6.8. QM ‣ Gaussian menu

It is a menu about Gaussian.

In order to use Gaussian you need to install Gaussian separately.

6.8.1. Configure

Set calculation conditions of Gaussian. To set up the calculations immediately after setting Run button, once to return to the main window please press OK button.

Behavior when clicking Run is see Run.

Return to the default state with Reset button. Save the current state as the default state with Save as Default button. Restore the default state to the factory condition with Save as Default ‣ Clear Default Settings.

Easy Setup
Show the simple setting window.
%nprocshared
Specify the parallel number.
Link0
#nproc=n
Specify the number of processors.
#Chk=file
Specify the checkpoint file.
# Mem = n
Specify the amount of dynamic memory in words. It is also possible to specify units of KB, MB, GB, KW, MB, GW. (Default: 6 MW)
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#
Specify the beginning of the route section.
#N
Output is done at the standard level. (Default)
#P
Perform detailed output. The execution time at the start and end of each link, and the information on convergence of SCF are output.
#T
Specify a concise output that only outputs important information and results.
Hamiltonian

Specify the Hamiltonian to use.

Ltd.
Perform Hartree-Fock calculation. Unless explicitly specified, RHF is used for singlet and UHF is used for higher multiplicity.
rhf
Restricted Hartree-Fock calculation is performed.
uhf
Unrestricted Hartree-Fock calculation is performed.
am1
We will perform semi-empirical calculations using AM1 Hamiltonian.
pm3
We perform semi-empirical calculation using PM3 Hamiltonian.
pm3mm
We perform semi-empirical calculations using PM3 Hamiltonian with molecular dynamics correction on HCON binding.
b3lyp
Compute the density functional method combining the Becke 3 functional with the LYP nonlocal correlation functional.
ub3lyp
Unrestricted version of b3lyp.
mp2
Following Hartree-Fock calculation, Moller-Plesset correlation energy correction up to the second order is performed.
ump2
It is an Unrestricted version of mp2.
mp4
Following Hartree-Fock calculation, Moller-Plesset correlation energy correction up to the fourth order is performed.
ump4
It is an Unrestricted version of mp4.
cis
Calculate the excited state using one-electron excitation CI.
cisd
Calculate the excited state using two electron excitation CI. (Synonymous with CI)
indo
We will perform semi empirical calculations using INDO Hamiltonian.
ondo
We will do semi-empirical calculations using CNDO Hamiltonian.
gvb
Perform general valence bond (GVB) calculation.
Basis
Specify the set of basis functions.
Pop

Control of molecular orbital output, electron density analysis, atomic charge distribution and so on.

none
It does not output molecular orbits and does not analyze electron density.
minimal
It outputs atomic charge and orbital energy.
regular
We output 5 occupied orbits and 5 virtual trajectories. Also output density matrix and Mulliken electron density analysis.
full
All occupied orbits and virtual trajectories are output. Also output density matrix and Mulliken electron density analysis.
Calc. Type

Perform structure optimization calculation by EF (Eigen Vector Following) method.

opt
Perform structure optimization.
opt=z-matrix
Structure optimization is performed with internal coordinates.
opt=modredundant
redundant Add, delete, and modify the definition of internal coordinates (including search and binding information). An input section is required after the structure specification.
opt=(ts,noeigentest,calcfc)
Optimize for transition state. We do not test curvature. Calculate the force constant for the first time
irc
Track reaction path
irc=(maxpoint=20, stepsize=20t, calcfc)
It tracks the reaction path. Specify the number of points on the route and the step size. Calculate the force constant for the first time
MaxCyc
Sets the maximum number of optimization steps.
Freq
freq
Calculate force constants and frequencies.
freq=raman
We calculate the Raman intensity in addition to the IR intensity.
freq=vcd
Calculate oscillating circular dichroism (VCD) intensity in addition to normal frequency analysis
freq = noraman
Hartree-Fock Raman intensity is not obtained by analytic frequency calculation.
freq=nraman
Calculate the polarizability derivative by numerically differentiating the analytical dipole derivative for the electric field.
freq=nnraman
Calculate the polarizability derivative by numerically differentiating the analytical polarizability on nuclear coordinates.
Charge
Specify the value of the charge.
Multiplicity
Specify multiplicity.
for example,
for example,
Calculate excited state energy using time-dependent Hartree-Fock or DFT method
td=(nstates=n)
For the n states, we obtain the energy of the excited state using the time dependent calculation method. (Default 3)
gfinput
Outputs the basis function system in the same format as the input format.
gfprint
It outputs the basis function system in tabular form.
nosymm
Do not reorient the coordinates and perform all calculations in Z-matrix orientation.
guess=read
Read initial wave function from checkpoint file
geom=check
Fetch the molecule specification section from the checkpoint file.
Others
Fill in other keywords.

