Turbomole User's Manual for ab initio calculations

328 Pages·2016·1.6 MB·English

Turbomole
Program Package for ab initio
Electronic Structure Calculations
USER’S MANUAL
Turbomole Version 5.10
17th February 2008

Contents
1 Preface 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
1.6 Installation of Turbomole . . . . . . . . . . . . . . . . . . . . . . . 25
1.7 How to Run Turbomole: A ‘Quick and Dirty’ Tutorial . . . . . . . 27
1.7.1 Single Point Calculations: Running Turbomole Modules . . 28
1.7.2 Energy and Gradient Calculations . . . . . . . . . . . . . . . 29
1.7.3 Calculation of Molecular Properties . . . . . . . . . . . . . . 30
1.7.4 Modules and Data Flow . . . . . . . . . . . . . . . . . . . . . 30
1.8 Parallel Runs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
1.8.1 Running Parallel Jobs . . . . . . . . . . . . . . . . . . . . . . 32
1.9 Running Turbomole using the script Tmole . . . . . . . . . . . . 36
1.9.1 Implementation . . . . . . . . . . . . . . . . . . . . . . . . . . 36
1.9.2 The file turbo.in . . . . . . . . . . . . . . . . . . . . . . . . 36
2 Preparing your input file with Define 43
2.0.1 Universally Available Display Commands in Define . . . . . 44
2.0.2 Specifying Atomic Sets. . . . . . . . . . . . . . . . . . . . . . 44
2.0.3 control as Input and Output File . . . . . . . . . . . . . . . 44
2.0.4 Be Prepared . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
2.1 The Geometry Main Menu. . . . . . . . . . . . . . . . . . . . . . . . 46
3
4 CONTENTS
2.1.1 Description of commands . . . . . . . . . . . . . . . . . . . . 48
2.1.2 Internal Coordinate Menu . . . . . . . . . . . . . . . . . . . . 51
2.1.3 Manipulating the Geometry . . . . . . . . . . . . . . . . . . . 56
2.2 The Atomic Attributes Menu . . . . . . . . . . . . . . . . . . . . . . 56
2.2.1 Description of the commands . . . . . . . . . . . . . . . . . . 59
2.3 Generating MO Start Vectors . . . . . . . . . . . . . . . . . . . . . . 61
2.3.1 The MO Start Vectors Menu . . . . . . . . . . . . . . . . . . 61
2.3.2 Assignment of Occupation Numbers . . . . . . . . . . . . . . 64
2.3.3 Orbital Specification Menu . . . . . . . . . . . . . . . . . . . 66
2.3.4 Roothaan Parameters . . . . . . . . . . . . . . . . . . . . . . 66
2.4 The General Options Menu . . . . . . . . . . . . . . . . . . . . . . . 67
2.4.1 Important commands . . . . . . . . . . . . . . . . . . . . . . 68
2.4.2 Special adjustments . . . . . . . . . . . . . . . . . . . . . . . 74
2.4.3 Relax Options . . . . . . . . . . . . . . . . . . . . . . . . . . 76
2.4.4 Definition of External Electrostatic Fields . . . . . . . . . . . 80
2.4.5 Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
3 Calculation of Molecular Structure and Ab Initio Molecular Dy-
namics 90
3.1 Structure Optimizations using the Jobex Script . . . . . . . . . . . 90
3.1.1 Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
3.1.2 Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
3.2 Program Statpt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
3.2.1 General Information . . . . . . . . . . . . . . . . . . . . . . . 92
3.2.2 Hessian matrix . . . . . . . . . . . . . . . . . . . . . . . . . . 93
3.2.3 Finding Minima . . . . . . . . . . . . . . . . . . . . . . . . . 94
3.2.4 Finding transition states . . . . . . . . . . . . . . . . . . . . . 94
3.3 Program Relax . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
3.3.1 Purpose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
3.3.2 Optimization of General Coordinates . . . . . . . . . . . . . . 96
3.3.3 Force Constant Update Algorithms . . . . . . . . . . . . . . . 98
3.3.4 Definition of Internal Coordinates . . . . . . . . . . . . . . . 99
CONTENTS 5
3.3.5 Structure Optimizations Using Internal Coordinates . . . . . 100
3.3.6 Structure Optimization in Cartesian Coordinates . . . . . . . 100
3.3.7 Optimization of Basis Sets (SCF only) . . . . . . . . . . . . . 101
3.3.8 Simultaneous Optimization of Basis Set and Structure . . . . 101
3.3.9 Optimization of Structure and a Global Scaling Factor . . . . 102
3.3.10 Conversion from Internal to Cartesian Coordinates . . . . . . 102
3.3.11 Conversion of Cartesian Coordinates, Gradients and Force
Constants to Internals . . . . . . . . . . . . . . . . . . . . . . 102
3.3.12 The m-Matrix . . . . . . . . . . . . . . . . . . . . . . . . . . 103
3.3.13 Initialization of Force Constant Matrices . . . . . . . . . . . . 103
3.3.14 Look at Results . . . . . . . . . . . . . . . . . . . . . . . . . . 104
3.4 Force Field Calculations . . . . . . . . . . . . . . . . . . . . . . . . . 104
3.4.1 Purpose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
