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The Institutional Challenges of Cyberinfrastructure and E-Research
E-Research and E-Scholarship The Institutional Challenges Cyberinfrastructureof and E-Research cholarly practices across an astoundingly wide range of dis- ciplines have become profoundly and irrevocably changed By Clifford Lynch by the application of advanced information technology. This collection of new and emergent scholarly practices was first widely recognized in the science and engineering disciplines. In the late 1990s, the term e-science (or occasionally, particularly in Asia, cyber-science) began to be used as a shorthand for these new methods and approaches. The United Kingdom launched Sits formal e-science program in 2001.1 In the United States, a multi-year inquiry, having its roots in supercomputing support for the portfolio of science and engineering disciplines funded by the National Science Foundation, culminated in the production of the “Atkins Report” in 2003, though there was considerable delay before NSF began to act program- matically on the report.2 The quantitative social sciences—which are largely part of NSF’s funding purview and which have long traditions of data curation and sharing, as well as the use of high-end statistical com- putation—received more detailed examination in a 2005 NSF report.3 Key leaders in the humanities and qualitative social sciences recognized that IT-driven innovation in those disciplines was also well advanced, though less uniformly adopted (and indeed sometimes controversial). In fact, the humanities continue to showcase some of the most creative and transformative examples of the use of information technology to create new scholarship.4 Based on this recognition of the immense disciplinary scope of the impact of information technology, the more inclusive term e-research (occasionally, e-scholarship) has come into common use, at least in North America and Europe. -
L2.3: Bulk MOS
Online simulations via nanoHUB: Molecular dynamics simulation of melting In this tutorial: • Setup an MD simulation for bulk Aluminum • Increase the system temperature with time • Explore melting Ale Strachan [email protected] School of Materials Engineering & Birck Nanotechnology Center Purdue University West Lafayette, Indiana USA © Alejandro Strachan – Online simulations: MD and melting 1 STEP 1: launch the nanoMATERIALS tool From your My HUB page launch nanoMATERIALS • From All Tools find: nano-Materials Simulation Toolkit • Launch tool by clicking on: © Alejandro Strachan – Online simulations: MD and melting 2 STEP 2: setup the atomistic simulation cell From the Input Model tab of the tool • Start with an Al unit cell • 4-atom cubic fcc cell: Cell vectors: a=a0(1,0,0) b=a0(0,1,0) c=a0(0,0,1) With a0=0.402 nm Fractional atomic positions (0,0,0) (0.0, 0.25, 0.25) (0.25, 0.0, 0.25) (0.25, 0.25, 0.0) • Replicate unit cell to create supercell Simulation cell will be infinitively • Replicate 5 times in each direction periodic with no free surfaces • Total number of atoms: 4x5x5x5 = 500 © Alejandro Strachan – Online simulations: MD and melting 3 STEP 3: setup the run parameters From the Driver Specification tab of the tool • NPT ensemble • Control temperature & pressure • Timestep to solve equations of motion: 0.002 ps (2 fs) • Number of MD steps 30,000 • Total simulation time: 30,000x0.002ps=60 ps • Temperature • Start simulation at room temp • Temperature increment • 30 K/ps • Temperature increase during run: 60ps x 30K/ps = 1800 • Final temperature: 1200 K + 300 K = 2100K © Alejandro Strachan – Online simulations: MD and melting 4 STEP 3 (cont.): setup the run parameters From the Driver Specification tab of the tool • Do not strain the simulation cell • Barostat will take care of thermal expansion and keep pressure at 1 atm. -
Cyberinfrastructure for High Energy Physics in Korea
