Pushing Back the Limit of Ab-Initio Quantum Transport Simulations On
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Effective Hamiltonians Derived from Equation-Of-Motion Coupled-Cluster
Effective Hamiltonians derived from equation-of-motion coupled-cluster wave-functions: Theory and application to the Hubbard and Heisenberg Hamiltonians Pavel Pokhilkoa and Anna I. Krylova a Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482 Effective Hamiltonians, which are commonly used for fitting experimental observ- ables, provide a coarse-grained representation of exact many-electron states obtained in quantum chemistry calculations; however, the mapping between the two is not triv- ial. In this contribution, we apply Bloch's formalism to equation-of-motion coupled- cluster (EOM-CC) wave functions to rigorously derive effective Hamiltonians in the Bloch's and des Cloizeaux's forms. We report the key equations and illustrate the theory by examples of systems with electronic states of covalent and ionic characters. We show that the Hubbard and Heisenberg Hamiltonians are extracted directly from the so-obtained effective Hamiltonians. By making quantitative connections between many-body states and simple models, the approach also facilitates the analysis of the correlated wave functions. Artifacts affecting the quality of electronic structure calculations such as spin contamination are also discussed. I. INTRODUCTION Coarse graining is commonly used in computational chemistry and physics. It is ex- ploited in a number of classic models serving as a foundation of modern solid-state physics: tight binding[1, 2], Drude{Sommerfeld's model[3{5], Hubbard's [6] and Heisenberg's[7{9] Hamiltonians. These models explain macroscopic properties of materials through effective interactions whose strengths are treated as model parameters. The values of these pa- rameters are determined either from more sophisticated theoretical models or by fitting to experimental observables. -
Introduction to the Physical Properties of Graphene
Introduction to the Physical Properties of Graphene Jean-No¨el FUCHS Mark Oliver GOERBIG Lecture Notes 2008 ii Contents 1 Introduction to Carbon Materials 1 1.1 TheCarbonAtomanditsHybridisations . 3 1.1.1 sp1 hybridisation ..................... 4 1.1.2 sp2 hybridisation – graphitic allotopes . 6 1.1.3 sp3 hybridisation – diamonds . 9 1.2 Crystal StructureofGrapheneand Graphite . 10 1.2.1 Graphene’s honeycomb lattice . 10 1.2.2 Graphene stacking – the different forms of graphite . 13 1.3 FabricationofGraphene . 16 1.3.1 Exfoliatedgraphene. 16 1.3.2 Epitaxialgraphene . 18 2 Electronic Band Structure of Graphene 21 2.1 Tight-Binding Model for Electrons on the Honeycomb Lattice 22 2.1.1 Bloch’stheorem. 23 2.1.2 Lattice with several atoms per unit cell . 24 2.1.3 Solution for graphene with nearest-neighbour and next- nearest-neighour hopping . 27 2.2 ContinuumLimit ......................... 33 2.3 Experimental Characterisation of the Electronic Band Structure 41 3 The Dirac Equation for Relativistic Fermions 45 3.1 RelativisticWaveEquations . 46 3.1.1 Relativistic Schr¨odinger/Klein-Gordon equation . ... 47 3.1.2 Diracequation ...................... 49 3.2 The2DDiracEquation. 53 3.2.1 Eigenstates of the 2D Dirac Hamiltonian . 54 3.2.2 Symmetries and Lorentz transformations . 55 iii iv 3.3 Physical Consequences of the Dirac Equation . 61 3.3.1 Minimal length for the localisation of a relativistic par- ticle ............................ 61 3.3.2 Velocity operator and “Zitterbewegung” . 61 3.3.3 Klein tunneling and the absence of backscattering . 61 Chapter 1 Introduction to Carbon Materials The experimental and theoretical study of graphene, two-dimensional (2D) graphite, is an extremely rapidly growing field of today’s condensed matter research. -
Dr. David Danovich
