Reference manuals
Gaussian
Petr Kulhánek
kulhanek@chemi.muni.cz
National Center for Biomolecular Research, Faculty of Science Masaryk University, Kotlářská 2, CZ-61137 Brno
nee manuals - Gaussian
Gaussian
http://www.gaussian.com
Help:
Support -> Gaussian 16 Documentation:
• Gaussian 16 Users Reference
• Keyword List
!!! All outputs below are only examples !!!
Their content is not related to the solved tasks.
nee manuals - Gaussian
Input file
LinkO commands are optional commands introduced after"%". They can specify the
archive name (checkpoint), amount of memory, number of processors, etc.
Command line    is specified after # (see Route (#)). It specifies QM method and type of
calculation.
basis set
>QM method
charge
%Chk^h2o. chk # RHF/cc-pVDZ*bpt
geometry optimization
multiplicity M= 2S + 1
optimization of water molecule geometry
0 1
0 0.000000 0.000000 -0.154167
H 0.000000 0.854766 0.538096
H 0.000000 -0.854766 0.538096
total spin of electrons
f
blank line comment
blank line
blank line
system geometry specification (Cartesian coordinates in A) terminated by a blank line
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How to run calculations (tests only
It is strictly prohibited to run calculations in Gaussian directly in home directories. All Gaussian jobs need to be submitted to a batch system (see next page).
For testing in the scratch directory only:
activate gaussian module
$ module add qaussian , . .
^  . n (only once in a terminal)
$ gib job.com
^ ^ name of input file
name of gaussian program
After completing the task, the result of the calculation will be saved in the job.log file, th last line of the file must state:
Normal termination of Gaussian 0 9 at Sun Oct
otherwise, the calculation is unsuccessful. The reason for premature termination of th calculation must be found in the output file.
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How to run calculations on WOLF
$ psubmit default job.com [ncpus=N]
/
batch system queue     input file name
[mem=XXg]
resources (optional)
[] is not part of specification
number of CPUs for parallel execution
amount of memory in GB
Example:
$ psubmit default job.com ncpus=2 mem=2 0g
nee manuals - Gaussian
Energy calculation (Single-point calculation)
Geometry optimization
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Energy calculation and optimizatio
%Chk=h2o.chk # RHF/cc-pVDZ
energy calculation   (water molecule)
0 1 0 0.000000 H 0.000000 H 0.000000
<-
0.000000 -0.154167 0.854766 0.538096 -0.854766 0.538096
%Chk=h2o.chk
# RHF/cc-pVDZ Opt
geometry optimization   (water molecule)
0 1 0 0.000000 H 0.000000 H 0.000000 <-
0.000000 -0.154167 0.854766 0.538096 -0.854766 0.538096
without the Opt keyword, only energy and WF are calculated including system properties
(single point calculation)
terminated by a blank line
request geometry optimization
terminated by a blank line
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Calculation progress
Single-point calculation
) )
Geometry optimization
for input geometry
Input geometry
Q
□
Estimation of the wave function (Guess)
Qi
Calculation of E and wave function (SCF)
the WF guess for the next step is taken from the previous step
gradient calculation
D
geometry change
No
a
Population analysis and calculation of system properties
Estimation of the wave function (Guess)
Calculation of E and wave function (SCF)
Population analysis and calculation of system properties
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Data extraction in CLI
Geometry optimization
1) Module activation:
$ module add qmutil | only once in a given terminal
2) Optimization process (energy):
It is advisable to analyze the course of $ extract-gopt-ene job. log optimization, in the GUI programs such as
vmd or Avogadro
3) Optimization process (all geometries): J
$ extract-gopt-xyz job.log > opt.xyz
4) Obtaining optimized geometry (last = optimized geometry): $ extract-xyz-str opt.xyz last > last.xyz
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Data extraction in CLI
Geometry optimization process (energy):
$ extract-gopt-ene job.log
# Coordinate:
# Step Energy [kcal/mol] Energy [au] #--------------------------------------
1
2
3
4
0 0 0 0
000 171 188 190
optimization step number
relative energy to the first geometry
028650961 028922822 028950914 02895393
absolute energy in Hartree
The energy (in a.u.) of the optimized structure, i.e., the geometry contained in opt.xyz. The opt.xyz geometry can be visualised in the programs: Avogadro, Nemesis, vmd.
