Gaussian & GaussView

• Gaussian is a general purpose electronic structure package

for use in computational chemistry.
• GaussView is a graphical user interface (GUI) designed to be
used with Gaussian to make calculation preparation and
output analysis easier, quicker and more efficient.
• Vendor’s website: http://www.gaussian.com
Gaussian/GaussView @ Lehigh
• Gaussian16 available for very small jobs via LUApps
• Gaussian16 can be installed (by LTS or the Fredin Group on a Lehigh Owned
Windows computer)
• Installed as a module on Sol
• Package name: gaussian/g09
• Add “module load Gaussian/g09” to your .bashrsc
• Scripts available for different partitions at /home/laf218/share/scripts/g09.*
• DO NOT compare Gaussian to other methods!
• DO Reference clearly!!!
Gaussian 16, Revision B.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E.
Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, G. A. Petersson,
H. Nakatsuji, X. Li, M. Caricato, A. V. Marenich, J. Bloino, B. G. Janesko, R.
Gomperts, B. Mennucci, H. P. Hratchian, J. V. Ortiz, A. F. Izmaylov, J. L.
Sonnenberg, D. Williams-Young, F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng,
A. Petrone, T. Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N. Rega, G.
Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M.
Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, K. Throssell, J. A.
Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. J. Bearpark, J. J. Heyd, E. N. Brothers,
K. N. Kudin, V. N. Staroverov, T. A. Keith, R. Kobayashi, J. Normand, K.
Raghavachari, A. P. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, J. M.
Millam, M. Klene, C. Adamo, R. Cammi, J. W. Ochterski, R. L. Martin, K. Morokuma,
O. Farkas, J. B. Foresman, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2016.
Gaussian Functionality
• Energies
• MM: AMBER, Dreiding, UFF force field
• Semiempirical: CNDO, INDO, MINDO/3, MNDO, AM1, PM3
• HF: closed-shell, restricted/unrestricted open-shell
• DFT: many local/nonlocal functionals to choose
• MP: 2nd-5th order; direct and semi-direct methods
• CI: single and double
• CC: single, double, triples contribution
• High accuracy methods: G1, G2, CBS, etc.
• MCSCF: including CASSCF
• GVB
• Gradients/Geometry optimizations
• Frequencies (IR/Raman, NMR, etc.)
• Other properties
• Populations analyses
• Electrostatic potentials
• NMR tensors
• Several solvation models (PCM, COSMOS)
• Two and three layer ONIOM – E, grad, freq
• Transition state search
• IRC for reaction path
Gaussian Input File Structure
• .com (this is a good default),.inp, or .gjf (Windows version)
• Free format, case insensitive
• Spaces, commas, tabs, forward slash as delimiters between keywords
• ! as comment line/section
• Divided into sections (in order)
• Link 0 commands (%)
• Route section – what calculation is to do
• Title
• Molecular specification
• Optional additional sections
%chk=water.chk
# HF/6-31G(d) !Route section
!Blank line
water energy !Title section
!Blank line
0 1 !Charge & multiplicity
O -0.464 0.177 0.0 !Geometry in Cartesian Coordinate
H -0.464 1.137 0.0
H 0.441 -0.143 0.0
!Blank line at the end
Input File – Gaussian Commands
• First “Link 0” options (defaults for LST Sol nodes)
• %chk=myjob.chk
• %mem=126GB
• %nprocshared=16
• enge (mem=190GB and nprocshared=32)
• Keyword line(s) – specify calculation type and other job options
• Starts with # symbol
• Can be multiple lines
• Terminate with a blank line
• Format
• keyword=option
• keyword(option)
• keyword(option1,option2,…)
• keyword=(option1,option2,…)
• User’s guide provides list of keywords, options, and basis set notion
http://gaussian.com/keywords/
• Title line – Brief description of calculation – for users benefit
• Terminate with a blank line
• Molecular Geometry – simplest is use the xyz coordinates
• 1st line charge and multiplicity
• Element label and location
• Cartesian coordinate
• Label x y z
• Z-matrix
• Label atoms bond length atom2 angle atm3 dihedral
• If parameters used instead of numerical values then variables section follows
• Again end in blank line
A More Complicated Example
%chkf33em5p77c.chk
%mem=4096MB
%NProc=4
#B3LYP/6-31G* opt geom=Checkpoint Guess=read nosymm scf=tight

Geometry optimization of a sample molecule

1 1

--Link1--
%chk=/scr/APPS_SCRDIR/f33em5p77c.chk
%mem=4096MB
%NProc=2
# B3LYP/6-311++G** sp pop=nbo nosymm guess=read geom=checkpoint

Single Point Energy for the "reference state" of molecule with

one more electron.

