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Turbomole USER's MANUAL

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Turbomole USER's MANUAL Turbomole Program Package for ab initio Electronic Structure Calculations USER’S MANUAL Turbomole Version 6.1 August 14, 2009 Contents 1 Preface and General Information 11 1.1 Contributions and Acknowledgements . 11 1.2 Features of Turbomole ......................... 13 1.3 How to Quote Usage of Turbomole .................. 13 1.4 Modules and Their Functionality . 21 1.5 Tools.................................... 23 2 Installation of Turbomole 26 3 How to Run Turbomole 28 3.1 A ‘Quick and Dirty’ Tutorial . 28 3.1.1 Single Point Calculations: Running Turbomole Modules . 30 3.1.2 Energy and Gradient Calculations . 30 3.1.3 Calculation of Molecular Properties . 31 3.1.4 Modules and Data Flow . 31 3.2 Parallel Runs . 31 3.2.1 Running Parallel Jobs — MPI case . 33 3.2.2 Running Parallel Jobs — OpenMP case . 37 4 Preparing your input file with Define 39 4.0.1 Universally Available Display Commands in Define ..... 40 4.0.2 Specifying Atomic Sets . 40 4.0.3 control as Input and Output File . 40 4.0.4 Be Prepared . 41 4.1 The Geometry Main Menu . 42 3 4 CONTENTS 4.1.1 Description of commands . 44 4.1.2 Internal Coordinate Menu . 47 4.1.3 Manipulating the Geometry . 52 4.2 The Atomic Attributes Menu . 52 4.2.1 Description of the commands . 55 4.3 Generating MO Start Vectors . 57 4.3.1 The MO Start Vectors Menu . 57 4.3.2 Assignment of Occupation Numbers . 60 4.3.3 Orbital Specification Menu . 62 4.3.4 Roothaan Parameters . 63 4.3.5 Start-MOs for broken symmetry treatments (”flip”) . 63 4.4 The General Options Menu . 66 4.4.1 Important commands . 67 4.4.2 Special adjustments . 73 4.4.3 Relax Options . 75 4.4.4 Definition of External Electrostatic Fields . 79 4.4.5 Properties . 80 5 Calculation of Molecular Structure and Ab Initio Molecular Dy- namics 89 5.1 Structure Optimizations using the Jobex Script . 89 5.1.1 Options . 89 5.1.2 Output . 90 5.2 Program Statpt ............................. 91 5.2.1 General Information . 91 5.2.2 Hessian matrix . 92 5.2.3 Finding Minima . 93 5.2.4 Finding transition states . 93 5.3 Program Relax . 94 5.3.1 Purpose . 94 5.3.2 Optimization of General Coordinates . 95 5.3.3 Force Constant Update Algorithms . 96 CONTENTS 5 5.3.4 Definition of Internal Coordinates . 98 5.3.5 Structure Optimizations Using Internal Coordinates . 98 5.3.6 Structure Optimization in Cartesian Coordinates . 99 5.3.7 Optimization of Basis Sets (SCF only) . 100 5.3.8 Simultaneous Optimization of Basis Set and Structure . 100 5.3.9 Optimization of Structure and a Global Scaling Factor . 101 5.3.10 Conversion from Internal to Cartesian Coordinates . 101 5.3.11 Conversion of Cartesian Coordinates, Gradients and Force Constants to Internals . 101 5.3.12 The m-Matrix . 102 5.3.13 Initialization of Force Constant Matrices . 102 5.3.14 Look at Results . 103 5.4 Force Field Calculations . 103 5.4.1 Purpose . 103 5.4.2 How to Perform a Uff Calculation . 104 5.4.3 The Uff implementation . 104 5.5 Molecular Dynamics Calculations . 106 5.6 Counterpoise-Corrections using the Jobbsse Script . 108 5.6.1 Options . 109 5.6.2 Output . 110 6 Hartree–Fock and DFT Calculations 111 6.1 Background Theory . 113 6.2 Exchange-Correlation Functionals Available . 114 6.3 Restricted Open-Shell Hartree–Fock . 117 6.3.1 Brief Description . 117 6.3.2 One Open Shell . 117 6.3.3 More Than One Open Shell . 120 6.3.4 Miscellaneous . 122 6.4 Two-component Hartree–Fock and DFT Calculations . 124 6.4.1 Background Theory . 124 6.4.2 How to use . 124 6 CONTENTS 6.5 Using the Douglas–Kroll–Hess (DKH) Hamiltonian . 126 6.6 Periodic Electrostatic Embedded Cluster Method . 127 6.6.1 General Information . 