3.4.2 How to Perform a Uff Calculation . . . . . . . . . . . . . . . 105
3.4.3 The Uff implementation . . . . . . . . . . . . . . . . . . . . 105
3.5 Molecular Dynamics Calculations . . . . . . . . . . . . . . . . . . . . 107
3.6 Counterpoise-Corrections using the Jobbsse Script . . . . . . . . . . 109
3.6.1 Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
3.6.2 Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
4 Hartree–Fock and DFT Calculations 112
4.1 Background Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
4.2 Exchange-Correlation Functionals Available . . . . . . . . . . . . . . 115
4.3 Restricted Open-Shell Hartree–Fock . . . . . . . . . . . . . . . . . . 118
4.3.1 Brief Description . . . . . . . . . . . . . . . . . . . . . . . . . 118
4.3.2 One Open Shell . . . . . . . . . . . . . . . . . . . . . . . . . . 118
4.3.3 More Than One Open Shell . . . . . . . . . . . . . . . . . . . 121
4.3.4 Miscellaneous . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
4.4 Two-component Hartree–Fock and DFT Calculations . . . . . . . . . 125
4.4.1 Background Theory . . . . . . . . . . . . . . . . . . . . . . . 125
4.4.2 How to use . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
4.5 Periodic Electrostatic Embedded Cluster Method . . . . . . . . . . . 127
6 CONTENTS
4.5.1 General Information . . . . . . . . . . . . . . . . . . . . . . . 127
4.5.2 Theoretical Background . . . . . . . . . . . . . . . . . . . . . 127
4.5.3 Calculation Setup . . . . . . . . . . . . . . . . . . . . . . . . 128
4.6 Empirical Dispersion Correction for DFT Calculations . . . . . . . . 135
5 Second-order Møller–Plesset Perturbation Theory 138
5.1 Functionalities of Mpgrad and Rimp2 . . . . . . . . . . . . . . . . . 138
5.2 Some Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
5.3 How to Prepare and Perform MP2 Calculations . . . . . . . . . . . . 139
5.4 General Comments on MP2 Calculations, Practical Hints . . . . . . 141
6 Hartree–Fock and DFT Response Calculations: Stability, Dynamic
Response Properties, and Excited States 143
6.1 Functionalities of Escf and Egrad . . . . . . . . . . . . . . . . . . 143
6.2 Theoretical Background . . . . . . . . . . . . . . . . . . . . . . . . . 144
6.3 Implementation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
6.4 How to Perform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
6.4.1 Preliminaries . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
6.4.2 Polarizabilities and Optical Rotations . . . . . . . . . . . . . 148
6.4.3 Stability Analysis . . . . . . . . . . . . . . . . . . . . . . . . . 149
6.4.4 Vertical Excitation and CD Spectra . . . . . . . . . . . . . . 149
6.4.5 Excited State Geometry Optimizations . . . . . . . . . . . . . 151
6.4.6 Excited State Force Constant Calculations. . . . . . . . . . . 152
6.4.7 Polarizability Derivatives and Raman Spectra . . . . . . . . . 152
7 Second-Order Approximate Coupled-Cluster (CC2) Calculations 154
7.1 CC2 Ground-State Energy Calculations . . . . . . . . . . . . . . . . 158
7.2 Calculation of Excitation Energies . . . . . . . . . . . . . . . . . . . 160
7.3 First-Order Properties and Gradients . . . . . . . . . . . . . . . . . . 163
7.3.1 Ground State Properties, Gradients and Geometries . . . . . 163
7.3.2 Excited State Properties, Gradients and Geometries . . . . . 166
7.3.3 Visualization of densities and Density analysis . . . . . . . . 168
7.3.4 Fast geometry optimizations with RI-SCF based gradients . . 170
CONTENTS 7
7.4 Transition Moments . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
7.5 RI-MP2-R12 Calculations . . . . . . . . . . . . . . . . . . . . . . . . 171
7.6 Parallel RI-MP2 and RI-CC2 Calculations . . . . . . . . . . . . . . . 172
7.7 Spin-component scaling approaches (SCS/SOS) . . . . . . . . . . . . 173
8 Calculation of Vibrational Frequencies and Vibrational Spectra 175
8.1 Analysis of Normal Modes in Terms of Internal Coordinates . . . . . 177
8.2 Calculation of Raman Spectra . . . . . . . . . . . . . . . . . . . . . . 178
8.3 Vibrational frequencies with fixed atoms using NumForce . . . . . 178
9 Calculation of NMR Shieldings 180
9.1 Prerequisites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
9.2 How to Perform a SCF of DFT Calculation . . . . . . . . . . . . . . 181
9.3 How to Perform a MP2 calculation . . . . . . . . . . . . . . . . . . . 181
9.4 Chemical Shifts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
9.5 Other Features and Known Limitations . . . . . . . . . . . . . . . . 182
10 Molecular Properties, Wavefunction Analysis, and Interfaces to Vi-
sualization Tools 183
10.1 Wavefunction analysis and Molecular Properties . . . . . . . . . . . 183
