Recent Posts

1

General Questions and Answers / Re: Can the Electron Density (or Converged State) Calculated from IV Characteristic

« Last post by dmicje12 on November 29, 2024, 04:11 »

Thanks for reply!
but,I still don’t understand
1.
I added configuration = nlread("file.hdf5", DeviceConfiguration)[-1] to the script.
If the metallic region in the DeviceConfiguration of file.hdf5 is at 0V, does that mean the calculated Veff result will be the "effective potential of the metallic region at 0V"?
But if I want to use the "DeviceConfiguration of the metallic region at 0V" as the initial state for calculating the "effective potential of the metallic region at -1V," is that possible?
2.
Also, where exactly should configuration = nlread("file.hdf5", DeviceConfiguration)[-1] be added in the script?
I tried adding it to both DeviceLCAOCalculator and DeviceConfiguration, but neither worked.
Thanks!
=======================================================
Thanks!
I already know how to import the initial state!

Just place the following:
job.setCalculator(
    calculator=calculator, initial_state=nlread("file.hdf5", DeviceConfiguration)[0]
)
before job.update()

2

General Questions and Answers / Re: How to build graphene/h-bn

« Last post by Anders Blom on November 28, 2024, 01:25 »

Looks like you are creating a bilayer material (van der Waals heterojunction) here, is that the intention, or did you want an in-plane junction?

Anyway I would rather use the Builder and the Interface Builder there, which is more of a single interface tool, whereas the one you have opted for is more suitable to make multiple interface structures and perhaps try different Miller indices etc, which is not too relevant for you. The Interface Builder has more interactive controls for a specific interface.

The in-plane junction is also easier to make with substitution probably, just make a BN sheet and replace parts of it with C atoms and relax the structure.

3

General Questions and Answers / Re: Query Regarding Transmission Spectra Analysis Features in QuantumATK

« Last post by Anders Blom on November 28, 2024, 01:16 »

There are different ways depending on what kind of system you are looking at, but fundamentally it's quite similar to the bulk case, except you have more "materials" involved. If your central region e.g. has a molecule and you are transporting through that, you want to compare the transmission peaks to the molecular eigenvalues (HOMO, LUMO, etc). If it's a bulk structure ABC you need to compare the DOS and projected DOS between all 3 materials.

I would suggest looking at published articles involving similar systems as yours, and checking what analysis they do. If you have trouble carrying that out in the code you can ask more specific questions.

4

General Questions and Answers / Interface MTP Training

« Last post by AsifShah on November 27, 2024, 23:03 »

Dear Admin,
Q1. I tried the code on "https://docs.quantumatk.com/manual/Types/CrystalInterfaceTrainingParameters/CrystalInterfaceTrainingParameters.html#NL.Study.MomentTensorPotential.CrystalInterfaceTraining.CrystalInterfaceTrainingParameters" for Iron/Copper interface but I get this error everytime. I tried changing random seed but still has same error. Kindly help resolve.

Master    : Handling exception in delegator process.
  Encountered TaskExecutionError: An exception was raised while executing task "a90b78e8ad0a11ef90b9801844e91328".
    Traceback (most recent call last):
      File "zipdir/NL/ComputerScienceUtilities/ParallelTools/DynamicTaskScheduler.py", line 1391, in __startParallelExecutionOnWorkerProcesses
      File "zipdir/NL/ComputerScienceUtilities/Workflow/Workflow.py", line 1187, in _runTask
      File "zipdir/NL/ComputerScienceUtilities/Workflow/Workflow.py", line 708, in run
      File "zipdir/NL/Study/MomentTensorPotential/FitMomentTensorPotential.py", line 464, in _execute
    NL.ComputerScienceUtilities.Exceptions.NLExecutionError: The training dataset contains no configurations. This error can probably be avoided by picking a different random seed.

Q2. Please answer the following. Step 1: I trained an MTP based with active learning of few configurations Step 2: I want to include more configurations so I combined reference data and active learning candidates from step 1 and passed onto Step 2. Step 3: I again want to include few more configurations. Now should I include all configurations from Step 1 and Step2 or only step 2? Also, in retaining should I change basis size as more configurations are being added or keep same for all Steps?

