DOCSLIB.ORG

Car-Parrinello Molecular Dynamics

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Car-Parrinello Molecular Dynamics CPMD Car-Parrinello Molecular Dynamics An ab initio Electronic Structure and Molecular Dynamics Program The CPMD consortium WWW: http://www.cpmd.org/ Mailing list: [email protected] E-mail: [email protected] January 29, 2019 Send comments and bug reports to [email protected] This manual is for CPMD version 4.3.0 CPMD 4.3.0 January 29, 2019 Contents I Overview3 1 About this manual3 2 Citation 3 3 Important constants and conversion factors3 4 Recommendations for further reading4 5 History 5 5.1 CPMD Version 1.....................................5 5.2 CPMD Version 2.....................................5 5.2.1 Version 2.0....................................5 5.2.2 Version 2.5....................................5 5.3 CPMD Version 3.....................................5 5.3.1 Version 3.0....................................5 5.3.2 Version 3.1....................................5 5.3.3 Version 3.2....................................5 5.3.4 Version 3.3....................................6 5.3.5 Version 3.4....................................6 5.3.6 Version 3.5....................................6 5.3.7 Version 3.6....................................6 5.3.8 Version 3.7....................................6 5.3.9 Version 3.8....................................6 5.3.10 Version 3.9....................................6 5.3.11 Version 3.10....................................7 5.3.12 Version 3.11....................................7 5.3.13 Version 3.12....................................7 5.3.14 Version 3.13....................................7 5.3.15 Version 3.14....................................7 5.3.16 Version 3.15....................................8 5.3.17 Version 3.17....................................8 5.4 CPMD Version 4.....................................8 5.4.1 Version 4.0....................................8 5.4.2 Version 4.1....................................8 5.4.3 Version 4.3....................................9 6 Installation 10 7 Running CPMD 11 8 Files 12 II Reference Manual 15 9 Input File Reference 15 9.1 Basic rules......................................... 15 9.2 Input Sections...................................... 16 9.3 List of Keywords by Sections.............................. 17 9.3.1 &CPMD ... &END................................ 17 9.3.2 &SYSTEM ... &END.............................. 21 9.3.3 &PIMD ... &END................................ 22 9.3.4 &PATH ... &END................................ 22 9.3.5 &PTDDFT ... &END.............................. 22 9.3.6 &ATOMS ... &END............................... 23 9.3.7 &DFT ... &END................................. 23 9.3.8 &PROP ... &END................................ 24 9.3.9 &RESP ... &END................................ 25 9.3.10 &LINRES ... &END............................... 25 9.3.11 &TDDFT ... &END............................... 26 9.3.12 &HARDNESS ... &END............................ 26 9.3.13 &CLASSIC ... &END.............................. 26 9.3.14 &VDW ... &END................................ 27 9.3.15 &QMMM ... &END............................... 27 9.3.16 &MTS ... &END................................. 28 9.4 Alphabetic List of Keywords.............................. 29 9.5 Further details of the input............................... 123 9.5.1 Pseudopotentials................................. 123 9.5.2 Constraints and Restraints........................... 124 9.5.3 Atomic Basis Set................................. 128 9.5.4 Van der Waals potential............................. 130 III Miscellaneous 131 10 Postprocessing 131 10.1 Density files........................................ 131 10.1.1 List........................................ 131 10.1.2 Postprocessing.................................. 131 10.2 xyz-files.......................................... 132 10.2.1 List........................................ 132 10.2.2 Postprocessing.................................. 132 10.3 TRAJECTORY-File................................... 132 10.3.1 List........................................ 132 10.3.2 Postprocessing.................................. 132 10.4 The MOVIE format................................... 133 11 Hints and Tricks 134 11.1 Pseudopotentials and Plane Wave Cutoff........................ 134 11.2 Wavefunction Initialization............................... 134 11.2.1 Using Vanderbilt Ultrasoft Pseudopotentials.................. 134 11.3 Wavefunction Convergence................................ 135 11.4 Cell Size for Calculations with SYMMETRY 0 ................... 136 11.5 Geometry Optimization................................. 137 11.6 Molecular Dynamics................................... 137 11.6.1 Choosing the Nos´e-Hoover chain thermostat parameters........... 137 11.7 Restarts.......................................... 138 11.7.1 General information............................... 138 11.7.2 Typical restart scenarios............................. 139 11.7.3 Some special cases................................ 139 11.8 TDDFT.......................................... 