September 2014 - Allocations-admins - mailman3.cels.anl.gov

[LCRC Accounts] Project Request: udmh_pyrolysis
by accounts＠lcrc.anl.gov 12 Sep '14

12 Sep '14

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: Alexander Landera Applicant's institution: ANL Applicant's division: CSE Project Name: udmh_pyrolysis Project title: Pyrolysis of UDMH and other propellants Associated funding: DOE-BSE and Army Research Office (ARO) Other Systems: linus.tcg.anl.gov pople.tcg.anl.gov Science: The Science objectives for this project is to investigate the long range interactions involved in the pyrolysis of UDMH and other similar propellants. This includes roaming reactions, which involves the partial dissociation of a fragment along with long range relative fragment reorientation, and finally abstraction by one of the fragments. This will aid in understanding the complicated dynamics involved in the pyrolysis of propellants containing heteratoms, such as nitrogen and oxygen. Project description: The project has as its main goal, the description of long range interactions involved in the pyrolysis of Unsymmetrical Di-methylhydrazine (UDMH), and other similar propellants. Further, as a separate goal, we will also obtain branching ratios for the products formed in these pyrolysis reactions. These propellants are used in the propulsion systems of many rocket systems. It will require the extensive use of the Molpro quantum Mechanical package. Molpro scales well with a small number of processors (16 or less), and for most molpro calculations, this is what we will need. We will also need access to a program called VaReCoF, which allows for the calculation of the flux involved in association reactions. It works by invoking multiple instances of molpro, and the code makes use of MPI and shows a speed-up efficiency of about 60% for up to 96 CPU’s (test performed on a 8 cpu/cores AMD Operton 2354 machine). This provides the efficiency that we need to complete this project successfully. Additionally, these two programs (molpro and VaReCoF) are already installed in both Blues and Fusion. When running VaReCoF, we will be using between 100 and 200 cores at once. The reference for the VaReCoF program is as follows: VaReCoF (Y. Georgievskii, S.J. Klippenstein, VaReCoF, Sandia National Laboratories and Argonne National Laboratory, 2006). Number of project members: 3 Industry partnership: None Project URL: Requested allocation: 80000 Q1: 20000 Q2: 20000 Q3: 20000 Q4: 20000 Justification: Storage requirements: 1 TB should be more than enough for storage 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 Metastable_Materials
by accounts＠lcrc.anl.gov 12 Sep '14

12 Sep '14

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Peter Zapol Project Name: Metastable_Materials Division: MSD Project title: First-principles studies of growth mechanisms for metastable materials Associated funding: ANL Strategic LDRD Other Systems: Science: The main objective of the project is to develop first-principles models describing the growth of Group-III nitrides in order to establish a firm basis for far-from-equilibrium nitride synthesis in a wide range of compositions. In particular, the growth of AlN and its alloys will be extensively studied in this work because of new applications in solid state lighting and power electronics. The needed understanding starts at the very beginning of the growth process where the detailed mechanisms of the creation of the AlN nucleation and diffusion barrier layer are poorly understood and extends through device processing and, ultimately, performance. Although metal organic chemical vapor deposition (MOCVD) is the most efficient and clean deposition process for production of nitride solid-state devices, the growth process for group III nitrides. The nitrogen activity produced by surface-catalyzed ammonia (NH3) decomposition may be responsible for the observed unusual beha vior, an atomistic model of the gas phase and surface chemistries, and catalytic reactions that govern such behavior needs to be developed. We propose calculations aimed at development of a kinetic model, which will help optimize synthesis conditions to grow nitride materials. Identification of rate-limiting reaction steps will lead to optimization of synthesis conditions and precursors based on this model. The results of the modeling will be validated by comparison to the experimental data obtained in ANL. This model is expected to be applicable to describe kinetically controlled processes in synthesis of other materials. Project description: We will continue our systematic study of the non-equilibrium growth of Group-III nitrides with NH3 and other precursors. Surface reaction pathways for AlN and for GaN on AlN will be calculated and used to determine lateral growth mechanisms. So far, we have investigated the interaction of NH3 and its moieties with the (0001) surfaces of InN and GaN, focusing on their adsorption energies and decomposition barriers. We have started work on AlN growth on different substrates and surface orientations. The species such as trimethyl Al will be placed on the surfaces along with appropriate NHx (x=0-3) precursors and the reaction energies will be calculated. Additional decomposition barriers for NH3 will be also computed on the nitride surfaces in the presence of the Al species. Additionally, we are planning to calculate kinetic barriers for diffusion and reactions on strained surfaces since the nitrides are currently grown on substrates with a large lat tice mismatch. We will use the results of our first-principles and kinetic calculations as input to coupled gas phase/surface modeling and to mesoscale modeling of growth processes, strain states, and defect distributions that are the focus of the imaging experiments. Industry partnership: Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 480000 Q1: 120000 Q2: 120000 Q3: 120000 Q4: 120000 Justification: Since VASP does not scale very well beyond 48 processors for our systems, it precludes the use of short-time large-scale capabilities of leadership class computer facilities. In fact, the scaling of the calculations is reduced with the number of processors beyond 48. The use of Blues cluster will allow us to overcome the computational challenges posed by the significantly large system sizes necessary for modeling various surfaces as well as decomposition and diffusion processes, which are computationally very demanding. The detailed estimate of the required computer time is given at the end of the project description. Storage requirements: Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Request: Modeling-HI-CEES2
by accounts＠lcrc.anl.gov 12 Sep '14

