652. N/EDA in GAMESS. 4. Running NEDA

Posts 1, 2 and 3.

For this you will need to have linked gamess and nbo.

Here's an example input that works:

andy@carbon:~$ less fast/gamess/mgme_tzvp/Mg_tzvp_opt_neda_2.inp
!   File created by the GAMESS Input Deck Generator Plugin for Avogadro
 $CONTRL SCFTYP=RHF RUNTYP=energy DFTTYP=PBE0 ICHARG=1 MULT=1 NOSYM=1 $END
! $PCM SOLVNT=NEPTANE $END
! $PCMCAV RADII=SUAHF $END
! $SCF DIRSCF=.TRUE. $END
 $BASIS EXTFIL=.TRUE. GBASIS=DEF2SVP $END
 $system mwords=2000 memddi=500 $end
 $INTGRL NOPK=1 $END
 $NBO MOLUNIT <1>  >
 <2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23> $END
 $DEL NEDA END $END
 $DATA 
Title
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

And here's the output:

Natural Energy Decomposition Analysis (Summary):

                                                            Component
                    Energy(wfn)        Energy(wfn)          (kcal/mol)
 ------------------------------------------------------------------------------
 C7H13N2Mg(+)   -583.0832392(scf)  -582.9738665(loc)      CT =  -68.632
                                                          ES = -394.694
                                                         POL = -353.983
                                                          XC =  -29.974
 1. Mg(+2)      -199.0566873(def)  -199.0582918(cp)  DEF(SE) =    1.007(  0.400)
 2. C7H13N2(-)  -382.6763191(def)  -383.3176043(cp)  DEF(SE) =  402.412(176.794)
                                                              ---------
                                                           E = -443.864


 Electrical (ES+POL+SE) :   -571.483
   Charge Transfer (CT) :    -68.632
       Core (XC+DEF-SE) :    196.251
                        ------------
  Total Interaction (E) :   -443.864

 ..... done with NBO analysis .....

A couple of things to note:
* It runs with PCM, but the results seem nonsensical, in addition to it finding a lot more fragments than without PCM (the latter thing can be amended with NAO)

* If I use DEF2TZVP with PBE0 and DIRSCF=.TRUE. It'll get stuck during the NBO run at

437. RY ( 5) H 23                      0.00000        0.00000       0.00000

 NEXT STEP:  Perform one SCF cycle to evaluate the energy of the new density
             matrix constructed from the deleted NBO Fock matrix.

 ------------------------------------------------------------------------------

          --------------------------
              R-PBE0 SCF CALCULATION
          --------------------------
         DENSITY MATRIX CONVERGENCE THRESHOLD=  2.00E-05
     COARSE -> FINE DFT GRID SWITCH THRESHOLD=  3.00E-04 (SWITCH IN $DFT)
                   HF -> DFT SWITCH THRESHOLD=  0.00E+00 (SWOFF IN $DFT)

 DIRECT SCF CALCULATION, SCHWRZ=T   FDIFF=T,  DIRTHR=  0.00E+00 NITDIR=10

                                                                                   NONZERO     BLOCKS
 ITER EX DEM     TOTAL ENERGY        E CHANGE  DENSITY CHANGE    DIIS ERROR      INTEGRALS    SKIPPED

It's not consuming any CPU at this point (nor is nbo). I'm running w/o DIRSCF now, but it's very slow, and requires ca 30 Gb of scratch space even for a small molecule like this one.

*  MOLUNIT <1> >
<2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23>

is not necessary for this run. You can simply use NBO $END instead.

649. N/EDA in GAMESS. 1. Recompiling GAMESS US with NBO6

I need to do energy decomposition analysis (EDA), but only have licenses for Gaussian and NBO6 (i.e. not ADF, turbomole, QChem etc.). NEDA isn't supported by NBO6 with gaussian (afaik).

NWChem, my usual gaussian alternative, doesn't support NBO6 beyond writing a .47 file.

Enter GAMESS US. I've been trying out gamess every few years, but I've found that it's slow and unreliable (very difficult to get SCF convergence) for the systems I work with (polyanions). Some of this may obviously be down to my lack of familiarity with the code -- there are probably plenty of satisified users of GAMESS US.

Either way, NBO6 suppports NEDA with GAMESS US. Also, GAMESS US does two different types  of   EDA: the common Morokuma-Kitaura (MOROKM) one (although only with HF) and an alternative approach by Su and Li that's referred to by GAMESS as LMOEDA (or CMOEDA).

MOROKM and LMOEDA as supported out of the box by GAMESS, but to get it to do NEDA you need to re-link it against NBO. Luckily it's even easier than the instructions in the NBO gamess file (i.e. no need to edit code).

NOTE: I could only link with gfortran 4.9 (jessie). gfortran 6.3 (stretch) failed to link (messages re -fPIC; recompiling gamess with -fPIC didn't solve it).

To compile gamess, see e.g. http://verahill.blogspot.com/2013/06/4xx-gamess-us-2013-r1-on-debian-wheezy.html

Once you've done the ddi/comp and compall steps, edit lked and search for NBO. Change to

set NBO=true
set NBOLIB="/opt/nbo6/bin/gmsnbo.i8.a"

assuming that this location is correct.

Then do lked as in the post above.