Introduction to First-Principles Method
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Solid-State NMR Techniques for the Structural Characterization of Cyclic Aggregates Based on Borane–Phosphane Frustrated Lewis Pairs
molecules Review Solid-State NMR Techniques for the Structural Characterization of Cyclic Aggregates Based on Borane–Phosphane Frustrated Lewis Pairs Robert Knitsch 1, Melanie Brinkkötter 1, Thomas Wiegand 2, Gerald Kehr 3 , Gerhard Erker 3, Michael Ryan Hansen 1 and Hellmut Eckert 1,4,* 1 Institut für Physikalische Chemie, WWU Münster, 48149 Münster, Germany; [email protected] (R.K.); [email protected] (M.B.); [email protected] (M.R.H.) 2 Laboratorium für Physikalische Chemie, ETH Zürich, 8093 Zürich, Switzerland; [email protected] 3 Organisch-Chemisches Institut, WWU Münster, 48149 Münster, Germany; [email protected] (G.K.); [email protected] (G.E.) 4 Instituto de Física de Sao Carlos, Universidad de Sao Paulo, Sao Carlos SP 13566-590, Brazil * Correspondence: [email protected] Academic Editor: Mattias Edén Received: 20 February 2020; Accepted: 17 March 2020; Published: 19 March 2020 Abstract: Modern solid-state NMR techniques offer a wide range of opportunities for the structural characterization of frustrated Lewis pairs (FLPs), their aggregates, and the products of cooperative addition reactions at their two Lewis centers. This information is extremely valuable for materials that elude structural characterization by X-ray diffraction because of their nanocrystalline or amorphous character, (pseudo-)polymorphism, or other types of disordering phenomena inherent in the solid state. Aside from simple chemical shift measurements using single-pulse or cross-polarization/magic-angle spinning NMR detection techniques, the availability of advanced multidimensional and double-resonance NMR methods greatly deepened the informational content of these experiments. In particular, methods quantifying the magnetic dipole–dipole interaction strengths and indirect spin–spin interactions prove useful for the measurement of intermolecular association, connectivity, assessment of FLP–ligand distributions, and the stereochemistry of adducts. -
TBTK: a Quantum Mechanics Software Development Kit
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Copenhagen University Research Information System TBTK A quantum mechanics software development kit Bjornson, Kristofer Published in: SoftwareX DOI: 10.1016/j.softx.2019.02.005 Publication date: 2019 Document version Publisher's PDF, also known as Version of record Document license: CC BY Citation for published version (APA): Bjornson, K. (2019). TBTK: A quantum mechanics software development kit. SoftwareX, 9, 205-210. https://doi.org/10.1016/j.softx.2019.02.005 Download date: 09. apr.. 2020 SoftwareX 9 (2019) 205–210 Contents lists available at ScienceDirect SoftwareX journal homepage: www.elsevier.com/locate/softx Original software publication TBTK: A quantum mechanics software development kit Kristofer Björnson Niels Bohr Institute, University of Copenhagen, Juliane Maries Vej 30, DK–2100, Copenhagen, Denmark article info a b s t r a c t Article history: TBTK is a software development kit for quantum mechanical calculations and is designed to enable the Received 7 August 2018 development of applications that investigate problems formulated on second-quantized form. It also Received in revised form 21 February 2019 enables method developers to create solvers for tight-binding, DFT, DMFT, quantum transport, etc., that Accepted 22 February 2019 can be easily integrated with each other. Both through the development of completely new solvers, Keywords: as well as front and back ends to already well established packages. TBTK provides data structures Quantum mechanics tailored for second-quantization that will encourage reusability and enable scalability for quantum SDK mechanical calculations. C++ ' 2019 The Author. -
Density Functional Theory
Density Functional Theory Fundamentals Video V.i Density Functional Theory: New Developments Donald G. Truhlar Department of Chemistry, University of Minnesota Support: AFOSR, NSF, EMSL Why is electronic structure theory important? Most of the information we want to know about chemistry is in the electron density and electronic energy. dipole moment, Born-Oppenheimer charge distribution, approximation 1927 ... potential energy surface molecular geometry barrier heights bond energies spectra How do we calculate the electronic structure? Example: electronic structure of benzene (42 electrons) Erwin Schrödinger 1925 — wave function theory All the information is contained in the wave function, an antisymmetric function of 126 coordinates and 42 electronic spin components. Theoretical Musings! ● Ψ is complicated. ● Difficult to interpret. ● Can we simplify things? 1/2 ● Ψ has strange units: (prob. density) , ● Can we not use a physical observable? ● What particular physical observable is useful? ● Physical observable that allows us to construct the Hamiltonian a priori. How do we calculate the electronic structure? Example: electronic structure of benzene (42 electrons) Erwin Schrödinger 1925 — wave function theory All the information is contained in the wave function, an antisymmetric function of 126 coordinates and 42 electronic spin components. Pierre Hohenberg and Walter Kohn 1964 — density functional theory All the information is contained in the density, a simple function of 3 coordinates. Electronic structure (continued) Erwin Schrödinger -