Dr. David Danovich ! 14 January 2021 (h-index: 34; 124 publications) Personal Information Name: Contact information Danovich David Private: Nissan Harpaz st., 4/9, Jerusalem, Date of Birth: 9371643 Israel June 29, 1959 Mobile: +972-54-4768669 E-mail: [email protected] Place of Birth: Irkutsk, USSR Work: Institute of Chemistry, The Hebrew Citizenship: University, Edmond Safra Campus, Israeli Givat Ram, 9190401 Jerusalem, Israel Marital status: Phone: +972-2-6586934 Married +2 FAX: +972-2-6584033 E-mail: [email protected] Current position 1992- present: Senior computational chemist and scientific programmer in the Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel Scientific skills Very experienced scientific researcher with demonstrated ability to implement ab initio molecular electronic structure and valence bond calculations for obtaining insights into physical and chemical properties of molecules and materials. Extensive expertise in implementation of Molecular Orbital Theory based on ab initio methods such as Hartree-Fock theory (HF), Density Functional Theory (DFT), Moller-Plesset Perturbation theory (MP2-MP5), Couple Cluster theories [CCST(T)], Complete Active Space (CAS, CASPT2) theories, Multireference Configuration Interaction (MRCI) theory and modern ab initio valence bond theory (VBT) methods such as Valence Bond Self Consistent Field theory (VBSCF), Breathing Orbital Valence Bond theory (BOVB) and its variants (like D-BOVB, S-BOVB and SD-BOVB), Valence Bond Configuration Interaction theory (VBCI), Valence Bond Perturbation theory (VBPT). Language skills Advanced Conversational English, Russian Hebrew Academic background 1. Undergraduate studies, 1978-1982 Master of Science in Physics, June 1982 Irkutsk State University, USSR Dr. David Danovich ! 2. Graduate studies, 1984-1989 Ph. -
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 -
Trends in Atomistic Simulation Software Usage [1.3]
A LiveCoMS Perpetual Review Trends in atomistic simulation software usage [1.3] Leopold Talirz1,2,3*, Luca M. Ghiringhelli4, Berend Smit1,3 1Laboratory of Molecular Simulation (LSMO), Institut des Sciences et Ingenierie Chimiques, Valais, École Polytechnique Fédérale de Lausanne, CH-1951 Sion, Switzerland; 2Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l’Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland; 3National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland; 4The NOMAD Laboratory at the Fritz Haber Institute of the Max Planck Society and Humboldt University, Berlin, Germany This LiveCoMS document is Abstract Driven by the unprecedented computational power available to scientific research, the maintained online on GitHub at https: use of computers in solid-state physics, chemistry and materials science has been on a continuous //github.com/ltalirz/ rise. This review focuses on the software used for the simulation of matter at the atomic scale. We livecoms-atomistic-software; provide a comprehensive overview of major codes in the field, and analyze how citations to these to provide feedback, suggestions, or help codes in the academic literature have evolved since 2010. An interactive version of the underlying improve it, please visit the data set is available at https://atomistic.software. GitHub repository and participate via the issue tracker. This version dated August *For correspondence: 30, 2021 [email protected] (LT) 1 Introduction Gaussian [2], were already released in the 1970s, followed Scientists today have unprecedented access to computa- by force-field codes, such as GROMOS [3], and periodic tional power. -
Density Functional Theory for Transition Metals and Transition Metal Chemistry
REVIEW ARTICLE www.rsc.org/pccp | Physical Chemistry Chemical Physics Density functional theory for transition metals and transition metal chemistry Christopher J. Cramer* and Donald G. Truhlar* Received 8th April 2009, Accepted 20th August 2009 First published as an Advance Article on the web 21st October 2009 DOI: 10.1039/b907148b We introduce density functional theory and review recent progress in its application to transition metal chemistry. Topics covered include local, meta, hybrid, hybrid meta, and range-separated functionals, band theory, software, validation tests, and applications to spin states, magnetic exchange coupling, spectra, structure, reactivity, and catalysis, including molecules, clusters, nanoparticles, surfaces, and solids. 