0 2
GaussView
• Sketch in molecules using its advanced 3D Structure
Builder, or load in molecules from standard files.
• Set up and submit Gaussian16 jobs right from the
interface, and monitor their progress as they run.
• Examine calculation results graphically via state-of-the-art
visualization features: display molecular orbitals and other
surfaces, view spectra, animate normal modes, geometry
optimizations and reaction paths.
• Online help: http://www.gaussian.com/g_gv/gvtop.htm
GaussView: Build
GuassView: Setup
• Molecule specification input is set up automatically.
• Specify additional redundant internal coordinates by clicking
on the appropriate atoms and optionally setting the value.
• Specify the input for any Gaussian 03 calculation type.
• Select the job from a pop-up menu. Related options automatically
appear in the dialog.
• Select any method and basis set from pop-up menus.
• Set up calculations for systems in solution. Select the desired solvent
from a pop-up menu.
• Set up calculations for solids using the periodic boundary conditions
method. GaussView specifies the translation vectors automatically.
• Set up molecule specifications for QST2 and QST3 transition state
searches using the Builder’s molecule group feature to transform one
structure into the reactants, products and/or transition state guess.
• Select orbitals for CASSCF calculations using a graphical MO editor,
rearranging the order and occupations with the mouse.
• Start and monitor local Gaussian jobs.
• Start remote jobs via a custom script.
GaussView: Setup
GuassView: Showing Results
• Show calculation results summary.
• Examine atomic changes: display numerical values or color atoms by charge
(optionally selecting custom colors).
• Create surfaces for molecular orbitals, electron density, electrostatic potential,
spin density, or NMR shielding density from Gaussian job results.
• Display as solid, translucent or wire mesh.
• Color surfaces by a separate property.
• Load and display any cube created by Gaussian 03.
• Animate normal modes associated with vibrational frequencies (or indicate the
motion with vectors).
• Display spectra: IR, Raman, NMR, VCD.
• Display absolute NMR results or results with respect to an available reference
compound.
• Animate geometry optimizations, IRC reaction path following, potential energy
surface scans, and BOMD and ADMP trajectories.
• Produce web graphics and publication quality graphics files and printouts.
• Save/print images at arbitrary size and resolution.
• Create TIFF, JPEG, PNG, BMP and vector graphics EPS files.
• Customize element, surface, charge and background colors, or select high
quality gray scale output.
GuassView: Showing Results
Surfaces
Reflection-Absorption Infrared Spectrum of AlQ3

N O

O Al N

N O

752 Wavenumbers (cm-1) 1473

1386
1116 1338 1580 1605

800 1000 1200 1400 1600

GaussView: VCD
(Vibrational Circular Dichroism) Spectra

GaussView can display a variety of computed spectra, including IR, Raman, NMR and VCD. Here we see the
VCD spectra for two conformations of spiropentyl acetate, a chiral derivative of spiropentane. See F. J. Devlin,
P. J. Stephens, C. Österle, K. B. Wiberg, J. R. Cheeseman, and M. J. Frisch, J. Org. Chem. 67, 8090 (2002).
Energy (scf) – Default
• simply calculates the energy, wave function and other requested
properties at a single fixed geometry
• Uses a variation method to search for the AO/basis function weighting
1. Single Point Energy (Hartrees)
2. Orbital symmetries
3. Mulliken atomic charges (short)
4. Dipole moments
• SCF=Tight is the default for G09.
• If SCF isn’t converging try scf=loose
• Or scf=qc
• scf=restart
• scf=(maxcycle=#), default 129
Functionals
• A functional is just a function that depends on a function

