Simple geometry optimisation and frequency calculation on water
0 1
o
0.000000 0.127170 0.000000
h
0.757997 -0.508679 0.000000
h -0.757997
-0.508679 0.000000
--------------------------------
#P CCSD(T)/6-311+G(2d,2p) Opt
Geometry optimisation of water with a Z-matrix (necessary with numerical gradients)
0 1
h
o,1,OH
h,2,OH,1,HOH
OH 0.9572
HOH 104.52
--------------------------------
%Chk=h2o.chk
%Mem=200MB
#P MP2=RW aug-cc-pVTZ MaxDisk=2000MB Pop=(Full,NO,MK,NBO)
Nosymm
Compound job with more input
0 1
o
0.000000 0.127170 0.000000
h
0.757997 -0.508679 0.000000
h -0.757997
-0.508679 0.000000
! RW
3, 0
--Link1--
%Chk=h2o.chk
#P MP2=RW aug-cc-pVTZ Pop=(Full,NO,MK,NBO) Density=Current
Guess(Read,Only) Geom=AllCheck
--------------------------------
%chk=PhO_VTZ
#t B3LYP/cc-pVTZ Freq(ReadFC,ReadISO) Geom=Check
Example of Freq calculations with new isotopes
O(18) Phenoxyl Radical; CCL 14 Jun 2001
0 2
298.150 1.00000
12
12
12
12
12
12
18
1
1
1
1
1
------------------------------------------------
#P B3LYP/6-31G* Scf(Conver=6) SCRF=(CPCM,Read)
Solvation calculation with non-default dielectric constant
Cu+, B3LYP/6-31G*, Vacuum, E8, 21/5-01
1 1
cu 0.0 0.0 0.0
! CPCM data
EPS=4.0
------------------------------------------------
%mem=200mw
#P HF/STO-3G SCRF(PCM,solvent=water)
Simple PCM input to get non-polar energies
1 1
cu 0.0 0.0 0.0
------------------------------------------------
Chk=APF03Monpmm
%Mem=28GB
%NProcShared=16
# TD(NStates=10)/lc-pbepbe/6-31G(d)
iop(3/107=0100000000,3/108=0100000000)
SCF(MaxCycles=512,XQC,Fermi) Geom(Connectivity)
Scrf(solvent=o-DiChloroBenzene)
APF03Monpmm
0 1
C
-7.60804968 -2.30417181 -0.22155883
C
-8.98640433 -2.16504207 -0.07565774
C
-9.54920751 -0.91947813 0.21091194
C
-8.74122111 0.21029755
0.35656787
C
-7.36721291 0.07870952
0.21260668
C
-6.80221512 -1.17580738 -0.07583145
H
-7.17416201 -3.27495209 -0.44537243
H
-9.62998425 -3.03306296 -0.18598201
H
-10.62602315 -0.82906697
0.32127531
H
-9.18925088 1.17558731
0.57929966
C
-4.33948705 -1.93732702 -0.42749252
C
-5.35252950 -1.01536584 -0.17135522
C
-5.03768557 0.33629795
0.05483102
C
-3.72451268 0.76823030
0.02975335
C
-2.69147025 -0.15054230 -0.23716495
C
-3.02176126 -1.49890999 -0.46246911
H
-4.56688645 -2.98431572 -0.60725972
H
-3.48130374 1.80730595
0.23491654
H
-2.23240826 -2.21083318 -0.68824507
C
-6.29381893 1.14931802
0.32383222
C
-6.26700716 1.77016074
1.72829846
H
-7.20466940 2.29743541
1.93142522
H
-6.13026215 1.00296054
2.49566119
H
-5.44882230 2.49264205
1.81369355
C
-6.48662270 2.24646998 -0.73325400
H
-7.42850449 2.77844255 -0.56492071
H
-6.50589005 1.82324431 -1.74156307
H
