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ADF Manual ADF Modeling Suite 2016

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ADF Manual ADF Modeling Suite 2016 ADF Manual ADF Modeling Suite 2016 www.scm.com November 18, 2016 CONTENTS 1 General 1 1.1 Introduction...............................................1 1.2 Release 2016...............................................4 1.3 Feature List................................................5 1.4 Technical remarks, Terminology.....................................7 1.5 Running the program........................................... 13 2 Input and Output 17 2.1 Minimal input.............................................. 17 2.2 Structure of the Input........................................... 18 2.3 Structure of the Output.......................................... 23 3 Coordinates, Basis sets, Fragments 27 3.1 Atomic coordinates............................................ 27 3.2 Basis sets and atomic fragments..................................... 31 3.3 Molecular fragments........................................... 40 4 Model Hamiltonians 45 4.1 Electronic Configuration......................................... 45 4.2 Density Functionals (XC)........................................ 56 4.3 Relativistic effects............................................ 72 4.4 Solvents and other environments..................................... 73 4.5 Electric Field: Homogeneous, Point Charges, Polarizability...................... 111 5 Structure and Reactivity 113 5.1 Run Types................................................ 113 5.2 Geometry Optimization......................................... 115 5.3 Transition State.............................................. 119 5.4 Linear Transit.............................................. 120 5.5 Intrinsic Reaction Coordinate...................................... 123 5.6 Climbing-Image Nudged Elastic Band.................................. 125 5.7 Special Features............................................. 127 5.8 Frequencies................................................ 133 6 Spectroscopic properties 143 6.1 IR spectra, (resonance) Raman, VROA, VCD.............................. 143 6.2 Time-dependent DFT.......................................... 150 6.3 Excitation energies: UV/Vis, X-ray, CD, MCD............................. 154 6.4 Excited state (geometry) optimizations................................. 173 6.5 Vibrationally resolved electronic spectra................................ 175 6.6 (Hyper-)Polarizabilities, ORD, magnetizabilities, Verdet constants................... 180 i 6.7 NMR................................................... 187 6.8 ESR/EPR................................................. 202 6.9 Nuclear Quadrupole Interaction (EFG)................................. 204 6.10 Mössbauer spectroscopy......................................... 205 7 Transport properties 207 7.1 Charge transfer integrals (transport properties)............................. 207 7.2 GREEN: Non-self-consistent Green’s function calculation....................... 210 8 Analysis 217 8.1 Molecules built from fragments..................................... 217 8.2 Bond energy analysis........................................... 218 8.3 Localized Molecular Orbitals...................................... 220 8.4 Advanced charge density and bond order analysis............................ 221 8.5 Controlling printed Output........................................ 230 8.6 Results on Output............................................ 243 8.7 Densf: Volume Maps........................................... 248 8.8 Dos: Density of States.......................................... 258 9 Accuracy and Efficiency 265 9.1 Precision and Self-Consistency..................................... 265 9.2 Basis Set Superposition Error (BSSE).................................. 279 9.3 Control of Program Flow......................................... 279 9.4 Technical Settings............................................ 281 10 Restarts 287 10.1 Restart files................................................ 287 10.2 The restart key.............................................. 288 10.3 Structure of the restart file........................................ 289 11 Recommendations, problems, Questions 293 11.1 Recommendations............................................ 293 11.2 Trouble Shooting............................................. 299 12 Appendices 309 12.1 Basis set file format........................................... 309 12.2 Elements of the Periodic Table...................................... 313 12.3 Multiplet States.............................................. 316 12.4 Dirac program: relativistic core potentials................................ 325 12.5 Symmetry................................................ 327 12.6 Binary result files, KF browser...................................... 329 13 Examples 351 13.1 Introduction............................................... 351 13.2 Model Hamiltonians........................................... 352 13.3 Structure and Reactivity......................................... 403 13.4 Spectroscopic Properties......................................... 440 13.5 Transport properties........................................... 516 13.6 Analysis................................................. 533 13.7 Accuracy and Efficiency......................................... 565 13.8 Scripting................................................. 573 13.9 List of Examples............................................. 575 14 Required Citations 579 14.1 General References............................................ 579 ii 14.2 Feature References............................................ 579 14.3 External programs and Libraries..................................... 588 15 References 589 16 Keywords 615 Index 619 iii iv CHAPTER ONE GENERAL 1.1 Introduction ADF (Amsterdam Density Functional) is a Fortran program for calculations on atoms and molecules (in gas phase or solution). It can be used for the study of such diverse fields as molecular spectroscopy, organic and inorganic chemistry, crystallography and pharmacochemistry. A separate program BAND is available for the study of periodic systems: crystals, surfaces, and polymers. The COSMO-RS program is used for calculating thermodynamic properties of (mixed) fluids. The underlying theory is the Kohn-Sham approach to Density-Functional Theory (DFT). This implies a one-electron picture of the many-electron systems but yields in principle the exact electron density (and related properties) and the total energy. If ADF is a new program for you we recommend that you carefully read the section Technical remarks, Terminology (page 7), which presents a discussion of a few ADF-typical aspects and terminology. This will help you to understand and appreciate the output of an ADF calculation. ADF has been developed since the early 1970s (at that time called HFS, later AMOL, see also Refs. [308-310 (page 607)]), mainly by the two theoretical chemistry groups of, respectively, the Vrije Universiteit in Amsterdam ( http://www.chem.vu.nl/en/research/division-theoretical-chemistry/index.asp) and the University of Calgary, Canada ( http://www.cobalt.chem.ucalgary.ca/group/master.html). Other researchers have also contributed. As a major re- search tool of these academic development groups, ADF is in continuous development and retains a firm basis in the academic world. Maintenance and distribution of the commercial (export) version of the program is done by Scientific Computing & Modelling NV (SCM) ( http://www.scm.com), a company based in Amsterdam, formally split off from the theoretical chemistry group in Amsterdam but practically still very much a part of it. Documentation such as User manuals, Installation instructions, Examples, Theoretical documents can be found at the SCM web site. Publications based on research with ADF should include appropriate references to the program. We recommend that references are made both to the program itself and to publications related to its development and structure. See the Required Citations (page 579). The installation of the Amsterdam Density Functional program package (ADF) is explained in the Installation manual. This User’s Guide describes how to use the program, how input is structured, what files are produced, and so on. Some special applications of ADF are described in the Examples (page 351). Where references are made to the operating system (OS) and to the file system on your computer the terminology of UNIX type OSs is used. The ADF package is in continuous development to extend its functionality and applicability, to increase its efficiency and user-friendliness, and of course to correct errors. We appreciate comments and suggestions for improvement of the software and the documentation. 1 ADF Manual, ADF Modeling Suite 2016 1.1.1 Functionality • Single Point calculation • Geometry Optimization • Transition States • Frequencies and thermodynamic properties • Tracing a Reaction Path • Computation of any electronic configuration • Excitation energies, oscillator strengths, transition dipole moments, (hyper)polarizabilities, Van der Waals dis- persion coefficients, CD spectra, ORD, using Time-Dependent Density Functional Theory (TDDFT) • ESR (EPR) g-tensors, A-tensors, NQCCs • NMR chemical shifts and spin-spin coupling constants • Various other molecular properties • Treatment of large systems and environment by the QM/MM (Quantum Mechanics / Molecular Mechanics) hybrid approach. 1.1.2 Applicability All elements of the periodic table can be used (Z = 1-118). For each of the elements, basis sets of different sizes are available, ranging from minimal to high quality.
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