12 Sep '14

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: hakim iddir Applicant's institution: ANL Applicant's division: MSD Project Name: Modeling-HI-CEES2 Project title: Modeling Battery Materials HI CEES2 Associated funding: DOE, EFRC Other Systems: PNNL Science: As a part of continuing effort to contribute to the battery research here at Argonne, and to the EFRC (CEES II) project. We will perform theoretical work based on density functional theory using “VASP”, to simulate the equilibrium particle shapes of non-stoichiometric and doped LiMn2O4 particles. As stated in the CEES II proposal, it is central to this task to understand the electrode structure instabilities induced electrochemically. LiMn2O4 is ideal as a high-capacity Li-ion battery cathode material by virtue of its low toxicity, low cost, and the high natural abundance of Mn. However, this material suffers from Mn dissolution problem that not only induces a capacity fade [1], but can also poison the anode. The dissolution is associated with the disproportionation of Mn3+, and is dependent on the surface structure, hence the crystal orientation as well [2, 3]. For example, (111) is expected to be more stable as the reconstruction moves Mn to th e surface sub-layers[4]. Previous works show that (111) surface is more stable than (100) and (110) surfaces with respect to Mn dissolution [3, 5]. To improve its stability with respect to Mn dissolution, one would like to predict the synthesis conditions that would preferentially enhance the (111) surface ratio over that of the other facets, not only in pristine stoichiometric state, but also non-stoichiometric and doped surfaces. However, it is also known that (111) is not favorable for Li diffusion, hence reducing the rate capability [3]. A truncated cubo-octahedron was proposed as a good compromise between stability and rate capability[3]. Karim et al. determined the equilibrium particle shape of pure stoichiometric LiMn2O4 particles, in which they predicted a stable reconstructed (111) facet [4], in agreement with the observed shapes at high temperatures for Li1+xMn2-xO4 (x=0.125)[6]. However, several experimental results show that the particle shapes obtained do not all exhibit the predicted shape by the model. This discrepancy could be due to the nature and stoichiometry of the different surfaces, which depend on the experimental conditions the particles were synthesized in. In this work we will investigate the particles shape for non-stoichiometric as well as with dopants, with the goal being an optimized particle shape that will provide both stability and good rate capability. A second focus will be on investigation of the effect of the support and hence the interface/strain of epitaxial thin films of LiMn2O4 grown on single crystals, such as SrTiO3 and MgO for three crystallographic orientations (111) (100) and (110). Here we will focus on the interplay between Jahn-Teller distortion, Mn dissolution and Strain. This work is in line with the two of the DOE Basic Research Needs Report on Electrical Energy Storage: • Rational design of interfaces and interphases in chemical energy storage. • Novel designs and strategies for electrochemical systems. References: 1. Tarascon, J.M. and D. Guyomard, Li Metal‐Free Rechargeable Batteries Based on Li1 + x Mn2 O 4 Cathodes ( 0 ≤ x ≤ 1 ) and Carbon Anodes. Journal of The Electrochemical Society, 1991. 138(10): p. 2864-2868. 2. Hirayama, M., et al., Dynamic Structural Changes at LiMn2O4/Electrolyte Interface during Lithium Battery Reaction. Journal of the American Chemical Society, 2010. 132(43): p. 15268-15276. 3. Kim, J.-S., et al., A Truncated Manganese Spinel Cathode for Excellent Power and Lifetime in Lithium-Ion Batteries. Nano Letters, 2012. 12(12): p. 6358-6365. 4. Karim, A., S. Fosse, and K.A. Persson, Surface structure and equilibrium particle shape of the LiMn2O4 spinel from first-principles calculations. Physical Review B, 2013. 87(7): p. 075322. 5. Thackeray, M.M., Manganese oxides for lithium batteries. Progress in Solid State Chemistry, 1997. 25(1–2): p. 1-71. 6. Takada, T., et al., Structure and electrochemical characterization of Li1+xMn2−xO4 spinels for rechargeable lithium batteries. Journal of Power Sources, 1999. 81–82(0): p. 505-509. Project description: In this work we will investigate the particles shape for non-stoichiometric as well as with dopants. We will perform theoretical work based on density functional theory using “VASP”, to simulate the equilibrium particle shapes of non-stoichiometric and doped LiMn2O4 particles, with the goal being an optimized particle shape that will provide both stability and good rate capability. Total energy calculations will be performed for different LiMn2O4 stoichiometries and compositions, in which Mn will be substituted with other candidate transition metals such as Ni, Mo, and Ti. This will require total energy calculations of surfaces (slab geometry) as well as corresponding bulk compositions. A second focus will be on investigation of the effect of the support and hence the interface/strain of epitaxial thin films of LiMn2O4 grown on single crystals, such as SrTiO3 and MgO for three crystallographic orientations (111) (100) and (110). Here we will focus on the interplay between Jahn-Teller distortion, Mn dissolution and Strain. Industry partnership: Project URL: Requested allocation: 480000 Q1: 120000 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: MBM_CEES2
by accounts＠lcrc.anl.gov 12 Sep '14

