Recent Posts

Pages: 1 [2] 3 4 ... 10
11
Thank you very, very much for going to the trouble of writing a converter just for this issue! The Cube files it produces are displayed correctly in both VMD and VESTA, so I'll use this from now on.

Kind regards & thank you once again
12
Hi,

cub files can be defined in different ways, especially the order of the data can vary. Usually tools like VMD check and use the options, but this does not seem to be always the case.

Turbomole cub files contain the line:

OUTER/INNER/MIDDLE LOOP: X,Y,Z

if this is ignored by the program you use, you will get wrong pictures.

Writing a plt -> cub converter is not a big issue, I will try to provide one here:

http://www.cosmologic.de/support-download/downloads/utilities-for-turbomole.html

as soon as possible.

Changing the defaults is a bit dangerous as there are others who use Turbomole cub files in the way they are defined now. Perhaps introducing a 2nd cub file format might be a reasonable addition...

Regards
13
Hello,

I've been trying to export Cube files using Turbomole's proper program, but it seems that the exported volumetric data is always spatially shifted for some reason.

Minimal reproducible example:

For a simple H2 molecule with the symmetry axis along z (cf. .xyz file at the bottom), this picture shows what the total density exported by Turbomole 7.3.1 as a Cube file looks like (visualized using VMD, but I've tried VESTA as well with similar results):



Clearly, there is some shift of the density that shouldn't be there. Note that this uses the atom positions contained in the Cube file itself; using those from the original .xyz file is even worse:



All of this works perfectly fine with .plt files, however, as shown here:



Unfortunately, I have to use Cube files, because some tools that I want to use only work with those, and I haven't found any utility that can convert .plt to .cub.

Am I doing anything wrong or is this just broken?

Thank you very much in advance for any suggestions!

Kind regards



.xyz file:

Code: [Select]
2
h2
h 0.0 0.0 -0.37
h 0.0 0.0 0.37



UPDATE: For the time being, I figured out a workaround: Export as .plt, convert this to .dx using https://www.mdanalysis.org/GridDataFormats/, then convert this to .cub using babel. This seems to produce correct Cube files. But it would still be nice if this could work correctly out-of-the-box in Turbomole.
14
Hello,

you can run static and dynamic first hyperpolarizabilities through escf.

For static just add this to the control file:
$scfinstab hyperpol <unit>

unit would be nm, ev, rcm. Default is a.u.

For dynamic it should look like this:
$scfinstab hyperpol <unit>
<freq1>
<freq2>
<pair1_a> <pair2_b>

A hyperpolarizability calculation will be performed using the pairs given on each line AND using all combinations of the single frequencies given alone on each line. Specifying no frequencies initiates a static calculation. The same unit specifications are accepted as for dynamic polarizability calculations. For example,

$scfinstab hyperpol nm
800
1000
1064 1064

will compute hyperpolarizability tensors with frequency pairs
1000nm,1000nm
1000nm,800nm
800nm,800nm
1064nm,1064nm

Hope that helps,

Arnim
15
Hello,

when you use define and come to this question
DO YOU ACCEPT THIS OCCUPATION ?  DEFAULT=y
Press n and and enter
u 2
for a triplet or
u 4
for a quintet or
u 6
of a septet.
That is chapter 4.3.2 in the manual of version 7.3.

Once you have intial MOs (alpha/beta), you can also edit directly the control file and change the values in
$alpha shells
and
$beta shells
according to your wishes.

In TmoleX you can select the multiplicity in the Molecular Attributes panel.

Cheers,

Arnim
16
Dear Turbomole developers and users,

We are currently struggling to calculate different multiplicities for a molecule.

We are studying some transition metal complexes and want to try out different multiplicities, for example singlet, triplet, quintet or septet. In Gaussian input file we can write an input line such as 1 3 where the first number is the charge of the molecule (here +1) and the second number is the multiplicity (here a triplet). Is there any way to modify control file, coord file or to use define script to quickly set any multiplicity such as triplet or septet?

We don't find this in the user manual.

What we are specifically interested in is doing ground state geometry optimization of transition metal complexes, which implies comparing energies of different spin states. The method we are using is the default Turbomole one (method BP86 basis set SV(P) with effective core potential for heavy metals)

Thank you in advance  :).

Best regards.
17
Hello!
I have one important question. Usually, the NACMEs have 1/bohr units. What is about in Turbomole?
I can see in egrad.out:
cartesian gradient of the energy (hartree/bohr)
dE/dx.....
dE/dy...
dE/dz...
----------
After I can see
cartesian nonadiabatic coupling matrix elements
dE/dx.....
dE/dy...
dE/dz...
So I assume that NACMEs have the hartree/bohr, too. Therefore I can (dE/dx)/E and have d/dx, for example.
However, there is a very interested situation.
the values of NACME (1/bohr) in GAMESS-US at CASSCF level of theory (only the static correlation) have the values which are similar (one order of magnitude) to NACME of Turbomole (with dynamic correlation). I was confused and therefore ask this question.
Thank you very much for the answer! 

18
Define / Re: Bug in damp within DEFINE script?
« Last post by Glxblt76 on April 02, 2019, 07:06:17 am »
Dear Uwe,

Thanks for your answer. I checked and there is no $restart keyword in the control file. Here is the list of commands I use in the define script:

Code: [Select]

title
a coord
desy
ired
*
*
eht
y
3
y
scf
iter
1000
damp
18

13
fermi
2
10
1
50

shift

0.1


dft
on

ri
on

*

On my machine, all entered input is taken into account there except the damping. The resulting damping is still:
Code: [Select]
$scfdamp   start=0.700  step=0.050  min=0.050where I expect:
Code: [Select]
$scfdamp   start=18  step=0.050  min=13
Best regards.
19
Define / Re: Bug in damp within DEFINE script?
« Last post by uwe on April 01, 2019, 10:51:29 am »
Hi,

you can check if define works correctly by opening the control file in an editor. Check the settings in the $scfdamp line:

$scfdamp   start=1.000  step=0.050  min=0.100

It should always contain the numbers you set when running define. If not, please send the input as bug report to the Turbomole support!

But the damping parameters are part of the restart information if the energy has not yet converged. So if you ran into the maximum number of SCF iterations limit ($scfiterlimit), the orbitals, the occupation numbers and the damping factors are stored and automatically re-used if you restart the job. In that case, running define and setting different damping values will not be sufficient. Either remove the $restart keyword in the control file or simply run the script

kdg restart

Then the $scfdamp keyword values will be taken.

Hope this helps,

Uwe
20
Define / Re: How to comment in define input file
« Last post by uwe on March 31, 2019, 07:37:20 pm »
Hi,

there is no option or menu within define to add comment lines. Well, at least not to my knowledge.

But you can of course open the control file with an editor and add whatever you like yourself. The control file is just a usual text file and can be modified and changed with your favorite text editor.

Regards,

Uwe

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