-5.67303173 2.97726158 -0.68152653
C
-1.30523481 0.30725727 -0.27985587
C
-0.82773658 1.57659766 -0.52004023
S
0.01746948 -0.78301193 0.00437106
C
0.58016347 1.67165140 -0.48651543
H
-1.47547948 2.41626100 -0.74496862
C
1.20896102 0.47189032 -0.22248974
H
1.13166856 2.58567577 -0.66116630
C
2.62541312 0.16881330 -0.12810343
C
3.63700733 1.18938865 -0.11636111
C
3.10577249 -1.12552930 -0.03734398
C
5.04560444 0.85625289 -0.01532928
C
4.47396023 -1.44777627 0.06782310
H
2.40340988 -1.95412930 -0.05020802
C
5.48759808 -0.50709262 0.07945153
H
4.72736500 -2.50124330 0.14615466
N
5.83412292 1.93256136 -0.02390614
N
3.41915069 2.50321035 -0.19186127
S
4.86921471 3.23341794 -0.14363884
C
6.89241016 -0.87157624 0.17497279
C
7.99670073 -0.07071519 0.37629717
S
7.38694842 -2.54126055 0.04157578
C
9.21613007 -0.79310270 0.42958351
H
7.91888882 1.00293999
0.48226461
C
9.04229259 -2.13839605 0.26545750
H
10.18491571 -0.33219811 0.58420162
H
9.79037443 -2.91969995 0.25837832
1 2 1.0 6 2.0 7 1.0
2 3 2.0 8 1.0
3 4 1.0 9 1.0
4 5 2.0 10 1.0
5 6 1.0 20 1.0
From G09 manual:
Long range corrected functionals. The non-Coulomb part of exchange functionals typically dies off too rapidly and becomes very inaccurate at large distances, making them unsuitable for modeling processes such as electron excitations to high orbitals. Various schemes have been devised to handle such cases. Gaussian 09 offers the following functionals which include long range corrections:
LC-wPBE: Long range-corrected version of wPBE.
CAM-B3LYP: Handy and coworkers’ long range corrected version of B3LYP using the Coulomb-attenuating method.
wB97XD: The latest functional from Head-Gordon and coworkers, which includes empirical dispersion. The wB97 and wB97X variations are also available. These functionals also include long range corrections.
In addition, the prefix LC- may be added to any pure functional to apply the long correction of Hirao and coworkers [Iikura01]: e.g., LC-BLYP.
IOp(3/107)
Example (scan of the last dihedral):
#P B3LYP/6-31G* Scan
Title
0 1
h
c 1 ch1
h 2 ch2 1 hch1
h 2 ch2 1 hch1 3 hch2 1
o 2 oc 1 hco1 4 hco2 1
h 5 oh 2 coh 1 hoch 0
ch1=1.093
ch2=1.101
oc =1.419
oh =0.969
hch1=108.080
hch2=108.419
hco1=106.675
hco2=112.693
coh =107.646
hoch=-180. 11 30.0
Another example:
#P MP2/6-311++G(3df,3pd) Scan
He2
0 1
he
he 1 r
r=1.1872 40 0.10
Most methods works with Oniom, e.g. optimisations and frequency
calculations. However, SCRF does not work (it is not available for
semiempirical or molecular mechanical methods).
changeparm command oo can set up a G09 Oniom calculation from an
ComQum (amber) calculation.
