Topics

1

Questions and Answers / ±isovalue option meaning in visualizing molecular orbitals

« on: February 23, 2021, 10:17 »

Dear all,

When I visualize molecular orbitals (for example HOMO or LUMO), when I tick the ±isovalue option, the orbitals will be shown with two colors red and blue. What do these colors mean? what is the difference between blue and red regions?

Thanks

2

Questions and Answers / Problem in finding HOMO-LUMO because of partial occupations

« on: February 22, 2021, 12:24 »

Dear all,

How can I determine HOMO-LUMO for this structure? there are some partial occupations in some orbitals! the script and the molecular energy spectrum have been attached.

 562  -1.457714e+00   2.000000e+00
  563  -1.396535e+00   2.000000e+00
  564  -2.405055e-01   1.999818e+00
  565  -7.608169e-02   1.899860e+00
  566   2.848218e-02   4.988281e-01
  567   3.148024e-01   1.029389e-05
  568   3.187673e-01   8.830246e-06
  569   3.190502e-01   8.734142e-06
  570   5.065160e-01   6.193482e-09
  571   5.070444e-01   6.068169e-09

Thanks
Best regards,

3

Questions and Answers / Bandstructure by using DFT+U

« on: February 12, 2021, 11:25 »

Dear ATK staff,

I am trying to calculate the ZnO bandstructure by using the GGA PBE + U method as it has been done in this paper: Ferromagnetism properties of Er-doped ZnO:a GGA +Ustudy (https://doi.org/10.1039/C6RA17921E)
I changed the lattice parameters to a=3.32 and c=5.34 which are the optimized numbers in the paper and selected 7 eV and 10.5 eV as U for oxygen and zinc atoms. Everything is similar to the ones in the paper but I can not calculate the bandstructure and the bandgap is 0 for my calculations. I attached the script and the log and the result. Would you please help me solve this problem?

Thanks.

4

Questions and Answers / Export images in vector format

« on: January 26, 2021, 11:03 »

Hi all,
Is there any way to export images from "viewer" in any vector format?
Thanks.
Hadi

5

Questions and Answers / Asking for help; I can not relax a ZnO surface!

« on: January 20, 2021, 10:02 »

Dear all,

I am trying to relax ZnO (10-10),(11-20), and (0001) slabs by using the semiempirical method, Slater-Koster. For (10-10) and (11-20) the calculations are fast and the surfaces are stable and in a good form and everything is reasonable. However, for the (0001) slab, I tried several slabs with different sizes and boundary conditions but the calculations will converge in a very long time (2-3 days!!!) while the surface finally collapses or deforms. I attached the script and a pic. Would you please guide me on what the problem could be and what the solution is? I have been struggling with this for one week, trying any solution I assumed may work 
Thanks.

Hadi

6

Questions and Answers / Slater-Koster method for charge transfer calculations

« on: January 12, 2021, 10:25 »

Dear QuantumATK staff,

I am using the semi-empirical method, particularly the Slater-Koster method (dftb.org parameters) to calculate the interactions between a ZnO surface with a molecule (look at the attached pic). I am calculating the charge transfer, HOMO-LUMO, binding energy and so on. I have two important and almost independent questions and I will be so grateful if you can help me:

FIRST QUESTION- Is the Slater-Koster method reliable for these calculations? I know that each method has its approximations but I want to know that generally, the Slater-Koster method (dftb.org parameters) performs correctly in calculating the parameters I am calculating or I must use for example Huckel method or even DFT?

The SECOND QUESTION- I would like to investigate the impacts of implicit solvent on my calculations. I mean I want my molecule to be in a solvent above the slab surface and not in a vacuum. I read the tutorial and I know that in the DFTB method I can change the dielectric constant in the poisson solver and in this way the solvent will be considered. I choose Multigrid solver and leave the boundary conditions for A and B periodic and choose Neumann and Dirichlet for C left and right respectively and 80 for dielectric constant. However, I never can see any differences between with-solvent and without-solvent calculations in any way and it seems to me that no solvent is considered at all. What could be the reason?

I am looking forward to your help. Thanks.

7

Questions and Answers / HOMO-LUMO of a slab+molecule system

« on: December 16, 2020, 11:30 »

Dear QuantumATK family,

I am trying to investigate the interactions between a molecule with ZnO surface. To do this I use a ZnO crystal and use the "cleave surface" and make a normal slab of ZnO with a vacuum on the top of the surface and relax it. Then I put the relaxed molecule on the vicinity of the surface and optimize the system and observe the trajectory to see what . You can see the system attached to this message.

