Gaussian 16 — Quantum Chemistry Software

Overview

Gaussian is the industry-standard quantum chemistry software for electronic structure calculations. It supports DFT (all major functionals), HF, MPn, CCSD(T), CASSCF, TDDFT, geometry optimization, frequency analysis, reaction pathways, and much more.

Installed on: marcus HPC cluster (remote server access via marcus2)

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Connection

ssh -p 8722 openclaw@124.16.75.110   # Login to marcus2
ssh marcus                               # Jump to compute node
module load gaussian/g16.c01-avx2       # Load Gaussian 16 Rev. C.01

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Input File Format (.gjf)

%chk=filename.chk          # Checkpoint file
%mem=60GB                  # Memory allocation
%nproc=64                  # Number of CPU cores
# route_section             # Method, basis set, job type, options

Title
Charge SpinMultiplicity     # Molecular charge and spin (0 1 = neutral singlet)
Cartesian or Z-Matrix coordinates

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Link0 Commands

Command	Description
%chk=file.chk	Checkpoint file path
%mem=60GB	Memory (any unit: MB, GB)
%nproc=64	CPU cores
%nprocshared=32	Shared memory parallelism
%oldchk=file.chk	Continue from existing checkpoint
%save	Force checkpoint saving

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Job Types

Keyword	Description	Common Options
SP	Single-point energy	Default calculation
Opt	Geometry optimization	Opt=CalcFC, Opt=TS, Opt=Tight, Opt=MaxStep=N
Freq	Frequency analysis	Freq=Raman, Freq=HPC
Opt Freq	Optimize then compute frequencies	Verify minima/transition states
Scan	Potential energy surface scan	Scan=ModRedundant, Scan=Bond, Scan=Angle
IRC	Intrinsic reaction coordinate	Follow reaction path from TS
Polar	Polarizability	Polar=EnOnly
ADMP	Car-Parrinello molecular dynamics
BOMD	Born-Oppenheimer MD
stable	Wavefunction stability test

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Methods

Hartree-Fock

# HF/6-31G*

• HF — Restricted (RHF), UHF — Unrestricted, ROHF — Restricted open-shell

DFT Functionals

Functional	Type	HF Exchange	Notes
B3LYP	Hybrid GGA	20%	Most popular, good all-round
PBE0	Hybrid GGA	25%	Based on PBE, reliable
M06-2X	Meta-GGA hybrid	54%	Good for non-covalent, thermochemistry
M06	Meta-GGA hybrid	27%	Minnesota functional
CAM-B3LYP	Range-separated hybrid	Variable	Long-range corrected
WB97X-D	Range-separated + D3	Variable	Dispersion-corrected
WB97X-D3BJ	Range-separated + D3(BJ)	Variable	Better dispersion
LC-WPBE	Long-range corrected	100% at long range	Charge-transfer states
wPBE	Long-range corrected	100% at long range	Same as LC-WPBE
TPSSH	Hybrid meta-GGA	10%
BP86	GGA	0%
PBE	GGA	0%
BLYP	GGA	0%
SVWN5	LDA	0%
HSEHJS	Range-separated	50% at short range	Screened Coulomb

Wave Function Methods

Method	Description
MP4	4th-order Møller-Plesset perturbation
MP3	3rd-order MP
MP2	2nd-order MP (also MP2=Full)
CCSD	Coupled-cluster singles + doubles
CCSD(T)	CCSD with perturbative triples
CCSD=T	CCSD with full triples (non-perturbative)
CCD, CCSD, CID, CISD	Other coupled-cluster variants
CASSCF(n,m)	Complete active space SCF (n electrons, m orbitals)
CASPT2	Multi-state second-order perturbation
EOMCCSD	Equation-of-motion CCSD (excited states)
SAC-CI	Symmetry-adapted cluster CI
GVB	Generalized valence bond
CIS	Configuration interaction singles
CIS(D)	CIS with perturbative doubles

Semi-Empirical

# CNDO, INDO, MINDO3, MNDO, AM1, PM3, ZINDO

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Basis Sets

Pople Split-Valence

Basis	Description
STO-3G	Minimal basis (fast)
3-21G	Split-valence, lightest
6-21G	Pople split-valence
6-31G	Double-zeta, standard for organics
6-31G*	With polarization on heavy atoms
6-31G**	With polarization on all atoms
6-31+G*	With diffusion on heavy atoms
6-31++G**	With diffusion on all
6-311G	Triple-zeta
6-311G*	Triple-zeta + polarization
6-311++G(2d,2p)	Highly extended

Correlation-Consistent (cc-pVnZ)

cc-pVDZ, cc-pVTZ, cc-pVQZ, cc-pV5Z, cc-pV6Z
aug-cc-pVDZ, aug-cc-pVTZ, aug-cc-pVQZ    # Augmented with diffuse functions

Def2 / Karlsruhe

def2-SVP, def2-TZVP, def2-QZVP
def2-TZVPP — with polarization functions

Effective Core Potentials (ECPs)