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Vibrational analysis
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Vibrational analysis
%Chk=h2o.chk # RHF/cc-pVDZ Freq
vibrational analysis
0 1
0 0.0000000 H 0.0000000 H 0.0000000 <-
0.0000000 -0.0780430 0.7492420 0.5000340 -0.7492420 0.5000340
request vibrational frequency calculation
terminated by a blank line
For optimized geometry (stationary point on PES), the type of stationary point can be determined from the number of imaginary frequencies of normal vibrations:
> 0 imaginary frequencies -> local minimum
> 1 imaginary (negative) frequency -> first order transition state
Vibrational analysis requires Hession calculation, which can be very computationally intensive.
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Calculation progress
Single-point calculation on optimized geometry
O
ut geometry
Estimation of the wave unction (Guess)
O
Calculation of E and wave function (SCF)
gradient calculation E
calculation Hessian E
D
The ideal gas model is used!
Harmonic approximation
i
pulation analysis calculation of em properties
Calculation of vibrational frequencies
The harmonic approximation is valid only for a stationary point on the PES
Thermodynamic properties
Stationary point test
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BSSE
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CP correction for BSSE
%Chk=ene.chk
# RHF/cc-pVDZ Counterpoise=2<-
SP calculation with BSSE correction
0 1
0(Fragment=l H (Fragment=l )" H(Fragment=l) 0(Fragment=2) H(Fragment=2) H(Fragment=2)
<-
231135 374693 074728 648273 166742 6494
0.063539 0.253491 -0.864502 1.893276 2.355543 1.311764
0
1 0 ■1 ■1
203312 116647 130817 229780 894982
-0.798971
request energy calculation with BSSE correction
terminated by a blank line
Fragments representing interacting molecules.
Counterpoise correction of BSSE requires 5 energy calculations (AB, A(B), (A)B, A, and B),
which are performed by Gaussian automatically.
This correction can be used during geometry optimization.
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Calculation progress
r
nput geometry
o
Estimation of the wa function (Guess)
■n
Estimation of the wa. function (Guess)
J
Calculation of E and wave function (SCF)
o
Calculation of E and wave function (SCF)
o
Population analysis and calculation of system properties
AB
Population analysis and calculation of system properties
A(B)
^cp ~ EAB + (EA E
Estimation of the wa. function (Guess)
Calculation of E and wave function (SCF)
D
Estimation of the ^ wave function (Guess)
Estimation of the ^ wave function (Guess)
Calculation of E and wave function (SCF)
o
Calculation of E and wave function (SCF)
o
Population analysis and calculation of system properties
Population analysis and calculation of system properties
sis of
es
(A)B
Population analysis and calculation of system properties
B
A(B)
) + (EB E(A)B)
Corrected energy
BSSE
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Finding a reaction path
SCD
Single Coordinate Driving
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Driving, strategy
The goal of SCD is to find an estimate of transition state. The driving is performed by changing the selected geometric parameter and optimizing all other degrees of freedom. The parameter can be, for example, a shortening of the length between the atoms between which a bond is formed during the reaction.
Selection of a suitable reaction coordinate describing the course of the reaction:
• The reaction coordinate is usually very complicated.
• It is necessary to use a simplified coordinate that best captures the intended change.
• The coordinate is chosen from simple geometric parameters (length, angle, torsion angle, etc.)
• The distances are natural choice in reactions, usually between atoms where bonds are formed or broken.
• Torsional angles are usually used for conformational transitions.
• The best choice for the starting geometry is to select a state with the smallest number of conformational degrees of freedom. Thus, driving need not to be necessary always performed from reactants to products.
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Driving, input
%Chk=driving.chk
# PM3 Opt=ModRedundant NoSymm
single coordinate driving
XX X X X
<-
B Al A2 S NStep StepSize
request driving
charge and multiplicity geometry
terminated by a blank line terminated by a blank line
distance
step size (positive or negative number), the number must contain a decimal point (for distance the optimal step length is about 0.1 A)
number of steps (integer)
SCD
indexes of atoms between which we will change the distance (indexed from one)
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Driving, example
blank lines
We shorten the length (B) between atoms 4 and 11 in fifteen steps, always by 0.1 A.
