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1
Introduction
1.1
About This Manual
1.1.1
Overview
1.1.2
Chapter Summaries
1.2
Q-Chem
, Inc.
1.2.1
Contact Information and Customer Support
1.2.2
About the Company
1.2.3
Company Mission
1.3
Q-Chem
Features
1.3.1
Overview of
Q-Chem
Features
1.3.2
New Features in
Q-Chem
6.1
1.3.3
New Features in
Q-Chem
6.0
1.3.4
New Features in
Q-Chem
5.4
1.3.5
New Features in
Q-Chem
5.3
1.3.6
New Features in
Q-Chem
5.2
1.3.7
New Features in
Q-Chem
5.1
1.3.8
New Features in
Q-Chem
5.0
1.3.9
New Features in
Q-Chem
4.4
1.3.10
New Features in
Q-Chem
4.3
1.3.11
New Features in
Q-Chem
4.2
1.3.12
New Features in
Q-Chem
4.1
1.3.13
New Features in
Q-Chem
4.0.1
1.3.14
New Features in
Q-Chem
4.0
1.3.15
Summary of Features in
Q-Chem
versions 3.
x
1.3.16
Summary of Features Prior to
Q-Chem
3.0
1.4
Citing
Q-Chem
1.4.1
Overview
2
Installation, Customization, and Execution
2.1
Installing
Q-Chem
2.1.1
Downloading and Licensing
2.1.2
Installation Requirements
2.1.3
Q-Chem
Auxiliary files (
$QCAUX
)
2.1.4
Q-Chem
Run-time Environment Variables
2.1.5
User Account Adjustments
2.1.6
Further Customization
2.2
Running
Q-Chem
2.2.1
General Usage
2.2.2
Integration with
IQmol
2.2.3
Testing and Exploring
Q-Chem
3
Q-Chem
Inputs
3.1
IQmol
3.1.1
Overview
3.2
General Form
3.2.1
Overview
3.3
Molecular Coordinate Input (
$molecule
)
3.3.1
Introduction
3.3.2
Specifying the Molecular Coordinates Manually
3.3.3
Reading Molecular Coordinates from a Previous Job or File
3.4
Job Specification: The
$rem
Input Section
3.4.1
Overview
3.5
Multiple Jobs in a Single File:
Q-Chem
Batch Jobs
3.5.1
Overview
3.6
Q-Chem
Output File
3.6.1
Overview
4
Self-Consistent Field Ground-State Methods
4.1
Introduction
4.1.1
Overview
4.2
Theoretical Background
4.2.1
SCF and LCAO Approximations
4.2.2
Hartree-Fock Theory
4.3
Basic SCF Job Control
4.3.1
Introduction
4.3.2
Job Control
4.3.3
Additional Options
4.3.4
Examples
4.3.5
Symmetry
4.4
SCF Initial Guess
4.4.1
Introduction
4.4.2
Initial Guess Types
4.4.3
Reading MOs from Disk
4.4.4
Modifying the Occupied Molecular Orbitals
4.4.5
Basis Set Projection
4.5
Converging SCF Calculations
4.5.1
Introduction
4.5.2
Basic Convergence Control Options
4.5.3
Direct Inversion in the Iterative Subspace (DIIS)
4.5.4
Damping
4.5.5
Level-Shifting
4.5.6
Pseudo-Fractional Occupation Number Method (pFON)
4.5.7
Geometric Direct Minimization (GDM)
4.5.8
Direct Minimization (DM)
4.5.9
Relaxed Constraint Algorithm (RCA)
4.5.10
Augmented Roothaan Hall Energy DIIS (ADIIS)
4.5.11
Newton Methods
4.5.12
User-Customized Hybrid SCF Algorithm
4.5.13
Maximum Overlap Method (MOM)
4.5.14
Square Gradient Minimization (SGM)
4.5.15
State-Targeted Energy Projection (STEP)
4.5.16
Internal Stability Analysis and Automated Correction for Energy Minima
4.6
Large Molecules and Linear Scaling Methods
4.6.1
Introduction
4.6.2
Continuous Fast Multipole Method (CFMM)
4.6.3
Linear Scaling Exchange (LinK) Matrix Evaluation
4.6.4
Incremental and Variable Thresh Fock Matrix Building
