Recent Posts

Pages: 1 2 [3] 4 5 ... 10
21
Aoforce and Numforce / reduced mass of diatomic molecule in aoforce output
« Last post by tonyst on May 11, 2020, 02:04:30 pm »
Dear Turbomole enthusiasts,

an analytical force constant calculation of IrN yielded the following output:

Code: [Select]
       mode               1        2        3        4        5        6

     frequency           0.00     0.00     0.00     0.00     0.00  1239.80

     symmetry                                                         a1 

        IR                -        -        -        -        -       YES
|dDIP/dQ|   (a.u.)     0.0000   0.0000   0.0000   0.0000   0.0000   0.0056
intensity (km/mol)       0.00     0.00     0.00     0.00     0.00    56.16
intensity (  %   )       0.00     0.00     0.00     0.00     0.00   100.00
 
       RAMAN              -        -        -        -        -       YES
 
  1   ir          x   0.00000  0.00000  1.00000  0.00000  0.00000  0.00000
                  y   0.00000  0.00000  0.00000  0.00000  1.00000  0.00000
                  z   0.00000  0.70711  0.00000  0.00000  0.00000 -0.07268
  2   n           x   0.00000  0.00000  0.00000  1.00000  0.00000  0.00000
                  y   1.00000  0.00000  0.00000  0.00000  0.00000  0.00000
                  z   0.00000  0.70711  0.00000  0.00000  0.00000  0.99736

reduced mass(g/mol)    14.007  103.113  192.220   14.007  192.220   14.948

The reduced mass is calculated to be 14.948, but should it not be 192.220*14.007/(192.220+14.007)=13.056? What am I missing?

Thank you for your help

/Edit: and for N2 it is 14?

Code: [Select]
       mode               1        2        3        4        5        6

     frequency           0.00     0.00     0.00     0.00     0.00  2348.41

     symmetry                                                         a1g

        IR                -        -        -        -        -       NO
|dDIP/dQ|   (a.u.)     0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
intensity (km/mol)       0.00     0.00     0.00     0.00     0.00     0.00
intensity (  %   )       0.00     0.00     0.00     0.00     0.00     0.00
 
       RAMAN              -        -        -        -        -       YES
 
  1   n           x   0.00000  0.00000  0.00000  1.00000  0.00000  0.00000
                  y   0.00000  1.00000  0.00000  0.00000  0.00000  0.00000
                  z   0.70711  0.00000  0.00000  0.00000  0.00000  0.70711
  2   n           x   0.00000  0.00000  1.00000  0.00000  0.00000  0.00000
                  y   0.00000  0.00000  0.00000  0.00000  1.00000  0.00000
                  z   0.70711  0.00000  0.00000  0.00000  0.00000 -0.70711

reduced mass(g/mol)    14.003   14.003   14.003   14.003   14.003   14.003

/Edit2:

Taking the wavenumber and force constant from that calculation I derive a reduced mass of 13.055474:

Code: [Select]
You have: (0.7594293 hartree / atomiclength^2)/(1239.80 cm^-1 * c * 2 * pi)^2*N_A
You want: g/mol
* 13.055474

I am really curious what that reduced mass in the aoforce output means.

22
Aoforce and Numforce / Re: Visualization vibration modes? aoforce2g98
« Last post by baishaotao on May 07, 2020, 12:46:27 pm »
Hello Uwe,

Many thanks. It works now.

Best,
Dr. Shaotao Bai
KU Leuven
23
Aoforce and Numforce / Re: Visualization vibration modes? aoforce2g98
« Last post by uwe on May 07, 2020, 12:15:22 pm »
Hello,

just copy the whole directory of your calculation from the Linux box to your Windows system. TmoleX does not need to read in the output file, as all results are stored in the control file or files referenced by it (like the vibspectrum file).

Then, in TmoleX, use File -> Open Job/Control File  to read in the control file. Switch to the Results panel. The buttons on the right side (vibrations , IR spectrum, thermochemical properties, etc. should be accessible).