Detailed documentation:
http://gaussian.com/opt/ -section Options/ModRedundant
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Calculation progress
Q
nput geometry
Estimation of the wave function (Guess)
Geometry optimization
■
parameter change
Population analysis and calculation of system properties
Q
geometry optimization
Calculation of E and wave function (SCF)
Q
D
gradient calculation E
geometry change
local inimum?
No
Yes
Optimized geometry
4
During optimization, the value of the SCD parameter is set a constant.
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Data extraction in CLI
1) qmutil module activation:
$ module add qmutil 's advisable to analyze the course of SCD,
in the GUI programs such as vmd or
2) Display the course of SCD (energy): $ extract-gdrv-ene job.log
3) Display the course of SCD (all geometries): $ extract-gdrv-xyz job.log > drv.xyz
4) Extract given geometry (geometry with index N): $ extract-xyz-p drv^cyz^N > TS_guess.xyz
The number of the structure we want to extract from the drv.xyz file.
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[Driving, results_
Example: Diels-Alder cycloaddition reaction
# Coordinate: R(4,7)
# Step Value Energy  [kcal/mol]    S Energy [au]
#--------------------------------------------------
1	1.	5380	0	.000	-	0	.002554791
2	1.	6380	2	. 648	/	0	.006774307
3	1.	7380	8	.526	/	0	.016141320
4	1.	8380	15	.826	/	0	. 027774776
5	1.	9380	23	.919	/	0	.040672342
6	2 .	0380	32	. 626	/	0	.054548199
7	2 .	1380	41	.714	/	0	.069029627
8	2 .	2380	50	.746	/	0	.083423613
9	2 .	3380	59	.194	/	0	.096886686
10	2.	4380	66	.597	/	0	.108683559
11	2.	5380	72	. 657	/	0	.118340986
	2.	6380	77	^5i_	/	0	. 125671188
	) 2.	7380	C"80	.400	L>	0	.130680500
14\	2.	8380	36	.19Í	\	0	.060228061
15\	2.	9380	35	.376\	\	0	.058929736
16 >	1 3.	0380	34	.774]	l\	0	.057970622
Structure number  Structure with maximum energy on the reaction path =>
estimate of transition state
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Driving, results
	90
	80
	70
1	60
~o	
E	50
ra	
o	40
LU	30
<	
	20
	10
	0
Example: Diels-Alder cycloaddition reaction
coordinate driving
product bond breaking
(input state for driving)
Structure with maximum energy on the reaction path
=>
estimate of transition state
The break indicates that the coordinate does not correctly describe the course of the reaction.
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Geometry optimization
of
transition state
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TS optimization, input
request optimization of the transition state
%Chk=ts.chk
# PM3 Opt(CalcFC,TS,NoEigenTest,MaxCycle=25)
transition sta\e optimization
XX
X......... ,
X......... ,
X......... ,
<-
CalcFC
CalcAII
terminated by a blank line
force constants (Hessian) are calculated on the input geometry
force constants (Hessian) are calculated on each geometry during optimization (Newton-Raphson method)
nee manuals - Gaussian
TS optimization, output
The output is processed in the same way as a regular geometry optimization.
• If the maximum number of steps is exceeded, you can try to continue the optimization (extract the last coordinates and perform the optimization again). The second option is to switch from CalcFC to CalcAII.
• If the TS is not found within about 30 optimization steps, it is necessary to find a better TS estimate.
• The TS must have only one imaginary ("negative") frequency.
• The vibrational motion corresponding to an imaginary frequency must follow the formation and termination of the bonds corresponding to the reaction step.
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Output file
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Output file: sections 1 and 2
1. Input geometry in internal coordinates
! Initial Parameters ! !   (Angstroms and Degrees) !
! Name Definition Value Derivative Info. !
! Rl R(l,2) 1.0999 estimate D2E/DX2 !
! R2 R(l,3) 1.0999 estimate D2E/DX2 !
! Al A(2,l,3) 101.9929 estimate D2E/DX2 !
2. WF initial guess
number of base siset functions = number of c coefficients, which need to be found during SCF
25 cartesian basis functions
Two-elegfj^efrintegral symmetry is turned off.