1. Introduction chemical systems, in part because its cost scales more favorably with system size than does the cost of correlated WFT, and yet Density functional theory (DFT) describes the electronic states it competes well in accuracy except for very small systems. This of atoms, molecules, and materials in terms of the three- is true even in organic chemistry, but the advantages of DFT dimensional electronic density of the system, which is a great are still greater for metals, especially transition metals. The simplification over wave function theory (WFT), which involves reason for this added advantage is static electron correlation. a3N-dimensional antisymmetric wave function for a system It is now well appreciated that quantitatively accurate 1 with N electrons. Although DFT is sometimes considered the electronic structure calculations must include electron correlation. B ‘‘new kid on the block’’, it is now 45 years old in its modern It is convenient to recognize two types of electron correlation, 2 formulation (more than half as old as quantum mechanics the first called dynamical electron correlation and the second 3,4 itself), and it has roots that are almost as ancient as the called static correlation, near-degeneracy correlation, or non- Schro¨ dinger equation. -
Arxiv:1601.03499V1 [Quant-Ph] 14 Jan 2016 Networks [23]
Non-Hermitian tight-binding network engineering Stefano Longhi Dipartimento di Fisica, Politecnico di Milano and Istituto di Fotonica e Nanotecnologie del Consiglio Nazionale delle Ricerche, Piazza L. da Vinci 32, I-20133 Milano, Italy We suggest a simple method to engineer a tight-binding quantum network based on proper coupling to an auxiliary non-Hermitian cluster. In particular, it is shown that effective complex non-Hermitian hopping rates can be realized with only complex on-site energies in the network. Three applications of the Hamiltonian engineering method are presented: the synthesis of a nearly transparent defect in an Hermitian linear lattice; the realization of the Fano-Anderson model with complex coupling; and the synthesis of a PT -symmetric tight-binding lattice with a bound state in the continuum. PACS numbers: 03.65.-w, 11.30.Er, 72.20.Ee, 42.82.Et I. INTRODUCTION self-sustained emission in semi-infinite non-Hermitian systems at the exceptional point [29], optical simulation of PT -symmetric quantum field theories in the ghost Hamiltonian engineering is a powerful technique regime [30, 31], invisible defects in tight-binding lattices to control classical and quantum phenomena with [32], non-Hermitian bound states in the continuum [33], important applications in many areas of physics such and Bloch oscillations with trajectories in complex plane as quantum control [1{4], quantum state transfer and [34]. Previous proposals to implement complex hopping quantum information processing [5{10], quantum simu- amplitudes are based on fast temporal modulations of lation [11{13], and topological phases of matter [14{19]. complex on-site energies [31, 32], however such methods In quantum systems described by a tight-binding are rather challenging in practice and, as a matter of Hamiltonian, quantum engineering is usually aimed at fact, to date there is not any experimental demonstration tailoring and controlling hopping rates and site energies, of non-Hermitian complex couplings in tight-binding using either static or dynamic methods. -
1 Advances in Electronic Structure Theory: Gamess a Decade Later Mark S. Gordon and Michael W. Schmidt Department of Chemistry A