• Local density approximation (LDA): Functional depends only on the

(local) density at a given point.
• Example: SVWN
• Gradient-corrected approximation (GGA): Functional depends on local
density and its gradient.
• Examples: PW91 and LYP correlation functionals, B88 exchange functional
• Meta-GGA: Functional depends on density, its gradient, and its
second derivative.
• Example: M06-L
• Hybrid DFT: Mixes in Hartree-Fock exchange.
• Most popular example: B3LYP (hybrid GGA). M05-2X and M06-2X are hybrid
meta-GGA’s.
Beyond HF
• Hartree Potential: each individual electron moves independently of each
other, only feeling the average electrostatic field due to all the other electrons
plus the field due to the atoms.
• neglects exchange and correlation effects.
• Kohn-Sham: Compute the kinetic energy of a density by assuming that the
density corresponds to a wavefunction consisting of a single Slater
determinant (“non-interacting limit”): we know how to compute the kinetic
energy of a Slater determinant (orbitals) --- looks same as HartreeFock
Theory
• Exchange-Correlation Functional: We can compute every piece of a Kohn-
Sham DFT energy exactly except for the “exchange correlation” piece, Exc[ρ].
(still KS)
• Unfortunately the exact exchange-correlation energy functional is not known and is
probably so complicated that even if it were known it would not be computationally
useful
• Hence, use various approximate exchange correlation functionals (S-VWN, B3LYP,
etc.)
• KS cost is similar to HF (similar equations) but quality can be better because
correlation is built in through the correlation functional
• Cost can actually be cheaper than HF if we replace the expensive, long-range
exchange integrals (K terms) from HF with a shorter range exchange potential
(which however might not be as accurate…)
 https://gaussian.com/basissets/
Basis Set
• Minimal basis set (e.g., STO-3G)
• Double zeta basis set (DZ)
• Split valence basis Set (e.g., 6-31G)
• K-LMG
• K = number of sp-type inner shell GTOs
• L = number of inner valence s- and p-type GTOs
• M = number of outer valence s- and p-type GTOs
• G = indicates that GTOs are used
• Polarization and diffuse functions (6-31+G*)
• Correlation-consistent basis functions (e.g., aug-cc-pvTZ)
• Pseudopotentials, effective core potentials
Geometry (opt)
• calculates the wave function and the energy at a starting geometry
• calculates the force on each atom by evaluating the gradient (first
derivative) of the energy with respect to atomic positions
• Minimal energy when the force is below some threshold
1. Atomic coordinates of optimized molecule
2. Optimized Parameters: atomic distances and angles
3. HOMO/LUMO eigenvalues (Hartrees)
4. Mulliken atomic charges (short)
5. Dipole moments
Tricks:
• If the first scf is taking a long time (over 500 steps) try a new guess
• Use maxstep=# to change the size of steps taken in opt
• Always check the freq for imaginary frequencies (negative)
Stable?
• The stability calculation determines whether the wavefunction
computed for the molecular system is stable or not:
• in other words, whether there is a lower energy wavefunction corresponding to
a different solution of the SCF equations.
• If the wavefunction is unstable, then whatever calculation you are
performing is not being done on the expected/desired state of the
molecule.
• SCF = self consistent field
• DFT = density functional theory
• Stable=Opt the wavefunction is allowed to be unrestricted if necessary
• Stable geometry message
• The wavefunction is stable under the perturbations considered.
• Unstable geometry messages
• The wavefunction has an RHF → UHF instability.
• The wavefunction has internal instability.
Vibrational Spectroscopy & Thermochemistry (freq)
• calculate the vibrations of the molecule in question, along with other parameters that you can choose to include or
erase from the output
• molecular frequencies depend on the second derivative of the energy with respect to the nuclear positions

• NOTE: You must use the same combination of theoretical model and basis set for both the Opt
and Freq calculations
1. Atomic coordinates of optimized molecule
2. Optimized parameters: atomic distances and angles
3. HOMO/LUMO eigenvalues (hartree)
4. Mulliken atomic charges (short)
5. Dipole moments
6. Single Point energy
7. Harmonic frequnecies (wavenumbers)
8. Reduced masses (amu)
9. Force constants
10. IR intensities
11. Raman intensities (not default)
12. Thermochemistry
(a) Temperature
(b) Pressure
(c) Isotopes used
(d) Molecular mass
(e) Thermal energy: E (Thermal)
(f) Constant volume molar heat capacity (CV)
(g) Entropy (S)
(h) Free Energy (sum of electronic and thermal Free Energies)
(i) Enthalpy (sum of electronic and thermal Enthalpies)

