Messages

16

General Questions and Answers / Re: MD simulation of vapor-deposition of metallic multilayer

« on: February 17, 2016, 03:36 »

To answer my own question....I have found a nice tutorial here....

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

As it is also mentioned in the tutorial that "The exact modified embedded atom model (MEAM) potential used in Ref. [1] is currently not available in VNL-ATK. Instead, you will use a Tersoff potential, which, unfortunately, will not produce the crystalline layers shown in the reference paper.", I am still expecting the MEAM to be implemented....

baizq

17

General Questions and Answers / MD simulation of vapor-deposition of metallic multilayer

« on: February 17, 2016, 03:19 »

Dear All,

I recently saw a paper (PRB 69, 144113 (2004)) which describes an MD simulation (using EAM potential) of vapor-deposition of CoFe/NiFe/CoFe multilayer on a Cu substrate. The main idea is to throw "hot" atoms onto the substrate at a specific rate, and let MD to determine the final position of the atoms.

This is an old work published more than 10 years ago. Just wondering whether/how we are able to model this with ATK.

Thanks,
baizq

18

General Questions and Answers / Re: dissociation temperature of solids

« on: January 30, 2016, 01:16 »

Thank you, zh. This is exactly the information I want.

19

General Questions and Answers / Re: NEB path

« on: January 30, 2016, 01:15 »

Thank you, Anders. Yes, the script you attached works for setting up the NEB run. However, when the job runs, it complaints the following strange error:

Assertion failed in file src/mpid/ch3/channels/nemesis/netmod/tcp/socksm.c at line 591: hdr.pkt_type == MPIDI_NEM_TCP_SOCKSM_PKT_ID_INFO || hdr.pkt_type == MPIDI_NEM_TCP_SOCKSM_PKT_TMPVC_INFO
internal ABORT - process 0

I am wondering what it is... I have attached the log file and input file for your reference.

Thanks,
baizq

20

General Questions and Answers / NEB path

« on: January 28, 2016, 18:41 »

Dear all,

I would like to set up an NEB path between two geometries (in both geometries there is a MgO slab with one oxygen vacancy inside. A carbon atom is diffusing from the surface (initial) into the vacancy in the slab (final)). However, when I put the two geometries into the VNL NEB builder, it complains "invalid". I have tried both relaxed and unrelaxed pairs.

Could anyone suggest me what happens here and how to solve the problem? I have attached the relaxed geometries for your reference.

Thanks in advance!
baizq

21

General Questions and Answers / Re: dissociation temperature of solids

« on: January 28, 2016, 18:30 »

Thank you, Julian. We are dealing with a SiO2 system. I was thinking that the dissociation energy should be the difference of energy between the solid and same number of separate atoms as in the solid model. And then we could somehow convert the dissociation energy to temperature...

22

General Questions and Answers / dissociation temperature of solids

« on: January 27, 2016, 02:50 »

Hi All,

We are recently looking into the dissociation temperature of a few solids (amorphous). Anyone knows whether there is a way to calculate it with ATK? Thanks in advance

Best,
baizq

23

General Questions and Answers / Re: Phonon transport calculation- ERROR: Dimension mismatch

« on: January 7, 2016, 18:29 »

Thank you, Anders. What would be the exact nlread command? I used the nlread but the program complained that there is no dynamic matrix read in.

baizq

24

General Questions and Answers / Re: Phonon transport calculation- ERROR: Dimension mismatch

« on: January 6, 2016, 18:30 »

Thank you, Jess. Looking forward to your reply.

baizq

25

General Questions and Answers / Phonon transport calculation- ERROR: Dimension mismatch

« on: January 4, 2016, 19:23 »

Hi All,

I was trying to do a phonon transport calculation on a gold/vacuum/carbon system while encountering an error at the phonon transport step after dynamic matrix calculation had been done:

** Back Engine Exception : Dimension mismatch
** Location of Exception : complexmatrix.cpp:319

1. Does anyone have an idea what the problem is? I tried a similar system of gold/vacuum/gold and the problem did not appear.

2. How could one resume a phonon calculation from the previous calculation where the dynamic matrix is available?

I have attached the phonon transport script for your reference.

Thanks,
baizq

26

General Questions and Answers / Re: generating gif movie

« on: November 11, 2015, 04:31 »

Thank you, Anders! Hope to hear back from you soon.

27

General Questions and Answers / Re: generating gif movie

« on: November 9, 2015, 23:43 »

Hi Anders,

Thank you. Here is the error msg:

Code

Traceback (most recent call last):
  File "./zipdir/NL/GUI/Graphics/GL/GLCanvas.py", line 896, in exportGIF
  File "./zipdir/NL/GUI/Core/AnimatedGIF.py", line 573, in writeGif
  File "./zipdir/NL/GUI/Core/AnimatedGIF.py", line 289, in handleSubRectangles
  File "./build/lib/python2.7/site-packages/PIL/Image.py", line 677, in convert
  File "./build/lib/python2.7/site-packages/PIL/Image.py", line 743, in copy
  File "./build/lib/python2.7/site-packages/PIL/ImageFile.py", line 164, in load
  File "./build/lib/python2.7/site-packages/PIL/PngImagePlugin.py", line 381, in load_prepare
  File "./build/lib/python2.7/site-packages/PIL/ImageFile.py", line 231, in load_prepare
  File "./build/lib/python2.7/site-packages/PIL/Image.py", line 37, in __getattr__
ImportError: The _imaging C module is not installed

You are right that the _imaging C module is not installed on my workstation. What should I do with the problem?

Thanks,
baizq

28

General Questions and Answers / generating gif movie

« on: November 9, 2015, 20:52 »

Hi All,

I am trying to generate an animation gif file for the relaxation process of a system from the nc file. Although it says "generating movie - please wait", it does not generate a movie at all even after several hours waiting

May I know whether it is a bug? I am running VNL 15.0 on Ubuntu 14.04.

Thanks,
baizq

29

General Questions and Answers / comb potential

« on: October 23, 2015, 02:24 »

Dear ATK developers,

I find from the ATK 2015 release note that the COMB classic potential is available. However, in the reference manual, no information about COMB is included. May I know whether there is any way to use this potential?

In addition, is there a way to use semi-empirical potential for MD calculation?

Thank you,
baizq

30

General Questions and Answers / Re: extract isovalue of the transmission eigenstates

« on: August 30, 2013, 17:37 »

Anders, you are right. Inserting a zero column in between the atomic number and coordinates solves the problem(see attach file). VESTA may by default treat the 3rd column as x, 4th as y, and 5th as z, following the format of the weird Gaussian cube file. Since we missed a column at first, it cannot find the fifth column and just sets the z coordinates as pure zero. This explains why in my first plot all atoms are accumulated at the two ends of the supercell.

The reason I insist to use VESTA is simply that.... I have plotted all the other figures in the manuscript with VESTA...just to make sure of style consistency...Anyway I promise next time I will use VNL for plotting...

Thanks for your help. Have a nice weekend.

baizq