Re: [lammps-users] [Non-DoD Source] Re: Problem with Ackland Analysis (UNCLASSIFIED)
"Barnes, Brian C CIV USARMY RDECOM ARL (US)" <brian.c.barnes11.civ@...2733...>
Fri, 4 May 2018 21:00:52 +0000
Thanks for the heads up, Chris. It has been quite some time since I've thought about the Ackland code, and unfortunately I don't have my old postdoc email address or archives from when that change was made. But yes, I wrote that patch. The algorithm itself is described in table II of Ackland and Jones, doi: 10.1103/PhysRevB.73.054104 . The original lammps-users thread discussing my change is available at: http://lammps.sandia.gov/threads/msg55921.html
I believe the original LAMMPS implementation was missing part of step (v) from table II in the paper, and other small discrepancies. I have not examined the Ovito implementation and therefore cannot comment on it. I do enjoy using Ovito (Hi, Alex S.! Nice work).
If there is a question of correctness, I would recommend referencing the Ackland/Jones paper and determining where the implementation, in any program, differs from algorithm described in the text. The n0 < 11 test, for example, is explicitly in the paper. I believe my patch improved the correctness of the LAMMPS implementation, and was trying to help based on a problem I encountered when analyzing my simulation. But, it's possible that someone else's analysis may encounter a difficulty in another part of the implementation.
US Army Research Laboratory
From: Shumeyko, Christopher M CTR USARMY RDECOM ARL (US)
From: Alexander Stukowski [mailto:stukowski@...503...]
Sent: Friday, May 4, 2018 11:20 AM
To: Axel Kohlmeyer <akohlmey@...24...>
Cc: Barnes, Brian C CTR USARMY ARL (US) <brian.c.barnes11.ctr@...2733...>; Olivier Politano <olivier.politano@...1102...>; LAMMPS Users Mailing List <email@example.com>
Subject: [Non-DoD Source] Re: [lammps-users] Problem with Ackland Analysis
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The implementation of the Ackland analysis found in OVITO is, according to my first assessment, is still based on the “old” algorithm version from LAMMPS. The algorithm in OVITO hasn’t changed since the very first program release as far as I can recall. The "n0 < 11” check, for example, mentioned by Brian Barnes in his contribution, is missing in OVITO’s implementation of the Ackland analysis.
On 4. May 2018, at 14:52, Axel Kohlmeyer <akohlmey@...24... < Caution-mailto:akohlmey@...24... > > wrote:
On Fri, May 4, 2018 at 5:40 AM, Olivier Politano <olivier.politano@...1102... < Caution-mailto:olivier.politano@...1102... > > wrote:
Dear Lammps users,
We are still working with Lammps 12Apr13. When we perform an ackland analysis with this version of LAMMPS, we obtain the following image for some atomic configuration. BCC atoms are represented in blue and FCC atoms are green.
I went through the file « compute_ackland_atom.cpp » in the USER-MISC directory and I found some modifications between the versions 12Apr13 and 7Dec15 (or later). However, I did not find mentions of these changes in the webpage "Latest Features and Bug Fixes in LAMMPS » or in the source file.
after a little digging in the git repository and the mailing list archives, i think i have found the origin of the change you noticed in this contribution posted to the mailing list:
Caution-https://sourceforge.net/p/lammps/mailman/message/34258128/ < Caution-https://sourceforge.net/p/lammps/mailman/message/34258128/ >
it comes with some detailed explanations, so please have a look.
So, I’m wondering if someone also noticed this drastic difference of result for the Ackland analysis and if there is a bug or a problem with the newer implementation of Ackland.
that e-mail claims to have removed some issues with the "old" implementation and the changes were approved by the original contributor of compute ackland/atom.
i am copying brian, who contributed these changes, in the hope, that he may be able to comment on his changes and your observations.
and i am also copying alex, the author of ovito in the hope, that he can provide some insight into what algorithm/implementation his code uses and how that stacks up with what the code in LAMMPS does.
it would be fairly easy to roll back the changes, but unless there is some tangible information that can prove what is correct for all cases and where the problem is at the implementation level, it is difficult to make a choice here.
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Dr. Axel Kohlmeyer akohlmey@...24... < Caution-mailto:akohlmey@...24... > Caution-http://goo.gl/1wk0 < Caution-http://goo.gl/1wk0 >
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.