Messages

406

General Questions and Answers / Re: question about tutorial

« on: April 12, 2016, 13:03 »

Dear Yasheng

If you do the calculations in serial, you can just save the new transmission spectra to the same file. They will end up as separate objects and can then be called as shown in the script.

407

General Questions and Answers / Re: How to build (AlN)12 nanocluster

« on: April 12, 2016, 10:13 »

Dear Nour

The structure in the paper is only fullerene-like, so it is unfortunately not available in our internal database. So you have several options:

1. You can ask the authors to provide you with a file, e.g. .xyz or .cif, which you can open with VNL and go from there.

2. You can search for the structure in databases you might have access to, and get a file from there, which you can open in VNL.

3. You can use a 24-atom fullerene from the VNL database and change the elements to fit your system, and then see if the  results are consistent with your expectations.

408

General Questions and Answers / Re: How to build (AlN)12 nanocluster

« on: April 11, 2016, 14:50 »

Thanks for linking to the answer you mentioned. That answer deals with a specific nanocluster structure - are you looking to model the same cluster structure, or are you looking for something else?

409

General Questions and Answers / Re: How to build (AlN)12 nanocluster

« on: April 11, 2016, 09:20 »

Dear Nour

Please also link to the answer you did not understand. It will help us to understand exactly what you are looking for.

410

General Questions and Answers / Re: How to restar the calculation because of exceeding walktime?

« on: April 8, 2016, 16:28 »

What you show should work - however, it seems that we have some problems with starting IV-curves using the checkpoint method, as an IV curve calculation is actually pretty complicated behind the scenes.  So if you are still having problems, that might be the cause, because your script looks correct.

411

General Questions and Answers / Re: Monte Carlo simulation of atomic diffusion in solids

« on: April 6, 2016, 09:29 »

Hi baizq

We have a more general introduction to the AKMC method in this tutorial: http://quantumwise.com/publications/tutorials/item/872-adaptive-kinetic-monte-carlo-simulation-of-pt-on-pt-100 Have you consulted this one? Please do so first, and then it will be easier to explain exactly what you would like to know.

We have two more tutorials you might also want to look at, if you have not already done so: http://quantumwise.com/publications/tutorials/item/879-adaptive-kinetic-monte-carlo-simulation-of-pt-island-ripening and docs.quantumwise.com/tutorials/akmc-empirical-sige.html

Regarding the practicality of modeling the system, you really need to do a test, and see how far it gets in a time that is reasonable for you. Using EAM potentials it should be possible, but it might still take a long time to get an adequate sampling.

412

General Questions and Answers / Re: Monte Carlo simulation of atomic diffusion in solids

« on: April 4, 2016, 14:32 »

Dear baizq

In principle, the AKMC implementation should be able to model the diffusion process. However, the XY layer is very thick, so depending on your model (DFT etc.), the time required might be impractically large.

413

General Questions and Answers / Re: Zig-zag graphene nanoribbon bandgap

« on: April 1, 2016, 09:03 »

You may also consult some tutorials about graphene in general and graphene nanoribbons, where the latter specifically deals with the bandstructure of GNRs:

http://docs.quantumwise.com/tutorials/exploring_graphene.html

http://docs.quantumwise.com/tutorials/spin_bloch_gnr.html

414

General Questions and Answers / Re: Resource reqirement

« on: March 30, 2016, 20:35 »

Well, that is the challenge in this case, as it is not possible to know beforehand. If you have a Geometry Optimization which has been interrupted, you can restart from the trajectory and look at the time per force step when estimating how much longer the simulation will run.

The absolute best help when estimating the length of a simulation is experience, and you should always allow for a lot more time than estimated. Personally I would set the time limit of at least twice my initial estimate unless I was very familiar with the system I was studying. For new systems I would give it at least 3 times longer than estimated.

Of course, all of this assumes that your supercomputer uses only actual running time for accounting. In this case I would say that it is always better to have too high estimate, to increase the chance of your calculation actually finishing.

415

General Questions and Answers / Re: How to restar the calculation because of exceeding walktime?

« on: March 29, 2016, 11:18 »

Thanks for providing the link, however, I cannot find the option for English, so I have no idea where I should click to access the file. Could you maybe upload it on a site where it is possible to change the language to English?

416

General Questions and Answers / Re: Resource reqirement

« on: March 29, 2016, 09:34 »

Hi Debarghya

Unfortunately, we do not have a way of automatically estimating the time required for a calculation. However, if you have calculations for similar systems you can use those to estimate the time required. If you only change a few things, it will probably not change the time much. However, you should always be skeptical when doing such estimates - the other calculation might take a lot longer than expected.

If your calculation involves geometry optimization, you can use that the time required for each force evaluation step is approximately the same for a given system.

417

General Questions and Answers / Re: How to restar the calculation because of exceeding walktime?

« on: March 22, 2016, 16:36 »

Can you maybe upload it somewhere else and provide a link?

It is important that the relative path to the checkpoint file is correct. The script you uploaded earlier will look for the checkpoint file in the same directory, so if the checkpoint file is not present, it cannot use it to start from. However, I am not sure if this is really the problem you are experiencing, so getting the .nc file will help me help you.

418

General Questions and Answers / Re: How to restar the calculation because of exceeding walktime?

« on: March 22, 2016, 15:52 »

Is this also the directory your script is running from?

I would like to take a closer look at your problem, so could you please upload or provide a link to the checkpoint .nc file?

419

General Questions and Answers / Re: How to restar the calculation because of exceeding walktime?

« on: March 22, 2016, 14:58 »

I do not see the checkpoint file in any of the folders, so I am not sure exactly where you have it? With the path you use in your script, it must be in the same folder as your script.

Also, I believe you need to set the initial state explicitly after line 620, as shown in this tutorial: http://www.quantumwise.com/publications/tutorials/item/502-restarting-stopped-calculations

420

General Questions and Answers / Re: How to restar the calculation because of exceeding walktime?

« on: March 22, 2016, 14:34 »

Please also provide the script, as you need to point to the specific location of the file.