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Q-Chem 4.0 User's Manual

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Q-Chem 4.0 User's Manual Q-Chem User's Manual Version 4.0.1 September, 2012 Version 4.0.1 September, 2012 Q-Chem User's Guide This version was edited by: Dr. Andrew Gilbert, Dr. Emil Proynov, and Prof. Anna Krylov Version 4.0 was edited by: Dr. Emil Proynov, Dr. Jing Kong, and Prof. John Herbert with contributions from those listed in the New Features Section 1.6.2 Version 3.2 was edited by: Dr. Yihan Shao with contributions from: Dr. Nick Besley (Partial Hessian) Dr. David Casanova (SF-XCIS) Dr. Jeng-Da Chai (Variations of !B97 functional) Dr. Deborah Crittenden (Wigner intracule) Dr. Evgeny Epifanovsky (Coupled-cluster parallelization) Prof. Steve Gwaltney (Onsager) Prof. John Herbert (LRC-DFT) Prof. Cherri Hsu (Electron transfer analysis) Dr. Rustam Khaliullin (ALMO, EDA, CTA) Dr. Ester Livshits (BNL functional) Dr. Alek Marenich (SM8) Prof. Young Min Rhee (SOS-CIS(D), SOS-CIS(D0)) Prof. David Sherrill (DFT-D) Dr. Vitalii Vanovschi (Distributed multipole analysis) Prof. Troy van Voorhis (Constrained DFT, Onsager, RCA) Dr. Lee Woodcock (QM/MM hessian) 3 Version 3.1 was edited by: Dr. Andrew Gilbert with contributions from: Dr. Greg Beran (Coupled-cluster active space methods) Prof. Dan Chipman and Dr. Shawn T. Brown (SS(V)PE solvation model) Dr. Laszlo Fusti-Molnar (Fourier Transform Coulomb Method) Prof. Martin Head-Gordon (Auxiliary bases, SOS MP2, perfect and imperfect pairing) Prof. John Herbert (Ab initio dynamics, Born-Oppenheimer dynamics) Dr. Jing Kong (Fast XC calculations) Prof. Anna Krylov (EOM methods) Dr. Joerg Kussman and Prof. Dr. Christian Ochsenfeld (Linear scaling NMR and optical properties) Dr. Ching Yeh Lin (Anharmonic Corrections) Dr. Rohini Lochan (SOS and MOS-MP2) Prof. Vitaly Rassolov (Geminal Models) Dr. Ryan Steele (Dual basis methods) Dr. Yihan Shao (Integral algorithm improvements, QM/MM and improved TS finder) Versions 3.1 and 3.2 are revisions and expansions based on version 2.1, which was written by: Dr. Jeremy Dombroski Prof. Martin Head-Gordon Dr. Andrew Gilbert Published by: Customer Support: Q-Chem, Inc. Telephone: (412) 687-0695 5001 Baum Blvd Facsimile: (412) 687-0698 Suite 690 email: [email protected] Pittsburgh, PA 15213 website: http://www.q-chem.com Q-Chem is a trademark of Q-Chem, Inc. All rights reserved. The information in this document applies to version 4.0.1 of Q-Chem. This document version generated on October 1, 2012. © Copyright 2012 Q-Chem, Inc. This document is protected under the U.S. Copyright Act of 1976 and state trade secret laws. Unauthorized disclosure, reproduction, distribution, or use is prohibited and may violate federal and state laws. Contents 1 Introduction 16 1.1 About This Manual . 16 1.2 Chapter Summaries . 17 1.3 Contact Information . 17 1.3.1 Customer Support . 17 1.4 Q-Chem, Inc. 18 1.5 Company Mission . 18 1.6 Q-Chem Features . 18 1.6.1 New Features in Q-Chem 4.0.1 . 18 1.6.2 New Features in Q-Chem 4.0 . 19 1.6.3 New Features in Q-Chem 3.2 . 22 1.6.4 New Features in Q-Chem 3.1 . 23 1.6.5 New Features in Q-Chem 3.0 . 24 1.6.6 Summary of Features Prior to Q-Chem 3.0 . 26 1.7 Current Development and Future Releases . 28 1.8 Citing Q-Chem ..................................... 28 References and Further Reading . 28 2 Installation 30 2.1 Q-Chem Installation Requirements . 30 2.1.1 Execution Environment . 30 2.1.2 Hardware Platforms and Operating Systems . 30 2.1.3 Memory and Hard Disk . 31 2.2 Installing Q-Chem ................................... 32 2.3 Q-Chem Auxiliary files ($QCAUX ) ......................... 32 2.4 Q-Chem Runtime Environment Variables . 32 2.5 User Account Adjustments . 33 2.6 Further Customization . 33 2.6.1 .qchemrc and Preferences File Format . 34 2.6.2 Recommendations . 34 2.7 Running Q-Chem ................................... 35 2.7.1 Running Q-Chem in parallel . 36 2.8 IQmol Installation Requirements . 37 2.9 Testing and Exploring Q-Chem ............................ 39 3 Q-Chem Inputs 40 3.1 IQmol .......................................... 