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Added Axilrod-Teller manybody potential #987
Adds Axilrod-Teller-Muto manybody potential (pair_style atm).
Does not break backward compatibility for inputs.
The code is adapted from in-house software.
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The code was ported to LAMMPS from the in-house code used in the following publication:
S. V. Lishchuk, "Role of three-body interactions in formation of bulk viscosity in liquid argon", J. Chem. Phys. 136 (2012) 164501.
Hi Sergey - I looked at the latest changes for the Axilrod-T-M
So I pushed changes to 2 files that I think are correct,
The doc file is to explain how to set K with
I also changed some things in the code
The answers in the log.9Jul18 log files
Also, for computational efficiency
Another thing you should check is
I made some changes to source and documentation:-
Hi Sergey @sergeylishchuk - thanks for the changes, we're close I think. However I
First, I think that you want to insure the same set of IJK triplets
So I think you need to compare rIJ and rIK to the force cutoff used to
Second, I assume you want to produce answers that are rotationally
Note that if you end up having to check all 3 distances < cutoff, than
@sergeylishchuk @sjplimp i've updated the branch to the latest master and thus resolved the indicated merge conflicts. in addition, i've integrated to documentation properly into the (refactored) manual and made a few formal corrections. there are still some SJP comments in the code, so i assume, those still need to be worked on. if not, please remove. thanks.
i have one more question: there are significant differences in energy and pressure when running the example input with 1 MPI rank vs. using 4 MPI ranks or when i add a small translation via the offset keyword to the lattice command. is this an intrinsic property/problem of the methodology employed or is there perhaps something missing in the example input?
good catch @akohlmey - the offset case is likely different b/c the velocities are initialized based on atom position. However the 1 vs 4 proc difference, even on step 0, for the as-is in.atm script is troubling.
@sjplimp File "pair_atm.cpp", line 121:
The code works fine for very small pair cutoffs, e.g.
Why this might be?
@sergeylishchuk Take a look at the pair_atm.cpp I just pushed. The issue with your 2 counters is that the 1st inner loop was to jmax-1, not jmax. This logic was correct (b/c the 2nd inner loop did the right thing), but when running in parallel, the order of what atoms appear in each atom's list of neighs will be permuted, depending on how many procs you run on. Thus you could get a different count for my count1 vs count2 (your previous message). Changing the first loop to jmax gives identical counts
However the real issue is with count3 = # of triplets computed,
ok @sergeylishchuk - here I think is a clearer explanation of the problem.
However it should also be possible to do the half double loop and find
Aug 29, 2018
On Fri, Dec 7, 2018 at 6:28 PM Stan Moore ***@***.***> wrote: @akohlmey <https://github.com/akohlmey> this style never got added to the .gitignore file, can we do this before the stable release?
yup. just been discussing something similar with @sjplimp. as for changes to the code, there would have to be a serious bug to warrant making changes there. ...and then the clock would be reset and we need to wait at least another week. but it looks like we already have some other "cosmetic" changes pending, i.e. no changes to the code itself. so we may have one more set of only cosmetic merges next week, step the version again, and declare that version immediately as stable. i think this makes sense after all the other cleaning up and making things consistent. that also gives me an opportunity to update a few more log files (not that that is crucial, but due to some corrections to the nose-hoover code, there are some small differences, especially for fix npt). axel.…
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