Recent Posts

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1
Escf and Egrad / Re: ESCF calculation with COSMO and symmetry
« Last post by finrod on August 29, 2019, 04:03:21 pm »
Disclaimer I don't claim to understand the technical aspects ("orthogonal subspace update") nor the uranyl chemistry.

However, in my experience excitations are quite sensitive to the given geometry, especially when electronic states are beginning to interact with each other. Have you tried re-optimising the geometry of your complex first (e.g. with solvent environment), and then run the excitation afterwards? Sometimes finding and reproducing sensible geometries takes up a lot of time.
Also, depending on your molecule or the properties of your specific excitation, e.g. excitations with strong CT character, you might also need to find a more adequate functional. Try screening the relevant literature.

Good luck!
2
Riper / Effective core potentials bug in the riper module
« Last post by Marek Sierka on August 14, 2019, 03:15:47 pm »
Dear Users:

Using effective core potentials (ECP) in the riper module may occasionally lead to wrong energies and gradients. This is usually accompanied by difficult SCF convergence. The energies are off by several hartree, which leads to unphysical relative energies. We are investigating this issue and will provide an updated bug-fixed Riper version as soon as possible.

Marek Sierka
3
News and Announcements / Turbomole 7.4 released
« Last post by uwe on July 26, 2019, 04:22:28 pm »
TURBOMOLE V7.4 has been released (July 2019)

New features:
Efficiency:
  • OMP parallelization of nearly all modules
  • Semi-numeric approximation in escf and aoforce
  • RI-K in egrad and aoforce
  • Improved efficiency, memory handling and symmetry exploitation in X2C gradients and energies [ https://doi.org/10.1021/acs.jctc.8b01084 ]
  • Extended DFT grids for relativistic all-electron calculations [ https://doi.org/10.1039/C9CP02382H ]
  • new and faster integrals for COSMO gradients
Usability:
  • New default: Usage of Intel MPI (version 2019)
          NOTE that Intel MPI might need additional settings for some
          network interconnects like Infiniband, but also affects the
          way the parallel MPI binaries are using CPU and core pinning.
  • TmoleX 4.5 now supports
    • New Methods:
      • RI-RPA
      • semi-empiric (MOPAC) and tight binding (xTB)
    • hyperpolarizabilities
    • extended and costumizable list of functionals
    • job templates redesigned
    • Combine Results feature extended
4
Well,  :-[
as boyz from Computational center in Aachen used to say RTFM

In readme-file of `Molden2AIM` is stated:

Code: [Select]
...
About the MOLDEN file
...
6. Turbomole Insert a command line
                        [Program] Turbomole
                        into the MOLDEN file or specify PROGRAM=3 in the m2a.ini file.

I added the `[Program] Turbomole` to molden.input and now it checks:
Code: [Select]
Do you want to check the *.47 file? ([Yes] / No)
 >

  Reading overlap matrix...
  Reading density matrix...

  Sum of MO Occupancies                       =      22.0000000000
  Analytically integrated number of electrons =      22.0000000010
  Difference                                  =       0.0000000010
  Difference per atom                         =       0.0000000003
 =============================================================================

I do not know if it solves all problems (test was on a CO2 molecule) but at least I have something to work on. If for bigger systems NBO does not work I'll let you know. I hope problem is solved.

It would be still nice to have also Fock-matrix in file.47 to use more options of NBO but it's a starter. As the Fock-matrix is not printed by `turbomole` this one stays in the hands of Cosmologic.
5
Sorry Uwe, I've been busy with broken machinery. I couldn't try anything sooner.

I did tested the "-norm" option and I can't say that I see in output anything about "NORM option found". As you can see I used turbomole 7.3 but I also tried 7.3.1 no difference.
Code: [Select]
tm2molden -norm

 tm2molden (wac2004.chemie.uni-wuerzburg.de) : TURBOMOLE V7.3 ( 22118 ) 1 Jul 2018 at 20:38:15
 Copyright (C) 2018 TURBOMOLE GmbH, Karlsruhe


    2019-07-18 13:48:20.874



              +--------------------------------------------------+
              | Atomic coordinate, charge and isotop information |
              +--------------------------------------------------+

                    atomic coordinates            atom    charge  isotop
          0.00000000    0.00000000    0.00000000    c      6.000     0
          0.00000000    0.00000000    2.21970934    o      8.000     0
          0.00000000    0.00000000   -2.21970934    o      8.000     0

       center of nuclear mass  :    0.00000000    0.00000000    0.00000000
       center of nuclear charge:    0.00000000    0.00000000    0.00000000

              +--------------------------------------------------+
              |               basis set information              |
              +--------------------------------------------------+

              we will work with the 1s 3p 5d 7f 9g ... basis set
              ...i.e. with spherical basis functions...

   type   atoms  prim   cont   basis
   ---------------------------------------------------------------------------
    c        1     24     14   def-SV(P)   [3s2p1d|7s4p1d]
    o        2     24     14   def-SV(P)   [3s2p1d|7s4p1d]
   ---------------------------------------------------------------------------
   total:    3     72     42
   ---------------------------------------------------------------------------

   total number of primitive shells          :   24
   total number of contracted shells         :   18
   total number of cartesian basis functions :   45
   total number of SCF-basis functions       :   42


 symmetry group of the molecule :   d6h

 the group has the following generators :
   c6(z)
   c2(x)
   mirror plane sigma(xy)