17th International Conference on Computing in High Energy and Nuclear Physics (CHEP09) IOP Publishing Journal of Physics: Conference Series 219 (2010) 072032 doi:10.1088/1742-6596/219/7/072032 Cyberinfrastructure for High Energy Physics in Korea Kihyeon Cho1, Hyunwoo Kim and Minho Jeung High Energy Physics Team Korea Institute of Science and Technology Information, Daejeon 305-806, Korea E-mail: [email protected] Abstract. We introduce the hierarchy of cyberinfrastructure which consists of infrastructure (supercomputing and networks), Grid, e-Science, community and physics from bottom layer to top layer. KISTI is the national headquarter of supercomputer, network, Grid and e-Science in Korea. Therefore, KISTI is the best place to for high energy physicists to use cyberinfrastructure. We explain this concept on the CDF and the ALICE experiments. In the meantime, the goal of e-Science is to study high energy physics anytime and anywhere even if we are not on-site of accelerator laboratories. The components are data production, data processing and data analysis. The data production is to take both on-line and off-line shifts remotely. The data processing is to run jobs anytime, anywhere using Grid farms. The data analysis is to work together to publish papers using collaborative environment such as EVO (Enabling Virtual Organization) system. We also present the global community activities of FKPPL (France-Korea Particle Physics Laboratory) and physics as top layer. 1. Introduction We report our experiences and results relating to the utilization of cyberinfrastrucure in high energy physics. According to the Wiki webpage on “cyberinfrastrucure,” the term “cyberinfrastructure” describes the new research environments that support advanced data acquisition, storage, management, integration, mining, and visulaization, as well as other computing and information processing services over the Internet. -
Nanohub.Org - Online Simulation and More Materials for Semiconductors and Nanoelectronics in Education and Research
Purdue University Purdue e-Pubs Other Nanotechnology Publications Birck Nanotechnology Center August 2008 nanoHUB.org - online simulation and more materials for semiconductors and nanoelectronics in education and research Gerhard Klimeck Purdue University - Main Campus, [email protected] Michael McLennan Purdue University - Main Campus Mark S. Lundstrom Purdue University - Main Campus George B. Adams III Purdue University - Main Campus Follow this and additional works at: https://docs.lib.purdue.edu/nanodocs Klimeck, Gerhard; McLennan, Michael; Lundstrom, Mark S.; and Adams, George B. III, "nanoHUB.org - online simulation and more materials for semiconductors and nanoelectronics in education and research" (2008). Other Nanotechnology Publications. Paper 144. https://docs.lib.purdue.edu/nanodocs/144 This document has been made available through Purdue e-Pubs, a service of the Purdue University Libraries. Please contact [email protected] for additional information. nanoHUB.org – online simulation and more materials for semiconductors and nanoelectronics in education and research Gerhard Klimeck, Michael McLennan, Mark S. Lundstrom, George B. Adams III. Purdue University, Network for Computational Nanotechnology, West Lafayette, IN 47907 [email protected] nanoHUB.org provides a community service to over 65,000 using interactive seminar content for more than 15 minutes, or users in over 172 countries annually with “online simulations and an IP address that downloads (not just views) a content item. and more”. Over 85 interactive simulation tools supported by tutorials and general nanotechnology information material are As of 2007-08, nanoHUB is receiving 3–5 million web hits available free of charge to anybody. In all there are over 1,000 monthly. Most of our users come from academic institutions resources on nanoHUB. -
National Nanotechnology Initiative (NNI) Is Managed by the Nanoscale Science, Engineering, and Technology (NSET) Subcommittee of the NSTC Committee on Technology
THE NATIONAL NANOTECHNOLOGY INITIATIVE Supplement to the President’s 2016 Budget About the National Science and Technology Council The National Science and Technology Council (NSTC) is the principal means by which the Executive Branch coordinates science and technology policy across the diverse entities that make up the Federal research and development enterprise. A primary objective of the NSTC is establishing clear national goals for Federal science and technology investments. The NSTC prepares research and development strategies that are coordinated across Federal agencies to form investment packages aimed at accomplishing multiple national goals. The work of the NSTC is organized under committees that oversee subcommittees and working groups focused on different