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Q–Chem User's Manual

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Q–Chem User's Manual Q{Chem User's Manual Version 3.0 March 2006 Version 3.0 April 2006 Q-Chem User's Guide This edition edited by: Dr Andrew Gilbert Contributions from: 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) Dr 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) Rohini Lochan (SOS and MOS{MP2) Prof. Vitaly Rassolov (Geminal Models) Ryan Steele (Dual basis methods) Dr Yihan Shao (Integral algorithm improvements, QM{MM and improved TS finder) This is a revised and expanded version of the previous (2.1) edition, written by: Dr Jeremy Dombroski Prof. Martin Head-Gordon Dr Andrew Gilbert Published by: Customer Support: Q-Chem, Inc. Telephone: (724) 325-9969 5001 Baum Blvd Facsimile: (724) 325-9560 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 3.0 of Q-Chem. This document version generated on May 5, 2006. Copyright 2006 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 1 1.1 About this Manual . 1 1.2 Chapter Summaries . 1 1.3 Contact Information . 2 1.3.1 Customer Support . 2 1.4 Q-Chem, Inc. 2 1.5 Company Mission . 2 1.6 Q-Chem Features . 3 1.6.1 New Features in Q-Chem 3.0 . 3 1.6.2 Summary of Existing Methods and Features . 5 1.7 Highlighted Features . 6 1.7.1 COLD PRISM . 7 1.7.2 Continuous Fast Multipole Method (CFMM) . 7 1.7.3 Parallel Computing . 7 1.7.4 Local MP2 . 7 1.7.5 High Level Coupled Cluster Methods . 7 1.7.6 Continuum Solvation Models . 8 1.7.7 Optimize . 8 1.7.8 Spartan . 8 1.8 Current Development and Future Releases . 8 1.9 Citing Q-Chem . 8 2 Installation 10 2.1 Q-Chem Installation Requirements . 10 2.1.1 Execution Environment . 10 2.1.2 Hardware Platforms and Operating Systems . 10 2.1.3 Memory and Hard Disk . 10 2.2 Installing Q-Chem . 11 CONTENTS iv 2.3 Environment Variables . 12 2.4 User Account Adjustments . 12 2.4.1 Example .login File Modifications . 12 2.5 The qchem.setup File . 13 2.6 Running Q-Chem . 13 2.6.1 Serial Q-Chem . 14 2.6.2 Parallel Q-Chem . 14 2.7 Testing and Exploring Q-Chem . 15 3 Q-Chem Inputs 16 3.1 General Form . 16 3.2 Molecular Coordinate Input ( ¡ molecule) . 17 3.2.1 Reading Molecular Coordinates From a Previous Calculation . 18 3.2.2 Reading molecular Coordinates from another file . 19 3.3 Cartesian Coordinates . 19 3.3.1 Examples . 19 3.4 Z {matrix Coordinates . 20 3.4.1 Dummy atoms . 22 3.5 Job Specification: The ¡ rem Array Concept . 22 3.6 ¡ rem Array Format in Q-Chem Input . 23 3.7 Minimum ¡ rem Array Requirements . 23 3.8 User–defined basis set ( ¡ basis) . 24 3.9 Comments ( ¡ comment) . 24 3.10 User–defined Pseudopotentials ( ¡ ecp) . 24 3.11 Addition of External Charges ( ¡ external charges) . 24 3.12 Intracules ( ¡ intracule) . 24 3.13 Isotopic substitutions ( ¡ isotopes) . 24 3.14 Applying a Multipole Field ( ¡ multipole field) . 25 3.15 Natural Bond Orbital Package ( ¡ nbo) . 25 3.16 User–defined occupied guess orbitals ( ¡ occupied) . 25 3.17 Geometry Optimization with General Constraints ( ¡ opt) . 25 ¡ 3.18 SS(V)PE Solvation Modeling ( ¡ svp and svpirf ) . 25 3.19 Orbitals, Densities and ESPs On a Mesh ( ¡ plots) . 26 3.20 User–defined Van der Waals Radii ( ¡ van der waals) . 26 3.21 User–defined exchange{correlation Density Functionals ( ¡ xc functional) . 26 3.22 Multiple Jobs in a Single File: Q-Chem Batch Job Files . 26 CONTENTS v 3.23 Q-Chem Output File . 28 3.24 Q-Chem Scratch Files . 29 4 Self{Consistent Field Ground State Methods 30 4.1 Introduction . 30 4.1.1 Overview of Chapter . 30 4.1.2 Theoretical Background . 31 4.2 Hartree{Fock Calculations . 33 4.2.1 The Hartree{Fock Equations . 33 4.2.2 Wavefunction Stability Analysis . 35 4.2.3 Basic Hartree{Fock Job Control . 36 4.2.4 Additional Hartree{Fock Job Control Options . 39 4.2.5 Examples . 41 4.2.6 Symmetry . 42 4.3 Density Functional Theory . 43 4.3.1 Introduction . 43 4.3.2 Kohn{Sham Density Functional Theory . 44 4.3.3 Exchange{Correlation Functionals . 45 4.3.4 DFT Numerical Quadrature . 47 4.3.5 Angular Grids . 47 4.3.6 Standard Quadrature Grids . 48 4.3.7 Consistency Check and Cutoffs for Numerical Integration . 49 4.3.8 Basic DFT Job Control . 49 4.3.9 User–Defined Density Functionals . 51 4.3.10 Example . 52 4.4 Large Molecules and Linear Scaling Methods . 52 4.4.1 Introduction . 52 4.4.2 Continuous Fast Multipole Method (CFMM) . 53 4.4.3 Linear Scaling Exchange (LinK) Matrix Evaluation . 55 4.4.4 Incremental and Variable Thresh Fock Matrix Building . 56 4.4.5 Incremental DFT . 57 4.4.6 Fourier Transform Coulomb Method . 59 4.4.7 Examples . 60 4.5 SCF Initial Guess . 61 4.5.1 Introduction . 61 4.5.2 Simple Initial Guesses . 62 CONTENTS vi 4.5.3 Reading MOs from Disk . 63 4.5.4 Modifying the Occupied Molecular Orbitals . 64 4.5.5 Basis Set Projection . 65 4.5.6 Examples . 66 4.6 Converging SCF Calculations . 68 4.6.1 Introduction . ..
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