24 bsreis functions,        47 primitive gaussians, 5 alpha electrons 5 beta electrons
nuclear repulsion energy 8.0071357792 Hartrees.
NAtoms=        3 NActive=        3 NUniq=        3  SFac= 1.00D+00 NAtFMM=      60 NAOKFM=F Big=F One-electron integrals computed using PRISM. NBasis=        24  RedAO= T    NBF= 24 NBsUse=        24  1.00D-06 NBFU= 24
Harris functional with IExCor=    205 diagonalized for initial guess.
initial guess of WF
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Output file: section 3
3. Energy and WF calculations
virial theorem
SCF Done:    E(RHF)  =    -75.9901319773 A.U.  after      10 cycles
Convg    =        0.5258D-08 -V/T = 2.0057
/
total energy
/
Number of SCF cycles needed to find E and WF Energy change in the last cycle of SCF
Energy is in a.u. (Hartree) Full SFC progress is printed, if #P is specified in the input file.
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Output file: section 3, cont.
Cycle      1    Pass 1    IDiag 1: E= -75.9710832672194
DIIS:  error= 4.94D-02 at cycle      1 NSaved= 1.
NSaved= 1 IEnMin= 1 EnMin= -75.9710832672194 IErMin= 1 ErrMin= 4.94D-02
ErrMax= 4.94D-02 EMaxC= 1.00D-01 BMatC= 1.08D-01 BMatP= 1.08D-01 IDIUse=3 WtCom= 5.06D-01 WtEn= 4.94D-01 Coeff-Com: 0.100D+01 Coeff-En: 0.100D+01 Coeff: 0.100D+01
Gap= 0.463 Goal=      None        Shift= 0.000
GapD=        0.4 63 DampG=2.000 DampE=0.500 DampFc=l.0000 IDamp=-l. RMSDP=6.04D-03 MaxDP=l.13D-01 OVMax= 1.12D-01
<- shortened
Cycle    10—Pass 1    IDiag 1:
E= -7 6.0418IN^4 8 07 68 Delta-E= 0.000000000000 Rises=F Damp=F
DIIS:  ^tfor= 2S^-08 at cycle    10 NSaved= 10.
NSaved=10^EnMin=l^\^nMin= -76.0418076480768 IErMin=10 ErrMin= 2.15D-08
ErrMax= 2.^D-08 EMaxCS^l. 00D-01 BMatC= 8.09D-15 BMatP= 1.54D-13 IDIUse=l WtC%n= 1. 00D+00 Rhs^n= 0.00D+00
Coeff-Com:   -0>^9D-06 0 .154D^,0 . 181D-04-0 . 155D-03 0.397D-03 0.649D-03 Coeff-Com:   -O.lSoD-01  0. 669D-01^N44lD+00 0.138D+01
Coeff: -0.199^06 0.154D-05 0.lS>S^04-0.155D-03 0.397D-03 0.649D-03
Coeff: -0.110D>^  0.669D-01-0.44lD+frss0.138D+01
Gap= 0.546 Goal=\None        Shift= O^Q.0
RMSDP=4.57D-09 MaxDP=4N^2D-08  DE=-3.84D-13 OVMaNt 8 . 92D-08
SCF Done:    E(RHF)  =    -76.0418076481 A.U.  after      10 cycles
Convg    =        0.4573D-08 -V/T = 2.0008
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Output file: section 4
4. Gradient calculation
forces = negative energy gradient (in atomic units)
\
Center	Atomic		Forces		(Hartrees/Bohr)		
Number	Number		X		Y		Z
1	8	0.	000000000	0.	000000000	0.	131133317
2	1	0.	000000000	-0.	085534245	-0 .	065566658
3	1	0.	000000000	0.	085534245	-0 .	065566658
Cartesian Forces
Max
0.131133317 RMS
0.06702083!
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Output file: section 5
5. Geometry ptimization
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization.