aspects of science and technology. The National Nanotechnology Initiative (NNI) is managed by the Nanoscale Science, Engineering, and Technology (NSET) Subcommittee of the NSTC Committee on Technology. More information is available at www.WhiteHouse.gov/administration/eop/ostp/nstc. About the Office of Science and Technology Policy The Office of Science and Technology Policy (OSTP) was established by the National Science and Technology Policy, Organization, and Priorities Act of 1976. OSTP’s responsibilities include advising the President in policy formulation and budget development on questions in which science and technology are important elements; articulating the President’s science and technology policy and programs; and fostering strong partnerships among Federal, state, -
Boston University Cyberinfrastructure Plan
Boston University Information Services & Technology 111 Cummington Street Boston, Massachusetts 02215 Boston University Cyberinfrastructure Plan I. BU Research Infrastructure o THE MASSACHUSETTS GREEN HIGH-PERFORMANCE COMPUTING CENTER (MGHPCC) BU recently partnered with government and regional institutions to establish the Massachusetts Green High Performance Computing Center (MGHPCC), operated by BU, Harvard, MIT, Northeastern, and the University of Massachusetts—five of the most research-intensive universities in Massachusetts—dedicated to serving our growing research computing needs more collaboratively efficiently, ecologically, and cost-effectively. BU high- performance computational resources are housed at the MGHPCC, taking advantage of an abundant source of clean renewable energy from the Holyoke Gas and Electric hydroelectric power plant on the Connecticut River. This project created a world-class high-performance computing center with an emphasis on green sustainable computing, offering unprecedented opportunities for collaboration among research, government, and industry in Massachusetts. MGHPCC is the first academic research computing center to achieve LEED Platinum certification, the highest level of green certification awarded by the Green Building Council. MGHPCC comprises 33,000 SF of space optimized for high performance computing, a 19 MW power feed, and high-efficiency cooling to support up to 10 MW of load with provisions for expansion to 30 MW. The MGHPCC owns the 8.6 acre site, providing substantial room for expansion. Network infrastructure includes a fiber loop passing through Boston, the Northern Crossroads (NoX), and New York City, connecting BU to the MGHPCC at 40 Gb/s. BU is also actively engaged in other national and regional consortia where we provide technical, strategic, and governance leadership. -
First Time User Guide to OMEN Nanowire**
Network for Computational Nanotechnology (NCN) UC Berkeley, Univ.of Illinois, Norfolk State, Northwestern, Purdue, UTEP First Time User Guide to OMEN Nanowire** Sung Geun Kim*, Saumitra R. Mehrotra, Ben Haley, Mathieu Luisier, Gerhard Klimeck Network for Computational Nanotechnology (NCN) Electrical and Computer Engineering *[email protected] ** https://nanohub.org/resources/5359 Outline • Introduction : Device →What is a nanowire? →What is a nanowire FET? →What can be measured in a nanowire FET? • What can be simulated by the OMEN Nanowire? -Input • What if you just hit “Simulate”? - Output • Examples – input-output relationship →What if the length of the channel is changed? →What if the diameter of nanowire is changed? • Limitation of the OMEN Nanowire tool • References Sung Geun Kim What is a nanowire? Nanowire : Wire-like structure with diameter or lateral dimension of nanometer(10-9m) ~10-9m=1nm ~Size of DNA http://en.wikipedia.org/wiki/DNA → Various material systems can be used to fabricate nanowires e.g.) Silver, Gold, Copper, …, etc. (metal) Si, Ge, GaAs, GaN, …, etc. (semiconductor) Sung Geun Kim What is a nanowire? Application of nanowires Fig. 1 **Nanowire memory cell Fig. 3 Nanowire FET National Institute of Standards and Technology Fig 1. http://www.eurekalert.org/pub_releases/2004-04/uosc-spn042004.php Fig 2. http://www.spectrum.ieee.org/oct07/5642 Fig. 2 ***Nanowire LED Fig 3. http://www.nist.gov/public_affairs/techbeat/tb2005_0630.htm#transistors B. Tian, Lieber Group, Harvard University Sung Geun Kim What is a nanowire FET? Nanowire FET : field effect transistor(FET) using nanowire Gate Drain Off On Current Source Insulator Channel » The current from the source to the drain is turned on and off by the voltage applied to the gate. -