   24 symmetry operations found

 there are 12 real representations :
 a1g  a2g  b1g  b2g  e1g  e2g  a1u  a2u  b1u  b2u  e1u  e2u

 maximum number of shells which are related by symmetry :  2




 ENTER NAME OF MOLDEN INPUT FILE (DEFAULT: molden.input):



    mo occupation :
   irrep   mo's   occupied
    a1g     10        4
    a2g      0        0
    b1g      0        0
    b2g      0        0
    e1g      4        1
    e2g      2        0
    a1u      0        0
    a2u      8        3
    b1u      0        0
    b2u      0        0
    e1u      5        1
    e2u      1        0

 number of basis functions   :                     42
 number of occupied orbitals :                     11

  MOs are in ASCII format !


 reading orbital data $scfmo  from file mos
 orbital characterization : scfconv=6
 all orbitals will be included in the transformation

 number of non-frozen orbitals          :    42
 number of non-frozen occupied orbitals :    11



 WRITE DATA GROUPS [GTO] AND [MO] (BASIS SET AND MOLECULAR ORBITAL DATA) TO
 molden.input (Y/N, DEFAULT: Y)?

y



 WRITE DATA GROUPS [FREQ] ETC. (VIBRATIONAL FREQUENCIES AND NORMAL MODES) TO
 molden.input (Y/N, DEFAULT: Y)?

y

   ***  vibrational spectroscopic data read from $vibrational spectrum
        file=<vibspectrum>  ***



 WRITE DATA GROUPS [GEOCONV] ETC. (GEOMETRY CONVERGENCE DATA) TO
 molden.input (Y/N, DEFAULT: Y)?

y

 Wrote data groups [Title] and [Atoms] to molden.input

 Wrote data groups [GTO] and [MO] to molden.input

 Wrote data groups [FREQ], [INT], [FR-COORD], and [FR-NORM-COORD] to molden.input

 Wrote data groups [GEOCONV] and [GEOMETRIES] to molden.input


    ------------------------------------------------------------------------
         total  cpu-time :   0.06 seconds
         total wall-time :  6 minutes and  6 seconds
    ------------------------------------------------------------------------

   ****  tm2molden : all done  ****


    2019-07-18 13:54:26.635

 tm2molden ended normally

`molden2aim.exe` still writes the warning `Normalization check failed`:
Code: [Select]
  Sum of MO Occupancies                       =      22.0000000000
  Analytically integrated number of electrons =      21.8483228688
  Difference                                  =       0.1516771312
  Difference per atom                         =       0.0505590437

 ### Warning! Normalization check failed.

When I tried `t2aomix` results were even worse -- but that's not a surprise --aomix is not listed as an input for Molden2AIM.

best regards
6
Treatment of Solvation Effects with COSMO / Re: Dummy atoms and COSMO
« Last post by cneiss on July 11, 2019, 03:34:03 pm »
Hi Uwe,

Quote
it would be sufficient to ask the program to calculate those at certain positions in space
This would be a nice option for the next release  ;)

Best,
Christian
7
Ridft, Rdgrad, Dscf, Grad / Re: $firstorder in TM 5.10
« Last post by cneiss on July 11, 2019, 02:14:26 pm »
Hi,

still does not work with TM 7.3...

Is the keyword "$firstorder" deprecated??

Best,
Christian
8
Ridft, Rdgrad, Dscf, Grad / Re: Controling linear dependence thresholding
« Last post by uwe on July 10, 2019, 08:45:11 pm »
Hi,

Quote
Normally such linear dependence would be projected out of the basis set for overlap matrix eigenvalues < some threshold.

I wonder what 'Normally' does mean  :). Probably other QC programs do that by default, but it was never a standard in Turbomole. Automatically changing the number of basis functions can be helpful for such interesting calculations you plan to run. But for applications it could also lead to discontinuities e.g. on the potential energy surface.

riper has the option to remove linearly dependent basis functions using the option lsdiag. Search the documentation for this keyword to see where it has to be added. It was initially implemented for periodic systems, but it might also work for molecules (but I have never tried it so far).

Regards,

Uwe
9
Ridft, Rdgrad, Dscf, Grad / Controling linear dependence thresholding
« Last post by jfurness on July 09, 2019, 11:58:54 pm »
I am running single point calculations using DFT from dscf and CCSD from ccsdf12 of hydrogen chains with the series of basis sets {cc-pVDZ, cc-pVTZ, cc-pVQZ, cc-pV5Z} for basis set extrapolations.

When the chain is compressed to short internuclear separations (~1.0 Bohr) the calculations with larger basis sets explode after a few iterations.

I was expecting this behaviour as the basis sets become linearly dependent. Normally such linear dependence would be projected out of the basis set for overlap matrix eigenvalues < some threshold.

Is it possible to set this threshold in the control file?

I have found the option lindep in $ricc2 for the coupled cluster calculations, though I am not certain this is doing what I want, and it definitely doesn't apply for the DFT calculations.

Many thanks,
James
10
Hi,

if you have Turbomole versions 7.3 or newer, try:

tm2molden -norm

The molden file export has been implemented about 20 years ago in Turbomole using a normalization which most tools do not expect, so some have a 'Turbomole option' which is used by default to modify the normalization.

To provide the meanwhile accepted standard but to avoid confusion, the option 'norm' was added. You can check if tm2molden did the job correctly by inspecting the output. You should find the lines:

NORM option found! The molecular orbital coefficients
will be normalized to standard MOLDEN format.

ENTER NAME OF MOLDEN INPUT FILE (DEFAULT: molden_std.input):


Another format which contains the non-Turbomole normalization and includes a lot of additional data is AOMix file (just use the t2aomix script).

Regards,
Uwe

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