Transport Phenomena in Nanomechanical Systems for Molecular Manufacturing
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Accessing the Accuracy of Density Functional Theory Through Structure
This is an open access article published under a Creative Commons Attribution (CC-BY) License, which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. Letter Cite This: J. Phys. Chem. Lett. 2019, 10, 4914−4919 pubs.acs.org/JPCL Accessing the Accuracy of Density Functional Theory through Structure and Dynamics of the Water−Air Interface † # ‡ # § ‡ § ∥ Tatsuhiko Ohto, , Mayank Dodia, , Jianhang Xu, Sho Imoto, Fujie Tang, Frederik Zysk, ∥ ⊥ ∇ ‡ § ‡ Thomas D. Kühne, Yasuteru Shigeta, , Mischa Bonn, Xifan Wu, and Yuki Nagata*, † Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan ‡ Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany § Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States ∥ Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Warburger Strasse 100, 33098 Paderborn, Germany ⊥ Graduate School of Pure and Applied Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8571, Japan ∇ Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan *S Supporting Information ABSTRACT: Density functional theory-based molecular dynamics simulations are increasingly being used for simulating aqueous interfaces. Nonetheless, the choice of the appropriate density functional, critically affecting the outcome of the simulation, has remained arbitrary. Here, we assess the performance of various exchange−correlation (XC) functionals, based on the metrics relevant to sum-frequency generation spectroscopy. The structure and dynamics of water at the water−air interface are governed by heterogeneous intermolecular interactions, thereby providing a critical benchmark for XC functionals. -
Density Functional Theory
Density Functional Approach Francesco Sottile Ecole Polytechnique, Palaiseau - France European Theoretical Spectroscopy Facility (ETSF) 22 October 2010 Density Functional Theory 1. Any observable of a quantum system can be obtained from the density of the system alone. < O >= O[n] Hohenberg, P. and W. Kohn, 1964, Phys. Rev. 136, B864 Density Functional Theory 1. Any observable of a quantum system can be obtained from the density of the system alone. < O >= O[n] 2. The density of an interacting-particles system can be calculated as the density of an auxiliary system of non-interacting particles. Hohenberg, P. and W. Kohn, 1964, Phys. Rev. 136, B864 Kohn, W. and L. Sham, 1965, Phys. Rev. 140, A1133 Density Functional ... Why ? Basic ideas of DFT Importance of the density Example: atom of Nitrogen (7 electron) 1. Any observable of a quantum Ψ(r1; ::; r7) 21 coordinates system can be obtained from 10 entries/coordinate ) 1021 entries the density of the system alone. 8 bytes/entry ) 8 · 1021 bytes 4:7 × 109 bytes/DVD ) 2 × 1012 DVDs 2. The density of an interacting-particles system can be calculated as the density of an auxiliary system of non-interacting particles. Density Functional ... Why ? Density Functional ... Why ? Density Functional ... Why ? Basic ideas of DFT Importance of the density Example: atom of Oxygen (8 electron) 1. Any (ground-state) observable Ψ(r1; ::; r8) 24 coordinates of a quantum system can be 24 obtained from the density of the 10 entries/coordinate ) 10 entries 8 bytes/entry ) 8 · 1024 bytes system alone. 5 · 109 bytes/DVD ) 1015 DVDs 2. -
Robust Determination of the Chemical Potential in the Pole
Robust determination of the chemical potential in the pole expansion and selected inversion method for solving Kohn-Sham density functional theory Weile Jia, and Lin Lin Citation: The Journal of Chemical Physics 147, 144107 (2017); doi: 10.1063/1.5000255 View online: http://dx.doi.org/10.1063/1.5000255 View Table of Contents: http://aip.scitation.org/toc/jcp/147/14 Published by the American Institute of Physics THE JOURNAL OF CHEMICAL PHYSICS 147, 144107 (2017) Robust determination of the chemical potential in the pole expansion and selected inversion method for solving Kohn-Sham density functional theory Weile Jia1,a) and Lin Lin1,2,b) 1Department of Mathematics, University of California, Berkeley, California 94720, USA 2Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA (Received 14 August 2017; accepted 24 September 2017; published online 11 October 2017) Fermi operator expansion (FOE) methods are powerful alternatives to diagonalization type methods for solving Kohn-Sham density functional theory (KSDFT). One example is the pole expansion and selected inversion (PEXSI) method, which approximates the Fermi operator by rational matrix functions and reduces the computational complexity to at most quadratic scaling for solving KSDFT. Unlike diagonalization type methods, the chemical potential often cannot be directly read off from the result of a single step of evaluation of the Fermi operator. Hence multiple evaluations are needed to be sequentially performed to compute the chemical potential to ensure the correct number of electrons within a given tolerance. This hinders the performance of FOE methods in practice. In this paper, we develop an efficient and robust strategy to determine the chemical potential in the context of the PEXSI method. -
Octopus: a First-Principles Tool for Excited Electron-Ion Dynamics
octopus: a first-principles tool for excited electron-ion dynamics. ¡ Miguel A. L. Marques a, Alberto Castro b ¡ a c, George F. Bertsch c and Angel Rubio a aDepartamento de F´ısica de Materiales, Facultad de Qu´ımicas, Universidad del Pa´ıs Vasco, Centro Mixto CSIC-UPV/EHU and Donostia International Physics Center (DIPC), 20080 San Sebastian,´ Spain bDepartamento de F´ısica Teorica,´ Universidad de Valladolid, E-47011 Valladolid, Spain cPhysics Department and Institute for Nuclear Theory, University of Washington, Seattle WA 98195 USA Abstract We present a computer package aimed at the simulation of the electron-ion dynamics of finite systems, both in one and three dimensions, under the influence of time-dependent electromagnetic fields. The electronic degrees of freedom are treated quantum mechani- cally within the time-dependent Kohn-Sham formalism, while the ions are handled classi- cally. All quantities are expanded in a regular mesh in real space, and the simulations are performed in real time. Although not optimized for that purpose, the program is also able to obtain static properties like ground-state geometries, or static polarizabilities. The method employed proved quite reliable and general, and has been successfully used to calculate linear and non-linear absorption spectra, harmonic spectra, laser induced fragmentation, etc. of a variety of systems, from small clusters to medium sized quantum dots. Key words: Electronic structure, time-dependent, density-functional theory, non-linear optics, response functions PACS: 33.20.-t, 78.67.-n, 82.53.-k PROGRAM SUMMARY Title of program: octopus Catalogue identifier: Program obtainable from: CPC Program Library, Queen’s University of Belfast, N. -
1-DFT Introduction
MBPT and TDDFT Theory and Tools for Electronic-Optical Properties Calculations in Material Science Dott.ssa Letizia Chiodo Nano-bio Spectroscopy Group & ETSF - European Theoretical Spectroscopy Facility, Dipartemento de Física de Materiales, Facultad de Químicas, Universidad del País Vasco UPV/EHU, San Sebastián-Donostia, Spain Outline of the Lectures • Many Body Problem • DFT elements; examples • DFT drawbacks • excited properties: electronic and optical spectroscopies. elements of theory • Many Body Perturbation Theory: GW • codes, examples of GW calculations • Many Body Perturbation Theory: BSE • codes, examples of BSE calculations • Time Dependent DFT • codes, examples of TDDFT calculations • state of the art, open problems Main References theory • P. Hohenberg & W. Kohn, Phys. Rev. 136 (1964) B864; W. Kohn & L. J. Sham, Phys. Rev. 140 , A1133 (1965); (Nobel Prize in Chemistry1998) • Richard M. Martin, Electronic Structure: Basic Theory and Practical Methods, Cambridge University Press, 2004 • M. C. Payne, Rev. Mod. Phys.64 , 1045 (1992) • E. Runge and E.K.U. Gross, Phys. Rev. Lett. 52 (1984) 997 • M. A. L.Marques, C. A. Ullrich, F. Nogueira, A. Rubio, K. Burke, E. K. U. Gross, Time-Dependent Density Functional Theory. (Springer-Verlag, 2006). • L. Hedin, Phys. Rev. 139 , A796 (1965) • R.W. Godby, M. Schluter, L. J. Sham. Phys. Rev. B 37 , 10159 (1988) • G. Onida, L. Reining, A. Rubio, Rev. Mod. Phys. 74 , 601 (2002) codes & tutorials • Q-Espresso, http://www.pwscf.org/ • Abinit, http://www.abinit.org/ • Yambo, http://www.yambo-code.org • Octopus, http://www.tddft.org/programs/octopus more info at http://www.etsf.eu, www.nanobio.ehu.es Outline of the Lectures • Many Body Problem • DFT elements; examples • DFT drawbacks • excited properties: electronic and optical spectroscopies. -
