Author Topic: How to generat file47 for gennbo (NBO7)  (Read 1601 times)

KrisR

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How to generat file47 for gennbo (NBO7)
« on: June 25, 2019, 10:24:05 am »
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
« Last Edit: June 25, 2019, 01:31:17 pm by KrisR »

KrisR

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Re: How to generat file47 for gennbo (NBO7)
« Reply #1 on: June 29, 2019, 06:47:07 pm »
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)



uwe

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Re: How to generat file47 for gennbo (NBO7)
« Reply #2 on: July 03, 2019, 10:53:19 pm »
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


KrisR

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Re: How to generat file47 for gennbo (NBO7)
« Reply #3 on: July 18, 2019, 02:13:07 pm »
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

KrisR

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Re: How to generat file47 for gennbo (NBO7)
« Reply #4 on: July 18, 2019, 02:56:45 pm »
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.
« Last Edit: July 19, 2019, 09:08:46 am by KrisR »