12 Sep '14

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: hakim iddir Applicant's institution: ANL Applicant's division: MSD Project Name: MBM_CEES2 Project title: Modeling Battery Materials CEES2 Associated funding: DOE, EFRC Other Systems: PNNL Science: As a part of continuing effort to contribute to the battery research here at Argonne, and to the EFRC (CEES II) project. We will perform theoretical work based on density functional theory using “VASP”, to simulate the equilibrium particle shapes of non-stoichiometric and doped LiMn2O4 particles. As stated in the CEES II proposal, it is central to this task to understand the electrode structure instabilities induced electrochemically. LiMn2O4 is ideal as a high-capacity Li-ion battery cathode material by virtue of its low toxicity, low cost, and the high natural abundance of Mn. However, this material suffers from Mn dissolution problem that not only induces a capacity fade [1], but can also poison the anode. The dissolution is associated with the disproportionation of Mn3+, and is dependent on the surface structure, hence the crystal orientation as well [2, 3]. For example, (111) is expected to be more stable as the reconstruction moves Mn to th e surface sub-layers[4]. Previous works show that (111) surface is more stable than (100) and (110) surfaces with respect to Mn dissolution [3, 5]. To improve its stability with respect to Mn dissolution, one would like to predict the synthesis conditions that would preferentially enhance the (111) surface ratio over that of the other facets, not only in pristine stoichiometric state, but also non-stoichiometric and doped surfaces. However, it is also known that (111) is not favorable for Li diffusion, hence reducing the rate capability [3]. A truncated cubo-octahedron was proposed as a good compromise between stability and rate capability[3]. Karim et al. determined the equilibrium particle shape of pure stoichiometric LiMn2O4 particles, in which they predicted a stable reconstructed (111) facet [4], in agreement with the observed shapes at high temperatures for Li1+xMn2-xO4 (x=0.125)[6]. However, several experimental results show that the particle shapes obtained do not all exhibit the predicted shape by the model. This discrepancy could be due to the nature and stoichiometry of the different surfaces, which depend on the experimental conditions the particles were synthesized in. In this work we will investigate the particles shape for non-stoichiometric as well as with dopants, with the goal being an optimized particle shape that will provide both stability and good rate capability. A second focus will be on investigation of the effect of the support and hence the interface/strain of epitaxial thin films of LiMn2O4 grown on single crystals, such as SrTiO3 and MgO for three crystallographic orientations (111) (100) and (110). Here we will focus on the interplay between Jahn-Teller distortion, Mn dissolution and Strain. This work is in line with the two of the DOE Basic Research Needs Report on Electrical Energy Storage: • Rational design of interfaces and interphases in chemical energy storage. • Novel designs and strategies for electrochemical systems. References: 1. Tarascon, J.M. and D. Guyomard, Li Metal‐Free Rechargeable Batteries Based on Li1 + x Mn2 O 4 Cathodes ( 0 ≤ x ≤ 1 ) and Carbon Anodes. Journal of The Electrochemical Society, 1991. 138(10): p. 2864-2868. 2. Hirayama, M., et al., Dynamic Structural Changes at LiMn2O4/Electrolyte Interface during Lithium Battery Reaction. Journal of the American Chemical Society, 2010. 132(43): p. 15268-15276. 3. Kim, J.-S., et al., A Truncated Manganese Spinel Cathode for Excellent Power and Lifetime in Lithium-Ion Batteries. Nano Letters, 2012. 12(12): p. 6358-6365. 4. Karim, A., S. Fosse, and K.A. Persson, Surface structure and equilibrium particle shape of the LiMn2O4 spinel from first-principles calculations. Physical Review B, 2013. 87(7): p. 075322. 5. Thackeray, M.M., Manganese oxides for lithium batteries. Progress in Solid State Chemistry, 1997. 25(1–2): p. 1-71. 6. Takada, T., et al., Structure and electrochemical characterization of Li1+xMn2−xO4 spinels for rechargeable lithium batteries. Journal of Power Sources, 1999. 81–82(0): p. 505-509. Project description: In this work we will investigate the particles shape for non-stoichiometric as well as with dopants. We will perform theoretical work based on density functional theory using “VASP”, to simulate the equilibrium particle shapes of non-stoichiometric and doped LiMn2O4 particles, with the goal being an optimized particle shape that will provide both stability and good rate capability. Total energy calculations will be performed for different LiMn2O4 stoichiometries and compositions, in which Mn will be substituted with other candidate transition metals such as Ni, Mo, and Ti. This will require total energy calculations of surfaces (slab geometry) as well as corresponding bulk compositions. A second focus will be on investigation of the effect of the support and hence the interface/strain of epitaxial thin films of LiMn2O4 grown on single crystals, such as SrTiO3 and MgO for three crystallographic orientations (111) (100) and (110). Here we will focus on the interplay between Jahn-Teller distortion, Mn dissolution and Strain. Industry partnership: Project URL: Requested allocation: 480000 Q1: 120000 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] Yearly Allocation Request for glassforms
by accounts＠lcrc.anl.gov 12 Sep '14

