Showing posts with label eda. Show all posts
Showing posts with label eda. Show all posts

20 August 2018

653. Energy decomposition analysis the manual/multiwfn way -- nwchem

I have a very large system (390 atoms, 3918 functions, 6474 primitives) where I want to analyse the bonding. Whereas I can reduce the size of the system a little bit, there's a large conjugated ad charged system in the middle which I can't really reduce. Either way, when I use GAMESS US to do NEDA, the calc seems to hang for days without ever progressing, and LMOEDA/CMOEDA keep running out of memory.

I recently had a look at Multiwfn, and section 4.100.8 in the manual shows how to do simple EDA as a multistep computation. The example uses multiwfn to input initial fragment wavefunctions to compute the DE_orb with Gaussian. Incidentally, this is something which is very easy to do with nwchem without using multiwfn.

I'll use NH3..BH3 as the example at RHF/6-31G*.


Nwchem:

1. Optimise NH3..BH3
scratch_dir /home/me/scratch Title "NH3BH3-nw" Start NH3BH3-nw charge 0 geometry noautosym noautoz units angstrom N 0.0720500 -0.00961700 -0.336156 H 0.871540 0.292859 -0.862886 H -0.685935 0.618297 -0.534511 H -0.187686 -0.922713 -0.663436 B 0.415920 -0.0366410 1.31774 H 0.709693 1.10584 1.58004 H -0.612009 -0.411733 1.83072 H 1.33214 -0.818018 1.41958 end basis "ao basis" cartesian print B library "6-31G*" H library "6-31G*" N library "6-31G*" END scf RHF nopen 0 end task scf optimize
Energy=-82.61181818

2. Run SE calcs on the BH3 and NH3 fragments:
scratch_dir /home/me/scratch Title "BH3-nw" Start BH3-nw charge 0 geometry noautosym noautoz units angstrom B 0.192902 -0.0151808 0.928551 H 0.486935 1.12724 1.19093 H -0.834959 -0.390362 1.44154 H 1.10930 -0.796437 1.03042 end basis "ao basis" cartesian print B library "6-31G*" H library "6-31G*" END scf RHF nopen 0 vectors output bh3.movecs end task scf energy
Energy=-26.368337779376
and
scratch_dir /home/me/scratch Title "NH3-nw" Start NH3-nw charge 0 geometry noautosym noautoz units angstrom N -0.150737 0.0117141 -0.725185 H 0.648571 0.314333 -1.25225 H -0.908696 0.639770 -0.923690 H -0.410582 -0.901249 -1.05260 end basis "ao basis" cartesian print N library "6-31G*" H library "6-31G*" END scf RHF nopen 0 vectors output nh3.movecs end task scf energy
Energy=-56.184296916045

3. Finally, use the two movecs created in step 2:
scratch_dir /home/andy/scratch Title "NH3BH3-nw" Start NH3BH3-nw charge 0 geometry noautosym noautoz units angstrom N 0.0720500 -0.00961700 -0.336156 H 0.871540 0.292859 -0.862886 H -0.685935 0.618297 -0.534511 H -0.187686 -0.922713 -0.663436 B 0.415920 -0.0366410 1.31774 H 0.709693 1.10584 1.58004 H -0.612009 -0.411733 1.83072 H 1.33214 -0.818018 1.41958 end basis "ao basis" cartesian print B library "6-31G*" H library "6-31G*" N library "6-31G*" END scf RHF nopen 0 vectors fragment nh3.movecs bh3.movecs output nh3bh3.movecs end task scf
4. Parse the output from step 4:
iter energy gnorm gmax time ----- ------------------- --------- --------- -------- 1 -82.5357150919 7.36D-01 2.88D-01 0.1 2 -82.6078664771 2.30D-01 5.23D-02 0.1 3 -82.6117699706 2.03D-02 7.47D-03 0.1 4 -82.6118181287 2.23D-04 5.79D-05 0.1 5 -82.6118181326 2.51D-06 7.28D-07 0.1 Final RHF results ------------------ Total SCF energy = -82.611818132574 One-electron energy = -190.292457149391 Two-electron energy = 67.248334359392 Nuclear repulsion energy = 40.432304657425 Time for solution = 0.1s
So, according to the Multiwfn Manual at 4.100.8, using the values from above:
DEtot=-82.61181818-(-26.368337779376-56.184296916045)= -37 kcal/mol (-155 kJ/mol)
DEorb=-82.611818132574-(-82.5357150919)= -48 kcal/mol (-200 kJ/mol)
DEsteric=DEtot-DEorb= 11 kcal/mol (45 kJ/mol)

This is essentially the Kitaura-Morokuma method.

See e.g. Frenking et al.in Energy Decomposition Analysis on page 44. Eq 2 defines Eint in the same way DEtot is defined above, and Eq 7 is the same Eorb as here.

DEstruc here is then DEelstat + DEPauli.

How to resolve these two factors from one another, is a problem for another day.
You can also run the calcs using a single input file:
scratch_dir /home/me/scratch Title "NH3BH3-nw-eda" Start NH3BH3-nw-eda echo charge 0 geometry molecule noautosym noautoz units angstrom N -0.150737 0.0117141 -0.725185 H 0.648571 0.314333 -1.25225 H -0.908696 0.639770 -0.923690 H -0.410582 -0.901249 -1.05260 B 0.192902 -0.0151808 0.928551 H 0.486935 1.12724 1.19093 H -0.834959 -0.390362 1.44154 H 1.10930 -0.796437 1.03042 end geometry ammonia noautosym noautoz units angstrom N -0.150737 0.0117141 -0.725185 H 0.648571 0.314333 -1.25225 H -0.908696 0.639770 -0.923690 H -0.410582 -0.901249 -1.05260 end geometry borohydride noautosym noautoz units angstrom B 0.192902 -0.0151808 0.928551 H 0.486935 1.12724 1.19093 H -0.834959 -0.390362 1.44154 H 1.10930 -0.796437 1.03042 end basis "ao basis" cartesian print N library "6-31G*" B library "6-31G*" H library "6-31G*" END set geometry ammonia scf vectors output ammonia.movecs end task scf set geometry borohydride scf vectors output borohydride.movecs end task scf set geometry molecule scf vectors input fragment ammonia.movecs borohydride.movecs output molecule.movecs end task scf

15 June 2018

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.