ECP	Description
LANL2DZ	Los Alamos ECP + DZ basis
LANL2DZdp	LANL2DZ with polarization
Stuttgart	Stuttgart-Cologne ECPs
CRENBL	Relativistic ECP

Other

Basis	Description
cc-pCVnZ	Core-valence (for core excitations)
pc-n	Polarization consistent basis
pcseg-n	Segmented polarization consistent
N07D	Density-fitting basis sets

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TDDFT — Excited States

# td=(nstates=10,root=1,singlets) b3lyp/6-31G*
# td=(nstates=10,triplets) b3lyp/6-31G*   # Triplet states only

Options:

• nstates=N — Number of excited states (default 10)
• root=N — Optimize/persist on state N
• singlets — Singlet excitations (default)
• triplets — Triplet excitations
• alltrans — Include all triplet-singlet transitions
• 50-50 — 50% CI coefficients for each determinant
• 50-50TDDFT — Special for degenerate states

For vertical emission:

# td=(nstates=5,singlets) b3lyp/6-31G*     # Excitation
# b3lyp/6-31G* td=(root=1) geom=check     # Emission from S1

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Solvent Effects (SCRF)

# b3lyp/6-31G* scrf=(smd,solvent=acetonitrile)
# b3lyp/6-31G* scrf=(pcm,solvent=water)

SCRF Models:

Model	Keyword	Notes
PCM	SCRF=PCM	Polarizable continuum
SMD	SCRF=SMD	Solvent model based on density (G16 default)
CPMF	SCRF=CM5
HCTH	SCRF=HCTH
SWIG	SCRF=SWIG

Common Solvents: water, ethanol, methanol, acetonitrile, dmso, dmf, chloroform, toluene, benzene, diethylether, thf, acetone

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Geometry Optimization Options

# opt=calcfc           # Compute force constants initially (default for TS)
# opt=ts               # Transition state search
# opt=tight            # Tight convergence criteria
# opt=gdiis            # Use GDIIS for optimization
# opt=modredundant     # Modredundant coordinates
# opt=maxstep=n        # Maximum step size (default 0.3 bohr)
# opt=readvariance     # Read variance data
# freq=hpc             # HPC-mode frequency scaling

ModRedundant examples (in input):

C 1 2 R    # Define bond between atoms 1-2
D 1 2 3 4 180.0 F    # Scan dihedral angle 1-2-3-4 to 180°

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Frequency Options

# freq=hindered rotor   # Include hindered rotor corrections
# freq=raman             # Raman activity
# freq=check            # Read frequency data from checkpoint
# freq=(hinderedrot,temperature=298.15,pressure=1.0)

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Population Analysis

# pop=full              # Full AO/MO analysis
# pop=full,nbomo        # Include NBOs
# pop=nbo               # Natural Bond Orbital analysis
# pop=npa               # Natural Population Analysis
# pop=mk                # Merz-Kollman ESP charges
# pop=chelpg            # CHELPG ESP charges
# pop=(bondorder)       # Wiberg/Mayer bond order
# pop=density          # Output density matrices

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NMR Properties

# nmr=cpa              # Continuous set of gauge transformations
# nmr=spin-spin        # Spin-spin coupling constants
# spinnuclear=         # Specify magnetic nuclei
# mag=                  # Magnetic properties

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SCF Convergence

# scf=qc               # Quadratic convergence (most robust)
# scf=xqc              # Extra quadratic convergence (try QC if this fails)
# scf=diis             # DIIS (default)
# scf=maxcyc=n         # Max SCF cycles (default 128)
# scf=conver=n         # Convergence criterion (10^-n)
# scf=tight            # Tight SCF convergence
# scf=novariational    # Non-variational MOs
# scf=direct           # Direct SCF (on-the-fly integral recomputation)
# scf=fermi            # Fermi-VWN5 for metals

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CBS Extrapolation

# cbs=QB3              # CBS-QB3 composite method
# cbs=APF              # CBS-APF method
# cbs=4s               # 4-parameter CBS extrapolation
# CBSExtrapolate=2/3   # Two-point extrapolation n=2,3

Composite Methods:

Method	Description
CBS-QB3	CBS-QB3 composite
CBS-APF	CBS-APF composite
W1U	W1 ultra-fine
W1	W1 method
W2	W2 method
W3	W3 method
W4	W4 method
CBS-4s	CBS with 4-parameter extrapolation
G1	G1 composite
G2	G2 composite
G3	G3 composite
G4	G4 composite

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IRC (Intrinsic Reaction Coordinate)

# irc=kalida            # Use Kupidonov-Khailenko algorithm
# irc=gs2               # Gonzalez-Schlegel second-order algorithm (default)
# irc=nproc=n           # Points per process in IRC
# ircmax=n             # Maximum points in IRC path

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External Potentials / Basis

# ExtraBasis=file        # Additional basis functions
# Gen                   # User-defined basis in input
# GenECP               # User-defined ECP in input
# Pseudo=read          # Read ECP from checkpoint
# densityfit           # Use density fitting (DF) for efficiency
# nodensityfit         # Disable density fitting

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Wavefunction Analysis

# Density=current       # Use current density
# guess=modify,alter    # Modify/alter initial MOs
# guess=hop            # Hückel initial guess
# guess=read           # Read MOs from checkpoint
# stable=opt           # Optimize unstable wavefunction
# prop=flex           # Flexible property output

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Stabilty Analysis

# stable                # Test wavefunction stability
# stable=opt            # Optimize to stable wavefunction

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Common Task Templates

Ground-State Optimization + Frequency

%chk=opt_freq.chk
%mem=60GB
%nproc=64
# opt freq b3lyp/6-31G**

Molecule optimization
0 1
C  0.0  0.0  0.0
...

