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

New LCRC report submitted for PrtnAdp_CG
by support＠lcrc.anl.gov 26 Oct '16

26 Oct '16

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2016/?project=PrtnAdp_CG

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New LCRC report submitted for IntensitySim
by support＠lcrc.anl.gov 25 Oct '16

25 Oct '16

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2016/?project=IntensitySim

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[LCRC Accounts] Project Request: Solvation_Challenges
by accounts＠lcrc.anl.gov 18 Oct '16

18 Oct '16

Hello, A new project on the LCRC cluster has been requested. Please forward the information on to the LCRC Allocation sub-committee. Applicant's name: Kenley Pelzer Applicant's institution: ANL Applicant's division: MSD Project Name: Solvation_Challenges Project title: Solvation Challenges in Polymer Chemistry and Nanotechnology: A Computational Approach Associated funding: Aneesur Rahman Named Postdoctoral Fellowship through Argonne Other Systems: None Science: A fundamental challenge in organic chemistry is the identification of appropriate solvents and detergents for solution phase systems. Finding an appropriate solvent for a solute molecule may be an endeavor in itself--however, even greater challenges arise when solvation must be maintained upon polymerization or aggregation of the solute. A small polymer solute may form a sturdy solvation shell with a particular solvent, but this solvation shell may experience major disruption when longer polymers are formed. Solvation of nanoscale colloids also presents difficulties, as aggregation of nanoparticles may cause precipitation in spite of the solubility of an isolated nanoparticle. All of these problems call for solvents that maintain strong interactions upon changes in the solute. In this work, we seek to develop a new computational approach to modeling solvation. Project description: While ab initio or classical molecular dynamics methods are traditionally used to model solvation, these methods are limited in the size of system and time scales that they can model. However, the simulation of thousands of molecules over long time scales may be necessary to observe solvation failures such as particle aggregation and precipitation. To allow simulation of large systems over long time scales, we suggest a coarse-grained approach that builds upon algorithms previously used to model self-assembly of colloids into ordered solid structures. We suggest that the assembly of solvent molecules into ordered solvation shells is analogous to the assembly of these solid structures, and with an appropriate representation of the solvent molecules, similar formalisms can be applied. The solvent molecules will be represented as hard shapes, with the shapes defined according to the electron density obtained with density functional theory (DFT) calculations. These hard shapes, which will contain enthalpic patches to incorporate electrostatic attraction and repulsion between molecules, will then be treated with Monte Carlo simulations. These Monte Carlo simulations will incorporate the directional entropic forces that have been shown to drive self-assembly in colloids. The Monte Carlo simulations will be GPU-based and we will pursue these resources elsewhere (probably at the ALCF and/or NERSC). However, prior to executing any Monte Carlo simulations, we must develop an appropriate method for defining the hard shapes and their enthalpic patches. We plan to define these properties using simple ground-state DFT calculations with the Gaussian software package. To test the validity of these shape definitions, we will perform ab initio molecular dynamics (AIMD) of a few explicit solvent molecules using the CPMD software package and confirm that our shape definition is consistent with the intermolecular spacings that we observe in AIMD. We will use this procedure to define hard shapes for several organic solvents that are commonly used in electrochemistry and nanomaterials. This information will then provide the basis for large-scale Monte Carlo simulations that can simulate thousands of molecules over the time scales relevant to solvation problem s. Industry partnership: Project URL: Requested allocation: 40000 Q1: 10000 Q2: 10000 Q3: 10000 Q4: 10000 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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Re: [allocations-admins] [LCRC Accounts] Project Request: zwitterion-brushes
by Bair, Raymond A. 12 Oct '16