An Overview on the Libxc Library of Density Functional Approximations
An overview on the Libxc library of density functional approximations Susi Lehtola Molecular Sciences Software Institute at Virginia Tech 2 June 2021 Outline Why Libxc? Recap on DFT What is Libxc? Using Libxc A look under the hood Wrapup GPAW 2021: Users' and Developers' Meeting Susi Lehtola Why Libxc? 2/28 Why Libxc? There are many approximations for the exchange-correlation functional. But, most programs I ... only implement a handful (sometimes 5, typically 10-15) I ... and the implementations may be buggy / non-standard GPAW 2021: Users' and Developers' Meeting Susi Lehtola Why Libxc? 3/28 Why Libxc, cont'd This leads to issues with reproducibility I chemists and physicists do not traditionally use the same functionals! Outdated(?) stereotype: B3LYP vs PBE I how to reproduce a calculation performed with another code? GPAW 2021: Users' and Developers' Meeting Susi Lehtola Why Libxc? 4/28 Why Libxc, cont'd The issue is compounded by the need for backwards and forwards compatibility: how can one I reproduce old calculations from the literature done with a now-obsolete functional (possibly with a program that is proprietary / no longer available)? I use a newly developed functional in an old program? GPAW 2021: Users' and Developers' Meeting Susi Lehtola Why Libxc? 5/28 Why Libxc, cont'd A standard implementation is beneficial! I no need to keep reinventing (and rebuilding) the wheel I use same collection of density functionals in all programs I new functionals only need to be implemented in one place I broken/buggy functionals only need to be fixed in one place I same implementation can be used across numerical approaches, e.g. -
Electron Density Functions for Simple Molecules (Chemical Bonding/Excited States) RALPH G
Proc. Natl. Acad. Sci. USA Vol. 77, No. 4, pp. 1725-1727, April 1980 Chemistry Electron density functions for simple molecules (chemical bonding/excited states) RALPH G. PEARSON AND WILLIAM E. PALKE Department of Chemistry, University of California, Santa Barbara, California 93106 Contributed by Ralph G. Pearson, January 8, 1980 ABSTRACT Trial electron density functions have some If each component of the charge density is centered on a conceptual and computational advantages over wave functions. single point, the calculation of the potential energy is made The properties of some simple density functions for H+2 and H2 are examined. It appears that for a diatomic molecule a good much easier. However, the kinetic energy is often difficult to density function would be given by p = N(A2 + B2), in which calculate for densities containing several one-center terms. For A and B are short sums of s, p, d, etc. orbitals centered on each a wave function that is composed of one orbital, the kinetic nucleus. Some examples are also given for electron densities that energy can be written in terms of the electron density as are appropriate for excited states. T = 1/8 (VP)2dr [5] Primarily because of the work of Hohenberg, Kohn, and Sham p (1, 2), there has been great interest in studying quantum me- and in most cases this integral was evaluated numerically in chanical problems by using the electron density function rather cylindrical coordinates. The X integral was trivial in every case, than the wave function as a means of approach. Examples of and the z and r integrations were carried out via two-dimen- the use of the electron density include studies of chemical sional Gaussian bonding in molecules (3, 4), solid state properties (5), inter- quadrature. -
Chemistry 1000 Lecture 8: Multielectron Atoms