12 Sep '14

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Peter Zapol Project Name: glassforms Division: MSD Project title: First-principles Calculations of Mineral and Glass Dissolution under Various pH Conditions Associated funding: DOE-NE Other Systems: Science: The dissolution of glass forms in nuclear waste disposal determines their long term stability, which is critical for evaluating disposal scenarios. The dissolution behavior of minerals and glasses has been found to strongly depend on the pH value of the aqueous environment. The delicate balance of ions at the solid-water interface in aqueous solutions is still a big challenge both for accurate computational modeling and for unambiguous experimental measurements. This project aims to develop physical models to simulate the water-borosilicate glass forms interface at the atomic level under various pH conditions and to calculate the rates of dissolution for Si, Al and other constituting elements under acidic, neutral and basic conditions. These studies are based on first-principles calculations and kinetic Monte Carlo simulations. The calculated reaction barriers by using DFT calculations can then be used as input in kinetic Monte Carlo simulations to estimate the over all dissolution rates and compare with experimental values. These investigations will be very important to better understanding of the dissolution behavior and prediction of dissolution rates. Project description: Next year we will extend our study from hydrolysis reactions of network formers in a sodium borosilicate glass to ion exchange reactions. In the past year, we have calculated hydrolysis reaction energies and barriers of the Si-O-Si bridges at surface sites of sodium borosilicate glass as a model system in different protonation states – neutral (≡SiOH), protonated (≡SiOH2+) and deprotonated (≡SiO-) using the Nudged Elastic Band (NEB) method. We will continue our studies for other constituting elements, e.g. Al, where we calculate the reaction barriers of T-O-T bridges (T=Si, Al, B) at surface sites in different protonation states – neutral (≡SiOH), protonated (≡SiOH2+) and deprotonated (≡SiO-) using the Nudged Elastic Band (NEB) method by using VASP code. We will address migration barriers of modifier cations throughout the network to address additional pathways for dissolution. The input parameters for Kinetic Monte Carlo simulations will be determined. Industry partnership: Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 600000 Q1: 150000 Q2: 150000 Q3: 150000 Q4: 150000 Justification: The first-principles calculations will be carried out using the electronic-structure code VASP. In the first part, NEB calculations will be performed to calculate the reaction pathways for a variety of composing elements under acidic, neutral and basic conditions. A single geometry optimization takes 48 hours on 32 processors. We are considering 60 supercell samplings of silicate glasses including multiple T sites (Si, Al, B). The calculation for possible reactants, intermediates, products will take about 300,000 core hours. It takes about 50 hours on 160 processors (5 images) to calculate a reaction barrier along the reaction pathway. The total estimated computer time for barrier calculation is 300,000 core hours. Storage requirements: Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request for lipidmovement
by accounts＠lcrc.anl.gov 12 Sep '14

12 Sep '14