10.2 Interfaces to Visualization Tools . . . . . . . . . . . . . . . . . . . . 185
11 Treatment of Solvation Effects with Cosmo 189
12 Keywords in the control file 193
12.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
12.2 Format of Keywords and Comments . . . . . . . . . . . . . . . . . . 193
12.2.1 General Keywords . . . . . . . . . . . . . . . . . . . . . . . . 193
12.2.2 Keywords for System Specification . . . . . . . . . . . . . . . 195
12.2.3 Keywords for redundant internal coordinates in $redund inp 197
12.2.4 Keywords for Module Uff. . . . . . . . . . . . . . . . . . . . 199
12.2.5 Keywords for Modules Dscf and Ridft . . . . . . . . . . . . 203
12.2.6 Keywords for Periodic Electrostatic Embedded Cluster Method225
12.2.7 Keywords for Cosmo . . . . . . . . . . . . . . . . . . . . . . 226
8 CONTENTS
12.2.8 Keywords for Modules Grad and Rdgrad . . . . . . . . . . 229
12.2.9 Keywords for Module Aoforce . . . . . . . . . . . . . . . . 230
12.2.10Keywords for Module Escf . . . . . . . . . . . . . . . . . . . 232
12.2.11Keywords for Module Egrad . . . . . . . . . . . . . . . . . . 235
12.2.12Keywords for Modules Mpgrad and Rimp2. . . . . . . . . . 235
12.2.13Keywords for Module Ricc2 . . . . . . . . . . . . . . . . . . 238
12.2.14Keywords for Module Relax . . . . . . . . . . . . . . . . . . 246
12.2.15Keywords for Module Statpt . . . . . . . . . . . . . . . . . . 254
12.2.16Keywords for Module Moloch . . . . . . . . . . . . . . . . . 256
12.2.17Keywordsforwavefunctionanalysisandgenerationofplotting
data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260
12.2.18Keywords for Module Frog . . . . . . . . . . . . . . . . . . . 266
12.2.19Keywords for Module Mpshift . . . . . . . . . . . . . . . . . 271
12.2.20Keywords for Parallel Runs . . . . . . . . . . . . . . . . . . . 272
13 Sample control files 277
13.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
13.2 NH Input for a RHF Calculation. . . . . . . . . . . . . . . . . . . . 278
3
13.2.1 Main File control . . . . . . . . . . . . . . . . . . . . . . . . 278
13.2.2 File coord . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279
13.2.3 File basis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 280
13.2.4 File mos . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 280
13.3 NO input for an unrestricted DFT calculation . . . . . . . . . . . . 282
2
13.3.1 Main File control . . . . . . . . . . . . . . . . . . . . . . . . 282
13.3.2 File coord . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 284
13.3.3 File basis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 284
13.4 TaCl Input for an RI-DFT Calculation with ECPs. . . . . . . . . . 286
5
13.4.1 Main File control . . . . . . . . . . . . . . . . . . . . . . . . 286
13.4.2 File coord . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 287
13.4.3 File basis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 288
13.4.4 File auxbasis . . . . . . . . . . . . . . . . . . . . . . . . . . . 290
13.5 Basisset optimization for Nitrogen . . . . . . . . . . . . . . . . . . . 293
CONTENTS 9
13.5.1 Main File control . . . . . . . . . . . . . . . . . . . . . . . . 293
13.5.2 File coord . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 294
13.5.3 File basis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 294
13.5.4 File mos . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295
13.6 ROHF of Two Open Shells . . . . . . . . . . . . . . . . . . . . . . . 296
13.6.1 Extracts from control for O in D Symmetry . . . . . . . 296
2 3d
13.6.2 Extracts from control for O in D Symmetry . . . . . . . 297
2 2h
14 Samples for turbo.in files 299
14.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299
14.2 RI-MP2 calculation of Phenyl . . . . . . . . . . . . . . . . . . . . . . 299
14.3 Vibrational Spectrum of Phenyl . . . . . . . . . . . . . . . . . . . . . 300
14.4 DFT calculation of Benzene . . . . . . . . . . . . . . . . . . . . . . . 301
14.5 Aoforce calculation of Benzene . . . . . . . . . . . . . . . . . . . . 301
14.6 Uff calculation of Water . . . . . . . . . . . . . . . . . . . . . . . . 302
14.7 Potential curve for the O–H bond in H O . . . . . . . . . . . . . . . 303
2
14.8 Bending potential for Ag . . . . . . . . . . . . . . . . . . . . . . . . 303
3
15 The Perl-based Test Suite Structure 305
15.1 General . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 305
15.2 Running the tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 305
15.3 Taking the timings and benchmarking . . . . . . . . . . . . . . . . . 307
15.4 Modes and options of the Ttest script . . . . . . . . . . . . . . . . 307
Bibliography 311
Index 318
10 CONTENTS