4.6.5
Fourier Transform Coulomb Method
4.6.6
Resolution of the Identity Fock Matrix Methods
4.6.7
PARI-K Fast Exchange Algorithm
4.6.8
occ-RI-K Exchange Algorithm
4.7
Dual-Basis Self-Consistent Field Calculations
4.7.1
Introduction
4.7.2
Dual-Basis MP2
4.7.3
Dual-Basis Dynamics
4.7.4
Basis-Set Pairings
4.7.5
Job Control and Example
4.8
Hartree-Fock and Density-Functional Perturbative Corrections
4.8.1
Introduction
4.8.2
Job Control
4.8.3
Examples
4.9
Unconventional SCF Calculations
4.9.1
Polarized Atomic Orbital (PAO) Calculations
4.9.2
SCF Metadynamics
4.9.3
Multiple SCF Solutions for Non-Orthogonal CI
4.9.4
Holomorphic Hartree-Fock Theory
4.9.5
Non-Hermitian SCF with complex basis functions
4.9.6
Scalar Relativistic Effects
5
Density Functional Theory
5.1
Introduction
5.1.1
Overview
5.2
Kohn-Sham Density Functional Theory
5.3
Overview of Available Functionals
5.3.1
Introduction
5.3.2
Suggested Density Functionals
5.3.3
Exchange Functionals
5.3.4
Correlation Functionals
5.3.5
Exchange-Correlation Functionals
5.3.6
Specialized Functionals
5.3.7
User-Defined Density Functionals
5.3.8
Semi-Empirical Functionals
5.4
Basic DFT Job Control
5.4.1
Overview
5.5
DFT Numerical Quadrature
5.5.1
Introduction
5.5.2
Angular Grids
5.5.3
Standard Quadrature Grids
5.5.4
Consistency Check and Cutoffs
5.5.5
Multi-resolution Exchange-Correlation (MRXC) Method
5.5.6
Incremental DFT
5.6
Range-Separated Hybrid Density Functionals
5.6.1
Introduction
5.6.2
Semi-Empirical RSH Functionals
5.6.3
User-Defined RSH Functionals
5.6.4
Tuned RSH Functionals
5.7
DFT Methods for van der Waals Interactions
5.7.1
Introduction
5.7.2
Non-Local Correlation (NLC) Functionals
5.7.3
Empirical Dispersion Corrections: DFT-D
5.7.4
Exchange-Dipole Model (XDM)
5.7.5
Tkatchenko-Scheffler van der Waals Model (TS-vdW)
5.7.6
Many-Body Dispersion (MBD) Method
5.8
Empirical Corrections for Basis Set Superposition Error
5.8.1
Overview
5.9
Double-Hybrid Density Functional Theory
5.9.1
Overview
5.10
Asymptotically Corrected Exchange-Correlation Potentials
5.10.1
Introduction
5.10.2
LB94 Scheme
5.10.3
Localized Fermi-Amaldi (LFA) Schemes
5.11
Methods Based on “Constrained” DFT
5.11.1
Introduction
5.11.2
Manner of Counting Electrons
5.11.3
Job Control
5.11.4
Examples
5.11.5
Configuration Interaction with Constrained DFT (CDFT-CI)
5.11.6
CDFT-CI Job Control and Examples
5.12
Unconventional DFT Methods
5.12.1
Density-Corrected DFT
5.12.2
Derivative Discontinuity Restoration
5.12.3
Thermally-Assisted-Occupation (TAO) DFT
6
Wave Function-Based Correlation Methods
6.1
Introduction
6.1.1
Overview
6.2
Treatment and the Definition of Core Electrons
6.2.1
Overview
6.3
Møller-Plesset Perturbation Theory
6.3.1
Overview
6.4
Exact MP2 Methods
6.4.1
Algorithm
6.4.2
Algorithm Control and Customization
6.5
Local MP2 Methods
6.5.1
Local Triatomics in Molecules (TRIM) Model
6.5.2
EPAO Evaluation Options
6.6
Auxiliary Basis (Resolution of the Identity) MP2 Methods
6.6.1
Introduction
6.6.2
RI-MP2 Energies and Gradients.