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Ursula Perez Salas Project Name: lipidmovement Division: MSD Project title: Curvature Effect on the Movement of Lipids Within and Between Membranes Associated funding: LDRD Other Systems: UIC extreme cluster Science: This project uses Molecular Dynamics simulations to investigate the diffusion of lipids, specifically cholesterol, in curved lipid (DPPC) membranes. We will calculate the free energy profile of extraction as well as flip-flop in a curved lipid membrane, i.e. a vesicle. The results will be compared to those obtained from MD simulations on planar membranes, which agree with experimental data of planar membranes (neutron reflectivity) but disagree substantially from data on highly curved lipid vesicles (small angle scattering). Scattering experiments appear to show that the flip-flop rates are fast in flat membranes and slow in the curved membranes. Thus curvature is expected to affect the transfer rate of lipids into the membrane as well as its movement across lipid leaflets. The results will provide an atomic-level explanation for the kinetic rates obtained in small angle neutron scattering experiments. The movement of lipids within membranes (flip-flop) together with the exchange between membranes under physiological conditions allows the creation of asymmetric distributions of lipids across cellular membranes. Further, the location of lipids and their rate of exchange have important biological consequences, especially for lipids involved in cellular signaling. Therefore decoding the underlying mechanisms that control lipid transfer between and within lipid membranes is critical for understanding lipid homeostasis in the cell as well as the metabolic pathways that sustain it. The proposed research seeks to identify key physical membrane properties, specifically curvature, which govern both exchange and flip-flop of lipids in membranes. Project description: We have used coarse-grained simulations utilizing the MARTINI force field to create a unilamellar lipid vesicle, 30nm in diameter, solvated in water consisting of 1M particles. This vesicle size is similar to those used in neutron scattering experiments to which we want to compare the simulations results. In our previous project we calculated the free energy profile of a single lipid (DPPC) across a flat bilayer as well as a vesicle (curved membrane) using the umbrella sampling technique. Our preliminary results show an increase in the energy barrier of lipid flip-flop across the membrane in the curved case compared to the flat bilayer which indicate slower flip-flop rates. We now plan to add cholesterol to the system at extremely low and high concentrations, which will eventually partition into the lipid (DPPC) vesicle. We will then calculate the free energy profile for cholesterol across the bilayer at each concentration and also comparing to the case of a flat membrane. In the Umbrella sampling technique the phase space is divided into many small regions, which are sampled independently and then combined using the Weighted Histogram Analysis method to provide a single energy profile. The umbrella sampling technique allows us to run many short simulations in parallel which are then combined through post-processing. We will use the molecular dynamics program NAMD, which is developed at University of Illinois at Urbana-Champaign and is freely available for download (http://www.ks.uiuc.edu/Research/namd/) NAMD is highly parallel and scales efficiently with the number of particles in the system. Our previous simulations on the Fusion cluster has shown a benchmark of 7ms/timestep on 512 cores. Using a time step of 10fs, we estimate that the proposed calculations require approximately 5 microseconds of simulation requiring a total of 495,000 core-hours. Industry partnership: Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 496000 Q1: 124000 Q2: 124000 Q3: 124000 Q4: 124000 Justification: Storage requirements: Thank You, The LCRC Accounts System

