Supercomputer Facility
A sample Gamess input file for H2O illustrating the use of a Z matrix to input the nuclear positions:
$CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE MPLEVL=2 UNITS=ANGS <---- job control parameters COORD=ZMT ISPHER=1 $END <---- job control parameters $SYSTEM MEMORY=1000000 $END <---- job control parameters $BASIS GBASIS=N31 NGAUSS=6 NPFUNC=1 NDFUNC=1 $END <---- job control parameters (basis set) $DATA <---- beginning of the $DATA group, where the geometry is described H2O, geometry optimization, 6-31G(d,p) basis set <---- your comment (ignored by Gamess) Cnv 2 <----molecular point group blank line O <------------------- Z matrix H 1 roh <------------------- Z matrix H 1 roh 2 ang <------------------- Z matrix blank line roh=0.957 <------------------- initial value of roh ang=104.5 <------------------- initial value of ang $END <---- end of the $DATA group
This input file corresponds to geometry optimization (RUNTYP=OPTIMIZE), using the closed-shell (SCFTYP=RHF) MBPT(2)=MP2 (MPLEVL=2) method and the 6-31G(d,p) (GBASIS=N31 NGAUSS=6 NPFUNC=1 NDFUNC=1) basis set. The lowest core orbital is kept frozen (the default in Gamess is to freeze all chemical core orbitals in the correlated calculations). The calculation utilizes the point symmetry of H2O (C2v; cf. "Cnv 2" in the input). ISPHER=1 means that the spherical components of d, f, etc. orbitals (5d, 7f, etc.) are used. COORD=ZMT means that the Gaussian style internal coordinates are used to describe nuclear geometry.
And here is another input, corresponding to coupled-cluster (CCSD(T)) energy calculations for glycine (Jensen and Gordon's GLY12 isomer, the AM1 geometry).
$CONTRL SCFTYP=RHF RUNTYP=ENERGY CCTYP=CCSD(T) UNITS=BOHR ISPHER=1 $END <---- job control parameters $SYSTEM MEMORY=2000000 $END <---- job control parameters $BASIS GBASIS=N31 NGAUSS=6 $END <---- job control parameters (basis set) $DATA <---- beginning of the $DATA group, where the geometry is described Glycine...H2N-CH2-COOH...GLY12 isomer...AM1 structure <---- your comment (ignored by Gamess) C1 <---- molecular point group O 8.0 -2.8770919486 1.5073755650 0.3989960497 <---- Cartesian coordinates of the O nucleus C 6.0 -0.9993929716 0.2223265108 -0.0939400216 C 6.0 1.6330980507 1.1263991128 -0.7236778647 O 8.0 -1.3167079358 -2.3304840070 -0.1955378962 N 7.0 3.5887721300 -0.1900460352 0.6355723246 H 1.0 1.7384347574 3.1922914768 -0.2011420479 H 1.0 1.8051078216 0.9725472539 -2.8503867814 H 1.0 3.3674278149 -2.0653924379 0.5211399625 H 1.0 5.2887327108 0.3011058554 -0.0285088728 H 1.0 -3.0501350657 -2.7557071585 0.2342441831 $END <---- end of the $DATA group
As you can see, you can use Carterian coordinates (default in Gamess) instead of Z-matrix and bohr instead of Angstroem. CCTYP=CCSD(T) means that you are interested in running the CCSD(T) calculation. Other coupled-cluster options or values of CCTYP include LCCD, CCD, CCSD, R-CC, and CR-CC. The choice CCTYP=CR-CC implies the standard, renormalized (R), and completely renormalized (CR) CCSD(T) calculations (all in one !!!). The CR-CCSD(T) method, proposed by Dr. Karol Kowalski and Professor Piotr Piecuch (included in this choice of CCTYP), provides the correct description of single bond breaking with the ease-of-use of the standard CCSD(T) method. The CR-CCSD(T) approach removes the failing of the otherwise very successful CCSD(T) method at larger internuclear separations. In the above example, the reference configuration is RHF (at present, SCFTYP=RHF is the only choice of the reference for the coupled-cluster calculations; this may change in the future). Please note that if you are interested in using the coupled-cluster option in Gamess, you are asked to cite the paper P. Piecuch, S.A. Kucharski, K. Kowalski, and M. Musial, Comp. Phys. Commun. 149, 71-96 (2002), in addition to the standard Gamess reference: M.W.Schmidt, K.K.Baldridge, J.A.Boatz, S.T.Elbert, M.S.Gordon, J.H.Jensen, S.Koseki, N.Matsunaga, K.A.Nguyen, S.J.Su, T.L.Windus, M.Dupuis, J.A.Montgomery J. Comput. Chem. 14, 1347-1363(1993).