http://gaussian.com/vib/
freq results
1. SCALING depends on the theoretical method and basis set used. Note that the scaling
factors for frequencies and for zero point energies are different! You can input the scale
factor to be used for thermochemistry analysis using the Scale keyword (ex: "Scale=0.95")
• https://cccbdb.nist.gov/vibscalejust.asp
2. STABILITY imaginary (negative) frequencies. Imaginary frequencies indicate instability of
molecular geometry.
• each molecule should have either 3N-6 or 3N-5 vibrational modes
• The others are the translational and rotational modes and their intensities should close to zero (+/- 10)
• Big intensities for these frequencies is another way to verify the stability of you molecule

3. IMAGINARY FREQUENCIES saddle points on the potential energy surface

• a transition state should have one (1st order saddle point)
4. ANHARMONIC FREQUENCIES By default, G09 computes frequencies based on harmonic
oscillator approximation (second order derivative with respect to the nuclei movement).
• anharmonic corrections, i.e. computing higher-order derivatives. anharmonic" keyword

5. RAMAN "Raman" keyword

6. THERMOCHEMSITRY By default, several thermodynamic values are computed
during a vibrational analysis. You can change the thermochemistry
parameters (temperature, pressure, ect) by writing Freq=ReadIsotopes in the
Route section.
Vibrational Normal Modes

1. Concerted motion of all atom

such that all atoms oscillate in
phase
2. The center of mass doesn’t
move
3. Each is ~ a single harmonic
oscillator with characteristic
frequency
Thermochemistry from ab initio Calculations
Thermochemistry
from ab initio Calculations
Thermochemistry from frequency calculation
Modeling System in Solution
Calculating Solvent Effect
Calculating Solvent Effect
Solvent Effect:
Menshutkin Model Reaction Transition State
Potential Energy Surfaces
• Many aspects of chemistry can be reduced to questions about potential
energy surfaces (PES)
• A PES displays the energy of a molecule as a function of its geometry
• Energy is plotted on the vertical axis, geometric coordinates (e.g bond
lengths, valence angles, etc.) are plotted on the horizontal axes
• A PES can be thought of it as a hilly landscape, with valleys, mountain
passes and peaks
• Real PES have many dimensions, but key feature can be represented by
a 3 dimensional PES
Calculating PES in Gaussian/GaussView
• Use the keyword “scan”

• Then change
input file properly
Transition State Search
Calculating Transition States
Locating Transition States
TS Search in Gaussian
TS Search in Gaussian/GaussView
TS Search
Animation of Imaginary Frequency
• Check that the imaginary
frequency corresponds to
the TS you search for.
Intrinsic Reaction Coordinate Scans
Input for IRC Calculation

• StepSize=N
Step size along the reaction path, in units of 0.01 amu-1/2-Bohr. The
default is 10.

• RCFC
Specifies that the computed force constants in Cartesian coordinates from
a frequency calculation are to be read from the checkpoint file.
ReadCartesianFC is a synonym for RCFC.
IRC Calculation in GaussView
Reaction Pathway Graph
Spectroscopy (TD or CIS or ZINDO)
• Most molecules have bound higher energy excited electronic states in
addition to the ground electronic state E0.
• These states may be thought of as arising from the promotion of one
of the electrons from the occupied orbital in the ground state to a
vacant higher energy orbital.
1. Ground to excited state transition
2. Excitation energies and oscillator strengths
3. Electronic Circular Dichroism (ECD)
4. Selected number of orbitals eigenvalues (hartree)
5. Orbitals’ population
6. Mulliken Analysis (short)
7. Dipole moments
Spectroscopy (TD or CIS or ZINDO)
• The classical Franck-Condon principle states that because the
rearrangement of electrons is much faster than the motion of nuclei,
the nuclear configuration does not change significantly during the
energy absorption process.
• Thus, the absorption spectrum (UV/Vis) of molecules is characterized
by the vertical excitation energies.
• TDDFT in general (singlets and triplets)
• Time Dependent calculation based on a DFT computational method.
• obtains the wave functions of MOs that oscillate between ground state and the
first excited states.
• td(nstates=#,type)
• default is 3 and singlets
• At least 40 states are normally needed to calculate a UV-Vis
NMR Shielding Tensors
 NMR Example Input

