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Q-Chem User’s Manual · PDF fileVersion 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

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  • Q-Chem Users Manual

    Version 4.0.1

    September, 2012

  • Version 4.0.1September, 2012

    Q-Chem Users 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 andDr. 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 andProf. 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 waswritten by:

    Dr. Jeremy DombroskiProf. Martin Head-GordonDr. Andrew Gilbert

    Published by: Customer Support:Q-Chem, Inc. Telephone: (412) 687-06955001 Baum Blvd Facsimile: (412) 687-0698Suite 690 email: support@q-chem.comPittsburgh, 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 November 14, 2012.

  • Copyright 2012 Q-Chem, Inc. This document is protected under the U.S. Copyright Act of1976 and state trade secret laws. Unauthorized disclosure, reproduction, distribution, or use isprohibited and may violate federal and state laws.

  • Contents

    1 Introduction 161.1 About This Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161.2 Chapter Summaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171.3 Contact Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

    1.3.1 Customer Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171.4 Q-Chem, Inc. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181.5 Company Mission . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181.6 Q-Chem Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

    1.6.1 New Features in Q-Chem 4.0.1 . . . . . . . . . . . . . . . . . . . . . . . . 181.6.2 New Features in Q-Chem 4.0 . . . . . . . . . . . . . . . . . . . . . . . . . 191.6.3 New Features in Q-Chem 3.2 . . . . . . . . . . . . . . . . . . . . . . . . . 221.6.4 New Features in Q-Chem 3.1 . . . . . . . . . . . . . . . . . . . . . . . . . 231.6.5 New Features in Q-Chem 3.0 . . . . . . . . . . . . . . . . . . . . . . . . . 241.6.6 Summary of Features Prior to Q-Chem 3.0 . . . . . . . . . . . . . . . . . . 26

    1.7 Current Development and Future Releases . . . . . . . . . . . . . . . . . . . . . . 281.8 Citing Q-Chem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28References and Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

    2 Installation 302.1 Q-Chem Installation Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . 30

    2.1.1 Execution Environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 302.1.2 Hardware Platforms and Operating Systems . . . . . . . . . . . . . . . . . 302.1.3 Memory and Hard Disk . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

    2.2 Installing Q-Chem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 322.3 Q-Chem Auxiliary files ($QCAUX ) . . . . . . . . . . . . . . . . . . . . . . . . . 322.4 Q-Chem Runtime Environment Variables . . . . . . . . . . . . . . . . . . . . . . 322.5 User Account Adjustments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 332.6 Further Customization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

    2.6.1 .qchemrc and Preferences File Format . . . . . . . . . . . . . . . . . . . . . 342.6.2 Recommendations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

    2.7 Running Q-Chem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352.7.1 Running Q-Chem in parallel . . . . . . . . . . . . . . . . . . . . . . . . . . 36

    2.8 IQmol Installation Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . 372.9 Testing and Exploring Q-Chem . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

    3 Q-Chem Inputs 403.1 IQmol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 403.2 General Form . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 403.3 Molecular Coordinate Input ($molecule) . . . . . . . . . . . . . . . . . . . . . . . 41

  • CONTENTS 6

    3.3.1 Reading Molecular Coordinates From a Previous Calculation . . . . . . . . 433.3.2 Reading Molecular Coordinates from Another File . . . . . . . . . . . . . . 44

    3.4 Cartesian Coordinates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 443.4.1 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

    3.5 Z -matrix Coordinates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 453.5.1 Dummy Atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

    3.6 Job Specification: The $rem Array Concept . . . . . . . . . . . . . . . . . . . . . 473.7 $rem Array Format in Q-Chem Input . . . . . . . . . . . . . . . . . . . . . . . . 483.8 Minimum $rem Array Requirements . . . . . . . . . . . . . . . . . . . . . . . . . 493.9 User-Defined Basis Sets ($basis) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 493.10 Comments ($comment) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 493.11 User-Defined Pseudopotentials ($ecp) . . . . . . . . . . . . . . . . . . . . . . . . . 493.12 User-defined Parameters for DFT Dispersion Correction ($empirical dispersion) . 503.13 Addition of External Charges ($external charges) . . . . . . . . . . . . . . . . . . 503.14 Intracules ($intracule) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 503.15 Isotopic Substitutions ($isotopes) . . . . . . . . . . . . . . . . . . . . . . . . . . . 503.16 Applying a Multipole Field ($multipole field) . . . . . . . . . . . . . . . . . . . . 503.17 Natural Bond Orbital Package ($nbo) . . . . . . . . . . . . . . . . . . . . . . . . 513.18 User-Defined Occupied Guess Orbitals ($occupied and $swap occupied virtual) . . 513.19 Geometry Optimization with General Constraints ($opt) . . . . . . . . . . . . . . 513.20 Polarizable Continuum Solvation Models ($pcm) . . . . . . . . . . . . . . . . . . 513.21 Effective Fragment Potential calculations ($efp fragmentsand $efp params) . . . 523.22 SS(V)PE Solvation Modeling ($svp and $svpirf ) . . . . . . . . . . . . . . . . . . 523.23 Orbitals, Densities and ESPs on a Mesh ($plots) . . . . . . . . . . . . . . . . . . 523.24 User-Defined van der Waals Radii ($van der waals) . . . . . . . . . . . . . . . . . 523.25 User-Defined Exchange-Correlation Density Functionals ($xc functional) . . . . . 523.26 Multiple Jobs in a Single File: Q-Chem Batch Job Files . . . . . . . . . . . . . . 533.27 Q-Chem Output File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 553.28 Q-Chem Scratch Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

    4 Self-Consistent Field Ground State Methods 564.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

    4.1.1 Overview of Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 564.1.2 Theoretical Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

    4.2 HartreeFock Calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 604.2.1 The Hartree-Fock Equations . . . . . . . . . . . . . . . . . . . . . . . . . . 604.2.2 Wavefunction Stability Analysis . . . . . . . . . . . . . . . . . . . . . . . . 614.2.3 Basic Hartree-Fock Job Control . . . . . . . . . . . . . . . . . . . . . . . . 624.2.4 Additional Hartree-Fock Job Control Options . . . . . . . . . . . . . . . . 654.2.5 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 684.2.6 Symmetry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

    4.3 Density Functional Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 704.3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 704.3.2 Kohn-Sham Density Functional Theory . . . . . . . . . . . . . . . . . . . . 714.3.3 Exchange-Correlation Functionals . . . . . . . . . . . . . . . . . . . . . . . 724.3.4 Long-Range-Corrected DFT . . . . . . . . . . . . . . .

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