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[LCRC Accounts] Yearly Allocation Request for metadissolve
by accounts＠lcrc.anl.gov 12 Sep '14

12 Sep '14

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: John J. Low Project Name: metadissolve Division: CLS Project title: Ab Initio Molecular Dynamics Simulations of Aqueous Reactions of AluminoSilicates Associated funding: Other Systems: Science: The reactions of Aluminosilicates in water are important in nuclear waste storage, zeolite synthesis, hydrothermal stability and mineralogy. These reactions involve changes in the coordination of reactants and products which can be difficult to model with continuum models of solvents often exploited in ab initio simulations of these reactions. We propose to model the kinetics of the polymerization reactions of aluminosilicates in solution and on surface of amorphous aluminosilicates. This study will establish the utility of advanced molecular dynamics with a explicit solvent models over implicit solvent models. Project description: The project will predict the rates of aqueous polymerization reactions of aluminosilicates with ab initio molecular dynamics. We will generate free energy surfaces for dimerization reactions of SiOH4 + SiOH4, Al(OH)3 + SiOH4 and B(OH3) + SiOH4 in water and vacuum. Each of these reactions will carried in pH neutral, acidic (1M HCl) and basic (1M NaOH) solutions to model the effect of pH on these reactions. We will use metadynamics to define the reaction coordinate and estimates of free energies. Umbrella sampling will be use to predict accurate free energies and estimates of rates. CPMD (http://www.cpmd.org) PLUMED (http://www.plumed-code.org) and WHAM (http://membrane.urmc.rochester.edu/content/wham) will be used in this project. CPMD is a plane-wave pseudopotential code which exploits Carr-Parrinello Molecular Dynamics. CPMD is very efficient method for ab initio molecular dynamics. PLUMED is an open source plugin, which works together with CPMD, for free energy calculations in molecular systems. Although CPMD can do metadynamics, PLUMED implements the reaction path collective variable (RPCV). The RPCV should increase the efficiency of metadynamics and umbrella sampling. WHAM is a program which performs a weighted histogram analysis of the trajectory from umbrella sampling to generate the free energy changes along the reaction coordinate. CPMD is a highly scalable parallel code. The hybrid MPI/openMP Version of CPMD 3.15.3 scales very well. CPMD can use 560 cores on either blues or fusion very efficiently for these models considered in this project. Additional scaling can be obtained with multiple walkers and task groups, which is available in CPMD. This will enable additional levels of parallelism could scale efficiently to thousands of cores. PLUMED implements a reaction path collective variable will allow us to simulate this reaction with one dimensional metadynamics. One dimensional metadynamics is at least two to three times more efficient than two or three dimensional sampling. PLUMED will increase the efficiency of our metadynamics and umbrella sampling by a factor of two to three. Industry partnership: Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 200000 Q1: 100000 Q2: 100000 Q3: 0 Q4: 0 Justification: Storage requirements: Thank You, The LCRC Accounts System

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Re: [allocations-admins] [LCRC Accounts] Project Request: hipgisaxs
by Low, John J. 12 Sep '14