Now I want to calculate the HOMO-LUMO of the whole system (ZnO +absorbed molecule). I read all the posts about HOMO-LUMO in the forum and I know that HOMO-LUMO are defined for a non-periodic isolated system but I think my system is periodic in A and B direction. I used "change the configuration to molecule" to eliminate the periodicity of the slab but when I try to relax it the whole structure of the ZnO will be changed (see the second attached pic). Do you have any idea how I can build up a system so I can investigate the interactions of a molecule with ZnO surface and also see the homo-lumo in the whole system?

Thank you in advance

8

Questions and Answers / QM/MM simulations

« on: November 23, 2020, 12:30 »

Hello,

I know that QuantumATK has the possibility for doing both MM and QM simulations. I want to know if there is the possibility of doing QM/MM simulations in ATK. In this simulation method you can choose a part of system for QM simulations while the calculations for other parts of the system will be MM. This method is very useful when size of  the system under study is large, yet you are interested in chemical reactions and bonding in a specific part of the system.
Thank you in advance.

Best regards,
Hadi

9

Questions and Answers / ERROR when I try to open ATK

« on: November 20, 2020, 14:59 »

Hello,
I have been using Quantum ATK on Win10 with no problem. The software crashed suddenly and now when I try to open it again I receive this ERROR:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "zipdir\NL\GUI\Main\Main.py", line 291, in main
  File "zipdir\NL\GUI\MainWindow\Project\OpenProjectWidget.py", line 590, in launchProjectBrowserOnStartUp
  File "zipdir\NL\GUI\MainWindow\Project\ProjectHandler.py", line 72, in currentProject
  File "zipdir\NL\GUI\MainWindow\Project\ProjectHandler.py", line 113, in projectList
  File "zipdir\NL\GUI\MainWindow\Project\ProjectHandler.py", line 113, in <listcomp>
  File "zipdir\NL\GUI\MainWindow\Project\Project.py", line 67, in __init__
  File "zipdir\NL\GUI\MainWindow\Project\Project.py", line 86, in setPath
  File "build\lib\ntpath.py", line 544, in abspath
ValueError: _getfullpathname: embedded null character in path


Would you please help me???
Thanks
 

10

Questions and Answers / QuantumATK2019 won't open on Linux(mint) on VirtualBox

« on: November 11, 2020, 13:44 »

Hello,
I installed Linux(mint) on VirtualBox on my Laptop. Then I installed the QuantumATK2019 on Linux(mint), but after installation I can not open it and when I try to open it nothing happens. Would you please help me with this problem?
Thank you very much in advance.
Best regards,
Hadi
P.S. I am a quite new Linux user so I will be so thankful if you consider this and give me instructions in details. Thanks again

11

Questions and Answers / IR absorption spectra

« on: October 2, 2020, 13:54 »

Hello,

Is it possible to somehow  get (directly or indirectly) the IR absorption spectra of a sample in QuantumATK? I am trying to obtain the IR absorption spectra of  a ZnO treated surface.

Looking forward to your responses.
Thank you
Hadi

12

Questions and Answers / Considering the effects of a solvent in interactions

« on: August 26, 2020, 14:30 »

Hello,
I am using Quantum-ATK to investigate the adsorption of a protein molecule (Albumin) on a surface of a slab like ZnO or diamond. Because of the large size of the system, I am using forcefield simulations. I did some simulations with the assumption of the protein molecule being in vaccum and over the surface of the slab. Now, I need to consider the protein being in a solvent (not vacuum)  and over the surface of the slab. I intend to go for implicit solvent strategy (although it is not accurate). These are my questions:

1. how I can introduce a solvent to be around my protein molecule instead of the vacuum?

2. Is using the different dielectric constant for the space (currently vacuum) above the surface a good idea for doing that? If yes how can I do that?

3. I used forcefield simulations so far (for the molecule in vacuum). What kind of calculations should I use for the molecule in solvent? Is using forcefield still possible? Generally would you please guide me on choosing the proper calculator in Script Generator for the new case? I need the
calculations be as fast as forcefield if it is possible.

Thank you very much for your responses in advance.

13

Questions and Answers / I need to have albumin molecule on ATK

« on: August 7, 2020, 15:05 »

Hello, I am investigating the interactions of different molecules with different surfaces and now I need to have albumin molecule. Do I have to build it or I can find it on web and import it into ATK? where can I find it? Thank you for your helps in advance. I found it on www.rcsb.org/structure/4F5S and in .cif format and I know ATK is supposed to support it but when I drag it into the builder it doesn't work. Any idea please?