Messages

46

General Questions and Answers / Re: Optimizing Geometry of 2D material sheet

« on: November 20, 2015, 12:02 »

Dears Anders,

With k being 9,1,9 the optimized sheet looks as if it is crumpled on one side of the surface of the sheet (asymmetrical crumpling) whereas with 5,1,5 as k-point sampling the optimized sheet looks more symetric. What could be the reason behind it? And which one could be considered more accurate?

Also, would please tell me, out of the two which would be a better way to optimize:
1. Optimizing the defective nanosheet first and then making a device
or
2. Making a device out of the defective sheet and then optimizing the whole thing

Thank you very much for your time!

47

General Questions and Answers / Re: Error in Geometry Optimization of nanosheet

« on: November 20, 2015, 11:46 »

While using Huckel the OptimizeGeometry option gets disabled, whereas with Slater Koster the error is showed after the simulation begins.
Moreover, on rechecking I found that with carbon nanosheet ATK is showing the same error, whereas with Si nanosheet the error persists.
I would be grateful if you explain the same. Thanks!

48

General Questions and Answers / Re: Error in Geometry Optimization of nanosheet

« on: November 20, 2015, 06:25 »

Okay, thank you!

But what about Slater Koster, what does the error mean?

49

General Questions and Answers / Parallelization over two cores of one CPU in one machine

« on: November 19, 2015, 07:19 »

I am trying to parallelize the simulation over two cores in one CPU (OS is CentOS 6.6).
Can anyone please guide me how to proceed with it?
I tried installing mpich2 (by following the tutorial http://quantumwise.com/publications/tutorials/item/509-mpi-setup-for-running-atk-in-parallel-on-a-simple-cluster ) but that's probably not the solution.

Thanks for you help!

50

General Questions and Answers / Error in Geometry Optimization of nanosheet

« on: November 19, 2015, 06:51 »

1. The following error flashes whenever I try to optimize the geometry of any nanosheet with Slater Koster. Could anyone please explain what it means?

Traceback (most recent call last):
  File "/tmp/9271670433236302.py", line 97, in <module>
    optimizer_method=LBFGS(),
  File "./zipdir/NL/Dynamics/Optimization/OptimizeGeometry.py", line 232, in OptimizeGeometry
  File "./zipdir/NL/Dynamics/Optimization/OptimizeGeometry.py", line 287, in runRelaxation
  File "./zipdir/NL/Dynamics/ASEAtomsInterface.py", line 264, in get_forces
  File "./zipdir/NL/Dynamics/ASEAtomsInterface.py", line 159, in _update
  File "./zipdir/NL/Analysis/Forces.py", line 29, in __init__
  File "./zipdir/NL/Calculators/HuckelCalculator/Analysis/Forces.py", line 23, in calculateHuckelForces
  File "./zipdir/NL/Calculators/HuckelCalculator/Analysis/EnergyForcesStressUtilities.py", line 168, in setupEnergyForcesStress
NL.ComputerScienceUtilities.Exceptions.NLValueError: No PairPotential given, which is required in order to calculate forces or stress.

2. Why can we not optimize the geometry using Extended Huckel? Is it a software problem or a practical one?

Thanks in advance!

51

General Questions and Answers / Re: Optimizing Geometry of 2D material sheet

« on: November 19, 2015, 06:24 »

Thank you for your reply.

Let me rephrase the question, should the k-point sampling in the new calculator (DFT) affect accuracy of the simulation?

52

General Questions and Answers / Optimizing Geometry of 2D material sheet

« on: November 7, 2015, 11:35 »

Hello!

1. Could anyone please tell me whether I must use SGGA or LSDA or MSGGA while using the 'new calculator' for optimizing a 2d material defective sheet with 'Optimize Geometry'?

2. While trying to optimize the geometry of the same, I tried keeping k = 9x1x9 (C being the direction of transmission, my sheet consists of 7x1x7 = 49 atoms) but it took huge time to simulate so I reduced the k to 3x1x3.
I notice that I got better result with low k.
With high k the sheet seemed more deformed on the right than on the left but with 3x1x3 it seems more symmetric. Why is that? (The defect is very near to the centre but, a little to the left)

Thanks for the help!!! 

53

General Questions and Answers / Line Defect

« on: July 6, 2015, 10:32 »

Please guide me on how to create Line defects in a 2D Nanosheet and a 2D Nanoribbon which are not perfectly 2D

54

General Questions and Answers / Passivation in non-perfect 2D nanosheet

« on: July 6, 2015, 10:29 »

Could you please tell me how to passivate (Hydrogen) 2D nanosheet and nanoribbon (after the formation of a defect) which is not perfectly 2D?