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Updates to dynamical_matrix #1359
Collected updates and fixes to the USER-PHONON dynamical_matrix command. See below for detailed list of changes.
This updates PR #1314.
Sebastian Hütter (OvGU)
By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).
Bugfixes to a brand new command. There will be changes, but not many users should be affected.
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This last commit changed the groupmap and some issues with MPI comm using the wrong element size/count. Now everything that is a global atom id should be a bigint. With this, I think I changed what the groupmap means (new definition: see comment in
"Works for me".
if i remember correctly, this primarily needs to be better documented (units of input and output and keyword to convert/not convert).
not worth doing now. we do it, when all changes, including the 3rd derivatives command are in.
athomps left a comment
I am okay with releasing this as is. However, there are problems with units:
But I'd be all for renaming that to something that makes this clear, as well as document it. There was also a python example for plotting PhDOS from the results using ASE, but that got discarded when the third_order part was separated out.
I hope, that @charlessievers will put these examples back in some form, but properly documented and with explanations for how to run LAMMPS through ASE (which would be a good addition to the manual in any case). At least, that was the original plan. As far as I read the python code, ASE was only used to set up the system, with a strategic use of a
Mar 21, 2019
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I am glad you like the ESKM style @martok!
I would prefer the style to be called ESKM, but that is for selfish reasons. If usability is a concern, we can change the style name to something else.
The Install.sh script needs to be changed until I finish fixing the third order calculator, which I am not sure when I will get to.
@akohlmey I would love to add my python scripts into the repo if you are all interested. There is a decent amount of documentation on ASE's end as to how to run lammps calculations.
On Wed, Mar 27, 2019 at 5:44 PM charlessievers ***@***.***> wrote: I am glad you like the ESKM style @martok <https://github.com/martok>! I would prefer the style to be called ESKM, but that is for selfish reasons. If usability is a concern, we can change the style name to something else. The Install.sh script needs to be changed until I finish fixing the third order calculator, which I am not sure when I will get to. @akohlmey <https://github.com/akohlmey> I would love to add my python scripts into the repo if you are all interested. There is a decent amount of documentation on ASE's end as to how to run lammps calculations. ASE documentation <https://wiki.fysik.dtu.dk/ase/ase/calculators/lammps.html> Do you have a little more direction for what type of documentation you would like?
please have a look at the "Tutorials howto" discussions listed under: https://lammps.sandia.gov/doc/Howto.html#tutorials-howto doesn't have to be that detailed like in those examples, but just some general remarks about how using LAMMPS through ASE is different from using it directly or through the library interface, particularly for system building, and what capabilities ASE offers, that LAMMPS doesn't have or is not as convenient to use for. perhaps also add one or two simple illustrative examples with a couple of screenshots for illustration. possibly with trying to do the same with standalone LAMMPS for one (or both) of those. axel.…
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