Internal    Forces:    Max 0.107734851 RMS 0.088033019
shortened
Variable
Old X
Rl 2.07857 R2 2.07857 Al 1.78011 I tern Maximum Force RMS Force Maximum Displacement RMS Displacement Predicted change in En^
-DE/DX     Delta X     Delta X (Linear) (Quad) 0.00000 -0.21160 0.00000 -0.21160 0.00000 -0.02126 TnreshulCh 0.000450 0.000300 0 .001800 0 .001200 -J.060008D-02
■0 . 10773 ■0 . 10773 ■0 . 00599 V
1*07735
0.088033 0 .177009 0.154831
Delta X (Total) -0.21160 -0.21160 -0. 02126 Lverged?
New X
1.86697 1.86697 1.75885
GradGradGradGradGradGXadGradGradGradGradGradGradGradGradGradGradGradGrad
convergence criteria for geometry optimization termination
planned geometry change
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Output file: section 6
6. Optimized geometry
Item Value Threshold Converged?
Maximum Force 0.000267 0.000450 YES
RMS Force 0.000172 0.000300 YES
Maximum Displacement 0.000999 0.001800 YES
RMS Displacement 0.000967 0.001200 YES
Predicted change in Energy=-2.315429D-07 Optimization completed.
-- Stationary point found.
!      Optimized Parameters !
!   (Angstroms and Degrees) !
!  Name    Definition Value Derivative Info. !
!   Rl        R(l,2) 0.9463 -DE/DX=      -0.0001 !
!   R2        R(l,3) 0.9463 -DE/DX=      -0.0001 !
!  Al        A(2,l,3) 104.696 -DE/DX=      -0.0003 !
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
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Output file: section 7
7. Population analysis and system property calculations (shortened)    ^ccupied orbiatals
Alpha occ. eigenvalues --Alpha virt.  eigenvalues --
-20 . 54839 0 .18742
■1.34218 0 .25779
■0 . 70556 0 .79793
■0 .56822 0.86396
■0 .49389 1.16257
energy of molecular orbitals
\
virtual orbitals
Mulliken atomic charges 1
1 0 -0.292462
2 H 0.146231
3 H 0.146231
Sum of Mulliken atomic charges
Mulliken atomic (point) charges
0. 00000
Dipole moment   (field-independent basis,  Debye):
X= 0.0000        Y= 0.0000 Z=
Quadrupole moment   (field-independent basis,  Debye-Ang): XX= -7.0085      YY= -4.1369 ZZ=
XY= 0.0000      XZ= 0.0000      YZ =
2.0430    Tot= 2.0430
-5.7327 0.0000
dipol and quadrupole electrostatic moments
Type of population analysis can be selected the pop keyword.
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Output file: section 8
Differentiating once with respect to electric field.
with respect to dipole field. Electric field/nuclear overlap derivatives assumed to be zero Keep Rl ints in memory in canonical form, NReq=873499. There are 3 degrees of freedom in the 1st order CPHF.
3 vectors produced by pass    0 Testl2= 3.17D-15 3.33D-08 XBigl2 AX will form 3 AO Fock derivatives at one time.
3 vectors produced by pass    1 Testl2= 3.17D-15 3.33D-0
IDoFFX=0. 1.15D+00
3 vectors produced by pass    2 Testl2 3 vectors produced by pass    3 Testl2 3 vectors produced by pass    4 Testl2 3 vectors produced by pass    5 Testl2 3 vectors produced by pass    6 Testl2 2 vectors produced by pass    7 Testl2 1 vectors produced by pass    8 Testl2 Inverted reduced A of dimension 24 End of Minotr Frequency-dependent properties file End of Minotr Frequency-dependent properties file Symmetrizing basis deriv contribution to polar: IMax=3 JMax=2 DiffMx= 0.00D+00
G2DrvN:  will do 4 centers at a time, making
3.17D-15 3.33D-0S 3.17D-15 3.33D-0S
3.17D-15 3.33D-0S 3.17D-15 3.33D-0S 3.17D-15 3.33D-0S 3.17D-15 3.33D-0S 3.17D-15 3.33D-0S
XBigl2 = XBigl2 = XBigl2 = XBigl2 = XBigl2 = XBigl2 = XBigl2 = XBigl2 =
5.63D-02 7.24D-03 2.25D-04 4.04D-06 2.96D-08 3.37D-10 1.95D-12 2D-15
9.8:
with in-core refinement.
