run a series of 100-500 ns MD simulations on all 6 available PpcA mutants. At the initial stages of the project we will focus on the systems with all three PpcA hemes either oxidized or reduced. 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 continue our work in collaboration with Dr. Xiaobing Zuo (XSD) on developing methods and techniques for generating sufficiently large protein conformational ensembles and rapidly matching X-ray scattering profiles calculated from MD snapshots with the actual experimental data. For this project we also plan to run all-atom MD and Steered MD simulations with CHARMM force field. Project URL: http://www.cse.anl.gov/fundamental_interactions/solar_conversion.html Current FY Hours Used: undetermined amount New FY Requested allocation: 600000 Q1: 150000 Q2: 150000 Q3: 150000 Q4: 150000 Justification: NAMD is a highly scalable molecular dynamics simulations code. Benchmarks on Fusion with wild-type 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, respectively. NAMD can be dramatically accelerated (~5-fold for typical protein simulations) with GPU support. Thank You, The LCRC Accounts System

1 0

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

27 Aug '12

Hello, A new project on the LCRC cluster has been requested. Please forward the information on to the LCRC Allocation sub-committee. Applicant's name: Maria Chan Applicant's institution: ANL Applicant's division: CNM Project Name: LiOnAu Project title: First principles investigations of the stress response of Au nanofilms to Li deposition Associated funding: DOE BES Other Systems: Argonne CNM -- Carbon Science: Lithium-ion batteries are ubiquitous in consumer electronics, but their widespread use in transportation applications remains elusive, partly due to the challenges involved in maintaining the long term stability of electrode materials. The surface stress response of electrodes during the initial formation of the solid-electrolyte interphase (SEI) and during charge/discharge cycles has great practical consequences for the longevity, since volume changes and stress variations can dramatically shorten the lifetime. In order to be able to optimize the mechanical aspects of the electrodes, it is important to achieve an atomistic understanding of factors and processes affecting the stress response. Gold nanofilms are an ideal model system for achieving such an understanding, due to its inertness, suitability as an SEI model electrode, and having lithiation voltage and capacities similar to other intermetallic anodes. The Gewirth group has performed optical stress measurements on cantilevers deposited with 50 nm thick Au. The results show a large compressive stress during lithium deposition on Au surfaces, tensile stress during lithium removal, and a lack of hysteresis when Li-Au alloy formation is prevented. Analysis of the cyclic voltammetry data indicate that a nanoscale Li film the equivalent of several atomic layers is deposited on the Au surface, but the precise distribution of Li atoms is unknown, nor are the voltages of Li deposition and removal understood. First principles calculations will be useful in building an atomistic model for the Li deposited on Au, corroborating the voltages of Li deposition and removal with experimental results, and therefore delineat ing the observed stress response Project description: The proposed work involves density functional theory (DFT) calculations of Li on the Au (111) surface, with the goals of (a) identifying thermodynamically favorable configurations, (b) determining the voltages at which surface deposition and reactions occur, and (c) deducing the stress response of the surface during different processes. Both Li overlayers and substitutions on the Au sites will be considered. For configurational sampling, we will use a genetic algorithm for Li overlayers, and a cluster expansion for Li substitutions. The resultant total energies will be translated into voltages vs the Li/Li+ couple. Together with the voltages, the calculated stress on the computational cell will allow us to interpret the experimental measurements. The proposed calculations will be performed using the plane wave DFT code VASP, with supplied projector augmented wave (PAW) atomic potentials for the core electrons. The generalized gradient approximation (GGA) of Perdew-Becke-Ernzerhof (PBE) is used for the exchange-correlation functional. Sufficiently high values of the kinetic energy cutoff for the plane wave basis set will be used to ensure convergence of the calculated stress. Two types of configurations of Li on the Au (111) surface will be considered: (a) Li overlayers on top of intact layers of Au, and (b) Li substitutions on the surface and subsurface layers of the Au surface. In order to obtain energetically favorable configurations, two different approaches will be used: for (a), since non-pseudomorphic Li layers are expected, a genetic algorithm will be used to find low energy configurations for these layers; for (b), since Li are expected to take on the Au lattice sites, a cluster expansion will be used on a random sampling of configurations to determine the energetics of surface and subsurface sites, pairs and triplet clusters. A Monte Carlo simulation will be used to determine, from the cluster expansion, low energy configurations. Detailed accounting of the computational time requested for each type of configurations is as follow: (a) The genetic algorithm requires the calculation of a large number of configurations, of order 300 for each value of the Li coverage. Since only the relative total energies are needed, the energy cutoff and kpoint density of these calculations do not have to be large. Previous testing shows that each calculation requires 3 hours on 32 cores. Once low energy configurations are found, higher precision calculations, requiring roughly 12 hours on 32 cores, are needed. However, only a few such calculations are needed for each coverage. We will consider 9 values of the Li coverage. All together we expect to need (300*3*32+4*12*32)*9 ~ 273,000 core-hours for investigating Li overlayers (b) The cluster expansion requires the calculation of approximately 150 random structures, each running for approximately 10 hours on 64 cores. These calculations are more computationally expensive than those in (a) due to the need for an additional layer of Au to accommodate subsurface Li. The stress from approximately 20 low energy structures obtained from the cluster expansion and Monte Carlo simulations will also be calculated. The total amount of time required to investigate Li substitutions is 109,000 core-hours. The total time requested for this project is 382,000 core hours. Project URL: Requested allocation: 380000 Q1: 80000 Q2: 100000 Q3: 100000 Q4: 100000 Justification: The requester has used undetermined amount hours of their initial startup project. In addition to approving an initial amount, please specify a Category and Subcategory for this project. For a list of the current selection of approved categories, please see: https://wiki.lcrc.anl.gov/wiki/Processes/Categories Once the Allocation committee has approved the project, please go to the Project Management page to create it: https://accounts.lcrc.anl.gov/projects.php Thank You, The LCRC Accounts System

1 0

New LCRC report submitted for Comp_Soft_Catalysts
by support＠lcrc.anl.gov 27 Aug '12

27 Aug '12

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2012/?project=Comp_Soft_Cat…

1 0