ADVANCES IN ELECTRONIC STRUCTURE THEORY: GAMESS A DECADE LATER MARK S. GORDON AND MICHAEL W. SCHMIDT DEPARTMENT OF CHEMISTRY AND AMES LABORATORY, IOWA STATE UNIVERSITY, AMES, IA 50011 Abstract. Recent developments in advanced quantum chemistry and quantum chemistry interfaced with model potentials are discussed, with the primary focus on new implementations in the GAMESS electronic structure suite of programs. Applications to solvent effects and surface science are discussed. 1. Introduction The past decade has seen an extraordinary growth in novel new electronic structure methods and creative implementations of these methods. Concurrently, there have been important advances in “middleware”, software that enables the implementation of efficient electronic structure algorithms. Combined with continuing improvements in computer and interconnect hardware, these advances have extended both the accuracy of computations and the sizes of molecular systems to which such methods may be applied. The great majority of the new computational chemistry algorithms have found their way into one or more broadly distributed electronic structure packages. Since this work focuses on new features of the GAMESS (General Atomic and Molecular Electronic Structure System1) suite of codes, it is important at the outset to recognize the many other packages that offer both similar and complementary features. These include ACES2 CADPAC3, DALTON4, GAMESS-UK5, HYPERCHEM6, JAGUAR7, MOLCAS8 MOLPRO9, NWChem10, PQS11, PSI312, Q-Chem13, SPARTAN14, TURBOMOLE15, and UT-Chem16. Some1,3,4,10 of these packages are distributed at no cost to all, or to academic users, while others are commercial packages, but all are generally available to users without restriction or constraint. Indeed, the developers of these codes frequently collaborate to share features, a practice that clearly benefits all of their users. -
CP2K: Atomistic Simulations of Condensed Matter Systems
Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2014 CP2K: Atomistic simulations of condensed matter systems Hutter, Juerg; Iannuzzi, Marcella; Schiffmann, Florian; VandeVondele, Joost Abstract: cp2k has become a versatile open-source tool for the simulation of complex systems on the nanometer scale. It allows for sampling and exploring potential energy surfaces that can be computed using a variety of empirical and first principles models. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern and massively parallel hardware. This review briefly summarizes the main capabilities and illustrates with recent applications thescience cp2k has enabled in the field of atomistic simulation. DOI: https://doi.org/10.1002/wcms.1159 Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-89998 Journal Article Accepted Version Originally published at: Hutter, Juerg; Iannuzzi, Marcella; Schiffmann, Florian; VandeVondele, Joost (2014). CP2K: Atomistic simulations of condensed matter systems. Wiley Interdisciplinary Reviews. Computational Molecular Science, 4(1):15-25. DOI: https://doi.org/10.1002/wcms.1159 cp2k: Atomistic Simulations of Condensed Matter Systems J¨urgHutter and Marcella Iannuzzi Physical Chemistry Institute University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Florian Schiffmann and Joost VandeVondele Nanoscale Simulations ETH Zurich Wolfgang-Pauli-Strasse 27 CH-8093 Zurich, Switzerland December 17, 2012 Abstract cp2k has become a versatile open source tool for the simulation of complex systems on the nanometer scale. It allows for sampling and exploring potential energy surfaces that can be computed using a variety of empirical and first principles models. -
Openmolcas: from Source Code to Insight Ignacio Fdez
Article Cite This: J. Chem. Theory Comput. XXXX, XXX, XXX−XXX pubs.acs.org/JCTC OpenMolcas: From Source Code to Insight Ignacio Fdez. Galvan,́ 1,2 Morgane Vacher,1 Ali Alavi,3 Celestino Angeli,4 Francesco Aquilante,5 Jochen Autschbach,6 Jie J. Bao,7 Sergey I. Bokarev,8 Nikolay A. Bogdanov,3 Rebecca K. Carlson,7,9 Liviu F. Chibotaru,10 Joel Creutzberg,11,12 Nike Dattani,13 Mickael̈ G. Delcey,1 Sijia S. Dong,7,14 Andreas Dreuw,15 Leon Freitag,16 Luis Manuel Frutos,17 Laura Gagliardi,7 Fredé rić Gendron,6 Angelo Giussani,18,19 Leticia Gonzalez,́ 20 Gilbert Grell,8 Meiyuan Guo,1,21 Chad E. Hoyer,7,22 Marcus Johansson,12 Sebastian Keller,16 Stefan Knecht,16 Goran Kovacevič ,́ 23 Erik Kallman,̈ 1 Giovanni Li Manni,3 Marcus Lundberg,1 Yingjin Ma,16 Sebastian Mai,20 Joaõ Pedro Malhado,24 Per Åke Malmqvist,12 Philipp Marquetand,20 Stefanie A. Mewes,15,25 Jesper Norell,11 Massimo Olivucci,26,27,28 Markus Oppel,20 Quan Manh Phung,29 Kristine Pierloot,29 Felix Plasser,30 Markus Reiher,16 Andrew M. Sand,7,31 Igor Schapiro,32 Prachi Sharma,7 Christopher J. Stein,16,33 Lasse Kragh Sørensen,1,34 Donald G. Truhlar,7 Mihkel Ugandi,1,35 Liviu Ungur,36 Alessio Valentini,37 Steven Vancoillie,12 Valera Veryazov,12 Oskar Weser,3 Tomasz A. Wesołowski,5 Per-Olof Widmark,12 Sebastian Wouters,38 Alexander Zech,5 J. Patrick Zobel,12 and Roland Lindh*,2,39 1Department of Chemistry − Ångström Laboratory, Uppsala University, P.O. -