6.6.3
OpenMP Implementation of RI-MP2
6.6.4
GPU Implementation of RI-MP2
6.6.5
Spin-Biased MP2 Methods (SCS-MP2, SOS-MP2, and MOS-MP2)
6.6.6
Orbital-Optimized MP2
6.6.7
Brueckner CC2
6.6.8
RI-TRIM MP2 Energies
6.6.9
Dual-Basis MP2
6.6.10
RI-MP2 Method for Complex Basis Functions
6.6.11
RI-MP2 Method with the Laplace Transformation
6.7
Attenuated MP2
6.7.1
Overview
6.8
Direct Random Phase Approximation Methods
6.8.1
Introduction
6.8.2
dRPA Job Control
6.9
Resolution-of-Identity MP3
6.9.1
Introduction
6.9.2
RI-MP3 Job Control
6.9.3
Examples
6.10
Coupled-Cluster Methods
6.10.1
Introduction
6.10.2
Coupled Cluster Singles and Doubles (CCSD)
6.10.3
Coupled Cluster Singles, Doubles and Triples (CCSDT)
6.10.4
Second-Order Approximate Coupled Cluster Singles and Doubles (CC2)
6.10.5
Quadratic Configuration Interaction (QCISD)
6.10.6
Optimized Orbital Coupled Cluster Doubles (OD)
6.10.7
Quadratic Coupled Cluster Doubles (QCCD)
6.10.8
Resolution of the Identity with CC (RI-CC)
6.10.9
Cholesky Decomposition with CC (CD-CC)
6.10.10
Job Control Options
6.10.11
Examples
6.11
Non-Iterative Corrections to Coupled Cluster Energies
6.11.1
(T) Triples Corrections
6.11.2
(2) Triples and Quadruples Corrections
6.11.3
(dT) and (fT) corrections
6.11.4
Job Control Options
6.11.5
Examples
6.12
Coupled Cluster Active Space Methods
6.12.1
Introduction
6.12.2
VOD and VOD(2) Methods
6.12.3
VQCCD
6.12.4
CCVB-SD
6.12.5
Local Pair Models for Valence Correlations Beyond Doubles
6.12.6
Convergence Strategies and More Advanced Options
6.13
Frozen Natural Orbitals in CCD, CCSD, OD, QCCD, and QCISD Calculations
6.13.1
Overview
6.14
Non-Hartree-Fock Orbitals in Correlated Calculations
6.14.1
Overview
6.15
Analytic Gradients and Properties for Coupled-Cluster Methods
6.15.1
Overview
6.16
Memory Options and Parallelization of Coupled-Cluster Calculations
6.16.1
Introduction
6.16.2
Serial and Shared Memory Parallel Jobs
6.16.3
Distributed Memory Parallel Jobs
6.16.4
Summary of Keywords
6.17
Using Single-Precision Arithmetic in Coupled-Cluster Calculations
6.17.1
Overview
6.18
Simplified Coupled-Cluster Methods Based on a Perfect-Pairing Active Space
6.18.1
Introduction
6.18.2
Perfect pairing (PP)
6.18.3
Coupled Cluster Valence Bond (CCVB)
6.18.4
Second-Order Correction to Perfect Pairing: PP(2)
6.18.5
Other GVBMAN Methods and Options
6.19
Complete Active Space Methods
6.19.1
Introduction
6.19.2
Theory
6.19.3
CAS-CI and CASSCF Job Control
6.20
Incremental Correlation Methods
6.20.1
Introduction
6.20.2
Theory
6.20.3
Job Control for iFCI
6.20.4
Example
6.21
Adaptive Sampling Configuration Interaction Method
6.21.1
Introduction
6.21.2
Theory
6.21.3
ASCI Job Control
6.22
Variational Two-Electron Reduced-Density-Matrix Methods
6.22.1
Introduction
6.22.2
Theory
6.22.3
v2RDM Job Control
6.22.4
Examples
7
Open-Shell and Excited-State Methods
7.1
General Excited-State Features
7.1.1
Overview
7.2
Uncorrelated Wave Function Methods
7.2.1
Introduction
7.2.2
Single Excitation Configuration Interaction (CIS)
7.2.3
Random Phase Approximation (RPA)
7.2.4
Extended CIS (XCIS)
7.2.5
Spin-Flip Extended CIS (SF-XCIS)
7.2.6
Spin-Adapted Spin-Flip CIS
7.2.7
CIS Analytical Derivatives
7.2.8
Basic CIS Job Control Options
7.2.9
CIS Job Customization
7.3
Time-Dependent Density Functional Theory (TDDFT)
7.3.1
Brief Introduction to TDDFT
7.3.2
TDDFT within a Reduced Single-Excitation Space
7.3.3
Job Control for TDDFT
7.3.4
TDDFT + PCM for Excitation and Emission Energies in Solution
7.3.5
Analytic Excited-State Hessian in TDDFT
7.3.6
Calculations of Spin-Orbit Couplings Between TDDFT States
7.3.7
Various TDDFT-Based Examples
7.4
Real-Time SCF Methods
7.4.1
Introduction
7.4.2
Theory
7.4.3
Job Control
7.4.4