139 11.8.1 Electronic spectra................................ 140 11.8.2 Geometry optimizations and molecular dynamics............... 140 11.9 Perturbation Theory / Linear Response........................ 141 11.9.1 General...................................... 141 11.9.2 &RESP section input.............................. 142 11.9.3 Response output................................. 143 11.9.4 Phonons...................................... 144 11.9.5 Lanczos...................................... 145 11.9.6 Raman...................................... 148 11.9.7 Nuclear Magnetic Resonance.......................... 148 11.9.8 FUKUI...................................... 150 11.9.9 KPERT: kdp k-point calculations........................ 150 11.10Metadynamics...................................... 150 11.10.1 MTD Algorithm................................. 151 11.10.2 The Shape of V (t)................................ 152 11.10.3 Metadynamics Keywords............................ 152 11.10.4 The Implemented Types of CV......................... 153 11.10.5 Other Keywords................................. 156 11.10.6 Output files.................................... 158 11.10.7 Using multiple walker metadynamics...................... 159 11.10.8 Shooting from a Saddle............................. 160 11.10.9 Keywords..................................... 160 11.11Restricted Open-Shell Calculations........................... 161 11.12Hints on using FEMD.................................. 161 11.12.1 Lanczos Parameters............................... 162 11.12.2 Other important FEMD parameters...................... 162 11.13The Davidson analysis and the shared electron number................ 162 11.14CDFT Theory...................................... 163 11.14.1 The density constraint.............................. 163 11.14.2 The weight.................................... 163 11.14.3 Constraint forces................................. 163 11.14.4 Transition Matrix Element calculation..................... 164 11.15Fragment Orbital DFT (FO-DFT)........................... 166 11.15.1 FODFT with CPMD............................... 167 11.16CPMD/Gromos QM/MM Calculations......................... 167 11.16.1 General Overview................................ 167 11.16.2 Input files for QM/MM CPMD......................... 168 11.16.3 Starting a QM/MM run............................. 168 11.16.4 Defining internal Gromos array dimensions.................. 168 11.16.5 Defining the QM system............................. 168 11.16.6 List of keywords in the &QMMM section................... 168 11.16.7 Keywords in the Gromos Input and Topology files.............. 177 11.16.8 Files generated by the interface code...................... 179 11.16.9 Hydrogen Capping vs. Link Atoms....................... 180 11.16.10What type of QM/MM calculations are available?.............. 181 11.16.11QM/MM Force Matching............................ 181 11.17Gromacs/CPMD QM/MM Calculations........................ 182 11.17.1 Technical Introduction.............................. 183 11.17.2 Compilation of Gromacs............................. 183 11.17.3 Execution of QM/MM runs........................... 183 11.17.4 QM/MM Examples............................... 183 11.18QM/(P)MM Interface to IPHIGENIE......................... 184 11.19CPMD on parallel computers.............................. 184 11.20Using the new xc driver and assembling functionals.................. 185 12 Questions and Answers 187 12.1 How to Report Problems................................. 187 12.2 Explanation of Warnings and Error Messages..................... 187 12.3 Pseudopotentials..................................... 189 12.4 File Formats and Interpretation of Data........................ 190 12.5 Input Parameter Values................................. 193 References 197 Index 205 CPMD 4.3.0 3 Part I Overview 1 About this manual Many members of the CPMD consortium (http://www.cpmd.org/) contributed to this manual. This version of the manual is based on a compilation by Barbara Kirchner, Ari P. Seitsonen and J¨urgHutter working at the Physical Chemistry Institute of the University of Zurich. Recent updates by Mauro Boero, Alessandro Curioni, J¨urgHutter, Axel Kohlmeyer, Nisanth Nair and Wolfram Quester. If you want to contribute or have constructive criticism please contact [email protected]. 2 Citation Publications of results obtained with CPMD should acknowledge its use by an appropriate citation of the following kind: CPMD, http://www.cpmd.org/, Copyright IBM Corp 1990-2019, Copyright MPI
Load more

Recommended publications
  • Benchmark Study of the Performance of Density
