Messages

1

Installation and License Questions / Re: Error in open quantumatk

« on: September 25, 2024, 17:12 »

Does the executable file /user/cad/synopsys/qatk/2023.12/quantumatk/V-2023.12/atkpython/bin/python3.11 exist? Probably not - most likely you moved the installation of QuantumATK to a different folder: you are trying to run it from the directory /usr/cad/synopsys/qatk/cur (notice even how it's /usr/.. and not /user/...).

You can't move a QuantumATK installation as the launcher scripts (quantumatk and atkpython) hardcode the path to the shipped python executable. So if you moved the QuantumATK installation, either move it back, or delete it and reinstall.

So,Need I upgrade the python version?

No, QuantumATK is self-contained: it doesn't require any (much) installed software and certainly doesn't depend on other Python installations on the system. It ships its own custom Python interpreter and you can use both side by side without problems (as long as you are careful). For more info see: https://docs.quantumatk.com/manual/Python.html#command-line-usage-with-qatk-shell-environments

2

General Questions and Answers / Re: Brodening in LCAO calculator

« on: September 24, 2024, 15:59 »

If you look at the second formula in the documentation (how the density is calculated) you will see that it involves an integral over the Brillouin zone. This is turned into a numerical integral, a.k.a. sum weighted by the k-grid volume element dk = Δk_x Δk_y Δk_z. The broadening should be chosen proportional to this value. If your system is long along one dimension then the Δk will be small along that direction given a constant k-point density as the Brillouin zone is inversely proportional to the length along that direction: for a cell with perpendicular lattice vectors you have Δk = 2π/(LN), where L is the length of the cell along that direction and N is the number of k-points. If you keep only one k-point along the C direction then the broadening should be proportional to Δk_x Δk_y = (2π)²/(L_x N_x L_y N_y)

As a rule of thumb you can use a broadening of 1000K for metals and 100K for semiconductors and if the metal has a hard time converging you can either 1) increase the k-point sampling (expensive) or 2) increase the broadening (cheap, but reduces quality of results due to artificial smearing)

3

General Questions and Answers / Re: Brodening in LCAO calculator

« on: September 24, 2024, 09:36 »

As explained in the documentation it depends on whether your system is metallic or has a gap (semiconductor or insulator). For gapped systems the broadening should be smaller than the gap and you can in fact set it to something close to zero (like 1e-9). For metals there is no "magic number that suits every situation". For metals the broadening is correlated with the k-point sampling: the denser the k-points, the smaller the broadening you generally need. A broadening is an approximation and a tool to make calculations converge faster, but for accurate results you generally want to have it as small as possible - but that often means you have to increase the k-point sampling increasing the computational cost. What the "best" broadening and k-point sampling is is up to you. I recommend trying to do some convergence studies for a small system similar to what you are actually interested in. Try changing the k-point sampling and the broadening and see how it affects the results.

4

General Questions and Answers / Re: Brodening in LCAO calculator

« on: September 23, 2024, 13:43 »

For general information on "broadening" in DFT: https://docs.quantumatk.com/manual/technicalnotes/occupation_methods/occupation_methods.html

When using a temperature such as 1000K as broadening it is automatically converted to an energy using E = kB T, so for T = 1000 K, E = 0.086 eV.

5

General Questions and Answers / Re: Is Planewave PAW Spin Orbit Coupling not supported?

« on: August 6, 2024, 11:14 »

Ok, this has been confirmed to be a bug.

As a workaround until it is fixed I suggest that you don't save the workflow, but instead save it has a script and run the script.

6

General Questions and Answers / Re: Is Planewave PAW Spin Orbit Coupling not supported?

« on: July 12, 2024, 20:09 »

Planewave PAW supports SOC. Can you share the script you are trying to run?

7

Scripts, Tutorials and Applications / Re: Heisenberg Exchange analyzer

« on: June 27, 2024, 13:59 »

You need to run the script with the atkpython executable, not the normal python program.

8

General Questions and Answers / Re: Analysis of calculated LSCC U values results

« on: June 17, 2024, 10:23 »

The two U values are for the two "3d like" orbitals in the basis set. The basis sets used are not exactly the true solutions to the Schrödinger to the isolated atom system - there will be some that resemble the typical occupied orbitals (the normal 3d orbitals) and some that somewhat resemble unbound states: polarization orbitals, and split orbitals, etc. To be honest: the basis sets and how additional orbitals are added are poorly described in the documentation: it is assumed that the user is already familiar with these concepts as it follows same practices as in the quantum chemistry community and many other software packages like Siesta. You can see plots of the basis set radial functions in basis set selection window.