Calculation of Absorption Spectra
7.5
Non-Orthogonal Configuration Interaction (NOCI)
7.5.1
Introduction
7.5.2
Job Control
7.6
Maximum Overlap Method (MOM) for
Δ
SCF Excited States
7.6.1
Overview
7.7
Non-Orthogonal Configuration Interaction with Single Substitutions (NOCIS) and Static Exchange (STEX)
7.7.1
NOCIS
7.7.2
Static Exchange
7.7.3
One-Center NOCIS (1C-NOCIS)
7.8
Electron-Affinity Time-Dependent Density Functional Theory (EA-TDDFT)
7.8.1
Job Control
7.9
Restricted Open-Shell and
Δ
SCF Methods
7.9.1
Introduction
7.9.2
Approximate Spin Purification
7.9.3
Restricted Open-Shell Kohn-Sham Method (ROKS)
7.9.4
Squared-Gradient Minimization
7.9.5
State-Targeted Energy Projection
7.9.6
Non-equilibrium Solvation for ROKS and
Δ
SCF Methods
7.10
Correlated Excited State Methods: The CIS(D) Family
7.10.1
Introduction
7.10.2
CIS(D) Theory
7.10.3
Resolution of the Identity CIS(D) Methods
7.10.4
SOS-CIS(D) Model
7.10.5
SOS-CIS(D
0
) Model
7.10.6
CIS(D) Job Control and Examples
7.10.7
RI-CIS(D), SOS-CIS(D), and SOS-CIS(D
0
): Job Control
7.10.8
Examples
7.11
Coupled-Cluster Excited-State and Open-Shell Methods
7.11.1
Introduction
7.11.2
Excited States via EOM-EE-CCSD
7.11.3
EOM-XX-CCSD and CI Suite of Methods
7.11.4
EOM-XX-CC2
7.11.5
Spin-Flip Methods for Di- and Triradicals
7.11.6
EOM-DIP-CCSD
7.11.7
EOM-DEA-CCSD
7.11.8
EOM-CC Calculations of Core-Level States
7.11.9
EOM-CC Calculations of Metastable States
7.11.10
Auger Spectra and Lifetimes of Core-Level States
7.11.11
Partial Auger Decay Widths from Complex-Variable Calculations
7.11.12
Charge Stabilization for EOM-DIP and Other Methods
7.11.13
Frozen Natural Orbitals in CC, IP-CC, and SF-CC Calculations
7.11.14
Single-Precision Arithmetic in EOM-CC Calculations
7.11.15
Approximate EOM-CC Methods: EOM-MP2 and EOM-MP2T
7.11.16
Approximate EOM-CC Methods: EOM-CCSD-S(D) and EOM-MP2-S(D)
7.11.17
EOM-CC Guess Formation and Iterative Diagonalization
7.11.18
EOM-CC Job Control
7.11.19
Examples
7.11.20
Non-Hartree-Fock Orbitals in EOM Calculations
7.11.21
Analytic Gradients and State and Transition Properties for the CCSD and EOM-XX-CCSD Methods
7.11.22
EOM-CC Optimization and Properties Job Control
7.11.23
EOM(2,3) Methods for Higher-Accuracy and Problematic Situations (CCMAN only)
7.11.24
Active-Space EOM-CC(2,3): Tricks of the Trade (CCMAN only)
7.11.25
Job Control for EOM-CC(2,3)
7.11.26
Non-Iterative Triples Corrections to EOM-CCSD and CCSD
7.11.27
Potential Energy Surface Crossing Minimization
7.11.28
Dyson Orbitals for Ionized or Attached States within the EOM-CCSD Formalism
7.11.29
Interpretation of EOM/CI Wave Functions and Orbital Numbering
7.11.30
Interface with OpenFermion package for quantum computing
7.12
Correlated Excited State Methods: The ADC(
n
) Family
7.12.1
Introduction
7.12.2
The Algebraic Diagrammatic Construction (ADC) Scheme
7.12.3
IP- and EA-ADC
7.12.4
Resolution of the Identity ADC Methods
7.12.5
Spin Opposite Scaling ADC(2) Models
7.12.6
Core-Excitation ADC Methods
7.12.7
Spin-Flip ADC Methods
7.12.8
CAP/ADC Methods for the Description of Metastable Electronic States
7.12.9
Properties and Visualization
7.12.10
Excited States in Solution with ADC/SS-PCM
7.12.11
Frozen-Density Embedding: FDE-ADC methods
7.12.12
ADC Job Control
7.12.13
Examples
7.13
Restricted Active Space Spin-Flip (RAS-SF) and Configuration Interaction (RAS-CI)
7.13.1
Introduction
7.13.2
The Restricted Active Space (RAS) Scheme
7.13.3
Second-Order Perturbative Corrections to RAS-CI
7.13.4
Short-Range Density Functional Correlation within RAS-CI
7.13.5
Excitonic Analysis of the RAS-CI Wave Function
7.13.6
Diabatization of RAS-CI Eigenstates
7.13.7
Spin-flip CAS with Perturbative External Singles Corrections (
