mcaroba / turbogap Goto Github PK

Dear sir,
When I use the commond "git clone -b turbosoap https://github.com/libAtoms/GAP.git" , an error occurred.

$ git clone -b turbosoap https://github.com/libAtoms/GAP.git
Cloning into 'GAP'...
fatal: Remote branch turbosoap not found in upstream origin

Is there a new command to download it？

Best regards,
Hao Wang

When running MD with TurboGAP, additional information from the initial structure file is lost. This applies both to data from the info line in extxyz files as well as per-atom arrays.
I believe that, for easier workflows, keeping this information in the output trajectory written by TurboGAP would be beneficial. (Of course, such information could be added back to the trajectory by the user in post-processing. This is just for convenience.) One example for a use case would be tags, indicating groups of atoms from the original structure (that would not be obvious from looking at the final structure of a MD run).

Hi,

in the generated potential.gap file, the path to gap_files/ is not added. For example,
gap_beg distance_2b
species1 = H
species2 = H
delta = 0.5
sigma = 0.5
rcut = 4.0
desc_sparse = "CH.xml.sparseX.GAP_2022_3_16_120_6_53_52_4881"
alphas_sparse = "alphas_distance_2b_1.dat"
gap_end
@richardjana

When fix_atoms is set, those atoms need to be excluded when evaluating the convergence by forces, now the code does not converge because of them being included

Could you please check the file: turbogap/src/soap_turbo/src/soap_turbo_radial.f90? For a binary collision simulation, there seems to be a problem running on Triton, but not in desktop. The previous version of this file is working fine on both Triton and desktop.

By default the new make_gap generates only alphas_hirshfeld.dat. In my case it means, that I get alphas only for C or H. Could you please @richardjana fix it? Previous script was generating the alphas_hirshfel_1.dat and alphas_hirshfeld_2.dat if several species found.

Greetings! I've been trying to use the TurboGAP code to do molecular dynamics fueled by the GAP provided in this repository and related paper. I'm running a melting process on a supercomputer, and the code seems to produce different results depending on the number of cores used. The related files can be found here.

The issue seems to stem from the process producing 0 or NaN for forces in the first step. When trying to use more cores, the issue is consistently reproduced. Any and all help with troubleshooting this issue would be greatly appreciated!

As discussed in some previous meetings, it would be a good idea to collect our testing procedures so they can be run in a more automatic, systematic fashion (especially as regression tests, i.e. to make sure new changes don't break previously working functionality). Organizing these tests so that they can be run automatically usually requires quite a bit of extra code to set up and run the tests, and to check their results. Luckily, we don't have to reinvent the wheel here, as many so-called unit testing frameworks have already been implemented in Fortran. One that looks good is test-drive - it's pure Fortran and can be integrated into the project fairly easily (by copying in one .F90 file).

However, this also brings in the issues of third-party dependency management, which hasn't really been touched on in the TurboGAP code development AFAICT. There's also the issue of possible license incompatibility -- @mcaroba do you know whether we can include and redistribute the code (which is Apache 2.0 and MIT licensed) under TurboGAP's current ASL license?

Thoughts/suggestions welcome.

@TiganyZ When I try to run swap and MD moves the MD moves only "perform" 0 MD steps, even though I'm requesting more:

n_mc_types = 2
mc_types = swap MD
thermostat = 'none'
md_nsteps = 20
md_step = 2.
t_beg = 900.
t_end = 900.

I get this kind of output and then no more MD steps follow:

 Hybrid md step: energy =         -425.40117480 , iteration         0 /       20

Is this an wrong usage issue or a possible bug?