For traditional Hubbard-U you are only interested in the occupied 3d orbital, so only the first U value is relevant. However, in the Nanolab GUI it is currently not possible to only calculate and use U for specific orbitals: one will always select all orbitals with a specific angular momentum. However, the U value of the additional 3d-like orbitals should not matter much in a DFT+U calculation as those orbitals will typically have very low occupation. It is possible to not include these orbitals in the Hubbard-U description in a Python script. You can send your workflow to script and see the basis set definition for how it's actually done and simply remove the selection of the second 3d-like orbital.

Also: I recommend using the Dual Hubbard term as it uses the Mulliken orbital charges for occupations which is a more local projection model than the Onsite and is a better fit for the U values calculated with the LSCC method, as it assumes projection on the actual orbitals (a projection method which we unfortunately currently do not support)

9

General Questions and Answers / Re: Extract 3D/2D potential profile as a text file

« on: March 13, 2024, 14:52 »

The columns in the text representation have no meaning - it's just a way to visually "compress" the output. It is just one long list of numbers, 111x111x431 = 5,310,351 numbers to be exact. So you can just take the "matrix" of numbers and split at whitespace and you get a 1-dimensional array of numbers. This is the potential. To convert a 3D index (i, j, k) into a 1D index n in this list you use: n = k + Nk * j + Nj * Nk * i as is somewhat documented at the top of of the text representation (outer loop: x, middle loop: y, inner loop: z)

If you know Python you can also more conveniently get the binary exact numbers as a numpy array by using the QuantumATK python API, see https://docs.quantumatk.com/manual/Python.html and https://docs.quantumatk.com/manual/Types/ElectrostaticDifferencePotential/ElectrostaticDifferencePotential.html This allows you to directly extract the data, do post-processing and plotting in the same Python script.

10

General Questions and Answers / Re: Complex Bandstructure with Hybrid Functionals (HSE06)

« on: February 28, 2024, 17:05 »

I can confirm that there is indeed a bug, and it has been reported in our internal issue tracker. Complex band structure calculations currently do not support hybrid functionals.

11

General Questions and Answers / Re: Complex Bandstructure with Hybrid Functionals (HSE06)

« on: February 23, 2024, 10:45 »

It looks like the HSE06 complex band structure is correct, but the Fermi level is wrong. We will take a look at it.

12

General Questions and Answers / Re: Error on Cluster

« on: February 5, 2024, 08:43 »

I'm not convinced this is a memory issue. More likely an incompatibility between the software and hardware.

Some questions we need answer to in order to investigate this issue:

• What are you trying to run? Please send script if you can
• How far does it get? Please send log output

On top of that it would be very valuable if you could rerun the script and set the environment variable I_MPI_DEBUG=5 in your submission script before the execution of atkpython. Then Intel MPI will output various diagnostics to the output log. Send that to us. Also please send the output of 'cat /proc/cpuinfo' on the node that is running the script (you can add this to the top of the submission script) as well as the name and version of the Operating System.

13

General Questions and Answers / Re: Optimize Cell Error

« on: January 15, 2024, 16:48 »

Note that the version of QuantumATK you have installed on your laptop may be different than the one installed on the cluster.

From the log file it is evident that you are running QuantumATK Q-2019.12-SP1[Build 2a77e01] on the cluster. If you have a newer version installed on the cluster you need to configure your jobs to use that in the machine settings, see: https://docs.quantumatk.com/tutorials/job_manager_remote/job_manager_remote.html

14

General Questions and Answers / Re: Bad termination

« on: January 10, 2024, 10:20 »

Hard for us to know for sure without more information. But the error message says the process was killed - in most cases, and I would assume it's the same reason here, it's because the job uses more memory or resources (e.g. runtime) than what it is allowed to by the job scheduler.

Check your cluster information page/wiki on how to configure job submission, you can typically configure your jobs to send you an email if the job fails or is stopped with the reason for why it was done. Otherwise ask your cluster admin.

To reduce memory you can try a few things:

• Increase the number of OpenMP threads and reduce the number of MPI processes accordingly
• Increase the number of processes per k-point or "processes per <task>" for operations that allows multilevel parallelism
• Decrease settings that have a big impact on memory usage, e.g. basis set size, grid size, etc

15

General Questions and Answers / Re: Name error in Cosmosolvationparameter

« on: December 21, 2023, 15:45 »

From the log output it states that you are using version T-2022.03. The Cosmo solvation model was first introduced in the U-2022.12, see release notes: https://www.synopsys.com/content/dam/synopsys/silicon/quantum-atk/pdf/qatk-datasheet-u-2022-12-release-notes.pdf

So solution is to upgrade to a newer version.