Camcasp 5.9 Alston J. Misquitta† and Anthony J
CamCASP 5.9 Alston J. Misquittay and Anthony J. Stoneyy yDepartment of Physics and Astronomy, Queen Mary, University of London, 327 Mile End Road, London E1 4NS yy University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW September 1, 2015 Abstract CamCASP is a suite of programs designed to calculate molecular properties (multipoles and frequency- dependent polarizabilities) in single-site and distributed form, and interaction energies between pairs of molecules, and thence to construct atom–atom potentials. The CamCASP distribution also includes the programs Pfit, Casimir,Gdma 2.2, Cluster, and Process. Copyright c 2007–2014 Alston J. Misquitta and Anthony J. Stone Contents 1 Introduction 1 1.1 Authors . .1 1.2 Citations . .1 2 What’s new? 2 3 Outline of the capabilities of CamCASP and other programs 5 3.1 CamCASP limits . .7 4 Installation 7 4.1 Building CamCASP from source . .9 5 Using CamCASP 10 5.1 Workflows . 10 5.2 High-level scripts . 10 5.3 The runcamcasp.py script . 11 5.4 Low-level scripts . 13 6 Data conventions 13 7 CLUSTER: Detailed specification 14 7.1 Prologue . 15 7.2 Molecule definitions . 15 7.3 Geometry manipulations and other transformations . 16 7.4 Job specification . 18 7.5 Energy . 23 7.6 Crystal . 25 7.7 ORIENT ............................................... 26 7.8 Finally, . 29 8 Examples 29 8.1 A SAPT(DFT) calculation . 29 8.2 An example properties calculation . 30 8.3 Dispersion coefficients . 34 8.4 Using CLUSTER to obtain the dimer geometry . 36 9 CamCASP program specification 39 9.1 Global data . -
The CECAM Electronic Structure Library and the Modular Software Development Paradigm
The CECAM electronic structure library and the modular software development paradigm Cite as: J. Chem. Phys. 153, 024117 (2020); https://doi.org/10.1063/5.0012901 Submitted: 06 May 2020 . Accepted: 08 June 2020 . Published Online: 13 July 2020 Micael J. T. Oliveira , Nick Papior , Yann Pouillon , Volker Blum , Emilio Artacho , Damien Caliste , Fabiano Corsetti , Stefano de Gironcoli , Alin M. Elena , Alberto García , Víctor M. García-Suárez , Luigi Genovese , William P. Huhn , Georg Huhs , Sebastian Kokott , Emine Küçükbenli , Ask H. Larsen , Alfio Lazzaro , Irina V. Lebedeva , Yingzhou Li , David López- Durán , Pablo López-Tarifa , Martin Lüders , Miguel A. L. Marques , Jan Minar , Stephan Mohr , Arash A. Mostofi , Alan O’Cais , Mike C. Payne, Thomas Ruh, Daniel G. A. Smith , José M. Soler , David A. Strubbe , Nicolas Tancogne-Dejean , Dominic Tildesley, Marc Torrent , and Victor Wen-zhe Yu COLLECTIONS Paper published as part of the special topic on Electronic Structure Software Note: This article is part of the JCP Special Topic on Electronic Structure Software. This paper was selected as Featured ARTICLES YOU MAY BE INTERESTED IN Recent developments in the PySCF program package The Journal of Chemical Physics 153, 024109 (2020); https://doi.org/10.1063/5.0006074 An open-source coding paradigm for electronic structure calculations Scilight 2020, 291101 (2020); https://doi.org/10.1063/10.0001593 Siesta: Recent developments and applications The Journal of Chemical Physics 152, 204108 (2020); https://doi.org/10.1063/5.0005077 J. Chem. Phys. 153, 024117 (2020); https://doi.org/10.1063/5.0012901 153, 024117 © 2020 Author(s). The Journal ARTICLE of Chemical Physics scitation.org/journal/jcp The CECAM electronic structure library and the modular software development paradigm Cite as: J. -
Jaguar 5.5 User Manual Copyright © 2003 Schrödinger, L.L.C
