Recent Posts

Pages: 1 ... 6 7 [8] 9 10
71
Molecular Properties, Wavefunction Analysis, and Interfaces to Visualization Tools / Re: [HowTo] Generate NTOs from TDDFT
« Last post by uwe on November 30, 2023, 08:54:15 AM »
Hello,

OK, if you have a plt or plv file (plv is the same as plt for scalar data while plv can also contain vectors on the grid) and the coord file, just Open the stand-alone COSMObuild tool. It is the same viewer as the 3D Molecular Builder within TmoleX, but as an own app it has a menu. There you can read in plt/plv files as well as coordinates, and you can simply open them in the same window. So you should see the molecule as well as the surface.
Right-click on the surface to change colour and opacity to change the level of transparency of the surface.

TmoleX 2023 should show all plv files in the job directory, they can have arbitrary names. Perhaps it is better not to name files you have created outside of TmoleX like a known file name like td (which is total density). Just rename plt files to .plv if plv works for you but not plt...

Hope this helps.
72
Molecular Properties, Wavefunction Analysis, and Interfaces to Visualization Tools / Re: [HowTo] Generate NTOs from TDDFT
« Last post by shafikoff on November 30, 2023, 02:58:09 AM »
Dear Uwe,

Thank you for your reply. However, my comment was more related to ricc2 calculations as I'm trying to visualize transition NTOs after a CC2 calculation. I did make .plt format hole and electron density files with proper, but Tmolex does not want to see them in the directory, neither after restart nor after job refresh. I can visualize a .plt file only by making it to pretend to be td.plv file by renaming it.  The original td.plv file, which is in the directory after cc2 calculation and seen by Tmolex, has first to be renamed to smth else. Other problem I have, is that after I trick Tmolex to visualize .plt like I described, I still see only the densities and not the molecular frame, which makes it not very useful for publication...

Best regards,
Marsel
73
Miscellaneous / Re: Really deep SCF energies DFT (with dscf)
« Last post by uwe on November 29, 2023, 06:23:41 PM »
Hi,

what did help for me was to
- use RI-DFT
- set $scftol 1d-15  as I described here: https://forum.turbomole.org/index.php/topic,401.0.html

With Turbomole 7.7 (should also work with 7.6 but probably not older versions), I used this simple control file as input:

$coord file=coord
$scftol 1d-15
$basis file=basis
$symmetry c1
$atoms
    basis = 6-31+G*
    jbas  = universal
$dft
  functional b3-lyp
$rij
$marij
$end

coord file contained your coordinates and basis file was what I have downloaded from https://www.basissetexchange.org/ .

Attached the input and the output of ridft. It converged in 15 SCF iterations.

I do not think that DFT is causing problems here as Hartree-Fock shows the same behavior.

The geometry has almost Cs  symmetry, and if you enforce Cs (call define and in the geometry menu 'desy 0.1', this will find Cs and also moves the coordinates to the exact positions of the symmetric structure), the calculation also runs fine without the need to set any keywords like $scftol.

Using other diffuse basis sets like def2-SVPD or aug-cc-pVDZ might be the better option.

Best Regards
74
Miscellaneous / Re: Really deep SCF energies DFT (with dscf)
« Last post by marilu98 on November 29, 2023, 05:10:12 PM »
I'm now trying the same calculation with HF (to have a better guess to feed a DFT calculation) and I still have extremely oscillating scf energies. Hereafter some cycles:

 ITERATION  ENERGY          1e-ENERGY        2e-ENERGY     NORM[dD(SAO)]  TOL
   2  -975974.79994451    -4311.6171875    -973025.53918    0.467D+11 0.102D-11
          Norm of current diis error:  4.4348
          max. resid. norm for Fia-block=  1.448D+05 for orbital     25a
          max. resid. fock norm         =  1.454D+05 for orbital     25a
          Delta Eig. = **************** eV

                                              current damping :  0.850
 ITERATION  ENERGY          1e-ENERGY        2e-ENERGY     NORM[dD(SAO)]  TOL
   3  -1019817.0084406    -4249.1926270    -1016930.1722    0.584D+09 0.102D-11
          Norm of current diis error:  5.1341
          max. resid. norm for Fia-block=  4.385D+01 for orbital      1a
          max. resid. fock norm         =  3.580D+02 for orbital      1a
          Delta Eig. = **************** eV