    DOI: 10.1002/open.201300012 Benchmark Study of the Performance of Density Functional Theory for Bond Activations with (Ni,Pd)-Based Transition-Metal Catalysts Marc Steinmetz and Stefan Grimme*[a] The performance of 23 density functionals, including one LDA, due to partial breakdown of the perturbative treatment for the four GGAs, three meta-GGAs, three hybrid GGAs, eight hybrid correlation energy in cases with difficult electronic structures meta-GGAs, and ten double-hybrid functionals, was investigat- (partial multi-reference character). Only double hybrids either ed for the computation of activation energies of various cova- with very low amounts of perturbative correlation (e.g., PBE0- lent main-group single bonds by four catalysts: Pd, PdClÀ , DH) or that use the opposite-spin correlation component only PdCl2, and Ni (all in the singlet state). A reactant complex, the (e.g., PWPB95) seem to be more robust. We also investigated barrier, and reaction energy were considered, leading to 164 the effect of the D3 dispersion correction. While the barriers energy data points for statistical analysis. Extended Gaussian are not affected by this correction, significant and mostly posi- AO basis sets were used in all calculations. The best functional tive results were observed for reaction energies. Furthermore, for the complete benchmark set relative to estimated CCSD(T)/ six very recently proposed double-hybrid functionals were ana- CBS reference data is PBE0-D3, with an MAD value of 1.1 kcal lyzed regarding the influence of the amount of Fock exchange molÀ1 followed by PW6B95-D3, the double hybrid PWPB95-D3, as well as the type of perturbative correlation treatment.
    [Show full text]
  • Exploring the Limit of Accuracy of the Global Hybrid Meta Density Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent Interactions
    J. Chem. Theory Comput. XXXX, xxx, 000 A Exploring the Limit of Accuracy of the Global Hybrid Meta Density Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent Interactions Yan Zhao and Donald G. Truhlar* Department of Chemistry and Supercomputing Institute, UniVersity of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431 Received June 25, 2008 Abstract: The hybrid meta density functionals M05-2X and M06-2X have been shown to provide broad accuracy for main group chemistry. In the present article we make the functional form more flexible and improve the self-interaction term in the correlation functional to improve its self-consistent-field convergence. We also explore the constraint of enforcing the exact forms of the exchange and correlation functionals through second order (SO) in the reduced density gradient. This yields two new functionals called M08-HX and M08-SO, with different exact constraints. The new functionals are optimized against 267 diverse main-group energetic data consisting of atomization energies, ionization potentials, electron affinities, proton affinities, dissociation energies, isomerization energies, barrier heights, noncovalent complexation energies, and atomic energies. Then the M08-HX, M08-SO, M05-2X, and M06-2X functionals and the popular B3LYP functional are tested against 250 data that were not part of the original training data for any of the functionals, in particular 164 main-group energetic data in 7 databases, 39 bond lengths, 38 vibrational frequencies, and 9 multiplicity-changing electronic transition energies. These tests include a variety of new challenges for complex systems, including large-molecule atomization energies, organic isomerization energies, interaction energies in uracil trimers, and bond distances in crowded molecules (in particular, cyclophanes).
    [Show full text]
  • Performance of DFT Procedures for the Calculation of Proton-Exchange
    Article pubs.acs.org/JCTC Performance of Density Functional Theory Procedures for the Calculation of Proton-Exchange Barriers: Unusual Behavior of M06- Type Functionals Bun Chan,*,†,‡ Andrew T. B. Gilbert,¶ Peter M. W. Gill,*,¶ and Leo Radom*,†,‡ † School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia ‡ ¶ ARC Centre of Excellence for Free Radical Chemistry and Biotechnology and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia *S Supporting Information ABSTRACT: We have examined the performance of a variety of density functional theory procedures for the calculation of complexation energies and proton-exchange barriers, with a focus on the Minnesota-class of functionals that are generally highly robust and generally show good accuracy. A curious observation is that M05-type and M06-type methods show an atypical decrease in calculated barriers with increasing proportion of Hartree−Fock exchange. To obtain a clearer picture of the performance of the underlying components of M05-type and M06-type functionals, we have investigated the combination of MPW-type and PBE-type exchange and B95-type and PBE-type correlation procedures. We find that, for the extensive E3 test set, the general performance of the various hybrid-DFT procedures improves in the following order: PBE1-B95 → PBE1-PBE → MPW1-PBE → PW6-B95. As M05-type and M06-type procedures are related to PBE1-B95, it would be of interest to formulate and examine the general performance of an alternative Minnesota DFT method related to PW6-B95. 1. INTRODUCTION protocol.13,14 In a recent study,15 however, it was shown that, Density functional theory (DFT) procedures1 are undeniably for complexation energies of water, ammonia and hydrogen the workhorse for many computational chemists.
