Showing posts with label neda. Show all posts
Showing posts with label neda. Show all posts

15 June 2018

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.