5

General Questions and Answers / Re: Removing Vacuum from Interface Structure and creating symmetrical interface

« Last post by Anders Blom on November 27, 2024, 20:05 »

The vacuum will automatically be removed if you use the "Device from Bulk" tool. The tricky bit here is the CoTi part. You could mirror the structure you have in the XY plane and combine the two pieces, but that could produce a grain boundary in the middle. That might be avoided if you also mirror it in XZ and/or YZ, you can experiment a bit.

6

General Questions and Answers / Re: Can the Electron Density (or Converged State) Calculated from IV Characteristic

« Last post by Anders Blom on November 27, 2024, 19:43 »

configuration = nlread("file.hdf5", DeviceConfiguration)

will return a list of all DeviceConfiguration objects in the file. You can either loop over them, or pick a specific one, like the last (and often only)

configuration = nlread("file.hdf5", DeviceConfiguration)[-1]

For an I-V calculation you need to identify the objects by bias, which is easiest in the GUI. Once you know which object ID to use, you can do

configuration = nlread("file.hdf5", DeviceConfiguration, object_id="DeviceConfiguration_0")[0]

Note that you will still need the [-1] since nlread always returns a list.

It will never recalculate if you read an already computed configuration from a file.

7

Installation and License Questions / Re: Error opening qATK on cluster

« Last post by Chandrasekar on November 27, 2024, 16:47 »

Hi Filipr,

Thanks for your response. Noted it. I will convey this message to our system admin and find a way to solve this issue.

Thank you again.

8

Installation and License Questions / Re: Error opening qATK on cluster

« Last post by filipr on November 27, 2024, 16:01 »

CentOS7 is no longer supported in v. 2024.09, see https://docs.quantumatk.com/intro/installation/technical_hardware.html#specific-platform-requirements. Specifically it is because 2024.09 is linked against a newer glibc (fundamental Linux library) that is incompatible with the one that is available on CentOS7.

You either have to continue to use v. 2023.12, see if the cluster has machines with a newer OS and run on those, or ask your cluster admin to install a supported OS on the nodes. Note that CentOS7 had its end-of-life June 30, 2024: https://www.redhat.com/en/topics/linux/centos-linux-eol

9

Installation and License Questions / Error opening qATK on cluster

« Last post by Chandrasekar on November 27, 2024, 15:08 »

Dear Developers,

We encountered the following error while opening the current version of atkpython (qATK_2024.09) on our laboratory server. The Version qATK_2023.12 works fine. Our license provider is TSRI in Taiwan. 

We use CentOS7 on our server.

Error message:
[joinet@sea101-sever-master ~]$ atkpython

cat: /usr/lib64/libc.so.6: version `GLIBC_2.25' not found (required by /cluster/cad/synopsys/qatk/2024.09/lib/pinned-libs/libstdc++.so.6)

cat: /usr/lib64/libc.so.6: version `GLIBC_2.18' not found (required by /cluster/cad/synopsys/qatk/2024.09/lib/pinned-libs/libstdc++.so.6)

(……)

Is it related to the new version of the qATK or our server OS version?

I really appreciate any help you can provide.

10

General Questions and Answers / Removing Vacuum from Interface Structure and creating symmetrical interface

« Last post by pshinyeong on November 27, 2024, 09:27 »

Hello,

I've created a Co/CoTi interface structure, as shown in the attached image. In this structure, two layers near the interface are relaxed, and there is a 10Å vacuum on both sides. Now, I want to construct a Co/CoTi/Co interface where CoTi/Co interface remains identical to the existing Co/CoTi interface to avoid repeating the relaxation process (as the structure contains many atoms). Additionally, I need to remove the vacuum regions to prepare the structure for a device configuration.

Is there an efficient way or a specific Builder tool in QuantumATK to
1. Remove the vacuum from the existing structure?
2. Create a symmetrical Co/CoTi/Co interface based on the relaxed Co/CoTi interface?

For clarity, I've included a second image to illustrate the structure I'm aiming to build. Thank you in advance for your guidance!