L2.3: Bulk MOS
Online simulations via nanoHUB: Exchange interaction in Oxygen In this tutorial: • Setup DFT simulation of oxygen • Explore how the total spin affects total energy • Quantify exchange energy Ale Strachan [email protected] School of Materials Engineering & Birck Nanotechnology Center Purdue University West Lafayette, Indiana USA © Alejandro Strachan – Online simulations: Getting Started 1 STEP 1: launch the SeqQuest tool From your My HUB page launch seqQuest • From All Tools find: nanoMaterials SeqQuest DFT • Launch tool by clicking on: © Alejandro Strachan – Online simulations: getting started 2 STEP 2: setup the atomistic simulation cell From the Input Geometry tab of the tool We will select the O2 molecule pre-build case and modify it Only 1 atom (1st line) Oxygen atom at position 0.0, 0.0, 0.0 (3rd line) Make sure there are no extra lines (even at the end) and do not use tabs Box for simulation (10 Angstroms on the side): 10.0 0.0 0.0 0.0 10.0 0.0 0.0 0.0 10.0 © Alejandro Strachan – Online simulations: electronic structure of the O atom 2 STEP 3: setup the spin state to be considered Spin 1 configuration • Set GGA-SP (for exchange & correlation) • Set spin polarization to 2 (this number is the difference between spin up and spin down) Spin 0 configuration • Set GGA • Spin polarization to 0 (same number of spin up as down) © Alejandro Strachan – Online simulations: getting started 2 STEP 4: set type of run and simulate! Calculation specification tab We have a single atom so the atomic force will always be zero. -
Online Simulations Via Nanohub: Nanoscale Thermal Transport Via MD
Online simulations via nanoHUB: Nanoscale thermal transport via MD In this tutorial: • Non-equilibrium MD simulations of thermal transport Keng-hua Lin and Ale Strachan [email protected] School of Materials Engineering & Birck Nanotechnology Center Purdue University West Lafayette, Indiana USA © Alejandro Strachan – Online simulaons: Geng Started 1 STEP 1: • From All Tools find: nanoMATERIALS nanoscale heat transport • Launch tool by clicking on: © Alejandro Strachan – Online simulaons: geng started 2 STEP 2: setup the atomistic simulation cell From the Input Model tab of the tool • Select prebuilt structures • Or create your own structure by checking the box We will create our own © Alejandro Strachan – Online simulaons: geng started 3 How the simulation cells are defined • Along the transport direc7on the simulaon contains: • 2 Heat baths (blue) • The middle bin defines the hot and cold regions • Interior material (red) • This can be defined to be a superlace • Periodic boundary condi7ons are applied along the transport direcon Material (5 bins) Heat bath (3 bins) Cold bin Hot bin F. Müller-Plathe, J. Chem. Phys. 106, 6082 (1997) Keng-Hua Lin and A. Strachan, Physical Review B, 87, 115302 (2013). © Alejandro Strachan – Online simulaons: geng started 3 STEP 2: setup the atomistic simulation cell • We would like to create a Si supercell by replicang the cubic Si unit cell • The tool allows users to build superlaces (laminates) so it is a bit convoluted Along the transport the system will be divided in bins Each bin is one unit cell long -
Reproducing MD Simulations In
Reproducible Science @ nanoHUB.org Reproducing MD simulations in Thermal transport in SiGe superlattice thin films and nanowires: Effects of specimen and periodic lengths Keng-hua Lin, and Alejandro Strachan Physical Review B 87, 115302 (2011) Jon Dunn and Ale Strachan Network for Computational Nanotechnology (NCN) School of Materials Engineering [email protected] The paper Ale Strachan Key results Studied thermal transport on various semiconductor superlattices SL Thin film SL Square Nanowire SL Circular Nanowire • Thin film and nanowire configurations • Focused on how characteristic sizes affect thermal transport • Superlattice period • Total specimen length Ale Strachan Key results Thermal conductivity vs. superlattice period for three specimen lengths 105.87 nm 70.52 nm 35.21 nm 10 Thin Film Thin Film Thin Film S quAre NAnowire S quare Nanowire S quare Nanowire 8 C irculAr NAnowire C ircular Nanowire C ircular Nanowire 6 (W/mK ) 4 κ 2 0 0 10 20 30 40 0 10 20 30 40 0 10 20 30 40 Periodic Length (nm) Periodic Length (nm) Periodic Length (nm) • Thermal conductivity decreases with decreasing period until it reaches a minimum, further reduction leads to an increase in thermal conductivity – this is well known • For long specimens thermal conductivity of wires is smaller than thin films – this is expected due to surface scattering • Reducing specimen length reduces thermal conductivity – also well known – but the decrease in thin film is much more marked -> key result of the paper • For short specimens thermal conductivity of thin films -