    [Show full text]
  • The Norbornene Mystery Revealed
    Supplementary Material (ESI) for Chemical Communications This journal is (c) The Royal Society of Chemistry 2010 Electronic Supporting Information The Norbornene Mystery Revealed Stephan N. Steinmann, Pierre Vogel, Yirong Mo, and Clémence Corminboeuf* To be published in Chemical Communication. The supplementary Data were prepared on June 22, 2010 and contains 14 pages. Contents: Method Section Figure S1: Molecules used for the comparisons between known experimental 1 Jcc-coupling constants (in Hertz) and the computed values. 1 Table S1 JCC-coupling comparison between experiment and computation. 1 Table S2: JCC-coupling constants for all compounds considered. Cartesian coordinates: B3LYP/6-311+G(d,p) (BLW and canonical) optimized structures for all compounds considered in the article. Contents: Computational Details 1 Table S1: JCC-coupling constants for all compounds considered. 1 Figure S1: Molecules for JCC-coupling comparison between experiment and computation. 1 Table S2: JCC-coupling comparison between experiment and computation. B3LYP/6-311+G(d,p) (BLW and canonical) optimized structures for all compounds considered in the article. Computational Details Standard geometries were optimized at the B3LYP1, 2/6-311+G** level using Gaussian 09.3 The BLW- constrained B3LYP/6-311+G** geometries (‘loc’) were optimized using a modified version of GAMESS-US (release 2008)4interfaced with the BLW-module.5, 6 Both the density and the J-coupling constants have been computed at the PBE7/IGLO-III level in Dalton 2.0.8 The BLW-eigenvalues and eigenvectors were optimized at the given DFT level with the SCF module of Dalton, SIRIUS, that has been interfaced with the BLW- module.
    [Show full text]
  • Computational Chemistry for Chemistry Educators Shawn C
    Volume 1, Issue 1 Journal Of Computational Science Education Computational Chemistry for Chemistry Educators Shawn C. Sendlinger Clyde R. Metz North Carolina Central University College of Charleston Department of Chemistry Department of Chemistry and Biochemistry 1801 Fayetteville Street, 66 George Street, Durham, NC 27707 Charleston, SC 29424 919-530-6297 843-953-8097 [email protected] [email protected] ABSTRACT 1. INTRODUCTION In this paper we describe an ongoing project where the goal is to The majority of today’s students are technologically savvy and are develop competence and confidence among chemistry faculty so often more comfortable using computers than the faculty who they are able to utilize computational chemistry as an effective teach them. In order to harness the student’s interest in teaching tool. Advances in hardware and software have made technology and begin to use it as an educational tool, most faculty research-grade tools readily available to the academic community. members require some level of instruction and training. Because Training is required so that faculty can take full advantage of this chemistry research increasingly utilizes computation as an technology, begin to transform the educational landscape, and important tool, our approach to chemistry education should reflect attract more students to the study of science. this. The ability of computer technology to visualize and manipulate objects on an atomic scale can be a powerful tool to increase both student interest in chemistry as well as their level of Categories and Subject Descriptors understanding. Computational Chemistry for Chemistry Educators (CCCE) is a project that seeks to provide faculty the J.2 [Physical Sciences and Engineering]: Chemistry necessary knowledge, experience, and technology access so that they can begin to design and incorporate computational approaches in the courses they teach.
