Hello everyone. I am new to molecular dynamics simulations and I have come across an issue regarding a code I have been working on in LAMMPS using openKIM and I’ve taken a few days working on it and am unsure how to progress from this point. Right now my issue is I’m trying to reference an openKIM model, which can be viewed here: https://openkim.org/id/Dipole_Umeno_YSZ__MO_394669891912_001, and for some reason I keep getting the error “ERROR: KIM Model name not found. (src/KIM/kim_init.cpp:189)”. I am referencing the openKIM model in my code by doing: kim_init Dipole_Umeno_YSZ__MO_394669891912_001 metal
and after calling the create_box command I have the following: kim_interactions Zr O Y
I believe I am calling doing the kim_init and kim_interactions correctly as I can replace the KIM ID and elements in the kim_interactions with another KIM Model and the program will compile, so I do not believe it is an error in how I am referencing them. Could someone please give me some feedback if they are able to access the openKIM model linked above? I tried referencing it through both the KIM ID, and the short KIM ID, and have had no luck. I’ve tried other various identifiers I found on the openKIM page but those too have not worked.
The model you are interested in is (currently) only available for an old version (v1.6) of the kim-api software. To use it you would need to use an old version of lammps that works with that version of the kim-api. I’m afraid that it would take some effort to figure out exactly what version is necessary and to build all of the right components to get this working.
We have been working with the developer to get this model updated to support the latest version of the kim-api, but progress has been slow. We’ll take your interest as a good prompt to redouble our efforts.
Thank you for taking the time to respond to my question.
As an individual, how feasible is it to modify the potential format from the database to be used in the new version of LAMMPS? Is this something I would be able to do or would it require the original creator to do so? I know at the bottom of the openKIM page, there is a download link which includes a .zip file containing various information about the model. Would it be possible to take the information from this download and use that in LAMMPS?
It is certainly possible, but likely will require a fairly advanced level of familiarity with atomistic simulation and programming. This is a “Portable Model” designed to work with the kim-api library which LAMMPS supports. It is not a “Simulator Model” that is just a packaged set of parameters and LAMMPS commands. So, it is not possible to just use the parameter files in LAMMPS without OpenKIM.
If you are experienced with compiling software on linux systems, then you might try building the necessary versions of the kim-api, your model of interest, and lammps.
I think the patch_11May2018 (Release patch_11May2018 · lammps/lammps · GitHub) release is the newest version that is likely to work with the YSZ model. You could try following the instructions found in the lammps/lib/kim directory for building the kim-api and adding the models of interest, and then building lammps.
We’ll keep you posted if there is any news on an updated version of this model.
Hello,
I still struggle using this potential with new version of lammps. Can you please guide me if 11May2018 version works with this potential of not?
Best,
Sepideh
Just to provide an update, I’ve written a new version of this model that conforms to KIM API v2, but am waiting on its original author, Prof. Yoshitaka Umeno, to verify its correctness and give me the OK to publish it on our site. I’ll post back here when it’s available.