40 3.2 General Form . 40 3.3 Molecular Coordinate Input ($molecule)....................... 41 CONTENTS 6 3.3.1 Reading Molecular Coordinates From a Previous Calculation . 43 3.3.2 Reading Molecular Coordinates from Another File . 44 3.4 Cartesian Coordinates . 44 3.4.1 Examples . 44 3.5 Z -matrix Coordinates . 45 3.5.1 Dummy Atoms . 47 3.6 Job Specification: The $rem Array Concept . 47 3.7 $rem Array Format in Q-Chem Input . 48 3.8 Minimum $rem Array Requirements . 49 3.9 User-Defined Basis Sets ($basis)............................ 49 3.10 Comments ($comment)................................. 49 3.11 User-Defined Pseudopotentials ($ecp)......................... 49 3.12 User-defined Parameters for DFT Dispersion Correction ($empirical dispersion) . 50 3.13 Addition of External Charges ($external charges).................. 50 3.14 Intracules ($intracule) ................................. 50 3.15 Isotopic Substitutions ($isotopes)........................... 50 3.16 Applying a Multipole Field ($multipole field) .................... 50 3.17 Natural Bond Orbital Package ($nbo) ........................ 51 3.18 User-Defined Occupied Guess Orbitals ($occupied and $swap occupied virtual) . 51 3.19 Geometry Optimization with General Constraints ($opt) . 51 3.20 Polarizable Continuum Solvation Models ($pcm) .................. 51 3.21 Effective Fragment Potential calculations ($efp fragmentsand $efp params) . 52 3.22 SS(V)PE Solvation Modeling ($svp and $svpirf ) .................. 52 3.23 Orbitals, Densities and ESPs on a Mesh ($plots) .................. 52 3.24 User-Defined van der Waals Radii ($van der waals) . 52 3.25 User-Defined Exchange-Correlation Density Functionals ($xc functional) . 52 3.26 Multiple Jobs in a Single File: Q-Chem Batch Job Files . 53 3.27 Q-Chem Output File . 55 3.28 Q-Chem Scratch Files . 55 4 Self-Consistent Field Ground State Methods 56 4.1 Introduction . 56 4.1.1 Overview of Chapter . 56 4.1.2 Theoretical Background . 57 4.2 Hartree{Fock Calculations . 60 4.2.1 The Hartree-Fock Equations . 60 4.2.2 Wavefunction Stability Analysis . 61 4.2.3 Basic Hartree-Fock Job Control . 62 4.2.4 Additional Hartree-Fock Job Control Options . 65 4.2.5 Examples . 68 4.2.6 Symmetry . 69 4.3 Density Functional Theory . 70 4.3.1 Introduction . 70 4.3.2 Kohn-Sham Density Functional Theory . 71 4.3.3 Exchange-Correlation Functionals . 72 4.3.4 Long-Range-Corrected DFT . 77 4.3.5 Nonlocal Correlation Functionals . 87 4.3.6 DFT-D Methods . 89 4.3.7 XDM DFT Model of Dispersion . 91 CONTENTS 7 4.3.8 DFT-D3 Methods . 95 4.3.9 Double-Hybrid Density Functional Theory . 98 4.3.10 Asymptotically Corrected Exchange-Correlation Potentials . 103 4.3.11 DFT Numerical Quadrature . 104 4.3.12 Angular Grids . 105 4.3.13 Standard Quadrature Grids . 105 4.3.14 Consistency Check and Cutoffs for Numerical Integration . 106 4.3.15 Basic DFT Job Control . 107 4.3.16 Example . 112 4.3.17 User-Defined Density Functionals . 112 4.4 Large Molecules and Linear Scaling Methods . 115 4.4.1 Introduction . 115 4.4.2 Continuous Fast Multipole Method (CFMM) . 116 4.4.3 Linear Scaling Exchange (LinK) Matrix Evaluation . 118 4.4.4 Incremental and Variable Thresh Fock Matrix Building . 119 4.4.5 Incremental DFT . 120 4.4.6 Fourier Transform Coulomb Method . 122 4.4.7 Multiresolution Exchange-Correlation (mrXC) Method . 124 4.4.8 Examples . 126 4.5 SCF Initial Guess . 127 4.5.1 Introduction . 127 4.5.2 Simple Initial Guesses . 127 4.5.3 Reading MOs from Disk . 129 4.5.4 Modifying the Occupied Molecular Orbitals . 129 4.5.5 Basis Set Projection . 131 4.5.6 Examples . 133 4.6 Converging SCF Calculations . 135 4.6.1 Introduction . 135 4.6.2 Basic Convergence Control Options . 135 4.6.3 Direct Inversion in the Iterative Subspace (DIIS) . 137 4.6.4 Geometric Direct Minimization (GDM) . 139 4.6.5 Direct Minimization (DM) . 140 4.6.6 Maximum Overlap Method (MOM) . 140 4.6.7 Relaxed Constraint Algorithm (RCA) . 141 4.6.8 Examples . 143 4.7 Dual-Basis Self-Consistent Field Calculations . ..
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