Jaguar 5.5 User Manual Copyright © 2003 Schrödinger, L.L.C. All rights reserved. Schrödinger, FirstDiscovery, Glide, Impact, Jaguar, Liaison, LigPrep, Maestro, Prime, QSite, and QikProp are trademarks of Schrödinger, L.L.C. MacroModel is a registered trademark of Schrödinger, L.L.C. To the maximum extent permitted by applicable law, this publication is provided “as is” without warranty of any kind. This publication may contain trademarks of other companies. October 2003 Contents Chapter 1: Introduction.......................................................................................1 1.1 Conventions Used in This Manual.......................................................................2 1.2 Citing Jaguar in Publications ...............................................................................3 Chapter 2: The Maestro Graphical User Interface...........................................5 2.1 Starting Maestro...................................................................................................5 2.2 The Maestro Main Window .................................................................................7 2.3 Maestro Projects ..................................................................................................7 2.4 Building a Structure.............................................................................................9 2.5 Atom Selection ..................................................................................................10 2.6 Toolbar Controls ................................................................................................11 -
Thomas–Fermi–Dirac–Von Weizsäcker Models in Finite Systems Garnet Kin-Lic Chan, Aron J
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Caltech Authors - Main Thomas–Fermi–Dirac–von Weizsäcker models in finite systems Garnet Kin-Lic Chan, Aron J. Cohen, and Nicholas C. Handy Citation: 114, (2001); doi: 10.1063/1.1321308 View online: http://dx.doi.org/10.1063/1.1321308 View Table of Contents: http://aip.scitation.org/toc/jcp/114/2 Published by the American Institute of Physics JOURNAL OF CHEMICAL PHYSICS VOLUME 114, NUMBER 2 8 JANUARY 2001 Thomas–Fermi–Dirac–von Weizsa¨cker models in finite systems Garnet Kin-Lic Chan,a) Aron J. Cohen, and Nicholas C. Handy Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, United Kingdom ͑Received 7 June 2000; accepted 8 September 2000͒ To gain an understanding of the variational behavior of kinetic energy functionals, we perform a numerical study of the Thomas–Fermi–Dirac–von Weizsa¨cker theory in finite systems. A general purpose Gaussian-based code is constructed to perform energy and geometry optimizations on polyatomic systems to high accuracy. We carry out benchmark studies on atomic and diatomic systems. Our results indicate that the Thomas–Fermi–Dirac–von Weizsa¨cker theory can give an approximate description of matter, with atomic energies, binding energies, and bond lengths of the correct order of magnitude, though not to the accuracy required of a qualitative chemical theory. We discuss the implications for the development of new kinetic functionals. © 2001 American Institute of Physics. ͓DOI: 10.1063/1.1321308͔ I. INTRODUCTION -
Simulation Studies of the Mechanisms of Interaction Between Carbon Nanotubes and Amino Acids
Simulation Studies of the Mechanisms of Interaction between Carbon Nanotubes and Amino Acids by George Bassem Botros Abadir B.Sc., Ain Shams University, Cairo, Egypt, 2000 M.Sc., Ain Shams University, Cairo, Egypt, 2005 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in The Faculty of Graduate Studies (Electrical and Computer Engineering) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) August 2010 c George Bassem Botros Abadir 2010 Abstract In this thesis, molecular dynamics and ab initio density functional theory/non- equilibrium Green’s function simulations are used to study the interaction between carbon nanotubes and amino acids. Firstly, rules for the proper choice of the parameters used in these simulations are established. It is demonstrated how the improper choice of these parameters (particularly the basis set used in ab initio simulations) can lead to quantitatively and qualitatively erroneous conclusions regarding the bandgap of the nanotubes. It is then shown that the major forces responsible for amino-acid adsorp- tion on carbon nanotubes are van der Waals forces, and that hydrophobic interactions may accelerate the adsorption process, but are not necessary for it to occur. The mechanisms of interaction between carbon nanotubes and amino acids are elucidated. It is found that geometrical deformations do not play a major role in the sensing process, and that electrostatic inter- actions represent the major interaction mechanism between the tubes and amino acids. Fully metallic armchair tubes are found to be insensitive to various amino acids, while small-radius nanotubes are shown to be inade- quate for sensing in aqueous media, as their response to the motion of the atoms resulting from the immersion in water is comparable to that of an- alyte adsorption. -