6.8.2. Import Keywords

Only keywords (calculation conditions) are read from the existing Gaussian input file.

6.8.3. Run

If Gaussian's input file is opened in the main window, use Gaussian to execute it. If it is not open, save the Gaussian input file and run Gaussian.

When saving the input file, output format of coordinates changes according to the selection of Coordinate Format choice (Z-Matrix or XYZ) and Z-Matrix / XYZ tab of Coordinate Viewer.

Gaussian's program path can be changed with:: menuselection: Tools –> Preferences –> Program Path.

Following file will be generated with execution. For example, the file/folder name when the input file is: file: water.gjf is shown together.

type Description
log file
water.log
 Calculation log file.
bat file
water.gjf.bat
 It is a batch file for running Gaussian.
Working directory
water_gau_tmp\
Working directory.

The job is run through Winmostar Job Manager.

6.8.4. Open Log File (log/out)

Open the log file with a text editor.

6.8.5. Animation

6.8.5.1. Optimization

Creates and displays animation of structural optimization calculation from information of log file.

For the animation display operation method, see Animation window.

6.8.5.2. IRC/modred

Creates and displays animation of IRC calculation from information of log file.

For the animation display operation method, see Animation window.

6.8.6. Analyses

6.8.6.1. MO, UV-Vis, Charge & NMR

Information on molecular orbital, UV-Vis, charge, NMR from the information of the log file is acquired and displayed.

Information on the charge read can be displayed in Viewport by selecting View ‣ Labels/Charges ‣ Show Mulliken Charge and so on.

Refer to Energy Level Diagram window, MO Plot window, UV-Vis Spectrum window, NMR Window for how to operate the subwindow.

6.8.6.2. IR/Raman

Select the log file and display the vibration spectrum (IR or Raman spectrum).

Refer to IR Spectrum Window for how to operate the subwindow.

6.8.6.3. RESP Charges

Calculate the point charge based on the RESP method from the esp file.

The esp file to be read must have been output from a calculation performed by selecting RESP/ESP in Configure ‣ Easy Setup. Spin multiplicity is assumed to be 1. Internally, RESP charge is calculated using Antechamber.

To use this function, you need to use G09.C.01 or later version; if you use the version before G09.C.01, you need to change the IOP.

Warning

To use this function, CygwinWM setup is required.

6.8.7. FormChk

G09W, G03W Activate Formchk of utility, create formatted .fch file from .chk file and display it.

6.8.8. Import Fchk (Cubegen) File

G09W, G03W Start Cubegen of the utility, read the .fch file and create the Cube file. If you do not have Cubegen, use OpenCubegen from Winmostar.

For how to operate the subwindow, please refer to MO Plot window and the following.

Property
MO
Molecular orbital
Density
Electron density
ESP
ESP
Spin
Spin density (α - β)
Alpha
α spin density
Beta
β spin density
Current Density
Current Density
Shielding Density
Shielding Density
Type
Specify the option of the Density keyword. (HF, MP 2, CI, QCI)
Cube
Output the Cube file.

6.8.9. Import Cube File

Read and display the Cube format file.

For GAMESS pun file, convert it to Cube file.

For how to operate the subwindow, please refer to MO Plot window and the following.

cube Manipulation

Perform operations on cube files specified in File 1 and File 2.

map
Map the data in the lower column to the data in the upper column. (Example mapping ESP to Density)
subtract
We will cover the difference between the data of the two cube files.
sub 2
We will cover the difference between the squares of the data of two cube files.
add
We will cover the sum of two cube files.
Cube
The calculation result of the cube file targeted by Map is output and displayed.
Cubegen
Start Cubegen, read the fch file and create a Cube file. For details, see Import Fchk (Cubegen) File.

6.8.10. Paired Interacting Orbitals

Paired Interacting Orbitals Executes analysis. For details, see PIO analysis window.