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1

Molecular Properties, Wavefunction Analysis, and Interfaces to Visualization Tools / hybrid functional and bandgap.

« Last post by Wonseok on July 16, 2024, 01:31:31 PM »

Dear all,

I am currently working on adjusting the parameters of hybrid functionals, specifically hse_own, to match the bandgap of a solid system with experimental values.

Below is a control file used for calculating a diamond structure composed of 8 carbon atoms, running the ‘riper’ module due to the periodic boundary conditions.

Code: [Select]

$title
$symmetry c1
$user-defined bonds    file=coord
$coord    file=coord
$optimize
 internal   off
 redundant  off
 cartesian  on
 global     off
 basis      off
$cell angs
  3.55103808   3.55103808   3.55103808   90.0   90.0   90.0
$periodic 3
$kpoints
    nkpoints 6 6 6 # Gamma point calculation
$atoms
c  1-8                                                                         \
   basis =c pob-TZVP                                                           \
   jbas  =c universal
$basis    file=basis
$scfmo   file=mos
$closed shells
 a       1-24                                   ( 2 )
$scfiterlimit      300
$thize     0.10000000E-04
$thime        5
$scfdamp   start=0.300  step=0.050  min=0.100
$scfdump
$scfintunit
 unit=30       size=0        file=twoint
$scfdiis
$scforbitalshift  automatic=.1
$maxcor    500 MiB  per_core
$drvopt
   cartesian  on
   basis      off
   global     off
   hessian    on
   dipole     on
   nuclear polarizability
$interconversion  off
   qconv=1.d-7
   maxiter=25
$coordinateupdate
   dqmax=0.3
   interpolate  on
   statistics    5
$forceupdate
   ahlrichs numgeo=0  mingeo=3 maxgeo=4 modus=<g|dq> dynamic fail=0.3
   threig=0.005  reseig=0.005  thrbig=3.0  scale=1.00  damping=0.0
$forceinit on
   diag=default
$energy    file=energy
$grad    file=gradient
$forceapprox    file=forceapprox
$dft
    functional   pbe
    gridsize   m5
$scfconv   7
$jbas    file=auxbasis
$ricore      500
$rij
$marij
$marij
$rundimensions
   natoms=8
   nbf(CAO)=152
   nbf(AO)=144
$last step     define
$end

After reading the manual, I understood that the HSE formula* corresponds to the hse_own parameters (alpha, beta, omega) as follows:

"""
alpha = a
beta  = 1 - a
omega = omega
"""

In the same control file, I varied the type of functional and the parameters as shown in the table below and checked the bandgap using the ‘eiger’ command.

functional  |   α    |    β     |     ω      |     Bandgap[eV]
pbe           |   X    |    X    |     X     |     4.86588
hse06        |  1/4  |    X    |   0.11  |     6.04238
hse_own    |  1/4  |   3/4  |   0.11  |     13.2466
hse_own    |  1/4  |   2/4  |   0.11  |     13.2466
hse_own    |  1/5  |   4/5  |   0.20  |     13.2466


However, the calculated bandgap using hse06 and hse_own shows a significant difference, with the values differing by about two times. Additionally, for hse_own, it is puzzling that the bandgap does not change despite adjusting the parameters.

I would like to confirm whether my understanding of the parameter relationships is correct. If it is not, I would appreciate an explanation of how each parameter (alpha, beta, omega) relates to the HSE formula*.

I would be grateful for any advice or suggestions.

Best regards,


*HSE formula* (Hybrid functional - wikipedia)

2

Ridft, Rdgrad, Dscf, Grad / Re: D4 - Edisp /kcal,au: NaN NaN

« Last post by rusakov on July 03, 2024, 06:35:23 PM »

Uwe, thank you very much! I am very much interested in knowing how to deal with the issue, so I sent you a private message.

3

Aoforce and Numforce / Re: Extreme IR Frequency of an Open-Shell Singlet Organic Cation with DFT

« Last post by uwe on July 02, 2024, 11:57:09 AM »

Did you also try the Ahlrichs/Weigend basis sets like def2-TZVPPD or def2-QZVPD ?