Regards,

Uwe
24
Aoforce and Numforce / Re: Visualization vibration modes? aoforce2g98
« Last post by baishaotao on May 07, 2020, 12:00:17 pm »
Hellow uwe,

Thanks for your kind suggestions.

I have looked into this TmoleX. Unfortunately, reading the control file from remote cluster does not work as expected because it cannot link to my aoforce.out and vib_normal_modes etc. I guess that is a missing excuting script, i.e. TmolexX, therefore the jobs performed in linux cluser cannot be read by TmoleX in windows. If you know how to solve this issue, please let me know.

Anyway, thanks again!

Best,
Dr. Shaotao Bai
KU Leuven
25
Hello,

yes, if you use Turbomole 7.4.1, just set:

export PARA_ARCH=SMP
export TM_PAR_OMP=yes
source $TURBODIR/Config_turbo_env

This will invoke the OpenMP version of ridft which is able to use arbitrary functionals and combinations of functionals from XCFun or libxc in the parallel SMP version.

For older versions of Turbomole you can set
export TM_PAR_FORK=yes
instead.

Note for other readers: To use the 'usual' M06-2X functional, it is sufficient to set:

$dft
   functional m06-2x

This will also work with the default parallel ridft version.

The input

$dft
   functional xcfun set-mgga
   functional xcfun m06x2x 1.0
   functional xcfun set-hybrid 0.2

includes only the exchange part of M06-2X and adds 20% exact HF exchange to it. This is not M06-2X as the correlation part is missing and the HF exchange for this functional is 54%.

Just to avoid any misunderstandings for those who read this post, searching for a way to use M06-2X in Turbomole...

Regards,

Uwe
26
Thanks Dr. UWE for your kind reply. I am running my job in Single Node with 16 cores. I would like to use M06-2x hybrid functional and it is not available in the libxc.

Do you have any suggestion regarding that?

Thanks
Subrata
27
Ricc2 / Problems generating plt files for nto orbitals (ricc2)
« Last post by doritsh on May 05, 2020, 07:28:43 pm »
I am trying to generate the natural transition orbitals as plt files using turbomole (with ADC(2)).
I have inserted into the control file: $pointval nto 1-5
I have tried to use the ricc2 module, or ricc2 -proper as suggested by the manual. The calculations run smoothly, but the plt files are not created. I also tried using the proper module as described in the manual (proper --> mos --> ntos), but this option generates different files, but not plt files. I need to plot the natural transition orbitals. The manual suggest to create plt files and open them with gOpenMol.
I am using Turbomole version 7.3.
Do I need another keyword in the control file? I could not find any explanation what is wrong with my input.
28
Aoforce and Numforce / Re: Visualization vibration modes? aoforce2g98
« Last post by uwe on May 03, 2020, 11:28:29 pm »
Hello,

hard to say what the problem is, but to visualize the modes, just run TmoleX and open the control file. In the Results section there is a button 'Vibrations' It opens the 3D builder which can visualize the modes or combination of modes.

TmoleX Client can do that too, that is the free version of the graphical user interface for Turbomole, available for download from here:

https://www.3ds.com/products-services/biovia/products/molecular-modeling-simulation/solvation-chemistry/turbomoler/

Just click on 'TmoleX - the graphical user interface' and you will find the download links.

Regards,

Uwe
29
Aoforce and Numforce / Visualization vibration modes? aoforce2g98
« Last post by baishaotao on May 03, 2020, 09:44:17 pm »
Dear friends,

I have a problem to visualize the vibration modes after aoforce calculations. I have tried 'aoforce2g98 aoforce.out > g98.out' to convert the turbomole output into GAUSSIAN98 formate. It still does not work!

I have copied the example from molden wibsite http://cheminf.cmbi.ru.nl/molden/examples/vibration.gal. This example works well.

Does anyone has an idea or suggestion to fix this problem or other suggestions?

Many thanks in advance!

Best,
Dr. Shaotao Bai
KU Leuven
30
Hello,

self-defined combinations of functionals are not supported in the MPI version at the moment. Do you run the job on several nodes, or on one machine only?

Regards,

uwe
Pages: 1 2 [3] 4 5 ... 10