127 6.6.2 Theoretical Background . 127 6.6.3 Calculation Setup . 128 6.7 Empirical Dispersion Correction for DFT Calculations . 135 7 Hartree–Fock and DFT Response Calculations: Stability, Dynamic Response Properties, and Excited States 138 7.1 Functionalities of Escf and Egrad . 138 7.2 Theoretical Background . 139 7.3 Implementation . 141 7.4 How to Perform . 142 7.4.1 Preliminaries . 143 7.4.2 Polarizabilities and Optical Rotations . 143 7.4.3 Stability Analysis . 144 7.4.4 Vertical Excitation and CD Spectra . 144 7.4.5 Excited State Geometry Optimizations . 146 7.4.6 Excited State Force Constant Calculations . 147 7.4.7 Polarizability Derivatives and Raman Spectra . 147 8 Second-order Møller–Plesset Perturbation Theory 149 8.1 Functionalities of Mpgrad, Rimp2, Ricc2 . 149 8.2 Some Theory . 150 8.3 How to Prepare and Perform MP2 Calculations . 151 8.4 General Comments on MP2 Calculations, Practical Hints . 153 9 Second-Order Approximate Coupled-Cluster (CC2) Calculations 155 9.1 CC2 Ground-State Energy Calculations . 159 9.2 Calculation of Excitation Energies . 161 9.3 First-Order Properties and Gradients . 165 9.3.1 Ground State Properties, Gradients and Geometries . 165 9.3.2 Excited State Properties, Gradients and Geometries . 167 CONTENTS 7 9.3.3 Visualization of densities and Density analysis . 169 9.3.4 Fast geometry optimizations with RI-SCF based gradients . 171 9.4 Transition Moments . 172 9.5 RI-MP2-F12 Calculations . 173 9.6 Parallel RI-MP2 and RI-CC2 Calculations . 178 9.7 Spin-component scaling approaches (SCS/SOS) . 179 9.7.1 Laplace-transformed SOS-RI-MP2 with O(N 4) scaling costs . 180 10 Calculation of Vibrational Frequencies and Vibrational Spectra 183 10.1 Analysis of Normal Modes in Terms of Internal Coordinates . 185 10.2 Calculation of Raman Spectra . 186 10.3 Vibrational frequencies with fixed atoms using NumForce . 186 11 Calculation of NMR Shieldings 188 11.1 Prerequisites . 188 11.2 How to Perform a SCF of DFT Calculation . 188 11.3 How to Perform a MP2 calculation . 189 11.4 Chemical Shifts . 190 11.5 Other Features and Known Limitations . 190 12 Molecular Properties, Wavefunction Analysis, and Interfaces to Vi- sualization Tools 191 12.1 Wavefunction analysis and Molecular Properties . 191 12.2 Interfaces to Visualization Tools . 193 13 Treatment of Solvation Effects with Cosmo 198 14 Keywords in the control file 203 14.1 Introduction . 203 14.2 Format of Keywords and Comments . 203 14.2.1 General Keywords . 203 14.2.2 Keywords for System Specification . 205 14.2.3 Keywords for redundant internal coordinates in $redund inp 207 14.2.4 Keywords for Module Uff . 209 8 CONTENTS 14.2.5 Keywords for Modules Dscf and Ridft . 213 14.2.6 Keywords for Periodic Electrostatic Embedded Cluster Method234 14.2.7 Keywords for Cosmo . 236 14.2.8 Keywords for Modules Grad and Rdgrad . 239 14.2.9 Keywords for Module Aoforce . 240 14.2.10 Keywords for Module Escf . 243 14.2.11 Keywords for Module Egrad . 245 14.2.12 Keywords for Modules Mpgrad and Rimp2 . 246 14.2.13 Keywords for Module Ricc2 . 249 14.2.14 Keywords for Module Relax . 259 14.2.15 Keywords for Module Statpt . 267 14.2.16 Keywords for Module Moloch . 269 14.2.17 Keywords for wave function analysis and generation of plotting data................................ 273 14.2.18 Keywords for Module Frog . 280 14.2.19 Keywords for Module Mpshift . 285 14.2.20 Keywords for Parallel Runs . 287 15 Sample control files 291 15.1 Introduction . 291 15.2 NH3 Input for a RHF Calculation . 292 15.3 NO2 input for an unrestricted DFT calculation . 296 15.4 TaCl5 Input for an RI-DFT Calculation with ECPs . 300 15.5 Basisset optimization for Nitrogen . 307 15.6 ROHF of Two Open Shells . 310 16 The Perl-based Test Suite.
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