Fail to follow the instructions given in 'Using Amp Potentials for Molecular Dynamics'

[kangyu zhang]

Hi! I followed the instruction given in 'Using Amp Potentials for Molecular Dynamics' to install kim-api and lammps. However, there are several errors occurred.

1. After I downloaded kim-api by git clone -b master-v2 https://github.com/openkim/kim-api.git and type ./configure in folder kim-api, I received an error -bash: ./configure: No such file or directory. So I installed kim-api followed the instructions given by INSTALL file in kim-api.

2. I downloaded lammps by git clone -b kim-v2-update https://github.com/ellio167/lammps.git per your request, but the Important bug-fixing step failed with error sed: 1: "./src/KIM/pair_kim.cpp": invalid command code . So I had to skip this step.

3. When I installed amp_model_driver with kim-api-v2-collections-management install user ./amp_model_driver, I received another error *** ERROR *** ./amp_parameterized_model not found at openkim.org. Aborting!

Here is a list of versions of packages: 1. GNU Wget 1.20 built on darwin18.2.0. 2. GNU Make 3.81 3. cmake version 3.13.2

And I'm using macOS.

[kangyu zhang]

I still cannot successfully install kim-api and lammps on my macbook followed the instructions, so I packed the trained neural network to be a readable calculator by ase, and do MD simulation using ase. However, I'm not sure how should I deal with those atoms that moved out of the supercell in the process. I know the neighbors found by ase will not be affected whether I mirror the atoms back or not, but the actual distances between two atoms will be changed by doing this.

Should I mirror the atoms back to the supercell for calculating $G_2$ and $G_4$?

[Jie Gong]

Hi Kangyu,

Have you resolved your issue 3? I followed the instructions as well, but as I do

kim-api-v2-collections-management install user ./amp_model_driver

I get the following error:

CMake Error: The source directory "/tmp/kim-api-v2-build-xaWUnsy463/item-source" does not appear to contain CMakeLists.txt.
Specify --help for usage, or press the help button on the CMake GUI.

Aborting!

[Alireza Khorshidi]

Hello everyone,

Sorry, I just had a chance to upgrade this. It should be solved with the last few commits, ending with the commit f580604.

Feel free to reopen this issue if the problem still exists.