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Messages - Anders Blom

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I note that you didn't add the torsion parts of the potential in the papers, but maybe that is just a small term.

However, upon opening the forcefield from the HDF5 file in the GUI (in the Editor) I think it might be possible that your forcefield generation script is not working as intended, with respect to the tags etc. There are terms generates for "Mo" with tag "sio2", and "Si" in "mos2" and other mismatched cross-terms it seems.

I checked the other post you mentioned, there was no resolution there. Are you using the same forcefield parameters? Where do these parameters come from? Is it well established that these values are correct and good? 

Maybe there are some parameter in the forcefield that causes very large forces on the atoms?

The "leaving the domain" only is an issue when running an MD calculation in parallel over MPI, and using domain decomposition. This can provide a nice performance boost, if each domain contains 1000+ atoms, as in your case. But, I would first start to check if the potential is generally stable by just running in serial. With 27000 atoms it will still be relatively fast, esp. if you run threaded on 16 cores or so. I don't see your submit script or output, it would be useful, but general advise is only use MPI if you go beyond a single node, since the MPI and OpenMP performance intranode is about equivalent, and OpenMP is easier and potentially more stable.

Also, you can save some code by using
from AddOns.VASPPlugins.IO import readPOSCAR
bulk_configuration = readPOSCAR("./POSCAR")

After the optimization you can again bring the structure into the Builder, or Viewer, and see each bond length. Just drag and drop the optimized structure from the Data view (or Lab Floor in older versions) onto the Builder or Viewer icon.

General Questions and Answers / Re: QATK unable to read files
« on: March 28, 2023, 18:52 »
Yes, the scanning is the problem. Do not set your project directory to your home directory with 100,000 files, use a specific subdirectory for each project, and keep the number of files in each directory small (<1000 is fine, even a bit more).

General Questions and Answers / Re: Charge Density Difference
« on: March 27, 2023, 07:23 »
Right, as I said, you are missing the index 0. It should be
density_full = nlread('Interface.hdf5', ElectronDensity)[0]
and so on

General Questions and Answers / Re: MPI batch script error
« on: March 27, 2023, 07:21 »
Ok, great that you solved those initial issues.

As for performance, this is very difficult to speculate on without seeing detailed input/output, however I would suggest not doing a device first, but rather test that the parallelization is behaving correctly for a standard bulk crystal simulation. Perhaps not the smallest possible, but say a larger crystal with 10-20 atoms and several k-points.

In earlier times it was possible to use "wrong" parallelization and get very slow behavior, in particular if trying to use OpenMPI with QuantumATK, which it is not compatible with. However, newer versions should block that. Still, it will be interesting to analyze the output of the simpler calculation when you have it done. I can also suggest some MPI parallel performance test commands to use after that.

General Questions and Answers / Re: MPI batch script error
« on: March 23, 2023, 05:40 »
Those error messages are not at all related to QuantumATK, since the software does not even start. The error says that wrong parameters are provided to mpiexec, which is launched through your srun.

In general you will first need to figure out how to run ANY application properly in parallel, because there is nothing about "internal scripting of QuantumATK" that is related to how you get your mpiexec to run.

So, just go back to basics: assuming you have a binary "a.out" that you want to run in parallel on your cluster, with a certain number of nodes, threads and MPI processes. What is the launch script for that? Based on this, one can backtrack how to run QuantumATK and set up the Job Manager.

It can be really useful to take advantage of the function to check the repetitions, instead of just blindly launching a calculation which may be extremely time-consuming. That said, no matter what value you set for the max_interaction_range, it will almost always correspond to an approximation, and is thus prone to inaccurate results, incl. negative frequencies. The exception is if you set a value for the range which is larger than the interaction range of all atoms, as then you just recover the default behavior, which is to include all atom interactions when determining the supercell size.

The real approximation you make is of course in the size of the supercell, but since any finite value of max_interaction_range gives a smaller supercell than the default, your second observation is logical: a smaller range will NOT eliminate imaginary frequencies, but rather increase their likelihood. As for the opposite case ("lower interaction range manages to eliminate imaginary frequencies"), I think that might just be luck, in some particular system; it is at least not something I would expect to be the general case.

Also note that imaginary frequencies are not only a result of a too small supercell. It is equally important to ensure the configuration itself is relaxed with high accuracy. This often requires a tighter tolerance on the forces and stress than the default values, which in turn typically can only be achieved with a lower convergence tolerance for the self-consistent loop.

Thus in conclusion, phonon calculations require tight SCF tolerance and well converged structures in forces and stress. Usually you can go with the default supercell; I usually check the supercell in the log file when the calculation starts, and interrupt it if I notice it's giving strange values, like not identifying a 2D sheet if there is not enough vacuum around it, or just generally giving too large cell compared to the computer hardware or time I am prepared to wait.

Finally, and I admit I might be wrong on this, but I suppose the main use for checking the supercell size with a given max_interaction_range is if you have a short-range forcefield, where using all atoms will yield an unnecessarily large supercell. But then again, forcefields are so fast that it doesn't really matter what supercell size is used.

General Questions and Answers / Re: MPI batch script error
« on: March 17, 2023, 20:44 »
It is possible that you need to run jobs under "srun" rather than mpiexec. This is a common case with SLURM. However, the exact details depend on your cluster setup, so you really need a sysadmin to show you what the proper way to submit a job is, manually.

So, talk to the admins about how the input script (that you attached) should be modified in order to run correctly, e.g. by changing the last line to "srun" and changing some of the resource allocation commands (and, in particular, srun probably doesn't recognize the -ppn option, but also doesn't need it).

After that, we can help you set up the Job Manager to automate this for future jobs.

Fortunately very easy :-) By pressing R on the keyboard, spatial regions are toggled on/off, both in the Builder and Viewer. You have to ensure that the 3D view is in focus by left-clicking in it with the mouse first. The option is also available in the menu, under Viewer>View

Well, the point was to use I_MPI_DEBUG=5, else there is no debug information to help solve the problem...

What specifically do you mean by "unrecognized"? If you share the exact input and output of your QuantumATK script it will be a lot easier to figure out how to solve this.

If you want to run a small test with the built-in potential, the attached scripts works in U-2022.12 provided you have an updated license file. I set it up very easily using the GUI.

General Questions and Answers / Re: Molecular Energy Spectrum
« on: March 14, 2023, 04:08 »
In the tutorial, the point is that the transmission occurs through some particular orbitals of the molecule. I am not sure that is applicable to your situation, it sounded more like you had an ad-atom (Fe) on top of a 2D sheet? Of course could compute the energy spectrum of the Fe atom in the presence of the ribbon (that is what the MPSH will give you). The atom indices for the MPSH define what the "molecule" is (in your case a single atom), where the quantum numbers select the eigenstates of the "molecule".

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