Chemistry 1000 Lecture 8: Multielectron atoms Marc R. Roussel September 14, 2018 Marc R. Roussel Multielectron atoms September 14, 2018 1 / 23 Spin Spin Spin (with associated quantum number s) is a type of angular momentum attached to a particle. Every particle of the same kind (e.g. every electron) has the same value of s. Two types of particles: Fermions: s is a half integer 1 Examples: electrons, protons, neutrons (s = 2 ) Bosons: s is an integer Example: photons (s = 1) Marc R. Roussel Multielectron atoms September 14, 2018 2 / 23 Spin Spin magnetic quantum number All types of angular momentum obey similar rules. There is a spin magnetic quantum number ms which gives the z component of the spin angular momentum vector: Sz = ms ~ The value of ms can be −s; −s + 1;:::; s. 1 1 1 For electrons, s = 2 so ms can only take the values − 2 or 2 . Marc R. Roussel Multielectron atoms September 14, 2018 3 / 23 Spin Stern-Gerlach experiment How do we know that electrons (e.g.) have spin? Source: Theresa Knott, Wikimedia Commons, http://en.wikipedia.org/wiki/File:Stern-Gerlach_experiment.PNG Marc R. Roussel Multielectron atoms September 14, 2018 4 / 23 Spin Pauli exclusion principle No two fermions can share a set of quantum numbers. Marc R. Roussel Multielectron atoms September 14, 2018 5 / 23 Multielectron atoms Multielectron atoms Electrons occupy orbitals similar (in shape and angular momentum) to those of hydrogen. Same orbital names used, e.g. 1s, 2px , etc. The number of orbitals of each type is still set by the number of possible values of m`, so e.g. -
Electronic Structure Study of Copper-Containing Perovskites
Electronic Structure Study of Copper-containing Perovskites Mark Robert Michel University College London A thesis submitted to University College London in partial fulfilment of the requirements for the degree of Doctor of Philosophy, February 2010. 1 I, Mark Robert Michel, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. Mark Robert Michel 2 Abstract This thesis concerns the computational study of copper containing perovskites using electronic structure methods. We discuss an extensive set of results obtained using hybrid exchange functionals within Density Functional Theory (DFT), in which we vary systematically the amount of exact (Hartree-Fock, HF) exchange employed. The method has enabled us to obtain accurate results on a range of systems, particularly in materials containing strongly correlated ions, such as Cu2+. This is possible because the HF exchange corrects, at least qualitatively, the spurious self-interaction error present in DFT. The materials investigated include two families of perovskite-structured oxides, of potential interest for technological applications due to the very large dielectric constant or for Multi-Ferroic behaviour. The latter materials exhibit simultaneously ferroelectric and ferromagnetic properties, a rare combination, which is however highly desirable for memory device applications. The results obtained using hybrid exchange functionals are highly encouraging. Initial studies were made on bulk materials such as CaCu3Ti4O12 (CCTO) which is well characterised by experiment. The inclusion of HF exchange improved, in a systematic way, both structural and electronic results with respect to experiment. The confidence gained in the study of known compounds has enabled us to explore new compositions predictively. -
Pyscf: the Python-Based Simulations of Chemistry Framework
PySCF: The Python-based Simulations of Chemistry Framework Qiming Sun∗1, Timothy C. Berkelbach2, Nick S. Blunt3,4, George H. Booth5, Sheng Guo1,6, Zhendong Li1, Junzi Liu7, James D. McClain1,6, Elvira R. Sayfutyarova1,6, Sandeep Sharma8, Sebastian Wouters9, and Garnet Kin-Lic Chany1 1Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125, USA 2Department of Chemistry and James Franck Institute, University of Chicago, Chicago, Illinois 60637, USA 3Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA 4Department of Chemistry, University of California, Berkeley, California 94720, USA 5Department of Physics, King's College London, Strand, London WC2R 2LS, United Kingdom 6Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA 7Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P. R. China 8Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO 80302, USA 9Brantsandpatents, Pauline van Pottelsberghelaan 24, 9051 Sint-Denijs-Westrem, Belgium arXiv:1701.08223v2 [physics.chem-ph] 2 Mar 2017 Abstract PySCF is a general-purpose electronic structure platform designed from the ground up to emphasize code simplicity, so as to facilitate new method development and enable flexible ∗[email protected] [email protected] 1 computational workflows. The package provides a wide range of tools to support simulations of finite-size systems, extended systems with periodic boundary conditions, low-dimensional periodic systems, and custom Hamiltonians, using mean-field and post-mean-field methods with standard Gaussian basis functions. To ensure ease of extensibility, PySCF uses the Python language to implement almost all of its features, while computationally critical paths are implemented with heavily optimized C routines. -
Arxiv:2005.05756V2