%chk=ethynenmr
#p hf/6-311+g(2d,p) nmr

nmr ethyne

0 1
C
C,1,r1
H,1,r2,2,a2
H,2,r3,1,a3,3,d3,0
Variables
R1=1.20756258
R2=1.06759666
R3=1.06759666
A2=180.0
A3=180.0
D3=0.0
Comparison of Calculated and
Experimental Chemical Shifts
 Other Gaussian Utilities
• formchk – formats checkpoint file so it can be used by other programs
• cubgen – generate cube file to look at MOs, densities, gradients, NMR in GaussView
• freqchk – retrieves frequency/thermochemsitry data from chk file
• newzmat – converting molecular specs between formats (zmat, cart, chk, cache, frac
coord, MOPAC, pdb, and others)
GaussView: ONIOM

Bacteriorhodopsin, set up for an ONIOM calculation (stylized). See T. Vreven and K. Morokuma,
“Investigation of the S0->S1 excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid
method,” Theor. Chem. Acc. (2003).
QM/MM: ONIOM Model
QM/MM: ONIOM Model
From GaussView menu: Edit -> Select Layer

Low Layer Medium Layer High Layer

QM/MM: ONIOM Setup
From GaussView menu: Calculate ->Gaussian->Method
 QM/MM: ONIOM Setup

• For the medium and low layers:

QM/MM: ONIOM Setup
Population analysis
• a mathematical way of partitioning a wave function or electron density into
charges on the nuclei, bond orders, and other related information.
• Atomic charges cannot be observed experimentally because they do not
correspond to any unique physical property.
• In reality, atoms have a positive nucleus surrounded by negative electrons, not
partial charges on each atom.
• However, condensing electron density and nuclear charges down to partial charges
on the nucleus results in an understanding of the electron density distribution.
• These are not integer formal charges, but rather fractions of an electron
corresponding to the percentage of time an electron is near each nucleus.
• Population are done once for SP energy calculation and at the first and last
step of geometry optimization.
1. Atomic coordinates of optimized molecule
2. Optimized parameters: atomic distances and angles
3. Selected number of orbitals eigenvalues (hartree)
4. Orbitals’ population
5. Atomic (partial) charges (full analysis)
6. Dipole moment
7. Single Point energy
8. Electrostatic potential derived charges (with ESP keyword)
Pop=X keyword
• PARTIAL CHARGES :
• Mulliken analysis is most common,
• it is also one of the worst and is used only because it is one of the oldest and
simplest.
• half the overlap population is assigned to each contributing orbital, giving the total
population of each AO. Summing over all the atomic orbitals on a specific atom
gives us the gross atomic population.
• WARNING! Mulliken method is extremely basis set sensitive! Usually, the smaller
the basis set, the better (opposite for energy calculations).
• X=NONE no orbital information displayed
• X=REG HOMO-5 up to LUMO+5 orbital information displayed
• X=FULL all orbitals information displayed
• X=NBO Mulliken analysis is replaced by Natural Bond-Order analysis
• NBOs are an orthonormal set of localized "maximum occupancy“ orbitals
whose leading N/2 members (or N members in the open-shell case) give
the most accurate possible Lewis-like description of the total N-electron
density.
• NBO uses eigenfunctions of the first order reduced density matrix,
localized and orthogonalized.
• X=MK, CHELP, OR CHELPG produce charges fit to electrostatic potential
(ESP)
• ESP This method uses electrostatic potential to compute charges on nuclei. ESP is
usually the best to describe charge interactions with other species, but require
significant amount of CPU time.
What Is NBO?
• Natural Bond Orbitals (NBOs) are localized few-center orbitals ("few" meaning typically 1 or
2, but occasionally more) that describe the Lewis-like molecular bonding pattern of electron
pairs (or of individual electrons in the open-shell case) in optimally compact form. More
precisely, NBOs are an orthonormal set of localized "maximum occupancy" orbitals whose
leading N/2 members (or N members in the open-shell case) give the most accurate
possible Lewis-like description of the total N-electron density.

