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QuantumATK => General Questions and Answers => Topic started by: adkins.99 on May 30, 2015, 20:51

Title: Molecular Dynamics Bombardment Simulation (Contraint Editor???)
Post by: adkins.99 on May 30, 2015, 20:51

Hello everyone, this is my first post.

I'm trying to follow the tutorial here:

 http://quantumwise.com/publications/tutorials/item/886-simulating-ion-bombardment-on-graphene-sheets

I'm having difficulty setting up the simulation. I take the carbon nanosheet with the bombardment atom to the script generator; I add the calculator and two MD blocks. In the tutorial there is shown a "constraint editor," and in the tutorial you can see in the picture there's an  "Add Constraints," button in the Molecular Dynamics window (just scroll down to "Setting up the Simulation" which brings up the "constraint editor". For me I don't see a button to "add constraints," so I don't know how to proceed. Everything else is there, just not that button.

Any help would be appreciated, thanks.

Title: Re: Molecular Dynamics Bombardment Simulation (Cohttp://quantuntraint Editor???)
Post by: adkins.99 on May 31, 2015, 00:47

Actually, it might be possible just to make modifications in the editor and put it in manually. I still don't see why the button isn't available in the script generator interface.

Title: Re: Molecular Dynamics Bombardment Simulation (Contraint Editor???)
Post by: Umberto Martinez on May 31, 2015, 13:20

The Screenshot and the instruction refer to VNL 2015 which is planned to be released soon.
Consider it a sneak peek of the new release :)

As reported in the tutorial just after the Figure you mention "In VNL 2014 it is sufficient to select the atom in the presenter window of the MolecularDynamics widget and the atom index will automatically appear in the Constraints field."

Hope you liked the tutorial and managed to complete it!

Title: Re: Molecular Dynamics Bombardment Simulation (Contraint Editor???)
Post by: adkins.99 on June 4, 2015, 00:59

Thanks for your reply. I am still having difficulty giving the bombardment atom a velocity. There are two molecule blocks, the first one runs fine, I use all the parameters given in the tutorial. The second molecule block is tricky. For one, the version I'm using doesn't have the "velocity configuration" option under "initial velocity," there's only the "Maxwell-Boltzmann" option.

I also need to understand how to make the modifications to the script in the editor similar to that shown in the tutorial.

Title: Re: Molecular Dynamics Bombardment Simulation (Contraint Editor???)
Post by: Jess Wellendorff on June 4, 2015, 11:44

Yes, there are certain new option for the Molecular Dynamics that are only available from the scripter as of VNL 2015. However, the ATK 2014 engine already has these. I have attached a script that should do exactly what the tutorial instructs. All you need to do is add the BulkConfiguration (the nanosheet + bombardment atoms).

Hope this helps.