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  • Q–Chem User’s Manual

    Version 3.2

    January 2009

  • Version 3.2 January 2009

    Q-Chem User’s Guide

    This version is edited by: Dr Yihan Shao

    with contributions from: Dr Nick Besley (Partial Hessian) Dr David Casanova (SF-XCIS) Dr Jeng-Da Chai (Variations of ωB97 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)

    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)

  • 3

    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 3.2 of Q-Chem. This document version generated on February 22, 2011.

  • © Copyright 2009 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 19

    1.1 About this Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

    1.2 Chapter Summaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

    1.3 Contact Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

    1.3.1 Customer Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

    1.4 Q-Chem, Inc. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

    1.5 Company Mission . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

    1.6 Q-Chem Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

    1.6.1 New Features in Q-Chem 3.2 . . . . . . . . . . . . . . . . . . . . . . . . . . 21

    1.6.2 New Features in Q-Chem 3.1 . . . . . . . . . . . . . . . . . . . . . . . . . . 22

    1.6.3 New Features in Q-Chem 3.0 . . . . . . . . . . . . . . . . . . . . . . . . . . 22

    1.6.4 Summary of Features Prior to Q-Chem 3.0 . . . . . . . . . . . . . . . . . . 25

    1.7 Current Development and Future Releases . . . . . . . . . . . . . . . . . . . . . . . 26

    1.8 Citing Q-Chem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

    2 Installation 28

    2.1 Q-Chem Installation Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

    2.1.1 Execution Environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

    2.1.2 Hardware Platforms and Operating Systems . . . . . . . . . . . . . . . . . . 28

    2.1.3 Memory and Hard Disk . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

    2.2 Installing Q-Chem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

    2.3 Environment Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

    2.4 User Account Adjustments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

    2.4.1 Example .login File Modifications . . . . . . . . . . . . . . . . . . . . . . . 30

    2.5 The qchem.setup File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

    2.6 Running Q-Chem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

    2.6.1 Serial Q-Chem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

    2.6.2 Parallel Q-Chem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

  • CONTENTS 6

    2.7 Testing and Exploring Q-Chem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

    3 Q-Chem Inputs 34

    3.1 General Form . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

    3.2 Molecular Coordinate Input ($molecule) . . . . . . . . . . . . . . . . . . . . . . . . 35

    3.2.1 Reading Molecular Coordinates From a Previous Calculation . . . . . . . . 36

    3.2.2 Reading molecular Coordinates from another file . . . . . . . . . . . . . . . 37

    3.3 Cartesian Coordinates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

    3.3.1 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

    3.4 Z–matrix Coordinates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

    3.4.1 Dummy atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

    3.5 Job Specification: The $rem Array Concept . . . . . . . . . . . . . . . . . . . . . . 40

    3.6 $rem Array Format in Q-Chem Input . . . . . . . . . . . . . . . . . . . . . . . . . 41

    3.7 Minimum $rem Array Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . 41

    3.8 User–defined basis set ($basis) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

    3.9 Comments ($comment) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

    3.10 User–defined Pseudopotentials ($ecp) . . . . . . . . . . . . . . . . . . . . . . . . . . 42

    3.11 User–defined parameters for DFT dispersion correction ($empirical dispersion) . . 42

    3.12 Addition of External Charges ($external charges) . . . . . . . . . . . . . . . . . . . 42

    3.13 Intracules ($intracule) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

    3.14 Isotopic substitutions ($isotopes) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

    3.15 Applying a Multipole Field ($multipole field) . . . . . . . . . . . . . . . . . . . . . 43

    3.16 Natural Bond Orbital Package ($nbo) . . . . . . . . . . . . . . . . . . . . . . . . . 43

    3.17 User–defined occupied guess orbitals ($occupied) . . . . . . . . . . . . . . . . . . . 43

    3.18 Geometry Optimization with General Constraints ($opt) . . . . . . . . . . . . . . . 43

    3.19 Polarizable Continuum Solvation Models ($pcm) . . . . . . . . . . . . . . . . . . . 44

    3.20 SS(V)PE Solvation Modeling ($svp and $svpirf ) . . . . . . . . . . . . . . . . . . . 44

    3.21 Orbitals, Densities and ESPs On a Mesh ($plots) . . . . . . . . . . . . . . . . . . . 44

    3.22 User–defined Van der Waals Radii ($van der waals) . . . . . . . . . . . . . . . . . 44

    3.23 User–defined exchange–correlation Density Functionals ($xc functional) . . . . . . 44

    3.24 Multiple Jobs in a Single File: Q-Chem Batch Job Files . . . . . . . . . . . . . . . 45

    3.25 Q-Chem Output File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

    3.26 Q-Chem Scratch Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

  • CONTENTS 7

    4 Self–Consistent Field Ground State Methods 48

    4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

    4.1.1 Overview of Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

    4.1.2 Theoretical Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

    4.2 Hartree–Fock Calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

    4.2.1 The Hartree–Fock Equations . . . . . . . . . . . . . . . . . . . . . . . . . . 52

    4.2.2 Wavefunction Stability Analysis . . . . . . . . . . . . . . . . . . . . . . . . 53

    4.2.3 Basic Hartree–Fock Job Control . . . . . . . . . . . . . . . . . . . . . . . . 54

    4.2.4 Additional Hartree–Fock Job Control Options . . . . . . . . . . . . . . . . . 57

    4.2.5 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

    4.2.6 Symmetry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

    4.3 Density Functional Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

    4.3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

    4.3.2 Kohn–Sham Density Functional Theory . . . . . . . . . . . . . . . . . . . . 62

    4.3.3 Exchange–Correlation Functionals . . . . . . . . . . . . . . . . . . . . . . . 64

    4.3.4 Long-range-corrected DFT . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

    4.3.5 Nonlocal correla