#P CCSD(T)/6-311+G(2d,2p) Opt
The next line should be blank (since the command line can be more than one line).
The third line is the Title. It can also be split in several lines and must be ended by a blank line. The next line gives the charge and the multiplicity of the calculation in this order.
The mulitiplicity specifies the spin state: (1=singlet=no unpaired electrons, 2=doublet, etc.). Most normal molecules are singlets.
The following lines give the geometry of the molecule. It can be specified in Cartesian coordinates (x, y, z, in ?ngstr?m), starting with the atomic symbol or number. Alternatively, it can be given as an Z-matrix (see Appendix E in Frank Jensen and the sample input below). The geometry is ended by a blank line.
The rest of the file contains additional input, is any (depending on the keywords). The file must end with a blank line. The job is started by: g98 input_file &
The output will be found in the file input_file.out.
You must specify the ampersand (\
If you run several similar calculations, it may be wise to save all important information in a checkpoint file. This is done with the line %Chk=file_name
which should be first in the file.
You can use the contents in the checkpoint file in other calculations by giving the same checkpoint file name. Guess=Read (in the command line) tells the program to read the wavefunction from the checkpoint file.
Geom=AllCheck (also in the command line) tells the program to read the title, charge, multiplicity and (final) geometry from the checkpoint file. The corresponding lines should then be ommitted from the input file. -------------------------------------------------------------------------------- Sample input files
-------------------------------- #P HF Sto-3G Opt Freq
Simple geometry optimization 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
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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
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------------------------------------------------ #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
------------------------------------------------
-------------------------------------------------------------------------------- Scan
This command is used to construct a rigid potential energy surface of one or more internal coordinates. The coordinates have to be specified in Z-matrix format. For the coordinate you want to scan, add after variable definition, the starting value, the number of steps -1, and the step size. 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
--------------------------------------------------------------------------------
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Oniom
This is a up to three layer combined QC/MM or QC/QC method. The input is similar to a normal input, but you specify two or three different after the oniom keyword and for each atom you specify which layer it belongs to: High (first method), Medium (second method) or Low (third method), and optionally the junction replacement atoms (typically H). Most methods work with Oniom, e.g. optimizations and frequency calculations. However, SCRF does not work (it is not available for semi-empirical or molecular mechanical methods). 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
-------------------------------------------------------------------------------- Gaussian
The current version is Gaussian-98, Revision A.9 The program is located in
/molcas/DIVPROG/lib/Gaussian/G98new/g98 (signe) /sw/gaussian/G98new/g98 (ask) /usr/local/software/G98/g98 (garm) /home/bio/G98new/g98 (husmodern) An older revision (A.5) is found in /molcas/DIVPROG/lib/Gaussian/g98 (signe) /sw/gaussian/g98 (ask)
Alternative versions of g98 A.5 with a higher maximum TSARE can be found in /molcas/DIVPROG/lib/Gaussian/New/g98 (signe) /sw/gaussian/New/g98 (ask)
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Gaussian-94 can be found in
/molcas/DIVPROG/lib/Gaussian/g94 (signe) /sw/gaussian/g94 (ask)
You can use the following script to run Gaussian (/teo/ulf/Bin/rung98). You should change the rows in bold face #!/bin/ksh
export g98root=/molcas/DIVPROG/lib/Gaussian/G98new 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/g98 <\
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 \-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().
-------------------------------------------------------------------------------- Compile the utility programs (formchk, newzmat, etc.)
To compile these programs, copy the corresponding row in the end of the file bldg98.log and replace util.so with util.a.
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 --------------------------------------------------------------------------------
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