“This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in Oliveira, M.J.T. [et al.]. The CECAM electronic structure library and the modular software development paradigm. "The Journal of Chemical Physics", 12020, vol. 153, núm. 2, and may be found at https://aip.scitation.org/doi/10.1063/5.0012901. The CECAM Electronic Structure Library and the modular software development paradigm Micael J. T. Oliveira,1, a) Nick Papior,2, b) Yann Pouillon,3, 4, c) Volker Blum,5, 6 Emilio Artacho,7, 8, 9 Damien Caliste,10 Fabiano Corsetti,11, 12 Stefano de Gironcoli,13 Alin M. Elena,14 Alberto Garc´ıa,15 V´ıctor M. Garc´ıa-Su´arez,16 Luigi Genovese,10 William P. Huhn,5 Georg Huhs,17 Sebastian Kokott,18 Emine K¨u¸c¨ukbenli,13, 19 Ask H. Larsen,20, 4 Alfio Lazzaro,21 Irina V. Lebedeva,22 Yingzhou Li,23 David L´opez-Dur´an,22 Pablo L´opez-Tarifa,24 Martin L¨uders,1, 14 Miguel A. L. Marques,25 Jan Minar,26 Stephan Mohr,17 Arash A. Mostofi,11 Alan O'Cais,27 Mike C. Payne,9 Thomas Ruh,28 Daniel G. A. Smith,29 Jos´eM. Soler,30 David A. Strubbe,31 Nicolas Tancogne-Dejean,1 Dominic Tildesley,32 Marc Torrent,33, 34 and Victor Wen-zhe Yu5 1)Max Planck Institute for the Structure and Dynamics of Matter, D-22761 Hamburg, Germany 2)DTU Computing Center, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark 3)Departamento CITIMAC, Universidad de Cantabria, Santander, Spain 4)Simune Atomistics, 20018 San Sebasti´an,Spain 5)Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA 6)Department of Chemistry, Duke University, Durham, NC 27708, USA 7)CIC Nanogune BRTA and DIPC, 20018 San Sebasti´an,Spain 8)Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain 9)Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom 10)Department of Physics, IRIG, Univ. -
Electronic Structure, Atomic Forces and Structural Relaxations by Wien2k
Electronic structure, atomic forces and structural relaxations by WIEN2k Peter Blaha Institute of Materials Chemistry TU Vienna, Austria R.Laskowski, F.Tran, K.Schwarz (TU Vienna) M.Perez-Mato (Bilbao) K.Parlinski (Krakow) D.Singh (Oakridge) M.Fischer, T.Malcherek (Hamburg) Outline: General considerations when solving H=E DFT APW-based methods (history and state-of-the-art) WIEN2k program structure + features forces, structure relaxation Applications Phonons in matlockite PbFI Phase transitions in Aurivillius phases Structure of Pyrochlore Y2Nb2O7 phase transitions in Cd2Nb2O7 Concepts when solving Schrödingers-equation Treatment of Form of “Muffin-tin” MT spin Non-spinpolarized potential atomic sphere approximation (ASA) Spin polarized pseudopotential (PP) (with certain magnetic order) Full potential : FP Relativistic treatment of the electrons exchange and correlation potential non relativistic Hartree-Fock (+correlations) semi-relativistic Density functional theory (DFT) fully-relativistic Local density approximation (LDA) Generalized gradient approximation (GGA) Beyond LDA: e.g. LDA+U, Hybrid-DFT 1 2 k k k V (r) i i i Schrödinger - equation 2 Basis functions Representation plane waves : PW, PAW augmented plane waves : APW non periodic of solid atomic oribtals. e.g. Slater (STO), Gaussians (GTO), (cluster, individual MOs) LMTO, numerical basis periodic (unit cell, Blochfunctions, “bandstructure”) DFT Density Functional Theory Hohenberg-Kohn theorem: (exact) The total energy of an interacting inhomogeneous electron gas in the presence of an external potential Vext(r ) is a functional of the density E V (r) (r)dr F [ ] ext Kohn-Sham: (still exact!) 1 (r)(r) E T [] V (r)dr drdr E [] o ext 2 | r r | xc Ekinetic Ene Ecoulomb Eee Exc exchange-correlation non interacting hom. -
HPC Applications on Shaheen (Bioscience/Chemistry/Materials Science/Physics)
HPC Applications on Shaheen (Bioscience/Chemistry/Materials Science/Physics) Zhiyong Zhu KAUST Supercomputing Core Lab 2018/10/15 Outline • Codes Available • Steps to Run – Use VASP as an example Codes Available • Bioscience/Molecular Dynamics – CP2k, CPMD, Gromacs, Lammps, Namd, etc • Chemistry/Materials Science/Physics – VASP, Wien2k, Quantum ESPRESSO, NWChem, Gaussian, ADF, etc • More information – WWW.hpc.kaust.edu.sa/app6 Example • VASP as an example – The Vienna Ab-initial Simulation Package (VASP) is a computer program for atomic scale materials modeling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics from first-principles (https://WWW.vasp.at). Steps to Run • Login Shaheen • Check Code Availability • Prepare Input Files for VASP • Prepare Jobscript for Slurm Job Scheduler • Job Submission using Slurm Commands • Check Output Files Login Shaheen • Logins – ssh -X [email protected] – ssh -X [email protected] (cdl[1,2,3,4]) Code Availability • module avail – module avail – module avail <code>/<version> Code Availability • WWW.hpc.kaust.edu.sa – WWW.hpc.kaust.edu.sa/app6 Prepare Input Files • 3 Different Working Directories – /home – Space is limited; Not mounted on compute nodes Prepare Input Files • 3 Different Working Directories – /project – Space is limited; Data are backed up Prepare Input Files • 3 Different Working Directories – /scratch – Files older than 60 days are deleted automatically Prepare Input Files • Examples under Installation Folder – /sw/xc40cle6/code/version/compilation/example -
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.