Example:
#P Oniom(B3LYP/6-31G*:PM3:Amber) Opt Freq
A three-layer oniom calculation of CH3-CH2-CHO
0 1
h 1.303312051
0.000000000 1.949234062 High
c 0.375760127
0.000000000 1.351034669 High
o -0.718742386 0.000000000
1.904192435 High
c 0.583631613 0.000000000
-0.143478503 Medium H
h 1.171836119 -0.887154331
-0.398970957 Medium
h 1.171836119 0.887154331
-0.398970957 Medium
c -0.720914899 0.000000000
-0.916455389 Low H
h -1.320117994 0.884637788
-0.676628009 Low
h -1.320117994 -0.884637788
-0.676628009 Low
h -0.526482757 0.000000000
-1.993329341 Low
%chk=test.chk
%mem=1000mb
#p hf sp nosymm iop(5/13=1)
scf=tight scrf=(PCM,solvent=Toluene,ExternalIteration,read)
xx
0 1
Coordinate here
dis rep cav
for x in ; do
# filename = Cavitation
Dispersion Repulsion Sum
echo "$x =
" $(grep 'Cavitation' $x.log | awk '{print $5}') $(grep
'Dispersion' $x.log | awk '{print $5}') $(grep 'Repulsion'
$x.log | awk '{print $5}') $(grep 'Total non e' $x.log | awk
'{print $6}') >>pcm.out
done
blyp IOp(3/76=1000001500) IOp(3/77=0720008500) IOp(3/78=0810010000)
bv5lyp IOp(3/76=1000001500) IOp(3/77=0720008500) IOp(3/78=0810010000)
#!/bin/sh #SBATCH -n 1 #SBATCH -t 168:00:00 export job=gauss export GAUSS_SCRDIR=$SNIC_TMP module add PGI/15.10-GCC-4.9.3-2.25 module add gaussian/g09 cd $GAUSS_SCRDIR cp $SLURM_SUBMIT_DIR/* . g09 <"$job" >$SLURM_SUBMIT_DIR/"$job".out
The program is located in
/temp4/bio/GAUSS/g98
g03 is not compiled on gefion, but g98 is compilded and can be run
with command rung98.
An older revision (A.5) is found in
/molcas/DIVPROG/lib/Gaussian/g98 (signe)
Alternative versions of g98 A.5 with a higher maximum TSARE can
be found in
/molcas/DIVPROG/lib/Gaussian/New/g98 (signe)
Gaussian-94 can be found in
/molcas/DIVPROG/lib/Gaussian/g94 (signe)
You can use the following script to run Gaussian
(/home/ulf/Bin/rung98).
You should change the rows in bold face
#!/bin/ksh
export g98root=/home/bio/GAUSS
export GAUSS_EXEDIR=$g98root/g98/bsd:$g98root/g98
export GAUSS_ARCHDIR=$PWD
export GMAIN=$GAUSS_EXEDIR
export PATH=$PATH:$GAUSS_EXEDIR
export LD_LIBRARY_PATH=$GAUSS_EXEDIR
export GAUSS_SCRDIR=/temp1/ulf/Gaussian
export G98BASIS="$g98root/g98/basis"
$g98root/g98/g98 <"$1" >>"$1".out
If you put this script in your bin directory with the name
rung98, you can then start a job with
rung98 input_file
and you will find the result in the file input_file.out.
Warnings of this type (with G98 Rev A.5) can safely be ignored:
1621782:/sw/gaussian/g98/l103.exe: rld:
Warning: Calling set_fpc_csr with (0x1000800)
1621782:/sw/gaussian/g98/l9999.exe: rld:
Warning: The aggregate IEEE exceptions required (OEX_FPU_MIN)
(0x10) not as complete as the aggregate IEEE exceptions
permitted (OEX_FPU_MAX>>8)(0x0).
1621782:/sw/gaussian/g98/l9999.exe: rld:
Warning: Use "elfdump -op " to see the floating-point
exceptions (OEX) flags for the latest object.
1621782:/sw/gaussian/g98/l9999.exe: rld:
Warning: Using aggregate 0x10 as OEX_FPU_MIN to add
floating-point exceptions flags with set_fpc_csr()
Originally on gefion, I got (Aug-12)
Erroneous write during file
extend. write -1 instead of 4096
Probably out of disk space.
Write error in NtrExt1: Bad address
Segmentation fault
Following a search in internet, it turned out that this could be
solved by inserting 0 in the file
/proc/sys/kernel/randomize_va_space
sudo echo 0 >
/proc/sys/kernel/randomize_va_space
This solved the problem
We can run gaussian03 on swegrid. It is limited to users who have
an SNAC account, but we are among those.
Install the nordugrid software on your local machine, cf. talk by
Valera and previous email from Jonas Lindeman. Get a Distinguished
Name (DN) by running the command:
grid-cert-info -subject
Then after a few days you will receive an email with your DN.