12 Oct '16

This is one that we can start with 200K (scaled), prio 3. Ray ----------------------------------------- Ray Bair Argonne National Laboratory On 10/6/16, 2:23 PM, "allocations-admins-bounces(a)lcrc.anl.gov on behalf of accounts(a)lcrc.anl.gov" <allocations-admins-bounces(a)lcrc.anl.gov on behalf of 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: Nicholas Jackson Applicant's institution: ANL Applicant's division: MSD/ALCF Project Name: zwitterion-brushes Project title: Structural Changes in Zwitterionic Brushes Associated funding: DOE, NIST Other Systems: UChicago Midway ANL - Blues - 20k Science: This project will use atomistic molecular dynamics to explore structural changes in a zwitterionic brush (PMPC) studied by ANL scientist Wei Chen, and ANL postdocs Jing Yu and Sean Mao in MSD. Dr. Chen has observed very unusual structural changes upon the addition of multivalent salts, an area which is almost completely unstudied computationally, but is vitally important biologically and technologically. X-ray and neutron scattering data taken by Dr. Chen indicate no change in brush height upon the addition of multivalent salt. However, x-ray scattering data indicates a clear change of structure within the brush resulting from the addition of multivalent salt ions. Specifically, the distribution of carbon and nitrogen atoms within the brush changes significantly upon the addition of divalent salt, however the brush height stays the same. These simulations will be used to directly assess the nature of this structural transition within the brush by directly monitoring the distributions of PMPC atoms within the brush, and its changes as a function of multivalent salt concentration. This will lend significant insight into the fundamental interaction between multivalent ions and polyzwitterions, while greatly assisting in the Dr. Chen's interpretation of experimental data. Project description: The computational model I will use for these simulations is atomistic molecular dynamics in the GROMACS package, which is compiled on Blues and utilizes MPI parallelization to accelerate the evaluation of the time-consuming kspace electrostatics calculations. GROMACS is the ideal software package for these calculations, as previous preliminary calculations of mine on atomistic polyelectrolytes on Blues exhibit a 10-fold increase in speed relative to the popular LAMMPS code for system sizes of ~100K atoms, achieving approximately 5ns/day for a given trajectory. System sizes will be approximately ~100K atoms. I will be running my simulation at 6 salt ion concentrations, and will need to simulate 30 ns of simulation time for each trajectory to capture the relevant relaxation processes. I intend for my simulations to occupy 5 nodes. I will be the sole project member. Industry partnership: Project URL: Requested allocation: 400000 Q1: 100000 Q2: 100000 Q3: 100000 Q4: 100000 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 _______________________________________________ allocations-admins mailing list allocations-admins(a)lcrc.anl.gov https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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[LCRC Accounts] Project Request: zwitterion-brushes
by accounts＠lcrc.anl.gov 06 Oct '16

06 Oct '16

Hello, A new project on the LCRC cluster has been requested. Please forward the information on to the LCRC Allocation sub-committee. Applicant's name: Nicholas Jackson Applicant's institution: ANL Applicant's division: MSD/ALCF Project Name: zwitterion-brushes Project title: Structural Changes in Zwitterionic Brushes Associated funding: DOE, NIST Other Systems: UChicago Midway ANL - Blues - 20k Science: This project will use atomistic molecular dynamics to explore structural changes in a zwitterionic brush (PMPC) studied by ANL scientist Wei Chen, and ANL postdocs Jing Yu and Sean Mao in MSD. Dr. Chen has observed very unusual structural changes upon the addition of multivalent salts, an area which is almost completely unstudied computationally, but is vitally important biologically and technologically. X-ray and neutron scattering data taken by Dr. Chen indicate no change in brush height upon the addition of multivalent salt. However, x-ray scattering data indicates a clear change of structure within the brush resulting from the addition of multivalent salt ions. Specifically, the distribution of carbon and nitrogen atoms within the brush changes significantly upon the addition of divalent salt, however the brush height stays the same. These simulations will be used to directly assess the nature of this structural transition within the brush by directly monitoring the distributions of PMPC atoms within the brush, and its changes as a function of multivalent salt concentration. This will lend significant insight into the fundamental interaction between multivalent ions and polyzwitterions, while greatly assisting in the Dr. Chen's interpretation of experimental data. Project description: The computational model I will use for these simulations is atomistic molecular dynamics in the GROMACS package, which is compiled on Blues and utilizes MPI parallelization to accelerate the evaluation of the time-consuming kspace electrostatics calculations. GROMACS is the ideal software package for these calculations, as previous preliminary calculations of mine on atomistic polyelectrolytes on Blues exhibit a 10-fold increase in speed relative to the popular LAMMPS code for system sizes of ~100K atoms, achieving approximately 5ns/day for a given trajectory. System sizes will be approximately ~100K atoms. I will be running my simulation at 6 salt ion concentrations, and will need to simulate 30 ns of simulation time for each trajectory to capture the relevant relaxation processes. I intend for my simulations to occupy 5 nodes. I will be the sole project member. Industry partnership: Project URL: Requested allocation: 400000 Q1: 100000 Q2: 100000 Q3: 100000 Q4: 100000 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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New LCRC report submitted for ElectrolyteRedoxFlow
by support＠lcrc.anl.gov 05 Oct '16

05 Oct '16

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2016/?project=ElectrolyteRe…

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LCRC Allocations
by Bair, Raymond A. 05 Oct '16

05 Oct '16

When: Monday, December 12, 2016 1:30 PM-2:45 PM. (UTC-06:00) Central Time (US & Canada) Where: 240/5172 *~*~*~*~*~*~*~*~*~* This is the Q2 allocations meeting.

