15 June 2018

651. N/EDA in GAMESS. 3. Running L/CMOEDA

As it turns out, while MOEDA works fine with pure and hybrid functionals, it does not appear to like PCM, giving weird results.

Here's an example of a run that works, with a few key words highlighted:
! File created by the GAMESS Input Deck Generator Plugin for Avogadro $BASIS EXTFIL=.TRUE. GBASIS=DEF2SVP $END ! $PCM SOLVNT=NEPTANE $END ! $PCMCAV RADII=SUAHF $END $CONTRL SCFTYP=RHF RUNTYP=EDA DFTTYP=PBE0 ICHARG=1 MULT=1 $END $CONTRL NOSYM=1 $END $SYSTEM MWORDS=2500 MEMDDI=500 $END $SCF DIRSCF=.TRUE. $END $lmoeda matom(1)=1,22 mcharg(1)=2,-1 mmult(1)=1,1 $end $DATA Test of MOEDA using a Mg coordination compound. C1 Mg 12.0 3.14572 1.02487 1.29474 N 7.0 4.95329 0.37304 1.62652 N 7.0 3.11530 2.89665 1.82263 C 6.0 5.44265 -0.98008 1.41792 C 6.0 5.80308 1.30078 2.07039 C 6.0 1.96130 3.78017 1.78886 C 6.0 4.28661 3.37927 2.23846 C 6.0 5.48149 2.64462 2.33178 H 1.0 6.31935 3.22840 2.68338 C 6.0 4.36331 4.81950 2.64988 H 1.0 5.37500 5.09552 2.93515 H 1.0 3.70056 5.01438 3.49762 H 1.0 4.03950 5.47541 1.83769 C 6.0 7.22682 0.90313 2.32491 H 1.0 7.68811 0.50750 1.41630 H 1.0 7.27827 0.11050 3.07627 H 1.0 7.81805 1.74612 2.67254 H 1.0 5.81529 -1.43220 2.34182 H 1.0 4.63475 -1.61377 1.04987 H 1.0 6.24793 -1.02060 0.67837 H 1.0 1.72108 4.18678 2.77556 H 1.0 2.10316 4.62224 1.10460 H 1.0 1.08587 3.22835 1.44552 $END
The ! comments out the PCM lines. I generated the input from an .xyz file through avogadro, and then edited the file manually to get the charges etc. right.

Here's the output:
DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=F, DIRTHR= 0.00E+00 NITDIR=10 DFT IS SWITCHED OFF, PERFORMING PURE SCF UNTIL SWOFF THRESHOLD IS REACHED. NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED *** ERROR *** IN -DAWRIT- ROUTINE ON NODE 0 DAWRIT HAS REQUESTED A RECORD WITH LENGTH DIFFERENT THAN BEFORE - ABORT FORCED. DAF RECORD 88 NEW LENGTH = 20100 OLD LENGTH = 190 EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT Thu Jun 14 23:30:05 2018 6712269 WORDS OF DYNAMIC MEMORY USED CPU 0: STEP CPU TIME= 1.73 TOTAL CPU TIME= 2.0 ( 0.0 MIN) TOTAL WALL CLOCK TIME= 2.1 SECONDS, CPU UTILIZATION IS 96.70% DDI Process 0: error code 911 ddikick.x: application process 0 quit unexpectedly. ddikick.x: Fatal error detected. The error is most likely to be in the application, so check for input errors, disk space, memory needs, application bugs, etc. ddikick.x will now clean up all processes, and exit... DDI Process 1: terminated upon request. DDI Process 2: terminated upon request. *** ERROR *** IN -DAWRIT- ROUTINE ON NODE 1 DAWRIT HAS REQUESTED A RECORD WITH LENGTH DIFFERENT THAN BEFORE - ABORT FORCED. DAF RECORD 88 NEW LENGTH = 20100 OLD LENGTH = 190 *** ERROR *** IN -DAWRIT- ROUTINE ON NODE 2 DAWRIT HAS REQUESTED A RECORD WITH LENGTH DIFFERENT THAN BEFORE - ABORT FORCED. DAF RECORD 88 NEW LENGTH = 20100 OLD LENGTH = 190 DDI Process 3: terminated upon request. DDI Process 4: terminated upon request. *** ERROR *** IN -DAWRIT- ROUTINE ON NODE 3 DAWRIT HAS REQUESTED A RECORD WITH LENGTH DIFFERENT THAN BEFORE - ABORT FORCED. DAF RECORD 88 NEW LENGTH = 20100 OLD LENGTH = 190 DDI Process 5: terminated upon request. *** ERROR *** IN -DAWRIT- ROUTINE ON NODE 4 DAWRIT HAS REQUESTED A RECORD WITH LENGTH DIFFERENT THAN BEFORE - ABORT FORCED. DAF RECORD 88 NEW LENGTH = 20100 OLD LENGTH = 190 *** ERROR *** IN -DAWRIT- ROUTINE ON NODE 5 DAWRIT HAS REQUESTED A RECORD WITH LENGTH DIFFERENT THAN BEFORE - ABORT FORCED. DAF RECORD 88 NEW LENGTH = 20100 OLD LENGTH = 190 ddikick.x: Sending kill signal to DDI processes. ddikick.x: Execution terminated due to error(s). unset echo

