Messages

1

General Questions and Answers / Using MEAM potential in ATK

« on: June 22, 2020, 17:28 »

Hi, We are developing MEAM potential and would like to test it in ATK.  Is there a standard format for MEAM potential coded in ATK.

The example provided in ATK is for SiO2, (potential name MEAM_SiOAu_2005).  This potential is developed by Kuo and Clancy and has a formalism which is different from other MEAM formalism. For example,  the embedding function for SiO2 is written as

F(rho) = A * E0 * rho * log(rho)

whereas some other formalisms use

F(rho) =  a * rho^(1/2) + b * rho^2 + c * rho^3

Can anyone recommend how to use MEAM potential in ATK.  We are using MEAMfit code to generate the MEAM potential and here is the paper that describes the formalism of MEAM potential.  http://dx.doi.org/10.1016/j.cpc.2015.05.016

The code that we used for generating MEAM potential can write output in LAMMPS format. Is there a way to use that in ATK?

Thanks
Amit

2

Installation and License Questions / Re: VNL OpenGL display question

« on: October 2, 2019, 15:53 »

I tried both 2017.12 and 2016.4

3

Installation and License Questions / VNL OpenGL display question

« on: October 1, 2019, 18:45 »

I am running VNL on a Linux machine I get the following error

Could not initialize OpenGL for RasterGLSurface, reverting to RasterSurface.
Could not initialize OpenGL
Aborted (core dumped)

Does VNL requires hardware acceleration from a GPU and NVIDIA driver installed?  Or is it that it only required OpenGL?
Any suggestions to fix the above error.

>>> lspci -k | grep -iA3 vga
08:00.0 VGA compatible controller: Matrox Electronics Systems Ltd. MGA G200e [Pilot] ServerEngines (SEP1) (rev 05)
   Subsystem: Intel Corporation Device 0103
   Kernel modules: mgag200
7f:08.0 System peripheral: Intel Corporation Xeon E7 v4/Xeon E5 v4/Xeon E3 v4/Xeon D QPI Link 0 (rev 01)

4

General Questions and Answers / Si EAM potential possibly incorrect source.

« on: December 21, 2017, 23:12 »

Hi,
I noticed, when working with ATK Classical, one of the available potential is EAM_PdSi_Sheng_2011. The Literature Reference for this potential is

Sheng, HW and Kramer, MJ and Cadien, A and Fujita, T and Chen, MW, Highly optimized embedded-atom-method potentials for fourteen fcc metals, Physical Review B, 83, p. 134118, 2011.

however, reading through the paper, there is no mention of Silicon. It seems to me that the source is incorrect. Or possibly the EAM potential. I haven't checked if this EAM potential will produce reasonable numbers for Silicon or not.

Best
Amit

5

General Questions and Answers / Re: Error in emulating wrap and hook function

« on: February 14, 2017, 20:09 »

I misread your response. You solution works.

Thanks
Amit

6

General Questions and Answers / Re: Error in emulating wrap and hook function

« on: February 14, 2017, 18:41 »

Julian,
Thank you for your reply and looking into the script. I tried your suggestion and I still got an error when running the complete simulation   (multiple MD)

In trying to resolve the issue I noticed that it was not the Tags that was generating the error but infact it is the reservoir_temperature that is generating the error. For example the line

reservoir_temperature = [('substrate',300*Kelvin)]  gives and error whereas if I replace the line with
reservoir_temperature = 300*Kelvin then the code runs fine with the same Atom tags, as was in my original file.

Also, what I dont understand is why does it work for the  Script_Sic  example and does not work for my script.

Any suggestion on how to set reservoir_temperature for a selected atoms?

Thanks
Amit

7

General Questions and Answers / Error in emulating wrap and hook function

« on: February 10, 2017, 21:49 »

Hi,
I am emulating the Thin film growth example with hook function - and in doing that I am getting the following error. The original example works fine. I am not sure what the error is telling me. Attached is the python script.