12 Sep '14

Nicola, Looks good to me by the way. Could you add the attached figure from Abinihav Appl Cyrst. Paper. Write something like ³HipGISAXS is a massively parallel code which shows good parallel scaling to 6000 cores allowing accurate simulations of complicated surface structures.² By the way he use 25 megacore hours to simulate an ³Organic photovoltaic three-dimensional complex morphology obtained from electron tomography measurements²!!!! Are you planning to do something like that? If so you should consider using the ALCF-BG or a GPU clusterŠ. John J. Low Principal Computational Science Specialist Computing, Environment and Life Sciences Building 240, 2143 9700 South Cass Avenue Argonne National Laboratory Argonne, IL 60439. 630-252-0045 www.linkedin.com/pub/john-low/15/8b0/5aa/ On 9/12/14, 1:21 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> wrote: >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: Nicola Ferrier >Applicant's institution: ANL > Applicant's division: MCS > Project Name: hipgisaxs > Project title: Simulation of Grazing Incident Small Angle >X-ray Scattering > Associated funding: Uchicago Institute for Molecular Engineering > Other Systems: > Science: Directed Self Assembly (DSA) of block copolymer >films on lithographically defined chemically nanopatterned surfaces is an >emerging technology originally developed by Nealey and de Pablo (our >UChicago collaborators) that is well-positioned for commercialization in >nanolithography and nanomanufacturing. A critical need is to capture >the details of the three-dimensional structure of individual block >copolymer domains, and the collective averages of three-dimensional >structure and pattern perfection over large areas, all as a function of >materials, processing and boundary conditions used in DSA. Our goal is >to develop computational tools for analysis of grazing incident small >angle x-ray scattering (GISAXS) data in order to accurately characterize >the 3D structure of materials. > Project description: John Low and I have been working to have >software from LBL, HiPGISAXS (High Performance GISAXS), operational at >ANL. This software simulates forward scattering spectra from complex >shapes (represented by triangulated surfaces). Accuracy scales >(inversely) with the size of the triangles, while computational demands >scales with the number of triangles. Thus accurate simulation of a large >area of material (many square microns) requires hundreds of millions of >triangles. We are currently starting to explore this space (accuracy vs. >computational load). > >The forward scattering (HiPGISAXS) will be integrated into a workflow >where output from MD simulations will be used to generate the >triangulated surface that is input to HiPGISAXS. Comparison with >experimental spectra will be used to ³feedback² to the simulations. >Currently MD simulation data (stored on disk) is used to generate >HiPGISAXS inputs (on a single core machine). Techniques for quantitative >comparison of simulated and experimental spectra is under development. > >In a related project (Manolis Doxastakis, MSD), 2D methods are being >explored. These projects are synergistic (with teams meeting weekly). > > Industry partnership: Intel funds my colloborators (Paul Nealey) at >UChicago Institute for Molecular Engineering on a projected called >"Narrowing the options for 16 nm full pitch DSA and below". Intel is >interested in characterization of materials used in the elcctronics >industry (i.e. block co-polymers). > Project URL: > Requested allocation: 100000 > Q1: 25000 > Q2: 25000 > Q3: 25000 > Q4: 25000 > Justification: > Storage requirements: < 1TB is needed. > > >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 lcrc-app-engr
by accounts＠lcrc.anl.gov 12 Sep '14

12 Sep '14

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: John Valdes Project Name: lcrc-app-engr Division: LCRC Project title: LCRC Application Engineer support work Associated funding: Other Systems: Science: Project description: This project will be used by the LCRC application engineers to do support work for users of the LCRC cluster. This support might be in the form of installation and debugging of both LCRC core and user applications, benchmarking and performance analysis, user startup help, etc. Industry partnership: Project URL: http://www.lcrc.anl.gov 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 DMDOHEMA_1
by accounts＠lcrc.anl.gov 12 Sep '14

