Messages

1

General Questions and Answers / Re: How is Defect Diffusivity Calculated with calculateDiffusivity method?

« on: April 11, 2024, 15:03 »

Thank you for your response.

In that case, is the calculatediffusivity method proceed to adaptive kinetic monte carlo? or does it only calculate the diffusivity of diffusion between the specified initial and final state.
If it's the latter, is there an equation or specific link to the document describing how defectdiffusivity is calculated?

Thank you,
Shinyeong

2

Installation and License Questions / Cannot assign more than 5 cores for AKMC

« on: March 19, 2024, 10:29 »

Hello,

I am trying to run AKMC with cluster but it seems that I can't assign more than 6 cores. When using low calculation parameter with lcao 1 node 7 cores, qatk_quantum licensed number of users already reached appears.. When using forcefield to run AKMC 1 node 7 cores, qatk_forcefield licensed number of users already reached appears too. 

Considering that AKMC is quite heavy calculation, I don't understand why the licenses stated above can only allow one core per license. It seems that I have 5 qatk_quantum and qatk_forcefield license each.

Is there a way around this?

Thank you

3

General Questions and Answers / Re: Using MTP forcefield that has more than required elements

« on: February 13, 2024, 03:36 »

Thanks all 

4

General Questions and Answers / Using MTP forcefield that has more than required elements

« on: February 5, 2024, 18:36 »

Hi all,

I was trying to generate GeTe amorphous structure using melt quench method.

This is a general question, is it safe to use MTP forcefield that has more elements than my required configuration?

More specifically, is it safe to use the built-in MTP for MD/Geo-opt of crystal GeTe which is QuantumATK_MTP_GST_2022_12 (Ge, Sb, Te)?

Thanks.

5

General Questions and Answers / Re: Reducing memory consumption for MTP training

« on: January 20, 2024, 14:47 »

Hello, I do not see any error message in the mtp_training_defectconfiguration_0_bundle_2.log,
I have attached the lmtp_training_defectconfiguration_0_bundle_2.log for reference

6

General Questions and Answers / Re: MD Final configuration is different from the last image of trajectory movie

« on: January 20, 2024, 14:40 »

Thanks

7

General Questions and Answers / MD Final configuration is different from the last image of trajectory movie

« on: January 19, 2024, 07:13 »

Hello all,

I tried MD simulation using the constant pressure Melt Quench template in the workflow on GeTe configuration.
The movie for trajectory looks fine but the final configuration of MD looks different from the final image shown in the movie and it is way off. Does anyone know what is causing this?

I used QuantumATK_MTP_GST_2022_12 (Ge, Sb, Te) as the forcefield

Thanks

8

General Questions and Answers / Re: Optimize Cell Error

« on: January 15, 2024, 15:36 »

from the log file it looks like you are running on 2019.12 version.
Maybe adjust the path variable so that you are executing the script by 2022.12 version?

9

General Questions and Answers / Can't find builder(bulk, selection, device etc.) tools on the right

« on: January 15, 2024, 11:53 »

Options such as bulk tools, builders, selection tools etc. suddenly went missing. Please refer to the image attached.
view -> restore builder layout does not do anything.
quitting atk and restarting it does not help.

Please help.

Thank you

10

General Questions and Answers / Reducing memory consumption for MTP training

« on: January 10, 2024, 08:35 »

I am trying to train MTP for silicon bulk with single boron dopant (as a test).
I created the script using defect training template in the workflow.
Pristine configuration was primitive silicon bulk (2 atoms), defect configuration generated has supercell repetition of 3x3x3.
I used 2x2x2 k-point density, pseudodojo medium basis set for silicon and boron, reduced the basis size to 400, used all available processes per task.
Most of the parameters were left as default settings.
I ran the script using intel MPI & SLURM with 3 nodes 18 cores each. Each node has 64GB memory.
Calculation file, log file and screenshot of the error is attatched below.

I also tried increasing the number of nodes, reducing the number of cores, increasing the number of processes per task, reducing the basis size etc. and same error appeared (I assume it is memory error)

My main goal is to do active learning MTP but if the above calculation faces memory error, I am pretty sure active learning MTP would also result in memory error.
Could anyone suggest any further ways to reduce memory consumption during MTP training?

Thank you

11

General Questions and Answers / Difference between IDPP interpolation for NEB in 23.12 version and 22.12 version

« on: January 3, 2024, 05:56 »

Hello,

Previously in 2022.12 version when I generate NEB configuration with Image Dependent Pair Potential interpolation, the python script would set generate_images parameter as false.

e.g
NudgedElasticBand(generate_images=False)

However in 2023.12 version, generating NEB configuration with IDPP sets generate_images parameter as ImageDependentPairPotential

e.g
NudgedElasticBand(generate_images=ImageDependentPairPotential())

Does this mean that in the 2022.12 version, image dependent pair potential was not implemented when generating NEB configurations even though I set the interpolation as IDPP (in the QATK interface, not the python script)?

12

General Questions and Answers / Re: Question regarding parallelization calculation using mpi

« on: December 21, 2023, 16:25 »

Thank you for your quick response. Using atkpython_system-mpi does the job.

13

General Questions and Answers / Question regarding parallelization calculation using mpi

« on: December 21, 2023, 15:18 »

Hello, I am trying to test mpi, for some reason mpirun works perfectly in QuantumATK 2020.09 & 2022.12 version but doesn't work in 2023.03 and 2023.12.

(Command I used)
mpirun -f hf78 -ppn 15 /home/edr_05/QuantumATK/QuantumATK-U-2022. 12-SP1/bin/atkpython mpi_test.py > mpi_test.log &

(output shown when I type "ps -ef | grep mpirun")
/bin/sh /opt/intel/oneapi/mpi/2021.10.0//bin/mpirun -f hf78 -ppn 15 /home/edr_05/QuantumATK/QuantumATK-U-2022. 12-SP1/bin/atkpython mpi_test.py 

This command works perfectly using node 7&8, 15 cores each and writes log as it is supposed to.

However, if I use the same command with atkpython from the bin folder in Quantumatk 2023.12 and 2023.03, it doesn't write any log file and doesn't proceed any calculation. Similarly, if I use mpiexec.hydra or mpiexec in the mpi file new versions, it also doesn't write any log. mpirun works well for 2023.03 and 2023.12 atkpython only when assigning one node but fails when assigning more than one node.

Can anyone help me solve this issue? Thank you

14

General Questions and Answers / Is it possible to create defect pair for defect block in defect training templat

« on: December 11, 2023, 12:06 »

Hello,

I want to train MTP for silicon with multiple defects in the crystal.
However I do not see an option for creating multiple defects from the defect block (interface), instead I only see that it's possible with scripts. Is it possible to create defect pair from the defect training (MTP) template?

Thanks in advance!

15

General Questions and Answers / Re: Dopant diffusion simulation in crystal Si

« on: December 4, 2023, 15:25 »

Dear Anders,

Thank you very much for your reply! Regarding the active learning on the NEB itself, I have the newest version and I prepared my NEB configuration. Could you possibly guide me on how I can apply active learning on NEB itself?

Also I have attached the python script and log file regarding the memory errors that appeared during MTP training.

Thanks alot!