If you have a doubly augmented basis set, there could be a lot of very small integrals which in the end sum up to a significant contribution. So increasing the integral threshold can be a test to see if that is a reason for the problem.

To increase accuracy (in general), first rerun energy and gradient calculations with:
- larger DFT grid (gridsize 5)
- converge the density in the dscf/ridft calculation before running aoforce ($denconv 1d-8)
- increase (or to be more correct: decrease the value of) the SCF integral threshold $scftol 1d-16
- make sure your gradients are very close to zero (they also contribute to the frequencies) by enabling weight derivatives in DFT and converge geometry sufficiently well

This might help if the problem comes from numerical noise. If not, you will not see any improvement...

If the frequency is so much off, also try to calculate the frequencies numerically with NumForce (just as a check).

4

Ridft, Rdgrad, Dscf, Grad / Re: D4 - Edisp /kcal,au: NaN NaN

« Last post by uwe on July 02, 2024, 11:48:35 AM »

Hi Alex,

sorry, you are right. DFT-D4 uses the nuclear charge and not the element symbol to determine the C6/C8 parameters.
I have another idea I can share offline. If you are interested, please send a personal message.

Best, Uwe

5

Ridft, Rdgrad, Dscf, Grad / Re: D4 - Edisp /kcal,au: NaN NaN

« Last post by rusakov on July 02, 2024, 01:12:00 AM »

Hello, Uwe,

I tried using an H atom with zero charge and no basis, but the result was exactly the same.

Alex

6

Aoforce and Numforce / Extreme IR Frequency of an Open-Shell Singlet Organic Cation with DFT

« Last post by emendezvega on July 02, 2024, 12:10:15 AM »

 
 Dear Turbomole Community,

 I am trying to compute the vibrational modes (IR) of an organic cation using DFT e.g. M06-2X and B3LYP // 6-311++G** in Turbomole 7.8.

 The closed-shell singlet (CSS) ground state and following excited states, triplet and open-shell singlet (OSS), lying ~0.4 and 0.5 eV higher in energy, were easily optimized within C2v symmetry.
 The energetic ordering nicely fits to our NEVPT2//CASSCF calculations and also to experimental photoelectron spectra.

 However, there is a vibrational mode in the OSS state (minimum) that is completely wrong, with an unreal frequency and intensity (see below). The mode is a CCC bending and should be below
 1300 cm-1. Consequently, the ZPE correction is affected and the ZPE-corrected energy of the OSS state, and relative instability, is shifted to much higher values.

                60        a1           3236.52             8.24940       YES     YES
                61        b1           3242.31             5.36910       YES     YES
                62        a1           3242.56             9.75005       YES     YES
 ----------  63        b1           5168.45    325387.74669       YES     YES -----------

 I also tried to optimize it in C1 symmetry with no success. This extreme frequency appears with both M06-2X and B3LYP. With other functionals the OSS state is a TS.

 Would you have any idea of how to proceed?

 Thanks in advance,
 Dr. Enrique Mendez-Vega
 Ruhr-Universität Bochum / OCII

7

Ridft, Rdgrad, Dscf, Grad / Re: D4 - Edisp /kcal,au: NaN NaN

« Last post by rusakov on July 01, 2024, 04:42:32 PM »

Uwe, thank you so much for your response. I will give it a try today.

8

Ridft, Rdgrad, Dscf, Grad / Re: D4 - Edisp /kcal,au: NaN NaN

« Last post by uwe on July 01, 2024, 04:40:43 PM »

Seems that DFT-D4 is not able to treat dummy atoms. I downloaded the original D4 code from https://github.com/dftd4/dftd4 and it refuses to treat a q, while the Turbomole implementation ignores the dummy atom in the energy but not in the gradient.
This can, however, be fixed for future versions.

You could try to use a hydrogen without basis functions and charge as a replacement for the element q to check if DFT-D4 accepts it. I think the additional dispersion energy and gradient from this single hydrogen can be neglected.