Newsletter 85
Ψk Newsletter AB INITIO (FROM ELECTRONIC STRUCTURE) CALCULATION OF COMPLEX PROCESSES IN MATERIALS Number 85 February 2008 Editor: Z. (Dzidka) Szotek Sponsored by: UK’s CCP9 E-mail: [email protected] and ESF Psi-k Programme 1 Contents 1 Editorial 4 2 General News 5 2.1 Psi-k Portal and Psi-k Mailing List . ........ 5 3 Psi-k School/Workshop/Conference Announcements 6 3.1 THIRD Psi-k/NANOQUANTA SCHOOL& WORKSHOP . 6 3.2 Psi-kTraining-MarieCurieSummerSchool . ........ 11 4 General School/Workshop/Conference Announcements 12 4.1 2nd International Workshop on “Ab initio Description of Iron and Steel (ADIS2008): MagnetismandPhaseDiagrams” . 12 4.2 TheCAMDSummerSchool............................. 13 4.3 International Center for Materials Research (ICMR) Summer School on Multi- ferroicMaterialsandBeyond . 16 4.4 15th WIEN2khands-onworkshop . 18 4.5 Meeting on Molecular Dynamics for Non-Adiabatic Processes ........... 19 4.6 12th European Conference ”Physics of Magnetism” . ........... 20 4.7 SymposiumG,EMRSFallMeeting. 21 4.8 Summer School on Ab Initio Modelling in Solid State Chemistry - MSSC2008 . 23 4.9 Computational Molecular Science 2008 . ......... 25 5 General Job Announcements 26 6 Abstracts 55 7 New Book Announcements 73 8 SCIENTIFIC HIGHLIGHT OF THE MONTH: Local Self-Interaction Cor- rection of a Scattering Resonance: The Atom in Jellium Model 74 1 Introduction 74 2 Local Self-interaction Correction (LSIC) 76 2 3 LSDA solution of an atom in jellium 77 4 LSIC solution for an atom in jellium 78 5 Self-interaction correction of scattering resonances for Ce in jellium 79 6 Effective Medium Theory of Ce metal 82 7 Conclusions 84 3 1 Editorial As we are currently trying to change the format of the future Psi-k newsletters, the present newsletter in a way already reflects this transition period. -
Quantum Chemical Calculations of NMR Parameters
Quantum Chemical Calculations of NMR Parameters Tatyana Polenova University of Delaware Newark, DE Winter School on Biomolecular NMR January 20-25, 2008 Stowe, Vermont OUTLINE INTRODUCTION Relating NMR parameters to geometric and electronic structure Classical calculations of EFG tensors Molecular properties from quantum chemical calculations Quantum chemistry methods DENSITY FUNCTIONAL THEORY FOR CALCULATIONS OF NMR PARAMETERS Introduction to DFT Software Practical examples Tutorial RELATING NMR OBSERVABLES TO MOLECULAR STRUCTURE NMR Spectrum NMR Parameters Local geometry Chemical structure (reactivity) I. Calculation of experimental NMR parameters Find unique solution to CQ, Q, , , , , II. Theoretical prediction of fine structure constants from molecular geometry Classical electrostatic model (EFG)- only in simple ionic compounds Quantum mechanical calculations (Density Functional Theory) (EFG, CSA) ELECTRIC FIELD GRADIENT (EFG) TENSOR: POINT CHARGE MODEL EFG TENSOR IS DETERMINED BY THE COMBINED ELECTRONIC AND NUCLEAR WAVEFUNCTION, NO ANALYTICAL EXPRESSION IN THE GENERAL CASE THE SIMPLEST APPROXIMATION: CLASSICAL POINT CHARGE MODEL n Zie 4 V2,k = 3 Y2,k ()i,i i=1 di 5 ATOMS CONTRIBUTING TO THE EFG TENSOR ARE TREATED AS POINT CHARGES, THE RESULTING EFG TENSOR IS THE SUM WITH RESPECT TO ALL ATOMS VERY CRUDE MODEL, WORKS QUANTITATIVELY ONLY IN SIMPLEST IONIC SYSTEMS, BUT YIELDS QUALITATIVE TRENDS AND GENERAL UNDERSTANDING OF THE SYMMETRY AND MAGNITUDE OF THE EXPECTED TENSOR ELECTRIC FIELD GRADIENT (EFG) TENSOR: POINT CHARGE MODEL n Zie 4 V2,k = 3 Y2,k ()i,i i=1 di 5 Ze V = ; V = 0; V = 0 2,0 d 3 2,±1 2,±2 2Ze V = ; V = 0; V = 0 2,0 d 3 2,±1 2,±2 3 Ze V = ; V = 0; V = 0 2,0 2 d 3 2,±1 2,±2 V2,0 = 0; V2,±1 = 0; V2,±2 = 0 MOLECULAR PROPERTIES FROM QUANTUM CHEMICAL CALCULATIONS H = E See for example M.