The parameterization of the new nanoENGINEER-1 simulator is being performed for molecules containing H through Cl at the B3LYP/6-31+G(d,p) level of theory. Unfortunately, the 6-31+G(d,p) basis set is not available for the 4th row elements (Ga,Ge,As,Se,Br), meaning an alternate basis set is required (for the 4th row, that is). In GAMESS-US, this is simple if the input files are in Cartesian format. This same approach cannot be used in Z-matrix input formats. A (maybe THE only) way to call mixed basis sets for Z-matrices in GAMESS-US is provided here. The procedure involves making an external basis set file with the required basis sets, changing the $BASIS control to read the external file, and modifying rungms to read the external basis set file.
Below is a sample input file. The only noteworthy differences between it and any other input file are (a) the $BASIS line, which tells GAMESS-US to use the external file (EXTFIL=.TRUE.) and (b) the call to use external basis sets named STO2GBAS. In this external file, you can have multiple groups of elements and basis sets, but not multiple basis set types for the SAME ELEMENT in the same group (so far as I know at the moment). This means that the external basis set example file I have available here has Hydrogen (H) and F (Fluorine) STO-2G (STO2GBAS) and 3-21G (321GBASI) basis set groups, but that you CANNOT call the STO2GBAS Hydrogen basis set and 321GBASI Fluorine basis set.
$CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE COORD=ZMT $END $BASIS EXTFIL=.TRUE. GBASIS=STO2GBAS $END $CONTRL NZVAR=1 $END $ZMAT IZMAT(1)=1,1,2 $END $DATA COMMENT: HF Z-matrix with mixed basis sets C1 H F 1 HFDist HFDist=1.00 $END
The edit to the rungms file is as follows. You will need to change the EXTBAS control from its default (/dev/null) to the location of the external basis set file (which I have named EXTFILE.txt). If the basis set file is in the same directory as your GAMESS-US executable, then change the EXTBAS to ./EXTFILE.txt.
set echo setenv ERICFMT ./ericfmt.dat setenv IRCDATA ./$JOB.irc setenv INPUT $SCR/$JOB.F05 setenv PUNCH ./$JOB.dat setenv EXTBAS ./EXTFILE.txt setenv AOINTS $SCR/$JOB.F08
The external basis sets can, of course, be downloaded from www.emsl.pnl.gov. My sample file, EXTFILE.txt, is below. Note the STO2GBAS and 321GBASI grouping. These labels MUST have 8 characters. Change the basis set choice by changing GBASIS in $BASIS in the input file.
H STO2GBAS S 2 1 1.309756377 0.4301284980 2 0.233135974 0.6789135310 F STO2GBAS S 2 1 63.73520200 0.4301280000 2 11.34483400 0.6789140000 L 2 1 2.498548000 0.4947200000E-01 0.5115410000 2 0.633698000 0.9637820000 0.6128200000 H 321GBASI S 2 1 5.4471780000 0.1562850000 2 0.8245470000 0.9046910000 S 1 1 0.1831920000 1.0000000000 F 321GBASI S 3 1 413.80100000000 0.5854830000E-01 2 62.24460000000 0.3493080000 3 13.43400000000 0.7096320000 L 2 1 9.7775900000 -0.4073270000 0.2466800000 2 2.0861700000 1.2231400000 0.8523210000 L 1 1 0.4823830000 1.0000000000 1.0000000000
You can download all of the program text and some brief comments in a single file located HERE.
In order to use the 6-31+G(d,p) and 6-311G(d,p) basis sets for a single molecule of mixed 1st/2nd/3rd row and 4th row elements, define an 8-character sequence for the group (like MIXEDBAS) and simply add all of the required basis sets for whatever elements into that group. Again, it is not obvious how to have two Hydrogen atoms in a single molecule have two different basis sets in a Z-matrix input by this (or any other) method in GAMESS-US, but the above goes a long way towards removing a major obstacle to running many molecules.
Sweet! I was asking people around my group if they have used external basis sets and apparently the work around is to use $ZMAT DCC=.T. AUTO=.T. $END with a cartesian $DATA and mixed basis set. But I think it is much less work for restarts if EXTBAS is used.
The "DCC=.T. AUTO=.T." trick never even occurred to me. I'll agree that the EXTBAS is MUCH easier for restarting jobs and (but why would anyone want to do this?!) for having tweaked repositories of basis sets. Now, all that said, if you want to use, for instance, high quality basis sets (like a 6-311++G(2d,p)) on the carbon atoms of a reactive site and lousy basis sets for carbon atoms 10 Angstroms away (3-21G or lower) while still using a Z-matrix, then the DCC/AUTO trick's the way to go (and thanks for this! I hadn't found a comfortable workaround for that yet. Will try and report back).
Sorry – it is DLC=.T. – I misread my coworkers handwriting.
If you plan to use this then in $CONTROL you need to specify NZVAR=(usually 3N-6)