TDDFT Excited States

%chk=tddft.chk
%mem=60GB
%nproc=64
# td=(nstates=10,singlets) b3lyp/6-31G*

S1 vertical excitations
0 1
C  0.0  0.0  0.0
...

S1 Optimization + Vertical Emission

%chk=s1_opt.chk
%mem=60GB
%nproc=64
# td=(nstates=5,root=1) b3lyp/6-31G* opt

S1 optimization
0 1
... (ground-state optimized geometry)

%chk=emission.chk
%mem=60GB
%nproc=64
# b3lyp/6-31G* td=(root=1) geom=check

S1 vertical emission
0 1
... (S1 optimized geometry)

Solvent Effect (SMD)

%chk=smd.chk
%mem=60GB
%nproc=64
# b3lyp/6-31G* scrf=(smd,solvent=acetonitrile)

SMD solvent model
0 1
...

CBS-QB3 Composite

%chk=cbs-qb3.chk
%mem=60GB
%nproc=64
# cbs-qb3

CBS-QB3 calculation
0 1
...

CASSCF

%chk=cas.chk
%mem=60GB
%nproc=64
# casSCF(10,8)/6-31G*

CAS(10,8) — 10 electrons, 8 orbitals in active space
0 1
...

ModRedundant Scan

%chk=scan.chk
%mem=60GB
%nproc=64
# b3lyp/6-31G* opt=modredundant

Dihedral scan
0 1
C 0 0 0
C 1 2 1.4
...
1 2 3 4 90.0 S 20 5.0   # Scan dihedral 1-2-3-4, 20 steps, 5° each

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Useful IOp Values

IOp	Description
IOp(3/76=055000)	Scale HF exchange in hybrid functionals
IOp(3/77=055000)	Scale correlation
IOp(3/78=...)	DFT integration grid
IOp(5/33=...)	Frozen core approximation
IOp(5/34=...)	Use spherical harmonics
IOp(5/41=...)	Population analysis options

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Converting Checkpoint Files

formchk filename.chk filename.fchk      # CHK → FCHK
# or
unfchk filename.chk filename.fchk       # Alternative

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Output Files

Extension	Description
.log	Main output file
.chk	Binary checkpoint file
.fchk	Formatted ASCII checkpoint
.out	(sometimes used)
.cub	Cube file for visualization
.int	Two-electron integrals
.sbn	Scratch binary file

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Official Keyword Index

Full keyword list from gaussian.com/keywords/:

ADMP, BD, BOMD, CacheSize, CASSCF, CBS Methods, CBSExtrapolate, CCD and CCSD, Charge, ChkBasis, CID and CISD, CIS, CNDO, Complex, Constants, Counterpoise, CPHF, Density, DensityFit and NoDensityFit, DFT Methods, DFTB and DFTBA, EET, EOMCCSD, EPT, External, ExtraBasis & ExtraDensityBasis, Field, FMM, Force, Freq, Gen and GenECP, GenChk, Geom, GFInput, GFPrint, Gn Methods, Guess, GVB, HF, Huckel, INDO, Integral, IOp, IRC, IRCmax, Link0 Commands, LSDA, MaxDisk, MINDO3, MNDO, MM Methods, MP Methods, Name, NMR, ONIOM, Opt, Output, PBC, Polar, Population, Pressure, Prop, Pseudo, Punch, QCI, Restart, SAC-CI, Scale, Scan, SCF, SCRF, Semi-Empirical Methods, SP, Sparse, Stable, Symmetry, TD, Temperature, Test, TestMO, TrackIO, Transformation, Units, Volume, W1 Methods, Window Keyword and Frozen Core Options, ZIndo

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Advanced Topics

###ONIOM (Embedded Fragment)

# oniom(b3lyp/6-31G*:pm3)=(...)

Layer definition in molecule section:
H  -1 0.0 0.0 0.0 q=0   # High layer
L  0  0.0 0.0 0.0 q=+1  # Low layer
...

EOM-CCSD (Excited States / Ionization)

# eomccsd                # EOM-CCSD for excited states
# eom(ip)                # Ionization potentials
# eom(ea)                # Electron affinities
# eom(ee)                # Two-electron excitations

Density Fitting

# densityfit             # Enable DF for all calculations
# scf=(nodensityfit)     # Disable DF for SCF only
# mp2=fulldensityfit     # Full density fitting for MP2

PBC (Periodic Boundary Conditions)

# pbc载体                 # Enable PBC calculations
# pbe0/pcs Solvent=...   # With SCRF