casman
)
7.13.8
Direct RAS-nSF-IP/EA (
librassf
)
7.13.9
librassf
Effective Hamiltonian Analysis
7.13.10
State-Specific PCM with RAS-SF
7.13.11
Job Control for the RASCI1 Implementation
7.13.12
Job Control Options for RASCI2
7.13.13
Job Control Options for
casman
7.13.14
Job Control Options for
librassf
7.13.15
Examples
7.14
Core Ionization Energies and Core-Excited States
7.14.1
Many-Body Methods for Core-Excited States
7.14.2
Calculations of X-Ray Spectroscopy with TDDFT
7.14.3
Methods Based on Kohn-Sham Eigenvalues
7.14.4
Calculations of Core Excitations with ROKS
7.15
Visualization of Excited States
7.15.1
Introduction
7.15.2
Attachment/Detachment Density Analysis
7.15.3
Natural Transition Orbitals
8
Basis Sets and Effective Core Potentials
8.1
Introduction to Basis Sets
8.1.1
Overview
8.2
Built-In Basis Sets
8.2.1
Overview
8.3
Basis Set Symbolic Representation
8.3.1
Symbolic Representation Overview
8.3.2
Customization
8.4
User-Defined Basis Sets (
$basis
)
8.4.1
Introduction
8.4.2
Job Control
8.4.3
Format for User-Defined Basis Sets
8.5
Mixed Basis Sets
8.5.1
Overview
8.6
Dual Basis Sets
8.6.1
Overview
8.7
Complex Basis Sets
8.7.1
Overview
8.8
Auxiliary Basis Sets for RI (Density Fitting)
8.8.1
Overview
8.9
Ghost Atoms and Basis Set Superposition Error
8.9.1
Overview
8.10
Introduction to Effective Core Potentials (ECPs)
8.10.1
Overview
8.11
ECP Fitting
8.11.1
Overview
8.12
Built-In ECPs
8.12.1
Introduction
8.12.2
Combining ECPs
8.12.3
Examples
8.13
User-Defined ECPs
8.13.1
Overview
8.14
ECPs and Electron Correlation
8.14.1
Overview
8.15
Forces and Vibrational Frequencies with ECPs
8.15.1
Overview
8.16
A Brief Guide to
Q-Chem
’s Built-In ECPs
8.16.1
Introduction
8.16.2
The fit-HWMB ECP at a Glance
8.16.3
The fit-LANL2DZ ECP at a Glance
8.16.4
The fit-SBKJC ECP at a Glance
8.16.5
The fit-CRENBS ECP at a Glance
8.16.6
The fit-CRENBL ECP at a Glance
8.16.7
The SRLC ECP at a Glance
8.16.8
The SRSC ECP at a Glance
8.16.9
The Karlsruhe “def2” ECP at a Glance
9
Exploring Potential Energy Surfaces: Critical Points and Molecular Dynamics
9.1
Equilibrium Geometries and Transition-State Structures with
Q-Chem
9.1.1
Introduction
9.1.2
Theoretical Background
9.1.3
Eigenvector-Following (EF) Algorithm
9.1.4
Delocalized Internal Coordinates
9.1.5
Constrained Optimization
9.1.6
Constrained Optimization in Delocalized Internal Coordinates
9.1.7
GDIIS
9.2
Geometry Optimization Job Controls
9.2.1
Job Control Overview
9.2.2
Optimize
Job Control
9.2.3
Hessian-Free Characterization of Stationary Points
9.2.4
Optimize
Job Examples
9.2.5
Libopt3
Job Control
9.2.6
Libopt3
Job Examples
9.3
Improved Algorithms for Transition-Structure Optimization
9.3.1
Introduction
9.3.2
Freezing String Method
9.3.3
Hessian-Free Transition-State Search
9.3.4
Improved Dimer Method
9.4
Constrained Optimization
9.4.1
Introduction
9.4.2
Geometry Optimization with General Constraints
9.4.3
Frozen Atoms
9.4.4
Dummy Atoms
9.4.5
Dummy Atom Placement in Dihedral Constraints
9.4.6
Additional Atom Connectivity
9.4.7
Atomic Confining Potentials as Alternatives to Constrained Optimization
9.5
Application of Pressure
9.5.1
Introduction
9.5.2
Hydrostatic Compression Force Field (HCFF)
9.5.3
eXtended Hydrostatic Compression Force Field (X-HCFF)
9.5.4
Gaussians On Surface Tesserae Simulate HYdrostatic Pressure (GOSTSHYP)
9.6
Application of External Forces (EFEI)
9.6.1
Overview
9.7
Potential Energy Scans
9.7.1
Overview
9.8
Intrinsic Reaction Coordinate
9.8.1
Overview
9.9
Nonadiabatic Couplings and Optimization of Minimum-Energy Crossing Points
9.9.1
Nonadiabatic Couplings
9.9.2
Job Control and Examples
9.9.3
Minimum-Energy Crossing Points
9.9.4
Job Control and Examples
9.9.5