                                              current damping :  0.900
 ITERATION  ENERGY          1e-ENERGY        2e-ENERGY     NORM[dD(SAO)]  TOL
   4  -1019817.9718195    -4261.4228516    -1016918.9054    0.251D+05 0.102D-11
          Norm of current diis error:  2.9852
          max. resid. norm for Fia-block=  7.470D+01 for orbital      1a
          max. resid. fock norm         =  6.127D+02 for orbital      1a
          Delta Eig. = **************** eV

                                              current damping :  0.950
 ITERATION  ENERGY          1e-ENERGY        2e-ENERGY     NORM[dD(SAO)]  TOL
   5   92468.401837716    -4271.7119141     95377.757324    0.251D+05 0.809D-11
          Norm of current diis error:  1.5651
          max. resid. norm for Fia-block=  3.087D+03 for orbital      1a
          max. resid. fock norm         =  1.669D+04 for orbital      1a
 mo-orthogonalization: Cholesky decomposition
          Delta Eig. = **************** eV



Note the positive energy of iteration 5.
Hereafter my control file generated using define:

$title
$symmetry c1
$user-defined bonds    file=coord
$coord    file=coord
$optimize
 internal   off
 redundant  off
 cartesian  on
 global     off
 basis      off
$atoms
h  1-14                                                                        \
   basis =h 6-31+G*
c  15-31                                                                       \
   basis =c 6-31+G*
o  32-33                                                                       \
   basis =o 6-31+G*
s  34                                                                          \
   basis =s 6-31+G*
$basis    file=basis
$scfmo    scfdump=30   format(4d20.14)
$scfiterlimit       100
$scfconv        7
$thize     0.10000000E-04
$thime        5
$scfdamp   start=1.000  step=0.050  min=0.100
$scfdump
$scfintunit
 unit=30       size=0        file=twoint
$scfdiis
$maxcor    500 MiB  per_core
$scforbitalshift  closedshell=.4
$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
$end


The basis file contains the external basis set.
I'm using Turbomole7.6
I have two questions:
1) is there any way to do basis set projection (i.e. use a smaller basis set first and the use the basis set needed).
2) I cannot impose hcore guess. By following the manual (i.e. using $scfmo none) I still have a EHT starting vectors in the output. Do you have any   experience with this? (dscf module)

Thank you to everybody in advance.
Best regards,
Marilu

 



75
Molecular Properties, Wavefunction Analysis, and Interfaces to Visualization Tools / Re: Create wfn file with natural orbitals for Multiwfn
« Last post by uwe on November 28, 2023, 11:43:29 AM »
Hello,

if you have the difference density (as it is generated by egrad) I wonder why you need NTOs in addition? NTOs are a quick way to get an idea of how the difference density does look like (where the electrons come from and where they are going to).
If you have the difference density available, you can simply plot it (using +/- view) to see the change in density directly.
Or do I miss something important?

Best Regards
76
Molecular Properties, Wavefunction Analysis, and Interfaces to Visualization Tools / Re: [HowTo] Generate NTOs from TDDFT
« Last post by uwe on November 28, 2023, 11:38:44 AM »
Hello,

first of all: Since TmoleX version 2023 NTOs from TDDFT can be generated and visualized directly in the graphical user interface without the need to run proper manually.

On the command line:
Proper (since version 2021, V7.6) has an option dftnto which does both steps in one run without asking any questions. So after an escf run where you have calculated N excited states, you can call

proper -dftnto 3

to get the NTOs of the 3rd excitation. It creates the first 10 occupied and virtual NTOs and writes the contribution to a file named tddft-nto-data.dat

Note that using this option when having symmetry is kind of dangerous because the name of the resulting plt files do not contain the IRREP name (a, b, a', e, ...). I'd recommend to run proper the non-automated way for symmetric cases. Or at least check the output of proper -dftnto <N>.

Final remark: Yes, TmoleX will show all plt files it finds in the job directory and lists them for visualization. So virtually everything can be put in there.
But the problem is that TmoleX does not re-read the content of the directory while it is running. Some tasks that are run do trigger this, but it is not easy to find out which ones... the only safe way is to end TmoleX and restart it. Or use COSMObuild (stand-alone version) and use File -> Open -> in Plot Viewer and change the 'Files of Type' to be shown from Molecules to TURBOMOLE plots.

There is an enhancement request for BIOVIA to also re-read in all plt files if a user uses the 'Refresh Job' option in the right-mouse menu when clicking on a  job directory.

Best Regards
77
Riper / Re: Is it possible to split a RT-TDDFT calculation into several sequential runs?
« Last post by manas.sharma on November 28, 2023, 10:40:21 AM »
RT-TDDFT calculations cannot be restarted and run from scratch right now. The restart feature may be added in the future.