Follow the instructions, and email your DN to Jonas Lindeman and
ask for access to swegrid under the SNIC account:
snic-021-03-22-vo
Follow the instructions on http://www.swegrid.se/re/gaussian/
regarding G03. Notice that the example is a parallel job.
The swegrid_manual is attached, and some useful links are:
http://www.swegrid.se/
(SWEGRID)
http://www.nordugrid.org/
(sofware, manuals, etc.)
http://www.teokem.lu.se/internal/grid/grid.ps
(Valera's talk)
It is far from easy to compile it on Linux.
The versions on whenim64 and husmodern are copied from garm
(executables; garm.tar).
I do no know how we (who?) managed to compile it on garm (probably
originally on husmodern).
Gaussian 98 Installation Instructions for Linux
For example (one row):
f77 -nocpp -w -mips4 -64 -align64 -r10000 -G 0
-O3 -LNO:blocking=OFF:prefetch=1 -r8const -trapuv
-OPT:roundoff=3:IEEE_arithmetic=3:IEEE_comparisons=1:liberal_ivdep=TRUE:Olimit=0:reorg_common=OFF
-o
formchk
formchk.o
util.a -lblas -lfastm
This is done by the script /molcas/DIVPROG/lib/Gaussian/G98new/g98/ulfmake
%rwf=f1,1500MB,f2,1900MB,f3,1900MB,f4,1900MB,f5,1900MB,f6,1900MB,f7,1900MB
%NoSave
%Chk=myoo2.hus.chk
%Mem=800MB
#P UB3LYP/Gen Freq SCF(Vshift=0,Conver=6,MaxCycle=300)
Geom=AllCheck Guess=Read MaxDisk=13000MB
! Gen basis set
@/teo/ulf/Myo/Vac/O2/B3lyp/myobas/N
Use a normal SCF calculation input file and add in the final
step:
TD(Nstates=12,Root=1,50-50) Density Pop=Full
where
Nstates is the number of interesting states and
Root is the root of interest (for population analysis and
geometry optimisation)
50-50 indicates that you are interested in both singlet
and triplet states.
SCF Done: E(RB+HF-LYP) =
-76.4070229620 A.U. after 10
cycles
Convg
=
0.9037D-08
-V/T
=
2.0052
S**2 = 0.0000
KE= 7.601163519654D+01 PE=-1.989603930100D+02 EE=
3.745590692757D+01
Leave Link 502 at Wed Mar 28 04:59:08 2001,
MaxMem= 6291456
cpu: 7.3
(Enter /usr/local/lib/Gaussian/G98new/g98/l801.exe)
Range of M.O.s used for correlation:
1 18
NBasis= 18 NAE= 5
NBE= 5 NFC= 0
NFV= 0
NROrb= 18
NOA= 5 NOB= 5
NVA= 13 NVB= 13
Leave Link 801 at Wed Mar 28 04:59:08 2001,
MaxMem= 6291456
cpu: 0.0
(Enter /usr/local/lib/Gaussian/G98new/g98/l1101.exe)
Using compressed storage.
Will process 3 atoms per pass.
Leave Link 1101 at Wed Mar 28 04:59:10 2001,
MaxMem= 6291456
cpu: 1.7
(Enter /usr/local/lib/Gaussian/G98new/g98/l1102.exe)
Use density number 0.
Leave Link 1102 at Wed Mar 28 04:59:11 2001,
MaxMem= 6291456
cpu: 0.4
(Enter /usr/local/lib/Gaussian/G98new/g98/l1110.exe)
Forming Gx(P) for the SCF density.
Integral derivatives from FoFDir, PRISM(SPDF).
Do as many integral derivatives as possible in FoFDir.
G2DrvN: MDV= 6291456.
G2DrvN: will do 3 atoms at a time,
making 1 passes doing MaxLOS=2.
Petite list used in FoFDir.
MinBra= 0 MaxBra= 2 Meth= 1.
IRaf= 0
NMat= 1 IRICut= 1
DoRegI=T DoRafI=F ISym2E= 1 JSym2E=1.