C-C Bond C-H Bond

NBO Analysis
NBO in GaussView
Natural Population Analysis
#rhf/3-21g pop=nbo

RHF/3-21G for formamide (H2NCHO)

0 1
H -1.908544 0.420906 0.000111
H -1.188060 -1.161135 0.000063
N -1.084526 -0.157315 0.000032
C 0.163001 0.386691 -0.000154
O 1.196265 -0.246372 0.000051
H 0.140159 1.492269 0.000126
 NPA
Output
Sample
Common Errors
• Typos!!!! 90% of computation is finding our own errors
• Memory: did you provide a value less than the total on the node? Try
reducing it more or try a node with more memory (enge)
• Erroneous Write: you have probably used all the disk space check with
quota
• Convergence failure:
• The SCF (self-consistent field) procedure has failed to converge.
• The SCF procedure might fail to converge if a poor guess is provided for the
molecular orbitals.
• Try using a better guess (guess=read) by carrying out an SCF using the same
starting structure, but at a lower level of theory such as HF/STO-3G.
• If this doesn't work, try using an alternate SCF converger such as SCF=QC or
SCF=XQC.
• In some cases, a poor geometry can result in an unconverged SCF, if a bond
is way too long or too short.
• Fixing the initial geometry may fix the problem.
• In some cases, the optimizer itself takes a bad step, resulting in this error.
• Resubmitting the job with the penultimate (or earlier) geometry and a newly
evaluated Hessian can fix this.
https://docs.computecanada.ca/wiki/Gaussian_error_messages
Running a Computational Project
STEP 1: DEFINE THE BOUNDRIES
• You should start by defining how much time, energy and CPU are available
for your study. There are some steps that could be skipped if results must be
obtained in little time. The choice of theoretical models and basis sets will
also heavly depend on time and CPU resources. If your computer is not
powerful enough, you will need much more computational time than when a
more powerful computer is used.
STEP 2: SET UP YOU COMPUTER
• To speed up computations, it is strongly recommended to turn off all the
programs (except G09) on your PC. Programs like Skype, open folders,
Internet browsers, etc., all demand CPU power. Shut them off! If you know
how to, also turn off all the other services (if you’re not sure, skip this). Make
sure your computer does not go into sleeping or hibernating mode
automatically after some period of time, this might kill a G09 job.
• This is why you should run jobs on HPC!!!
STEP 3: DEFINE A GOOD WAY TO NAME THE JOBS
• It is crucial to have a strict notation for all of your G09 jobs. For example, you
could use something like this:
trans_azo_UFF(MP2_6-31G(d))_Opt
• This notation puts the name of the molecule followed by the MM method that
was used initially to optimize the geometry, followed by the theoretical model,
followed by the basis set and finally by the type of calculation performed.
• Make notes in your notebook or in a file in your file tree about how things are
named!
Computational Project …
STEP 4: DEFINE A PARENT MOLECULE
• (skip if not working with library of molecules)
• Starting with a parent molecule will aid you to choose the right theoretical model and basis
set. Run several calculations using the same theoretical model, but with increasingly better
basis sets, compare with literature values. Then restart with a different model. This will show
you which combination outputs the smallest error, and therefore suites the best for this case.
STEP 5: SUCCESFULL SEQUENCE OF CALCULATIONS
• The following sequence of calculations is what is recommended:
• (more important for hard or large systems)
1. Geometry Opt in Avogadro using MM (UFF or MMFF).
2. Geometry Opt and Freq calculation in G09 .
3. Check for imaginary frequencies (none for ground state, 1 for TS, etc).
4. If frequencies are alright, continue, otherwise restart the geometry opt.
5. Compute any property that you need.
6. Re-opt and re-compute frequencies in solvent (if needed).
7. Re-compute any property that you need in solvent (if needed).
STEP 6: READ THE OUTPUT
• Write Python scripts to analyze data you look at a lot: bond distances, angles, MO energy
levels
• Make Batch scripts that batch make cubes or other visual output (WAY WAY faster than
doing each in GaussView)
• You can use a script called "G09\output\interpreter" that can be found on the desktop of the
Gaussian workstation (PC). This program lists all the .out files found in
C:\G09W\IO\COMPUTED\BATCH\done directory, asks which file you want to work with and
lets you extract only the pertinent information out of it. This avoids scrolling up and down to
find the right values, and saves you lots of time. Don’t forget that the .out file must be copied
into the directory mentioned above, otherwise the list will be empty!