State-Tracking Algorithm
9.10
Ab Initio
Molecular Dynamics
9.10.1
Introduction
9.10.2
Overview and Basic Job Control
9.10.3
Additional Job Control and Examples
9.10.4
Thermostats: Sampling the
NVT
Ensemble
9.10.5
Vibrational Spectra
9.10.6
Quasi-Classical Molecular Dynamics
9.10.7
Fewest-Switches Surface Hopping
9.10.8
Meyer-Miller Nonadiabatic Dynamics
9.11
Ab Initio
Path Integrals
9.11.1
Theory
9.11.2
Job Control and Examples
9.12
Ab Initio
Molecular Dynamics with Complex Absorbing Potentials
9.12.1
Introduction
9.12.2
Some tips for finding electronic resonance states of temporary anions with the CAP-HF method
9.12.3
CAP-AIMD job control and examples
9.13
Optimizing the Structure of Clusters
9.13.1
Introduction
9.13.2
Cluster Optimization Job Control
10
Molecular Properties and Analysis
10.1
Introduction
10.1.1
Overview
10.2
Wave Function Analysis
10.2.1
Introduction
10.2.2
Atomic Partial Charges
10.2.3
Multipole Moments
10.2.4
Symmetry Decomposition
10.2.5
Localized Orbital Bonding Analysis
10.2.6
Oxidation State Localized Orbitals
10.2.7
Intrinsic Atomic Orbitals
10.2.8
Basic Excited-State Analysis of CIS and TDDFT Wave Functions
10.2.9
General Excited-State Analysis
10.3
Orbital Analysis
10.3.1
Interface to the NBO Package
10.3.2
Orbital Localization
10.3.3
Donor–Acceptor Orbital Overlaps
10.4
Density Analysis
10.4.1
Spin and Charge Densities at the Nuclei
10.4.2
Atoms in Molecules
10.5
Visualizing and Plotting Volumetric Quantities
10.5.1
Introduction
10.5.2
Visualizing Orbitals Using
MolDen
and
MacMolPlt
10.5.3
Visualization of Natural Transition Orbitals
10.5.4
Generation of Volumetric Data Using
$plots
10.5.5
Direct Generation of “Cube” Files
10.5.6
Noncovalent Interactions (NCI) Plots
10.5.7
Electron Localization Function
10.5.8
Electrostatic Potentials
10.6
Electric Fields
10.6.1
Overview
10.7
Harmonic Vibrational Analysis
10.7.1
Introduction
10.7.2
Treatment of Low-Frequency Vibrational Modes
10.7.3
Isotopic Substitutions
10.7.4
Partial Hessian Vibrational Analysis
10.7.5
Localized Mode Vibrational Analysis
10.7.6
Resonance Raman intensities
10.7.7
Vibrationally-Resolved Electronic Spectra and Resonance Raman Simulations
10.8
Anharmonic Vibrational Frequencies
10.8.1
Introduction
10.8.2
Vibration Configuration Interaction Theory
10.8.3
Vibrational Perturbation Theory
10.8.4
Transition-Optimized Shifted Hermite Theory
10.8.5
Job Control
10.9
Linear-Scaling Computation of Electric Properties
10.9.1
Introduction
10.9.2
$fdpfreq
Input Section
10.9.3
Job Control for the MOProp Module
10.9.4
Examples
10.10
NMR and Other Magnetic Properties
10.10.1
Introduction
10.10.2
NMR Chemical Shifts and
J
-Couplings
10.10.3
Linear-Scaling NMR Chemical Shift Calculations
10.10.4
Additional Magnetic Field-Related Properties
10.11
Vibrational Circular Dichroism (VCD)
10.11.1
Introduction
10.12
Finite-Field Calculation of (Hyper)Polarizabilities
10.12.1
Introduction
10.12.2
Numerical Calculation of Static Polarizabilities
10.12.3
Romberg Finite-Field Procedure
10.13
General Response Theory
10.13.1
Introduction
10.13.2
Job Control
10.13.3
$response
Section and Operator Specification
10.13.4
Examples Including
$response
Section
10.14
Electronic Couplings for Electron- and Energy Transfer
10.14.1
Eigenstate-Based Methods
10.14.2
Diabatic-State-Based Methods
10.14.3
Fragment-Based Methods for Electronic Coupling
10.15
Population of Effectively Unpaired Electrons
10.15.1
Overview
11
Molecules in Complex Environments: Solvent Models, QM/MM and QM/EFP Features, Density Embedding
11.1
Introduction
11.1.1
Overview
11.2
Chemical Solvent Models
11.2.1
Introduction
11.2.2
Kirkwood-Onsager Multipole Expansion Method
11.2.3
Polarizable Continuum Models
11.2.4
PCM Job Control