9

Ridft, Rdgrad, Dscf, Grad / Re: D4 - Edisp /kcal,au: NaN NaN

« Last post by rusakov on June 25, 2024, 11:16:00 PM »

Hello, Uwe,

I've just faced the same problem. Here is my control file. The rest is in the attachment.

$title
AtAu4
$symmetry c1
$user-defined bonds    file=coord
$coord    file=coord
$redund_inp
  metric 1
$optimize
 internal   on
 redundant  on
 cartesian  off
 global     off
 basis      off
$atoms
q  1
    basis =none
    jbas  =none
au 2-5
    basis =au dft_g
    ecp   =au gatchina
    jbas  =au dft_g
at 6
    basis =at dft_g
    ecp   =at gatchina
    jbas  =at dft_g
$basis    file=basis
$ecp    file=basis
$newecp
$uhfmo_alpha   file=alpha
$uhfmo_beta   file=beta
$uhf
$scfiterlimit       500
$thize     0.10000000E-04
$thime        5
$scfdamp   start=2.000  step=0.050  min=0.50
$scfdump
$scfintunit
 unit=30       size=0        file=twoint
$scfdiis
$maxcor    500 MiB  per_core
$drvopt
   cartesian  on
   basis      off
   global     off
   hessian    on
   dipole     on
   nuclear polarizability
$interconversion  off
   qconv=1.d-7
   maxiter=25
$coordinateupdate
   dqmax=0.3
   interpolate  on
   statistics    5
$forceupdate
   ahlrichs numgeo=0  mingeo=3 maxgeo=4 modus=<g|dq> dynamic fail=0.3
   threig=0.005  reseig=0.005  thrbig=3.0  scale=1.00  damping=0.0
$forceinit on
   diag=default
$energy    file=energy
$grad    file=gradient
$forceapprox    file=forceapprox
$gdiis
$soghf
$soghf
$scftol 1d-16
$omp_cpus 40
$coulex
$rij
$jbas file=auxbasis
$statpt
$dft
   functional pbe0
   gridsize   7
$scfconv   7
$disp4
$fermi tmstrt=400.00 tmend=50.00 tmfac=0.900 hlcrt=1.0E-01 stop=1.0E-03
$gdiis
$scforbitalshift  closedshell=.05
$rundimensions
   natoms=6
   nbf(CAO)=495
   nbf(AO)=399
$redundant    file=coord
$intdef    file=coord
$alpha shells
 a       1-51                                   ( 1 )
$beta shells
 a       1-50                                   ( 1 )
$actual step      relax
$spinor shells
 a       1-101                                  ( 1 )
$orbital_max_rnorm  0.0000000000000
$last SCF energy change = -808.23441
$subenergy  Etot         E1                  Ej                Ex                 Ec                 En                 Disp
-808.2344132397    -2844.748051236     1390.630536822    -66.28585299480    -4.417380296856     716.6005302506    -.1419578455483E-01
$charge from ridft
          0.000 (not to be modified here)
$dipole from ridft
  x    -0.00498505410922    y     0.00025876325979    z    -0.16748520203162    a.u.
   | dipole | =    0.4258971729  debye
$spinor_real       file=spinor.r
$spinor_imag       file=spinor.i
$maximum norm of cartesian gradient =            NaN
$maximum norm of internal gradient =  0.0000000
$end

10

TmoleX - general topics / Re: RICC2 NTOs visualization with TMOLEX or others

« Last post by uwe on June 21, 2024, 05:01:44 PM »

Hi,

call proper in the directory where your job did run. Create NTOs by

• first, enter the mos menu and then enter 'nto' there. The list of excitations is shown and you are asked to specify for which excited state you want to generate NTOs for. The NTOs are then written to disk. proper will also print to the screen how many NTOs are contributing to which amount
• then 'end' proper, not quit, so you will go back to the main menu again.
• there, enter 'grid' to get into the menu which is taking care of generating 3D grid data for a lot of properties
• one of the options in the grid sub-menu is 'nto'. It needs as option which (how many) NTOs to generate, e.g. 'nto 1-5' will create the first 5.
• the 3D grid files are written to disk, default format is plt and can be opened in TmoleX or VMD. You can also ask for cube format before generating the NTOs for other viewers.