    [Show full text]
  • The Empirical Pseudopotential Method
    The empirical pseudopotential method Richard Tran PID: A1070602 1 Background In 1934, Fermi [1] proposed a method to describe high lying atomic states by replacing the complex effects of the core electrons with an effective potential described by the pseudo-wavefunctions of the valence electrons. Shortly after, this pseudopotential (PSP), was realized by Hellmann [2] who implemented it to describe the energy levels of alkali atoms. Despite his initial success, further exploration of the PSP and its application in efficiently solving the Hamiltonian of periodic systems did not reach its zenith until the middle of the twenti- eth century when Herring [3] proposed the orthogonalized plane wave (OPW) method to calculate the wave functions of metals and semiconductors. Using the OPW, Phillips and Kleinman [4] showed that the orthogonality of the va- lence electrons’ wave functions relative to that of the core electrons leads to a cancellation of the attractive and repulsive potentials of the core electrons (with the repulsive potentials being approximated either analytically or empirically), allowing for a rapid convergence of the OPW calculations. Subsequently in the 60s, Marvin Cohen expanded and improved upon the pseudopotential method by using the crystalline energy levels of several semicon- ductor materials [6, 7, 8] to empirically obtain the potentials needed to compute the atomic wave functions, developing what is now known as the empirical pseu- dopotential method (EPM). Although more advanced PSPs such as the ab-initio pseudopotentials exist, the EPM still provides an incredibly accurate method for calculating optical properties and band structures, especially for metals and semiconductors, with a less computationally taxing method.
    [Show full text]
  • The Plane-Wave Pseudopotential Method
    The Plane-wave Pseudopotential Method i(G+k) r k(r)= ck,Ge · XG Chris J Pickard Electrons in a Solid Nearly Free Electrons Nearly Free Electrons Nearly Free Electrons Electronic Structures Methods Empirical Pseudopotentials Ab Initio Pseudopotentials Ab Initio Pseudopotentials Ab Initio Pseudopotentials Ab Initio Pseudopotentials Ultrasoft Pseudopotentials (Vanderbilt, 1990) Projector Augmented Waves Deriving the Pseudo Hamiltonian PAW vs PAW C. G. van de Walle and P. E. Bloechl 1993 (I) PAW to calculate all electron properties from PSP calculations" P. E. Bloechl 1994 (II)! The PAW electronic structure method" " The two are linked, but should not be confused References David Vanderbilt, Soft self-consistent pseudopotentials in a generalised eigenvalue formalism, PRB 1990 41 7892" Kari Laasonen et al, Car-Parinello molecular dynamics with Vanderbilt ultrasoft pseudopotentials, PRB 1993 47 10142" P.E. Bloechl, Projector augmented-wave method, PRB 1994 50 17953" G. Kresse and D. Joubert, From ultrasoft pseudopotentials to the projector augmented-wave method, PRB 1999 59 1758 On-the-fly Pseudopotentials - All quantities for PAW (I) reconstruction available" - Allows automatic consistency of the potentials with functionals" - Even fewer input files required" - The code in CASTEP is a cut down (fast) pseudopotential code" - There are internal databases" - Other generation codes (Vanderbilt’s original, OPIUM, LD1) exist It all works! Kohn-Sham Equations Being (Self) Consistent Eigenproblem in a Basis Just a Few Atoms In a Crystal Plane-waves
    [Show full text]
  • Introduction to DFT and the Plane-Wave Pseudopotential Method
    Introduction to DFT and the plane-wave pseudopotential method Keith Refson STFC Rutherford Appleton Laboratory Chilton, Didcot, OXON OX11 0QX 23 Apr 2014 Parallel Materials Modelling Packages @ EPCC 1 / 55 Introduction Synopsis Motivation Some ab initio codes Quantum-mechanical approaches Density Functional Theory Electronic Structure of Condensed Phases Total-energy calculations Introduction Basis sets Plane-waves and Pseudopotentials How to solve the equations Parallel Materials Modelling Packages @ EPCC 2 / 55 Synopsis Introduction A guided tour inside the “black box” of ab-initio simulation. Synopsis • Motivation • The rise of quantum-mechanical simulations. Some ab initio codes Wavefunction-based theory • Density-functional theory (DFT) Quantum-mechanical • approaches Quantum theory in periodic