The final example describes the 2nd order MC-QDPT calculation (using the multi-configurational quasi-degenerate or multi-reference second-order perturbation theory). This job finds the Full Optimized Reaction Space or CASSCF wavefunction for water and then performs the 2nd order MC-QDPT calculation of the energy. The initial molecular orbitals (in the $VEC group) were obtained in a separate RHF calculation (they can always be found in the .dat short output file; in this case, in the .dat file produced by the RHF calculation).
$CONTRL SCFTYP=MCSCF MPLEVL=2 $END <---- job control parameters (theory level) $SYSTEM TIMLIM=8 MEMORY=300000 $END <---- job control parameters $GUESS GUESS=MOREAD NORB=13 $END <---- job control parameters (initial guess for MOs) $DET NCORE=1 NACT=6 NELS=8 $END <---- job control parameters (1 core orbital doubly occupied in all reference determinants; 6 active orbitals; 8 active electrons) $MCQDPT NSTATE=1 ISTSYM=1 REFWGT=.TRUE. $END<---- job control parameters (NSTATE=1, one state to be determined; ISTSYM=1 means state of the A1 symmetry) $BASIS GBASIS=N21 NGAUSS=3 $END<---- job control parameters (basis set) $DATA <---- beginning of the $DATA group, where the geometry is described WATER...3-21G BASIS...FORS-MCSCF...EXPERIMENTAL GEOMETRY <---- your comment (ignored by Gamess) Cnv 2 <---- molecular point group blank line Oxygen 8.0 0.0 0.0 0.0 <---- Cartesian coordinates of the O nucleus Hydrogen 1.0 0.0 0.7572157 0.5865358 $END <---- end of the $DATA group $VEC <----initial molecular orbitals (obtained in the RHF calculation) 1 1 0.98323195E+00 0.95883436E-01 0.00000000E+00 0.00000000E+00 0.35370268E-02 1 2-0.38015713E-01 0.00000000E+00 0.00000000E+00-0.67933232E-02 0.26157699E-02 1 3 0.69075022E-02 0.26157699E-02 0.69075022E-02 2 1-0.22915183E+00 0.21751680E+00 0.00000000E+00 0.00000000E+00 0.83482416E-01 2 2 0.70627255E+00 0.00000000E+00 0.00000000E+00 0.93448600E-01 0.11715069E+00 2 3 0.19083329E-01 0.11715069E+00 0.19083329E-01 3 1 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.39852684E+00 0.00000000E+00 3 2 0.00000000E+00 0.00000000E+00 0.36975524E+00 0.00000000E+00-0.23386378E+00 3 3-0.18332401E+00 0.23386378E+00 0.18332401E+00 4 1-0.88424758E-01 0.82203534E-01 0.00000000E+00 0.00000000E+00-0.44197156E+00 4 2 0.40499817E+00 0.00000000E+00 0.00000000E+00-0.50792220E+00-0.13089427E+00 4 3-0.10523065E+00-0.13089427E+00-0.10523065E+00 5 1 0.00000000E+00 0.00000000E+00 0.52129122E+00 0.00000000E+00 0.00000000E+00 5 2 0.00000000E+00 0.63210541E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 5 3 0.00000000E+00 0.00000000E+00 0.00000000E+00 6 1-0.10921346E+00 0.34847757E-01 0.00000000E+00 0.00000000E+00 0.20920102E+00 6 2 0.10449784E+01 0.00000000E+00 0.00000000E+00 0.46616469E+00-0.46425782E-01 6 3-0.86310980E+00-0.46425782E-01-0.86310980E+00 7 1 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.30311516E+00 0.00000000E+00 7 2 0.00000000E+00 0.00000000E+00 0.77474462E+00 0.00000000E+00 0.36159920E-01 7 3 0.11766731E+01-0.36159920E-01-0.11766731E+01 8 1 