The Seamless Cyberinfrastructure: the Challenges of Studying Users of Mass Digitization and Institutional Repositories
The Seamless Cyberinfrastructure: The Challenges of Studying Users of Mass Digitization and Institutional Repositories Dawn Schmitz April 2008 Seamless Cyberinfrastructure Contents 1 Introduction......................................................................................................................1 1.1 Scope of this Report ................................................................................................1 1.2 Rationale for this Report ........................................................................................2 2 Background on Mass Digitization................................................................................4 2.1 Definition of Mass Digitization .............................................................................4 2.1.1 Selection and Copyright..................................................................................6 2.2 Anticipated Users of Mass Digitization ...............................................................7 2.3 User Issues Related to Mass Digitization............................................................8 3 Background on Institutional Repositories .................................................................8 3.1 Definition of Institutional Repository..................................................................9 3.2 Prevalence of Institutional Repositories ...........................................................11 3.3 User Issues Related to Institutional Repositories............................................11 3.3.1 Who Is Depositing -
What Is Cyberinfrastructure? Craig A
What is Cyberinfrastructure? Craig A. Stewart* Stephen Simms Beth Plale 812-855-4240 812-855-7211 812-855-4373 Pervasive Technology Institute & Research Technologies, UITS & School of Informatics and Computing Research Technologies, UITS** Pervasive Technology Institute & Pervasive Technology Institute [email protected] [email protected] [email protected] Matthew Link David Y. Hancock Geoffrey C. Fox 812-855-633 812-855-4021 812-856-7977 Research Technologies, UITS & Research Technologies, UITS & School of Informatics and Computing Pervasive Technology Institute Pervasive Technology Institute & Pervasive Technology Institute [email protected] [email protected] [email protected] *All authors at Indiana University, Bloomington, IN 47405 **UITS is University Information Technology Services ABSTRACT General Terms Cyberinfrastructure is a word commonly used but lacking a single, precise definition. One recognizes intuitively the analogy Management, Performance, Design, Security, Human Factors, with infrastructure, and the use of cyber to refer to thinking or Standardization. computing – but what exactly is cyberinfrastructure as opposed to information technology infrastructure? Indiana University has Keywords developed one of the more widely cited definitions of Cyberinfrastructure, e-Science, Infrastructure, Open Science cyberinfrastructure: Grid, TeraGrid. Cyberinfrastructure consists of computing systems, data storage systems, advanced instruments and data 1. INTRODUCTION repositories, visualization environments, and people, The term ‘cyberinfrastructure’ was coined in the late 1990s, and all linked together by software and high performance its usage became widespread in 2003 with the publication of networks to improve research productivity and “Revolutionizing Science and Engineering Through enable breakthroughs not otherwise possible. Cyberinfrastructure: Report of the National Science Foundation Blue-Ribbon Advisory Panel on Cyberinfrastructure” by Atkins A second definition, more inclusive of scholarship generally and et al.