boundaries • Plane-wave and other basis sets Density Functional • Theory SCF solvers • Molecular Dynamics Electronic Structure of Condensed Phases Recommended Reading and Further Study Total-energy calculations • Basis sets Jorge Kohanoff Electronic Structure Calculations for Solids and Molecules, Plane-waves and Theory and Computational Methods, Cambridge, ISBN-13: 9780521815918 Pseudopotentials • Dominik Marx, J¨urg Hutter Ab Initio Molecular Dynamics: Basic Theory and How to solve the Advanced Methods Cambridge University Press, ISBN: 0521898633 equations • Richard M. Martin Electronic Structure: Basic Theory and Practical Methods: Basic Theory and Practical Density Functional Approaches Vol 1 Cambridge University Press, ISBN: 0521782856
    [Show full text]
  • An Ion Mobility-Aided, Quantum Chemical Benchmark Analysis of H+GPGG Conformers Daniel Beckett, Tarick J
    Article Cite This: J. Chem. Theory Comput. 2018, 14, 5406−5418 pubs.acs.org/JCTC Electronic Energies Are Not Enough: An Ion Mobility-Aided, Quantum Chemical Benchmark Analysis of H+GPGG Conformers Daniel Beckett, Tarick J. El-Baba, David E. Clemmer, and Krishnan Raghavachari* Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States *S Supporting Information ABSTRACT: Peptides and proteins exist not as single, lowest energy structures but as ensembles of states separated by small barriers. In order to study these species we must be able to correctly identify their gas phase conformational distributions, and ion mobility spectrometry (IMS) has arisen as an experimental method for assessing the gas phase energetics of flexible peptides. Here, we present a thorough exploration and benchmarking of the low energy conformers of the small, hairpin peptide H+GPGG with the aid of ion mobility ). spectrometry against a wide swath of density functionals (35 dispersion-corrected and uncorrected functionals represented by 21 unique exchange−correlation functionals) and wave function theory methods (15 total levels of theory). The three experimentally resolved IMS peaks were found to correspond to three distinct pairs of conformers, each pair composed of species differing only by the chair or boat configuration of the proline. Two of the H+GPGG conformer pairs possess a cis configuration about the Pro−Gly1 peptide bond while the other adopts a trans configuration. While the experimental spectrum reports a higher intensity for the o legitimately share published articles. cis-1 conformer than the trans conformer, 13 WFT levels of theory, including a complete basis set CCSD(T) extrapolation, obtain trans to be favored in terms of the electronic energy.
    [Show full text]
  • The Plane-Wave Pseudopotential Method
    The Plane-Wave Pseudopotential Method Eckhard Pehlke, Institut für Laser- und Plasmaphysik, Universität Essen, 45117 Essen, Germany. Starting Point: Electronic structure problem from physics, chemistry, materials science, geology, biology, ... which can be solved by total-energy calculations. Topics of this (i) how to get rid of the "core electrons": talk: the pseudopotential concept (ii) the plane-wave basis-set and its advantages (iii) supercells, Bloch theorem and Brillouin zone integrals choices we have... Treatment of electron-electron interaction and decisions to make... Hartree-Fock (HF) ¿ ÒÌ Ò· Ú ´ÖµÒ´Öµ Ö Ú ¼ ¼ ½ Ò´ÖµÒ´Ö µ ¿ ¿ ¼ · Ö Ö · Ò Configuration-Interaction (CI) ¼ ¾ Ö Ö Quantum Monte-Carlo (QMC) ÑÒ Ò ¼ Ú Ê ¿ Ò´Ö µ ÖÆ Density-Functional Theory (DFT) ¼ ½ Ò´Ö µ ¾ ¿ ¼ ´ Ö · Ú ´Öµ· Ö · Ú ´Öµµ ´Öµ ´Öµ ¼ ¾ Ö Ö Æ Ò ¾ Ò´Öµ ´Öµ Ú ´Öµ Æ´Öµ Problem: Approximation to XC functional. decisions to make... Simulation of Atomic Geometries Example: chemisorption site & energy of a particular atom on a surface = ? How to simulate adsorption geometry? single molecule or cluster Use Bloch theorem. periodically repeated supercell, slab-geometry Efficient Brillouin zone integration schemes. true half-space geometry, Green-function methods decisions to make... Basis Set to Expand Wave-Functions ½ ¡Ê ´Øµ ´ Öµ Ù ´Ö Ê µ Ô Æ linear combination of Ê atomic orbitals (LCAO) ´ Öµ ´µ ´ Öµ simple, unbiased, ½ ´·µ¡Ö ´ Öµ ´ · µ plane waves (PW) Ô independent of ª atomic positions augmented plane waves . (APW) etc. etc. I. The Pseudopotential Concept Core-States and Chemical Bonding? Validity of the Frozen-Core Approximation U. von Barth, C.D.