Scale QM/MM-MD Simulations and Its Application to Biomolecular Systems
PUPIL: a Software Integration System for Multi- scale QM/MM-MD Simulations and its Application to Biomolecular Systems Juan Torras, 1 * B.P. Roberts, 2 G.M. Seabra, 3and S.B. Trickey 4 * 1Department of Chemical Engineering, EEI, Universitat Politècnica de Catalunya, Av. Pla de la Massa 8, Igualada 08700, Spain 2 Centre for eResearch, The University of Auckland, Private Bag 92019, Auckland 1142 New Zealand 3Departamento de Química Fundamental, Universidade Federal de Pernambuco, Cidade Universitária, Recife, Pernambuco CEP 50.740-540, Brazil 4Department of Physics, Department of Chemistry, and Quantum Theory Project, Univ. of Florida, Gainesville Florida 32611-8435, USA * Corresponding Authors: [email protected] and [email protected] 1 Abstract PUPIL (Program for User Package Interfacing and Linking) implements a distinctive multi-scale approach to hybrid quantum mechanical/molecular mechanical molecular dynamics (QM/MM-MD) simulations. Originally developed to interface different external programs for multi-scale simulation with applications in the materials sciences, PUPIL is finding increasing use in the study of complex biological systems. Advanced MD techniques from the external packages can be applied readily to a hybrid QM/MM treatment in which the forces and energy for the QM region can be computed by any of the QM methods available in any of the other external packages. Here we give a survey of PUPIL design philosophy, main features, and key implementation decisions, with an orientation to biomolecular simulation. We discuss recently implemented features which enable highly realistic simulations of complex biological systems which have more than one active site that must be treated concurrently. -
Organic & Biomolecular Chemistry
Organic & Biomolecular Chemistry Accepted Manuscript This is an Accepted Manuscript, which has been through the Royal Society of Chemistry peer review process and has been accepted for publication. Accepted Manuscripts are published online shortly after acceptance, before technical editing, formatting and proof reading. Using this free service, authors can make their results available to the community, in citable form, before we publish the edited article. We will replace this Accepted Manuscript with the edited and formatted Advance Article as soon as it is available. You can find more information about Accepted Manuscripts in the Information for Authors. Please note that technical editing may introduce minor changes to the text and/or graphics, which may alter content. The journal’s standard Terms & Conditions and the Ethical guidelines still apply. In no event shall the Royal Society of Chemistry be held responsible for any errors or omissions in this Accepted Manuscript or any consequences arising from the use of any information it contains. www.rsc.org/obc Page 1 of 6 CREATED USING THE RSC ARTICLEOrganic TEMPLATE & Biomolecular (VER. 3.0 OOo) - SEE WWW.RSC.ORG/ELECTRONICFILESChemistry FOR DETAILS www.rsc.org/xxxxxx | XXXXXXXX Expanding DP4: Application to drug compounds and automation Kristaps Ermanis,a Kevin E. B. Parkes,b Tatiana Agbackb and Jonathan M. Goodman*c Received (in XXX, XXX) Xth XXXXXXXXX 200X, Accepted Xth XXXXXXXXX 200X First published on the web Xth XXXXXXXXX 200X DOI: 10.1039/b00000000x The DP4 parameter, which provides a confidence level for NMR assignment, has been widely used to help assign the structures of many stereochemically-rich molecules.