11.2.5
Linear-Scaling QM/MM/PCM Calculations
11.2.6
Isodensity Implementation of SS(V)PE
11.2.7
Composite Method for Implicit Representation of Solvent (CMIRS)
11.2.8
COSMO
11.2.9
SM
x
Models
11.2.10
Langevin Dipoles Model
11.2.11
Poisson Boundary Conditions
11.3
Stand-Alone QM/MM Calculations
11.3.1
Introduction
11.3.2
Available QM/MM Methods and Features
11.3.3
Using the Stand-Alone QM/MM Features
11.3.4
Additional Job Control Variables
11.3.5
QM/MM Examples
11.4
Q-Chem
/
Charmm
Interface
11.4.1
Overview
11.5
Effective Fragment Potential Method
11.5.1
Introduction
11.5.2
Theoretical Background
11.5.3
Excited-State Calculations with EFP
11.5.4
Pairwise Fragment Energy Decomposition and Pairwise Fragment Excited-State Energy Decomposition Analysis
11.5.5
Extension to Macromolecules: Fragmented EFP Scheme
11.5.6
Running EFP Jobs
11.5.7
Library of Fragments
11.5.8
Calculation of User-Defined EFP Potentials
11.5.9
fEFP Input Structure
11.5.10
Input keywords
11.5.11
Examples
11.6
Projection-Based Density Embedding
11.6.1
Introduction
11.6.2
Theory
11.6.3
Job Control for DFT-in-DFT and WFT-in-DFT Calculations
11.6.4
Previous Implementation Based on “EmbedMan”
11.7
Frozen-Density Embedding Theory
11.7.1
Introduction
11.7.2
FDE-Man
11.7.3
FDE-Man Job Control
11.7.4
Single-fragment Calculations
11.7.5
Examples
11.7.6
FDE-Man output
11.8
Polarizable Embedding Model
11.8.1
Introduction
11.8.2
Job Control
11.8.3
Interpreting the Output
11.9
Atomic Interactions Represented By Empirical Dispersion (AIRBED)
11.9.1
Introduction
11.9.2
AIRBED Job Control
12
Fragment-Based Methods
12.1
Introduction
12.1.1
Overview
12.2
Specifying Fragments in the
$molecule
Section
12.2.1
Overview
12.3
FRAGMO Initial Guess for SCF Methods
12.3.1
Overview
12.4
Automated Evaluation of BSSE and Counterpoise-Corrected Interaction Energies
12.4.1
Overview
12.5
The Original Locally-Projected SCF and First-Generation ALMO-EDA Methods
12.5.1
Introduction to Locally-Projected SCF
12.5.2
Roothaan-Step Corrections on Locally-Projected SCF or
FRAGMO
Initial Guess
12.5.3
The First-Generation ALMO-EDA and Perturbative Charge-Transfer Analysis (CTA)
12.5.4
Perturbative Charge-Transfer Analysis Based on Complementary Occupied/Virtual Pairs (COVPs)
12.5.5
Job Control for the Original Locally-Projected SCF and the First- Generation ALMO-EDA Methods
12.6
The Second-Generation ALMO-EDA Method
12.6.1
Introduction
12.6.2
Generalized SCFMI Calculations and Additional Features
12.6.3
Polarization Energy with a Well-defined Basis Set Limit
12.6.4
Further Decomposition of the Frozen Interaction Energy
12.6.5
Job Control for EDA2
12.6.6
ALMO-EDA with Implicit Solvent Models
12.6.7
ALMO-EDA with non-
aufbau
Electronic Configurations
12.6.8
ALMO-EDA with Non-Perturbative Polarization and Charge Transfer Analysis
12.6.9
Visualization Tools Associated with ALMO-EDA
12.7
The MP2 ALMO-EDA Method
12.7.1
Overview
12.8
ALMO-EDA Method for Bonded Interactions
12.8.1
Overview
12.9
The Adiabatic ALMO-EDA Method and VFB Analysis
12.9.1
Overview
12.10
The ALMO Force Decomposition Analysis Method
12.10.1
Overview
12.11
ALMO-EDA Involving Excited-State Molecules
12.11.1
Theory
12.11.2
Job Control
12.12
The Explicit Polarization (XPol) Method
12.12.1
Theory
12.12.2
Supplementing XPol with Empirical Potentials
12.12.3
Job Control Variables for XPol
12.12.4
Examples
12.13
Symmetry-Adapted Perturbation Theory (SAPT)
12.13.1
Theory
12.13.2
Job Control for SAPT Calculations
12.14
The XPol+SAPT (XSAPT) Method
12.14.1
Introduction
12.14.2
Theory
12.14.3
Dispersion Models
12.14.4
Running an XSAPT+MBD Job
12.15
Energy Decomposition Analysis based on SAPT/cDFT
12.15.1
Overview
12.16
The Many-Body Expansion Method
