Topics

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 / 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)

3

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

4

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.

5

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

6

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

7

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

8

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

9

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

10

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

11

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

12

General Questions and Answers / version 2015 for Mac OS ?

« on: October 29, 2015, 19:07 »

I downloaded the binary of v2015 on linux workstation (2x Intel Xeon E5 2.1 GHz (6-Core)  64 GB RAM, PNY NVIDIA Quadro K600 GPU, 1GB DDR3) and tried to setup and run the non-equilibrium momentum exchange simulation  (from tutorial).  I notice that the builder runs very slow on Linux platform.  I think the hardware is quite reasonable for this calculation. Do you agree?  Not sure why the software is so slow.

On Macbook pro laptop the response of builder is faster than linux box. However, there is no non-equilibrium MD in version 2014. Is v2015 out for Mac os X ?

13

General Questions and Answers / display bonds in builder - tolerance

« on: October 25, 2015, 22:41 »

I am new to VNL so maybe this issue has been addressed before, however, I could not find a satisfactory solution. In a simple FCC lattice I want to display the structure such that all atoms are not bonded to all other atoms. Presently they look like as shown in the attached figure. I would like to control how the bonds are drawn - something like draw bond only if the distance is less than xx angstrom. Is there a way to do that in builder?

The reason is I want to play around with interstitials and its easy to visualize those if the lattice is cleared of the clutter.  I tried "Bond Control" - Fuzz factor but it does not do what I want.
Thanks in advance.
Amit