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.18247792E+00 0.00000000E+00 8 2 0.00000000E+00 0.00000000E+00 0.45271854E+00 0.00000000E+00 0.96497497E+00 8 3-0.68407554E+00-0.96497497E+00 0.68407554E+00 9 1-0.68462918E-01 0.98778424E-01 0.00000000E+00 0.00000000E+00 0.27668306E+00 9 2 0.11645921E+00 0.00000000E+00 0.00000000E+00 0.30171282E+00-0.98500862E+00 9 3 0.48555609E+00-0.98500862E+00 0.48555609E+00 10 1 0.00000000E+00 0.00000000E+00 0.10292728E+01 0.00000000E+00 0.00000000E+00 10 2 0.00000000E+00-0.96518900E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 10 3 0.00000000E+00 0.00000000E+00 0.00000000E+00 11 1-0.45193228E-01 0.13566837E+00 0.00000000E+00 0.00000000E+00-0.10100340E+01 11 2 0.17234151E+00 0.00000000E+00 0.00000000E+00 0.11527420E+01-0.26046385E+00 11 3-0.92175886E-01-0.26046385E+00-0.92175886E-01 12 1 0.00000000E+00 0.00000000E+00 0.00000000E+00-0.10670424E+01 0.00000000E+00 12 2 0.00000000E+00 0.00000000E+00 0.13962359E+01 0.00000000E+00 0.13746917E+00 12 3 0.50761817E+00-0.13746917E+00-0.50761817E+00 13 1-0.84642669E-01 0.16413752E+01 0.00000000E+00 0.00000000E+00 0.16053837E+00 13 2-0.19938626E+01 0.00000000E+00 0.00000000E+00-0.49752222E+00 0.28728587E+00 13 3 0.35961579E+00 0.28728587E+00 0.35961579E+00 $END
A complete manual for Gamess is available from the web. Please click here for further details.
After creating your input file with an editor (e.g. vi), save
it under some name with extension of .inp (e.g. gamess_file.inp ) and
submit it to the queue.
Command to send your Gamess job to the queue is:
gmssub gamess_file
Note: in the above line, your input file is assumed to be named gamess_file.inp.
The output file will be called gamess_file.out
You will also see the extra file gamess_file.dat, which contains, in particular,
molecular orbitals for various restart calculations. The coupled-cluster calculations
will produce the gamess_file.restart file with the information needed to restart
the coupled-cluster calculations, if you are interested in using the results of the
earlier coupled-cluster calculations as an initial guess for some new coupled-cluster
calculations (you can erase these files if you are not interested in using them).
In the above examples, the basis set
was defined via the $BASIS group. Another possibility is to incorporate
the basis set in the $DATA group or to create the external file with the basis sets.
In the latter case, you should use
the EXTFIL=.TRUE. option in $BASIS and -b flag in gmssub.
For more information about EXTFIL, see the
Gamess web site.
You can use the command qstat -a to see the status of your and all other jobs. If you see a line with your name in it and some other job information, your job is in the queue (if the job status is R, the job is running).
To learn more about the NQS queue system running in the department, go here.
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Last Updated: October 3, 2003 - WebMaster URL: http://www.chemistry.msu.edu/Facilities/ Supercomputer/gamess_doc.shtml |4.01|css|508|A|[D] |
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