Thanks
Amit

Traceback (most recent call last):
  File "He_deposit_Tungsten (100).py", line 719, in <module>
    method=method
  File "./zipdir/NL/Dynamics/MolecularDynamics/MolecularDynamics.py", line 262, in MolecularDynamics
  File "./zipdir/NL/Dynamics/MolecularDynamics/NVTNoseHoover.py", line 102, in _initialize
  File "./zipdir/NL/Dynamics/MolecularDynamics/NVTNoseHoover.py", line 248, in _initializeThermostats
NL.ComputerScienceUtilities.Exceptions.NLValueError: Nose-Hoover requires at least one unconstrained degree of freedomwithin each temperature group.

8

General Questions and Answers / reset the graphics properties of selected atoms.

« on: January 5, 2017, 17:33 »

I am observing that using Quick Optimizer is resetting graphics properties of selected atoms. Inside Builder I change the color of a select atom but when I perform quick optimization the color changes back. Is this a bug?

A similar bugfix was listed for 2015 version.
Using the Move Tool would reset the graphics properties of selected atoms.

Thanks
Amit

9

General Questions and Answers / Potential for W He

« on: July 22, 2016, 05:06 »

I notice that there are no potential for W-He system. May I please request to add W-He and W-H-He potential to ATK.

Here is the link with potential for this system
http://www.ctcms.nist.gov/potentials/W.html#W-H-He

http://www.ctcms.nist.gov/potentials/W.html

Thanks
Amit

10

General Questions and Answers / visualizing vacancy movement.

« on: July 22, 2016, 03:40 »

I have a large structure with 100s of atoms and few vacancies. It becomes hard to visualize the movement of vacancy embedded deep into the structure. So the question is

Is there a way to only display vacancy (may be as a ball) and not show all other atoms in the simulation box?

Also, if I toggle an atom to ghost atom then is that the same as removing the atom from the crystal and creating a vacancy?

Thanks
Amit

11

General Questions and Answers / periodic BC for molecular dynamics

« on: July 22, 2016, 03:25 »

How do we apply periodic boundary condition in Molecular Dynamics calculation.  If applied, the atom leaving the box from one end should appear at the opposite end.  I see in my MD simulation that the atoms are leaving the box and stay outside the box.

Thanks
Amit

12

General Questions and Answers / Save movie from Movie Tool on MAC OS X

« on: July 22, 2016, 03:03 »

Hi,
How do I save animated GIF or movie (avi or mov) using MOVIE TOOL of VNL on Mac OS X.  I only option to save images in various formats.

Thanks
Amit

13

General Questions and Answers / RF response similar to optical properties of Si

« on: March 24, 2016, 17:29 »

My question is based on the tutorial on Optical properties calculation with Meta-GGA. In that example Qwise calculates the optical spectrum followed by 'n' and 'k'.
Can the same approach be used to compute complex-epsilon in MHz or GHz  range or other frequency ranges?  Or is the underlying theory only applicable in the optical range?

Thanks in advance.
Amit

14

General Questions and Answers / Re: adaptive KMC optimized structure.

« on: March 8, 2016, 16:54 »

Thank you! I will give this a try.
Amit

15

General Questions and Answers / adaptive KMC optimized structure.

« on: March 3, 2016, 14:13 »

In following the aKMC tutorial - I delete all atoms except for 7 non-contiguous and then perform geometry optimization. I am seeing that my optimized geometry is coming out to be different from the one shown in the tutorial and due to this the aKMC results are very different. I tried a few times but I am having no luck reproducing the results of the tutorial. I am not seeing island formation on the Pt surface.

Can anyone please share with me the starting Pt structure either in the form of image or Python file so I can see which 7 atoms to keep in the starting structure. Also it would be helpful if you can share the geometry optimization script so I can see if there are differences due to optimization.

If needed I  can post some screenshots.

Thanks for your help.
Amit