650. N/EDA in GAMESS. 2. Defining an external basis set

This is post number two in a series. Post 1 is here: http://verahill.blogspot.com/2018/06/649-neda-in-gamess-1-recompiling-gamess.html

Defining external basis sets isn't hard, but I find that the gamess documentation isn't great, and there isn't as much online as one would hope.


1. Either way, I'll create an external basis set file with def2svp and def2tzvp at /opt/gamess/gamess_nbo/EXTFILE.txt

2. Get the basis set definition from https://bse.pnl.gov/bse/portal -- select the atoms you want, and the basis set, set format to GAMESS US, and click Get Basis Set.


3. When you paste the data into the EXTFILE.txt,
a) skip the $DATA tag, and
b) change the atom definition to their corresponding symbols (e.g. H instead of Hydrogen) and append the name of the basis set,

so the beginning looks like this:
MG DEF2SVP S 5 1 4953.8339196 -0.57778967498E-02 2 745.18044154 -0.43124761082E-01 3 169.21604972 -0.19268216987 4 47.300672019 -0.48641439116 5 14.461336973 -0.42550894077 S 3 1 24.768174789 0.87956969984E-01 2 2.4940945349 -0.55165058128 3 0.87807584533 -0.53443294833 S 1 1 0.87212782497E-01 1.0000000 S 1 1 0.33599293780E-01 1.0000000 P 5 1 98.053010494 -0.14480564601E-01 2 22.586932277 -0.95495750787E-01 3 6.8391509842 -0.30787672651 4 2.2332843818 -0.49936292886 5 0.71606599387 -0.31503476213 P 1 1 0.18914796195 1.0000000 P 1 1 0.53768755187E-01 1.0000000 D 1 1 0.1010000 1.0000000 H DEF2SVP S 3 1 13.0107010 0.19682158E-01 2 1.9622572 0.13796524 3 0.44453796 0.47831935 S 1 1 0.12194962 1.0000000 P 1 1 0.8000000 1.0000000 C DEF2SVP
and the end like this:
D 1 1 0.64500000 1.0000000 F 1 1 1.42800000 1.0000000 MG DEF2TZVP S 7 1 31438.3495550 0.60912311326E-03 2 4715.5153354 0.47066196465E-02 3 1073.1629247 0.24135820657E-01 4 303.57238768 0.93628959834E-01 5 98.626251042 0.26646742093 6 34.943808417 0.47890929917 7 12.859785199 0.33698490286 S 3 1 64.876913004 0.19180889307E-01 2 19.725520777 0.90913704392E-01 3 2.8951804339 -0.39563756125 S 2 1 1.1960454710 1.6827603373 2 0.54329451156 0.52141091954 S 1 1 0.10099104092 1.0000000 S 1 1 0.36865728085E-01 1.0000000 P 5 1 179.87189612 0.53799549018E-02 2 42.120069376 0.39318014098E-01 3 13.120503032 0.15740129476 4 4.6257503609 0.35919094128 5 1.6695211016 0.45533379310 P 1 1 0.58551012105 1.0000000 P 1 1 0.18914796195 1.0000000 P 1 1 0.53768755187E-01 1.0000000 D 1 1 3.4440000 1.0000000 D 1 1 0.2900000 1.0000000 D 1 1 0.0700000 1.0000000


4. Edit the gms-files.csh in your gamess root (e.g. /opt/gamess/gamess_nbo)
setenv EXTBAS /opt/gamess/gamess_nbo/EXTFILE.txt


5. To use, put
$BASIS EXTFIL=.TRUE. GBASIS=DEF2TZVP $END
or
$BASIS EXTFIL=.TRUE. GBASIS=DEF2SVP $END
in your gamess input file.