For a faster simulation, you can try turning the SCF scheme off within the $rttddft block using scf off, which will then enable the predictor-corrector scheme.

Alternatively, you can also try using a larger time step of 0.4 or 0.5 au depending on the desired energy range of the spectrum.
78
Miscellaneous / Re: Really deep SCF energies DFT (with dscf)
« Last post by marilu98 on November 17, 2023, 06:01:53 PM »
Hi,
thank you very much once again. In fact, I have problems with systems that contain triple CC bonds.
Here an example (it is from the paper J. Chem. Theory Comput. 2022, 18, 2, 1046–1060):
$coord
    9.27006233815159     -4.56563200912835      0.00013379544421       h
    4.64141236904137     -4.32483962923246      0.00013182805034       h
    5.05918122897159      3.75748513925418     -0.00010634112513       h
    9.66505382813530      3.54143798936859     -0.00010887127944       h
   -3.67501791919848     -3.89309077933371     -0.00010509711842       h
   -3.25648850932071      4.19556853915043      0.00011925041120       h
   -8.32979991840199     -3.64789074931242     -0.00010594314881       h
   -7.93772671848856      4.41415218923358      0.00011623176269       h
  -15.81144469698963     -0.50727138483899     -1.67389502958465       h
  -15.75527819702021     -3.44057121940902     -0.00010840943037       h
  -15.81145089699207     -0.50737682191914      1.67386171976020       h
   16.41873589675920      2.04080322952146     -0.00006053284106       h
   13.80513209730624      3.27359241934086     -1.68893740959647       h
   13.80512039725591      3.27368692926867      1.68873124973594       h
    8.35084343836196     -2.73888994941181      0.00007836070629       c
    5.74629668879938     -2.60666967941831      0.00007860126843       c
    4.49886966908027     -0.26110449798891      0.00001062063877       c
    5.97959980891925      1.93352382967140     -0.00005539221908       c
    8.59585792826932      1.80436951956161     -0.00005627037481       c
    9.81767446813259     -0.53413285394070      0.00001026385847       c
    1.82241367963363     -0.12226715902900      0.00000922356424       c
   -0.45911807593796     -0.00608386365412      0.00000770327957       c
   -3.13570901941989      0.13323481802946      0.00000705000125       c
   -4.60739961919282     -2.07607416960626     -0.00005649241763       c
   -4.37115621920461      2.48437982950287      0.00006990720545       c
   -7.21746430856807     -1.93788686959910     -0.00005681008059       c
   -6.97894704856623      2.61135661953761      0.00006833816584       c
   -8.43051093826820      0.40687496393239      0.00000522736041       c
  -11.22667899787731      0.66458740692910      0.00000708666194       c
  -15.12622359708390     -1.48762030975725     -0.00004640146910       c
   14.37355899722264      2.24752188963408     -0.00007215975899       c
  -12.34226999752111      2.65789218946130      0.00005136653552       o
  -12.41664749751367     -1.59239539976045     -0.00004424018933       o
   13.13702549744587     -0.95154658274258      0.00001396280839       s
$end

I agree with you: 6-31+G* has less diffuse functions with respect to aug-cc-pVDZ... this is why I can't spot properly the problem.
The only difference is that aug-cc-pVDZ is implemented and I used 6-31+G* as implemented in QChem.

Best regards


79
Miscellaneous / Re: Really deep SCF energies DFT (with dscf)
« Last post by uwe on November 15, 2023, 07:24:55 PM »
Hi,

is the input structure prone to linear dependencies of the basis set if diffuse functions are used? Like a fullerene where all diffuse functions 'flood' the inner part of the fullerene?
As far as I can see aug-cc-pVDZ is not less diffuse than 6-31+G* (I just downloaded both basis sets for carbon from https://www.basissetexchange.org/ and compared them).
Is it possible to post the structure of one of those cases (coord file and also the basis set file you have used)?
Best Regards
80
Miscellaneous / Re: Really deep SCF energies DFT (with dscf)
« Last post by marilu98 on November 15, 2023, 09:47:45 AM »
Thank you for your reply.

I don't think that is a problem of the functional (I tried also other xcf like tpssh and pbe0).
With aug-cc-pVDZ I have no problems, as well as with bs (external or built in) without diffuse functions (6-31G*, 3-21G*, cc-pVDZ,...).

The problem is that B3LYP/6-31+G* level is not working for some of my systems (namely 12 out of 48), so it is not a systematic error. My guess it's that for these systems linear dependencies are more crucial....thus, I'd like to remove some of them (if it is possible).

Thank you once again

Best regards
Pages: 1 ... 6 7 [8] 9 10