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1
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
2
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
3
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
4
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
5
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

6
Ridft, Rdgrad, Dscf, Grad / Re: prinitng fock, density and overlap matrices
« Last post by uwe on June 30, 2019, 08:34:23 pm »
Hi,

there is an undocumented keyword which prints some of the matrices, but since it is undocumented you need to contact the Turbomole Support Team to find out how to do it  ;)

Regards,

Uwe
7
Ridft, Rdgrad, Dscf, Grad / prinitng fock, density and overlap matrices
« Last post by KrisR on June 30, 2019, 09:01:29 am »
Apparently during DSCF above matrices are computed.

Following info appears in DSCF output:
Code: [Select]
density matrices ---> file = dens
 fock matrices ---> file = fock
But as I haven't see any additional files I assume these are binary scratch only.

I tried to search through Manual but except remarks like:
Quote
To accelerate local hybrid calculations, the analytical integrals for exact exchange
 are screened using the overlap and the density matrix
I couldn't find anything.

Is there any way to print them in some text format to la og- or an external-file?

best regards,
Kris
8
I tried to use tm2molden followed by Molden2AIM
Unfortunately the 2nd program claims that sum of occupations is wrong in molden-file generated with tm2molden.
Here example for CO2

Code: [Select]
tm2molden

 tm2molden : TURBOMOLE V7.3 ( 22118 ) 1 Jul 2018 at 20:38:15
 Copyright (C) 2018 TURBOMOLE GmbH, Karlsruhe

              +--------------------------------------------------+
              | 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)?

...
 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
 ...
 tm2molden ended normally

end then the Molden2AIM

Code: [Select]
./molden2aim.exe


 *****************************************************************************
                               *  Molden2AIM  *
                          Version 4.3.0,  02/09/2019
      It converts the format from MOLDEN to AIM-WFN, AIM-WFX, and NBO-47.
 *****************************************************************************
...
 Type in the MOLDEN/GABEDIT file name within 50 characters:
 (extension mol/mold/molden/gab can be omitted; default: MOLDEN)
 > molden.input

 The MOLDEN/GABEDIT file molden.input has been found.
 _____________________________________________________________________________

 >>> Cartesian basis functions are used.

 >>> SUMMARY

     Number of atoms:                                 3
     Maximum angular momentum:                        2
     Number of primitive Cartesian functions:        75
     Number of contracted Cartesian functions:       45
     Number of primitive spherical functions:        72
     Number of contracted spherical functions:       42
     Number of orbitals to be printed:               11
 =============================================================================
...
 A NBO 47 file is generated successfully!
  File Name = molden.47

 Do you want to check the *.47 file? ([Yes] / No)
 > Yes

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

  Sum of MO Occupancies                       =      22.0000000000
  Analytically integrated number of electrons =      21.8483236278
  Difference                                  =       0.1516763722
  Difference per atom                         =       0.0505587907

 ### Warning! Normalization check failed.
 =============================================================================

NBO7 generates then the same error on the FILE47

Code: [Select]
gennbo.i8.exe molden.47

 *********************************** NBO 7.0 ***********************************
             N A T U R A L   A T O M I C   O R B I T A L   A N D
          N A T U R A L   B O N D   O R B I T A L   A N A L Y S I S
 ************************                                ************************
  (c) Copyright 1996-2018 Board of Regents of the University of Wisconsin System
      on behalf of the Theoretical Chemistry Institute.  All rights reserved.

          Cite this program [NBO 7.0.2 (2-Jan-2019)] as:

          NBO 7.0.  E. D. Glendening, J. K. Badenhoop, A. E. Reed,
          J. E. Carpenter, J. A. Bohmann, C. M. Morales, P. Karafiloglou,
          C. R. Landis, and F. Weinhold, Theoretical Chemistry Institute,
          University of Wisconsin, Madison, WI (2018)

       /NLMO   / : Form natural localized molecular orbitals
       /BNDIDX / : Print bond indices based on the NAO density matrix

 Job title:  Molden2AIM, Version 4.3.0 (02/09/2019)           Time: Sat Jun 29 1

 Invalid density: Tr(P*S) = 21.84832 is not an integer number of electrons

 NBO analysis completed in 0.02 CPU seconds (0 wall seconds)
 Maximum scratch memory used by NBO was 40000 words (0.31 MB)
 Maximum scratch memory used by GENNBO was 1332 words (0.01 MB)


9
Actually title says all of it.
Could somebody tell me how to generate an input for NBO7 using turbomole or tmolex?
I would prefer to not bypass it with gaussian's recalculation.

best regards, Kris
10
Treatment of Solvation Effects with COSMO / Re: Dummy atoms and COSMO
« Last post by uwe on June 19, 2019, 11:24:30 pm »
Hi,

dummy atoms have a lot of disadvantages, as they might carry charges, masses, basis sets, COSMO radii, ...

I guess for nuclear independent chemical shieldings it would be sufficient to ask the program to calculate those at certain positions in space. That would be much easier to implement.

Regards,
Uwe
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