FoFDir used for L=0 through L=2.
Leave Link 1110 at Wed Mar 28 04:59:19 2001,
MaxMem= 6291456
cpu: 6.1
(Enter /usr/local/lib/Gaussian/G98new/g98/l1002.exe)
Minotr: Closed-shell wavefunction.
Direct CPHF
calculation.
Solving
linear equations simultaneously.
Using
symmetry in CPHF.
Requested
convergence is 1.0D-08 RMS, and 1.0D-07 maximum.
Secondary
convergence is 1.0D-12 RMS, and 1.0D-12 maximum.
Differentiating once with respect to electric field.
with
respect
to
dipole field.
Differentiating once with respect to nuclear coordinates.
NewPWx=T
KeepS1=F KeepF1=F KeepIn=F MapXYZ=F.
MDV= 6291456
Using
IRadAn= 2.
Store
integrals in memory, NReq= 876501.
Symmetry not used in FoFDir.
MinBra= 0 MaxBra= 2 Meth= 1.
IRaf= 0
NMat= 1 IRICut= 1
DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0.
There
are 12 degrees of freedom in the 1st order CPHF.
10 vectors were produced by pass 0.
AX will form 10 AO Fock derivatives at one time.
9 vectors were produced by pass 1.
9 vectors were produced by pass 2.
9 vectors were produced by pass 3.
5 vectors were produced by pass 4.
3 vectors were produced by pass 5.
Inv2: IOpt= 1 Iter= 1 AM= 1.09D-15 Conv= 1.00D-12.
Inverted reduced A of dimension 45 with in-core
refinement.
Leave Link 1002 at Wed Mar 28 04:59:27 2001,
MaxMem= 6291456
cpu: 5.5
(Enter /usr/local/lib/Gaussian/G98new/g98/l601.exe)
Copying SCF densities to generalized density rwf, ISCF=0
IROHF=0.
**********************************************************************
Population analysis using the SCF density.
**********************************************************************
...
Leave Link 601 at Wed Mar 28 04:59:28 2001,
MaxMem= 6291456
cpu: 0.5
(Enter /usr/local/lib/Gaussian/G98new/g98/l701.exe)
Compute integral second derivatives.
... and contract with generalized density number 0.
Leave Link 701 at Wed Mar 28 04:59:31 2001,
MaxMem= 6291456
cpu: 2.5
(Enter /usr/local/lib/Gaussian/G98new/g98/l702.exe)
L702 exits ... SP integral derivatives will be done
elsewhere.
Leave Link 702 at Wed Mar 28 04:59:32 2001,
MaxMem= 6291456
cpu: 0.0
(Enter /usr/local/lib/Gaussian/G98new/g98/l703.exe)
Compute integral second derivatives.
Integral derivatives from FoFDir, PRISM(SPDF).
Petite list used in FoFDir.
MinBra= 0 MaxBra= 2 Meth= 1.
IRaf= 0
NMat= 1 IRICut= 1
DoRegI=T DoRafI=F ISym2E= 1 JSym2E=1.
Leave Link 703 at Wed Mar 28 04:59:52 2001,
MaxMem= 6291456
cpu: 13.9
(Enter /usr/local/lib/Gaussian/G98new/g98/l716.exe)
Dipole =
1.97314156D-05-8.22036304D-01 0.00000000D+00
Polarizability= 7.33514026D+00 1.70957942D-03 5.34051953D+00
2.28341401D-04
1.91679577D-05
2.73823266D+00
Full mass-weighted force constant matrix:
Low frequencies --- -54.4316
-0.0023 -0.0019 -0.0016
46.0086 70.3001
Low frequencies --- 1712.8326 3718.8261 3841.6059
Harmonic frequencies (cm**-1), IR intensities (KM/Mole),
Raman scattering activities (A**4/AMU), Raman depolarization
ratios,
reduced masses (AMU), force constants (mDyne/A) and normal
coordinates:
1
2
3
A'
A'
A'
Frequencies --
1712.8326
3718.8261
3841.6059