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[LCRC Accounts] Yearly Allocation Request for SHARP_ARC
by accounts＠lcrc.anl.gov 04 Oct '16

04 Oct '16

Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Justin W. Thomas Project Name: SHARP_ARC Division: NE, MCS Project title: Multi-physics Simulation of SFR Core Radial Expansion with SHARP Associated funding: DOE-NE Advanced Reactor Concepts Other Systems: NE Division clusters, MCS Cosmea cluster Science: Following multi-year efforts for development of coupled neutronics, computational fluid dynamics (CFD), and computational structural mechanics (CSM) analysis capabilities, the SHARP multi-physics nuclear reactor analysis toolkit was released for distribution (via an end-user license agreement) at the end of March 2016. In FY17, our main focus will therefore shift toward testing, validation and verification of SHARP component codes and multi-physics toolkit in application to challenge problems for advanced reactor designs. The objective is to assess SHARP capabilities in addressing the high-fidelity modeling and simulation needs that have been identified as important to customers in the nuclear industry and other DOE R&D programs (particularly the Advanced Reactor Technologies program). One challenge problem that has been identified is the need to assess hot pin/hot channel factors for sodium-cooled fast reactor designs. Hot pin and hot channel factors are a means of accounting for deviations between the actual manufactured nuclear fuel pins and the design specifications, as well as deviations in the actual operating flow conditions from the idealized flow field assumed for design calculations. In this effort, SHARP will be used to explicitly model the standard assumptions made in conservative analyses by reassessing hot-channel and hot-pin factors for Argonne’s AFR-100 reactor concept. The fuel assembly with peak power-to-flow ratio, and the peak-to-average pin power, temperature and flow distributions within that fuel assembly under nominal conditions will be identified. The impact of inlet flow maldistribution and resulting temperature variations, cladding circumferential temperature variation, uncertainties and tolerances in fuel manufacturing, core lo ading errors, and uncertainties in heat transfer correlations will also be assessed. If successful, reliable prediction of these factors will enhance the safety margins and therefore improve the economic competitiveness of new reactor concepts. A second challenge problem is to demonstrate “SHARP Zoom”, a multi-scale modeling capability for a focused view of a select region of an otherwise homogenized core model. The “SHARP Zoom” concept is a multi-scale modeling technique aimed to achieve a high-fidelity (focused) view of a select zone (i.e., fuel assembly) as part of a homogenized whole-core analysis to reduce the computational requirements and cost significantly in comparison to a full-core pin-by-pin analysis. Further, the allocation will be used to support international collaborations for code validation activities. The first is a U.S.-Japan Bilateral collaboration on sodium-cooled fast reactor technology development. For the advanced modeling & simulation task under the U.S.-Japan Bilateral Commission on Civil Nuclear Cooperation, benchmark simulation of a sodium experiment using wire-wrapped 37-pin bundles from JAEA’s Plant Dynamic Test Loop facility will be pursued to validate SHARP CFD solvers for liquid metal coolants. Under a collaboration between the U.S. and European Union, there are tasks earmarked for further SHARP CFD validation, including exercises related to flow in wire-wrapped fuel assemblies, and validation of approaches that couple conventional 1-D codes with 3-D CFD. Project description: As the SHARP modeling and simulation toolkit is maturing, the focus is on customer-oriented applications and further validation exercises. This allocation will help with those applications, for performing small to moderate scale simulations and for scaling up to ALCF. The SHARP toolkit is regularly compiled on Blues using Intel or GNU compilers. The components of SHARP—the Nek5000 computational fluid dynamics code and the PROTEUS neutron transport code—have already been demonstrated to scale well not only on Blues but on Blue Gene/P. This project will be used by 4-5 analysts in the NE and MCS Divisions. Industry partnership: Project URL: http://energy.gov/ne/advanced-modeling-simulation/advanced-nuclear-reactors Current FY Hours Used: undetermined amount New FY Requested allocation: 1000000 Q1: 250000 Q2: 250000 Q3: 250000 Q4: 250000 Justification: FY17 efforts for SHARP are highly focused on solving challenge problems for customers and code validation. FY16 efforts were focused on code development, as there was a major release, and so computational requirements were lower than usual. If the project is successful, we anticipate that FY17 and beyond will be highly resource intensive. The components of SHARP—the Nek5000 computational fluid dynamics code and the PROTEUS neutron transport code—have already been demonstrated to scale well not only on Fusion but on Blue Gene/P. Nek5000 has demonstrated > 80% parallel efficiency on BG/P (strong scaling) out to P=131,072 processors, using only 7300 points/processor at the largest scale. PROTEUS has demonstrated greater than 90% strong space-angle scaling at the 100,000 processer level and was nominated for the Gordon Bell Prize for its parallel performance. Storage requirements: 4 TB would provide convenience, considering the relatively large number of collaborators working simultaneously. Thank You, The LCRC Accounts System

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New LCRC report submitted for Atmos_Chem
by support＠lcrc.anl.gov 04 Oct '16

04 Oct '16

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2016/?project=Atmos_Chem

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New LCRC report submitted for Atmos_Chem
by support＠lcrc.anl.gov 04 Oct '16

04 Oct '16

Full project report at https://accounts.lcrc.anl.gov/reporting/project/2016/?project=Atmos_Chem

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