12.16.1
Introduction
12.16.2
Job Control
12.17
Ab Initio
Frenkel Davydov Exciton Model (AIFDEM)
12.17.1
Theory
12.17.2
Job Control Variables
12.17.3
Examples
12.18
TDDFT for Molecular Interactions
12.18.1
Introduction
12.18.2
Job Control
12.19
The ALMO-CIS/TDA method and its Charge-Transfer Correction
12.19.1
Introduction
12.19.2
Job Control
12.19.3
ALMO-CIS/TDA with selected fragment occupied-virtual pairs
13
Specialized Topics
13.1
Geminal Models
13.1.1
Introduction
13.1.2
Perturbative Corrections
13.2
Intracules
13.2.1
Introduction
13.2.2
Position Intracules
13.2.3
Momentum Intracules
13.2.4
Wigner Intracules
13.2.5
Intracule Job Control
13.2.6
Format for the
$intracule
Section
13.3
CASE Approximation
13.3.1
Overview
13.4
Molecular Junctions
13.4.1
Overview
13.5
Nuclear–Electronic Orbital Method
13.5.1
Introduction
13.5.2
NEO-Hartree-Fock
13.5.3
NEO-DFT
13.5.4
NEO-PCM
13.5.5
NEO-TDDFT
13.5.6
NEO-DFT(V)
13.5.7
NEO-CC
13.5.8
Job Control for the NEO-SCF methods
13.5.9
Examples
13.6
Construction of Effective Hamiltonians from EOM-CC Wave Functions
13.6.1
Overview
A
AOInts
A.1
Introduction
A.1.1
Overview
A.2
Historical Perspective
A.2.1
Overview
A.3
AOInts
: Calculating ERIs with
Q-Chem
A.3.1
Overview
A.4
Shell-Pair Data
A.4.1
Overview
A.5
Shell-Quartets and Integral Classes
A.5.1
Overview
A.6
Fundamental ERI
A.6.1
Overview
A.7
Angular Momentum Problem
A.7.1
Overview
A.8
Contraction Problem
A.8.1
Overview
A.9
Quadratic Scaling
A.9.1
Overview
A.10
Algorithm Selection
A.10.1
Overview
A.11
More Efficient Hartree–Fock Gradient and Hessian Evaluations
A.11.1
Overview
A.12
User-Controllable Variables
A.12.1
Overview
B
Q-Chem
Quick Reference
B.1
Q-Chem
Text Input Summary
B.1.1
Introduction
B.1.2
Keyword:
$molecule
B.1.3
Keyword:
$rem
B.1.4
Keyword:
$basis
B.1.5
Keyword:
$comment
B.1.6
Keyword:
$ecp
B.1.7
Keyword:
$empirical_dispersion
B.1.8
Keyword:
$external_charges
B.1.9
Keyword:
$intracule
B.1.10
Keyword:
$isotopes
B.1.11
Keyword:
$multipole_field
B.1.12
Keyword:
$nbo
B.1.13
Keyword:
$occupied
B.1.14
Keyword:
$opt
B.1.15
Keyword:
$svp
B.1.16
Keyword:
$svpirf
B.1.17
Keyword:
$plots
B.1.18
Keyword:
$localized_diabatization
B.1.19
Keyword:
$van_der_waals
B.1.20
Keyword:
$xc_functional
B.2
Geometry Optimization with General Constraints
B.2.1
Overview
B.3
$rem
Variable List
B.3.1
Overview
B.3.2
General
B.3.3
SCF Control
B.3.4
DFT Options
B.3.5
Large Molecules
B.3.6
Correlated Methods
B.3.7
Correlated Methods Handled by CCMAN and CCMAN2
B.3.8
Perfect pairing, Coupled cluster valence bond, and related methods
B.3.9
Excited States: CIS, TDDFT, SF-XCIS and SOS-CIS(D)
B.3.10
Excited States: EOM-CC and CI Methods
B.4
Geometry Optimizations
B.4.1
Overview
B.4.2
Vibrational Analysis
B.4.3
Reaction Coordinate Following
B.4.4
NMR Calculations
B.4.5
Wave function Analysis and Molecular Properties
B.4.6
Symmetry
B.4.7
Printing Options
B.4.8
Resource Control
B.5
Alphabetical Listing of
$rem
Variables
B.5.1
Overview
C
Third-party Components
C.1
Introduction
C.1.1
Overview
C.2
Armadillo
C.2.1
Overview
C.3
ctx
C.3.1
Overview
C.4
dftd4
C.4.1
Overview
C.5
libecpint
C.5.1
Overview
C.6
libefp
C.6.1
Overview
C.7
libtensor
C.7.1
Overview
C.8
libxm
C.8.1
Overview
Q-Chem 6.1 User’s Manual
10.15.1
Overview
11.1
Introduction
Chapter 11
Molecules in Complex Environments: Solvent Models, QM/MM and QM/EFP Features, Density Embedding
(April 13, 2024)
11.1
Introduction
11.2
Chemical Solvent Models
11.3
Stand-Alone QM/MM Calculations
11.4
Q-Chem
/
Charmm
Interface
11.5
Effective Fragment Potential Method
11.6
Projection-Based Density Embedding
11.7
Frozen-Density Embedding Theory
11.8
Polarizable Embedding Model
11.9
Atomic Interactions Represented By Empirical Dispersion (AIRBED)
