Messages

1

General Questions and Answers / Interface MTP Training

« 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?

2

General Questions and Answers / Re: TorchX_MACE_MP_0_L0_2023

« on: November 17, 2024, 14:48 »

Hi,

I think its available in latest 2024 package

3

General Questions and Answers / Re: Trying to install QATK W 2024

« on: October 21, 2024, 20:45 »

Do I have to upgrade license server OS too from CentOS to ubuntu 20.04? or just installing new SCL will work?

4

General Questions and Answers / Trying to install QATK W 2024

« on: October 21, 2024, 00:52 »

Dear Admin,

I upgraded my server OS from CentOS 7 to Ubuntu with following description:
Description:   Ubuntu 20.04.6 LTS
Release:   20.04
ldd (Ubuntu GLIBC 2.31-0ubuntu9.16) 2.31

And installed QATK_W version which was installed successfully as displayed in the message (attached pic).
However, the license servers still have CentOS7.

Then, I ran a py file which was created on QATK_2023_SP1 software. But ran into this error as below. Kindly help in this regard.

[SCL] Error:  FLEXlm version of the application is higher than the license daemon version. Please upgrade the license daemon to latest version (SCL-601)

License Error: Unable to obtain a required license for the
requested license feature. It could mean there are no valid
licenses left, a problem with the connection to the license
server, or the license file does not contain the requested feature.
See below for more details.

Cannot check out base license. SCL error message:
Version of vendor daemon is too old.
FlexNet Licensing error:-83,234

5

General Questions and Answers / Re: Error in MoS2 forcefield implementation in QuantumATK

« on: October 9, 2024, 12:03 »

Dear Anders Blom,

Thanks a lot for your response.
Yes, the Mo-S bonds are overestimated. Also, though there is O2 molecule but the distortion is high than what is obtained from DFT.

I tested the script u shared on Gold and the results do not make sense. The Au atom does not bond at S vacancy which is clearly in contrast with DFT. (See attached pic)

I think you are right the authors perhaps do not want to share the real forcefield. This one looks useless.

6

General Questions and Answers / Re: Error in MoS2 forcefield implementation in QuantumATK

« on: October 8, 2024, 22:43 »

Dear Anders Blom,

Sure. Please find the attached pics highlighting errors. The yellow lines indicate places where mismatch is found between Reax parameters from article (left side) and QATK implementation (Right side). Also, torsion has one missing line and Angles also misplaced or missing line.
I am also attaching a original reactive forcefield (with parameters from article) file but unfortunately it gives some runtime error. Please help fix it if possible.

PS: This is a quick manual check I did. There might be other errors as well.

Thanks
regards
Asif Altaf Shah

7

General Questions and Answers / Error in MoS2 forcefield implementation in QuantumATK

« on: October 7, 2024, 00:12 »

Dear Admin,

The actual MoS2 forcefield given in the original paper "https://www.frontiersin.org/journals/nanotechnology/articles/10.3389/fnano.2022.1034795/full#supplementary-material" is quite different from what is implemented in QuantumATK ReaxFF_CHOSMoNiAuTi_2022. Upon inspecting the implementation in QuantumATK against with original paper it, I found multiple lines have errors and one line is completely missing.

When using this forcefield it gives so many distortions in MoS2. Kindly, check into this or please let me know if I am missing anything.'

regards
Asif

8

General Questions and Answers / Charged vacancy in a device configuration for transmission

« on: October 3, 2024, 20:46 »

Dear Admin,

How to introduce charged vacancy in a device configuration for transmission?

9

General Questions and Answers / Re: Setting different temperature for different regions

« on: September 6, 2024, 22:32 »

Thanks a lot.

10

General Questions and Answers / Re: Setting different temperature for different regions

« on: August 31, 2024, 21:35 »

Dear Ander Bloms,
It's for simulating Joule's heating in a small region.
I would love to share but I am still improving upon the code. I am not able to maintain temperature properly. I used manual code in hook method but I was thinking if I could utilize velocity distribution from class MaxwellBoltzmannDistribution in QuantumATK. I have been trying to obtain velocities from this distribution but i run into errors.
Can you help me with that? I am trying to set velocities using this method for a configuration but it runs into error. Kindly help in this case.
Also, is there a direct way to extract say 10 random velocities from class MaxwellBoltzmannDistribution?

Code

# %% Molybdenite (1)

# Set up lattice
lattice = Hexagonal(3.1604*Angstrom, 12.295*Angstrom)

# Define elements
elements = [Molybdenum, Sulfur, Molybdenum]

# Define coordinates
fractional_coordinates = [[ 0.333333333333,  0.666666666667,  0.25          ],
                          [ 0.666666666667,  0.333333333333,  0.121         ],
                          [ 0.666666666667,  0.333333333333,  0.379         ]]

# Set up configuration
molybdenite_1 = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates,
    )
molybdenite_1_name = "molybdenite_1"

molybdenite_1.setVelocities(
    velocities=MaxwellBoltzmannDistribution(
        temperature=300*Kelvin
        )
    )

11

General Questions and Answers / Re: Setting different temperature for different regions

« on: August 27, 2024, 07:27 »

Dear Anders Blom,
Thanks for your response.
I was able to do it manually using post_step_hook. Looks like post_step_hook is a nice way to do many things.

12

General Questions and Answers / Setting different temperature for different regions

« on: August 16, 2024, 21:55 »

Dear Admin,

How can one set a heating rate only for a specific tag of atoms? In QuantumATK by default heating rate is set for all atoms.

13

General Questions and Answers / Re: Relaxation of devices (optimize the geometry of a two-probe system)

« on: July 5, 2024, 12:20 »

As a rule, you need to optimize electrodes separately first and then create the structure you want.
After that the central region should include some portion of electrodes and your molecule and then optimize all of central region.

PS: During optimization - electrode and electrode extensions will be fixed.

Thanks

14

General Questions and Answers / Re: Geometric optimization

« on: July 5, 2024, 12:18 »

You can do it in the device optimizer in QATK. You can set voltage values in LCAO calculator. However, there maybe convergence issues due to high bias.

15

General Questions and Answers / Re: Questions about MD reservoir temperature and its analysis

« on: June 17, 2024, 16:01 »

The instan. temperature will always fluctuate around reservoir temperature and it is normal.
May I know:
1. What type of forcefield you are using?
2.  If you can provide a longer time scale graph?
3. What time do you set for thermostat timescale and barostate timescale?