Re: [Jmol-users] Error loading GAMESS-US input file with symmetry

[Mark P. <pe...@so...>]

Hi Bob,


That works perfectly, thanks for the quick update.


I have a related question:  Is there any function or script to nudge the atom positions so that this molecule is perfectly symmetric?  I'm only using 2 decimal places for the coordinates which helps on most molecules, but GAMESS has a very low threshold for imperfections and it crashes because this benzene isn't perfectly D6h.  I'm trying to automate the process.


Thanks,

Mark



!generalInstructions.xml
!2
!
!   GAMESS Calculation input file
!
!
 $CONTRL SCFTYP=RHF MAXIT=99 RUNTYP=OPTIMIZE
         COORD=PRINAXIS MULT=1
         ICHARG=0
         DFTTYP=B3LYP
         MOLPLT=.FALSE. PLTORB=.FALSE.  $END
 $SYSTEM TIMLIM=2879 MWORDS=300  $END

 $FORCE METHOD=SEMINUM NVIB=2 $END
 $STATPT OPTTOL=0.0005 NSTEP=99 IHREP = 20 HSSEND=.TRUE. $END

 $DFT    METHOD=GRID  NLEB=590  $END

 $BASIS  GBASIS=N31 NGAUSS=6
         NDFUNC=1   NPFUNC=0  $END

 $SCF    DIRSCF=.T. $END
 $GUESS  GUESS=HUCKEL  $END

 $DATA

  Dnh 6

C     6.0     0.17    -1.38     0.00
C     6.0    -1.12    -0.84     0.00
C     6.0    -1.28     0.55    -0.00
C     6.0    -0.17     1.38    -0.00
C     6.0     1.12     0.84    -0.00
C     6.0     1.28    -0.55     0.00
H     1.0     0.29    -2.46     0.00
H     1.0    -1.98    -1.49     0.00
H     1.0    -2.28     0.98    -0.00
H     1.0    -0.29     2.46    -0.00
H     1.0     1.98     1.49    -0.00
H     1.0     2.28    -0.98     0.00
 $END


________________________________
From: Robert Hanson <ha...@st...>
Sent: Thursday, January 18, 2018 3:29 AM
To: jmo...@li...
Subject: Re: [Jmol-users] Error loading GAMESS-US input file with symmetry

Mark,

Yes, I see that Jmol only supported 'C1' symmetry.

Just released 14.28.2, but I did not see this message. I have built a Jmol.jar file for you to check, though. It is at:

https://chemapps.stolaf.edu/jmol/temp/Jmol.jar

Note that Jmol does not support reading of input decks that mess with the orientation, as described by
http://www.msg.ameslab.gov/gamess/GAMESS_Manual/input.pdf page 41.

Bob