12 Sep '14

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Ross Ellis Project Name: DMDOHEMA_1 Division: CSE Project title: Metal Ion Transport through Nano-Structured Lipophilic Systems: Atomistic MD Simulations Associated funding: DOE-BES Other Systems: There are two computer clusters available in addition to LCRC, i.e., the TARDIS at Prof. Monica Olvera de la Cruz’s group, and the QUEST, both at Northwestern University. Involved in several projects, the collaborating user Dr. Baofu Qiao has uses aroud 100,000 CPU hours on QUEST, and more than 1,000,000 CPU hours on TARDIS. Science: The interactions and transport mechanisms of metal ions through nano-structured soft matter systems is woefully lacking in fundamental understanding. Such systems are imported in a huge range of applications, such as: extractive separations; forming meso-porous catalytic supports; nano-particle synthesis; life-mimicking systems; etc. Understanding multi-scale structures and interactions is key to developing these important applications and is at the forefront of meso-science. However, soft-matter systems containing coordinating metal ions are notoriously difficult to probe structurally, with the best techniques being synchrotron SAXS and EXAFS giving information on the atomic metal-centric scale and supramolecular scale, respectively. Interpreting such experimental data from these complex systems can give a general idea of coordination environment and the morphology of the supramolecular solvent. However, in order to gain a truly multi-scale understanding with atomi c resolution, we must couple these experimental data with MD simulations, which can be done conveniently and powerfully by directly fitting SAXS and EXAFS data with the simulated systems. This methodology will provide a breakthrough in new fundamental insights into the structural complexity of metal ion – soft matter systems. Project description: In the last few months, we have performed some preliminary simulation runs in understanding the supra-molecular aggregate structure in organic phases under the project DMDOHEMA_1 on LCRC. Some findings have been unveiled, e.g., the presences of water, acid, Eu(NO3)3 all affect the supra-molecular aggregate structure of extractant (i.e., DMDOHEMA) in organic phased. These findings agree with the existing experimental data. However, due to the small size of those simulation systems, the aggregation behaviors are not converged well. Therefore, in the renewal period of project DMDOHEMA_1, we are aiming to enlarge our simulation boxes so that such findings can be solidified. Moreover, one already finished large simulation supports that larger simulation box decreases the calculated error bar of the aggregation number of DMDOHEMA. With the simulations on large enough simulation boxes, the effects of water, acid, Eu(NO3)3 will be distinguished, which will surel y provide significant insight for the rational design of higher efficient extractants. Our project is expected to highly spark the development of rare earth element related technologies. In this project, classical molecular dynamics (MD) simulations will be performed at the all-atom resolution, in addition to the concurrent solvent extraction experiments at ANL. All-atom MD simulations have been well proven in predicting supra-molecular aggregate structures. The open source package GROMACS will be employed for the simulations. GROMACS is one of the highly recommended packages for MD simulations. GROMACS has been reported to be able to scale well up to around 1,000 CPU processors. Based on our experience on LCRC, the simulations can be LINEARLY scaled up to 256 CPU cores, under which condition the simulation speed is around 3 hours/ns for a system of the size of around 17 × 17 × 17 = 5000 nm3. Two users will use this allocation time, Dr. Ross J. Ellis and Dr. Baofu Qiao, both at the CSE division at ANL. In the first phase of this project, we are studying the influence of a variety of components, i.e., water, acid, Eu(NO3)3, on the aggregate structures of DMDOHEMA extractants dissolved in n-heptane organic phases. As aforementioned, this project is currently ongoing. With the allocation from LCRC, we are able to collects some conclusions in the near fure. In the second phase, we plan to study the effect of extractant on the supra-molecula aggregate structure. The extraction of DMDBTDMA, which is the preceding extractant of DMDOHEMA, will be simulated and compared with the simulation results of DMDOHEMA systems. According to the available experimental data, the effects of some factors will be explore, such as the concentration of water, the concentration of Eu(NO3)3 complexes, the concentration of acidic molecule of HNO3. Industry partnership: Project URL: Current FY Hours Used: undetermined amount New FY Requested allocation: 600000 Q1: 200000 Q2: 200000 Q3: 100000 Q4: 100000 Justification: Table. Benchmark of the simulation speed on LCRC #CPU cores 16 32 64 256 Speed (ns/day) 0.51 1.0 2.0 7.7 Based on the benchmark simulations, we can conclude that the scaling on LCRC can be linearly up to at least 256 CPU cores for our simulations. Storage requirements: 1TB storage is large enough for our project. Thank You, The LCRC Accounts System

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