    [Show full text]
  • Ab Initio Search for Novel Bxhy Building Blocks with Potential for Hydrogen Storage
    Utah State University DigitalCommons@USU All Graduate Theses and Dissertations Graduate Studies 12-2010 Ab Initio Search for Novel BxHy Building Blocks with Potential for Hydrogen Storage Jared K. Olson Utah State University Follow this and additional works at: https://digitalcommons.usu.edu/etd Part of the Physical Chemistry Commons Recommended Citation Olson, Jared K., "Ab Initio Search for Novel BxHy Building Blocks with Potential for Hydrogen Storage" (2010). All Graduate Theses and Dissertations. 844. https://digitalcommons.usu.edu/etd/844 This Dissertation is brought to you for free and open access by the Graduate Studies at DigitalCommons@USU. It has been accepted for inclusion in All Graduate Theses and Dissertations by an authorized administrator of DigitalCommons@USU. For more information, please contact [email protected]. AB INITIO SEARCH FOR NOVEL BXHY BUILDING BLOCKS WITH POTENTIAL FOR HYDROGEN STORAGE by Jared K. Olson A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in Chemistry (Physical Chemistry) Approved: Dr. Alexander I. Boldyrev Dr. Steve Scheiner Major Professor Committee Member Dr. David Farrelly Dr. Stephen Bialkowski Committee Member Committee Member Dr. T.C. Shen Byron Burnham Committee Member Dean of Graduate Studies UTAH STATE UNIVERSITY Logan, Utah 2010 ii Copyright © Jared K. Olson 2010 All Rights Reserved iii ABSTRACT Ab Initio Search for Novel BxHy Building Blocks with Potential for Hydrogen Storage by Jared K. Olson, Doctor of Philosophy Utah State University, 2010 Major Professor: Dr. Alexander I. Boldyrev Department: Chemistry and Biochemistry On-board hydrogen storage presents a challenging barrier to the use of hydrogen as an energy source because the performance of current storage materials falls short of platform requirements.
    [Show full text]
  • Surface Modification of Mgni by Perylene
    Materials Transactions, Vol. 43, No. 11 (2002) pp. 2711 to 2716 Special Issue on Protium New Function in Materials c 2002 The Japan Institute of Metals Surface Modification of MgNi by Perylene Tiejun Ma, Yuji Hatano, Takayuki Abe and Kuniaki Watanabe Hydrogen Isotope Research Center, Toyama University, Toyama 930-8555, Japan Amorphous MgNi was modified by ball milling with perylene and its effects on the charge/discharge capacity were examined by using a conventional two-electrode cell. It was found that both the ball milling time and perylene/MgNi ratio had great influence on the discharge capacity and cycle life of MgNi. Three types of effects were identified, depending on ball-milling conditions. One of them was the increase in the discharge capacity at the first cycle, the second type was the deceleration of the degradation of the discharge capacity with charge/discharge cycle, and the last type was the reduction in the charge/discharge capacity. Chemical states of modified surfaces were analyzed by Auger electron spectroscopy (AES) as well as ab-inito calculation. Both AES and ab-initio calculations indicated that carbon atoms can form bonding with both magnesium and nickel atoms, but bonding with magnesium atoms is most preferable. The change in the charge/discharge capacity is attributed to such kind of reactions, and the three distinct effects are ascribed to the presence of different MgNi-perylene composites, formed during the ball milling on the surface, resulting in the retardation or acceleration of Mg(OH)2 formation on the electrode. (Received May 20, 2002; Accepted July 16, 2002) Keywords: magnesium, nickel, aromatic compound, surface modification, battery, electrode 1.
    [Show full text]