721 does not exist
722 does not exist
1 passes doing MaxLOS=2
Calling FoFCou,   ICntrl=    3107 FMM=F IlCent= FoFDir/FoFCou used for L=0 through L=2. End of G2Drv Frequency-dependent properties file End of G2Drv Frequency-dependent properties file
0 AccDes= 0.00D+00
721 does not exist.
722 does not exist.
6.84D-01
1.22D-01 3.79D-02 7.06D-03 8.17D-04 7.41D-05 9.10D-06 5.99D-07 4.57D-08
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Output file: section 9
6(5) vibrací musí mít nízké frekvence (ideálně nulové) - 3 translační a 3 rotační stupně volnosti systému
Full mass-weighted force constant matrix:
Low frequencies --- -40.7995      -0.0019      -0.0015        0.0005 37.6815
Low frequencies --- 1774.9584  4112.7795 4211.8138
Harmonic frequencies   (cm**-l),   IR intensities   (KM/Mole),  Raman scattering activities   (A**4/AMU),  depolarization ratios for plane and unpolarized incident light,  reduced masses   (AMU),   force constants   (mDyne/A), and normal coordinates:
55.2358
Frequencies Red. masses Frc consts IR Inten Raman Activ Depolar (P) Depolar (U) Atom AN
1 8
2 1
3 1
1 Al
1774.9584
1
2 SO
4 0 0
0818 0080 8414 7861 5271
6903 v
2
4112.7795
1 10 21 68
0
X
0.00 0. 00 0. 00
0460 4246 1644 9225 1703 0.2910 Y
0.00 0 . 58 -0.58
B2
4211.8137 1. 0821 11.3093
60 34 0 0
Z
0 . 05 -0.40 -0.40
X
0.00 0. 00 0. 00
8089 7495 7500 8571 Y
0.07 -0 .56 -0 .56
frequencies of normal vibrational modes
z
0 . 00 0.43 -0.43
direction of atom movements during the normal mode vibration
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Output file: section 10
E(RHF)
-76.0270533118
IDEAL GAS MODEL
Ek ~ Em (R0pt,m ) + EyRTJ
- Thermochemistry -
Temperature
Zero-point correction Thermal correction to Thermal correction to Thermal correction to Sum of electronic and Sum of electronic and Sum of electronic and Sum of electronic and
aceno
Energy= Enthalpy= Gibbs Free Energy= zero-point Energies= thermal Energies= thermal Enthalpies= thermal Free Energies
0.02300! 0.025843 0 . 026787 0.005411
-76 . 004045 -76 . 001211 -76.000267 -76.021642
zero-point vibrational energy
Gibbs energy
Total
Electronic Translational Rotational Vibrational
E (Thermal) KCal/Mol 16.216 0.000 0.889 0.889 14 .439
CV
Cal/Mol-Kelvin 5. 989 0. 000 2 . 981 2 . 981 0. 028
S
Cal/Mol-Kelvin 44 . 988
0.000 34.608 10.376
0.004
http://gaussian.com/g_whitepap/thermo.htm
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Output file: section 11
7. Calculations with BSSE corrections
Counterpoise: corrected energy Counterpoise:  BSSE energy =
-152.060077655641 0.002829142358
BSSE correction
final interaction energy with BSSE correction
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Output file: section 12
		! Initial	Parameters !		
		! (Angstroms	and Degrees) !		
! Name	Definition	Value	Derivative Info.		!
! Rl	R(l,2)	1.4982	estimate	D2E/DX2	,
! R2	R(l,6)	1.3351	estimate	D2E/DX2	!
! R3	R(l,17)	1.0954	estimate	D2E/DX2	!
! R4	R(2,3)	1.4982	estimate	D2E/DX2	!
! R5	R(2,7)	1.6028	estimate	D2E/DX2	!
! R6	R(2,13)	1.5363	estimate	D2E/DX2	!
! R7	R(3,4)	1.3351	estimate	D2E/DX2	!
! R8	R(3,18)	1.0954	estimate	D2E/DX2	!
! R9	R(4,5)	1.5075	estimate	D2E/DX2	!
! RIO	R(4,ll)	3.7721	Scan		!
! Rll		1.0^24	esmmate	D2E/DX2	!
R - distance between atoms 4 and 11
initial value
indicates that the coordinate is subject of SCD
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