Topics

1

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

2

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.

3

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

4

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

5

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

6

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)?

7

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

8

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!

9

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

« on: November 26, 2023, 13:55 »

Hello,

In the manual for DefectDiffusivity class in https://docs.quantumatk.com/manual/Types/DefectDiffusionRates/DefectDiffusionRates.html

Does calculateDiffusivity method use Harmonic Transition State Theory to calculate the diffusivity of defects?

10

General Questions and Answers / Dopant diffusion simulation in crystal Si

« on: November 23, 2023, 07:42 »

Hello,

I am trying to simulate dopant diffusion (B,P,Ga,Te) in crystal Si for a start.
I am trying different methods such as NEB, AKMC and it seems using MTP is much less time consuming than other potentials. On top of that, I couldn't find any suitable force field potential.

1. To create MTP for a single dopant in crystalline Si, do I use the Defect Training template in the workflow?
If so, my reference configuration will be just pristine Si?
2. Would batch learning be enough or would you suggest active learning MTP for this case?
3. Is there a tutorial or a description/manual for defect training template?
4. Any ways to reduce the memory consumption while training MTP? (most of the MTP training attempts gave memory errors)

Thanks!

11

General Questions and Answers / I can't open defect list analyzer

« on: August 3, 2023, 09:32 »

Hello everyone,

I encountered an error while trying to open defect list analyzer. I am using QuantumATK2022.12 version.
Whenever I try to open VacancyList, SubstitutionalList, InterstitialList with defect list analyzer, the following error appears:

Traceback (most recent call last):
  File "zipdir/NL/GUI/Tools/Data/DataCatalogWidget.py", line 793, in _onDoubleClicked
  File "zipdir/NL/GUI/Tools/Data/DataCatalogWidget.py", line 894, in open
  File "/tmp/tmpik9qca59CustomAddOns/SMWDefectListPlugins/DefectListAnalyzer/DefectListAnalysisPlugin.py", line 62, in createWidget
  File "/tmp/tmpik9qca59CustomAddOns/SMWDefectListPlugins/DefectListAnalyzer/DefectListAnalyzerWidget.py", line 165, in __init__
  File "zipdir/NL/GUI/ModelViewControl/Views.py", line 86, in __init__
  File "zipdir/NL/GUI/ModelViewControl/Views.py", line 129, in connect
  File "/tmp/tmpik9qca59CustomAddOns/SMWDefectListPlugins/DefectListAnalyzer/DefectListAnalyzerWidget.py", line 419, in plotTypeChanged
  File "/tmp/tmpik9qca59CustomAddOns/SMWDefectListPlugins/DefectListAnalyzer/PlotManager.py", line 128, in setPlotType
  File "zipdir/NL/GUI/Graphics/Plotter/PlotView/PlotView.py", line 107, in setPlotLayout
  File "zipdir/NL/GUI/Graphics/Plotter/PlotView/BasicPlotView.py", line 107, in setPlotLayout
  File "zipdir/NL/GUI/Graphics/Plotter/PlotView/PlotController.py", line 172, in plot
  File "zipdir/NL/GUI/Graphics/Plotter/PlotView/PlotController.py", line 201, in _constructDelegatesInLayout
  File "zipdir/NL/GUI/Graphics/Plotter/PlotView/PlotController.py", line 239, in _constructDelegatesInFrame
  File "zipdir/NL/GUI/Graphics/Plotter/PlotView/PlotController.py", line 262, in _constructDelegatesInFrameForModel
  File "zipdir/NL/GUI/Graphics/Plotter/PlotView/PlotController.py", line 306, in _constructDelegateInFrameForItem
  File "zipdir/NL/GUI/Graphics/Plotter/PlotView/Delegates/FillAreaDelegates.py", line 66, in plot
  File "build/atkpython/lib/python3.8/site-packages/matplotlib/__init__.py", line 1361, in inner
  File "build/atkpython/lib/python3.8/site-packages/matplotlib/axes/_axes.py", line 5386, in fill_between
  File "build/atkpython/lib/python3.8/site-packages/matplotlib/axes/_axes.py", line 5306, in _fill_between_x_or_y
ValueError: where size (1) does not match x size (2)

Can anyone help me solve this issue?
I have attached the python file for reference.
Any help would be much appreciated. Thank you!

12

General Questions and Answers / AKMC saddle search error

« on: July 19, 2023, 03:53 »

Hello,

I found an error while following through this tutorial : https://docs.quantumatk.com/tutorials/boron_diffusion_in_si/boron_diffusion_in_si.html

I attached a python file which was used for the Adaptive Kinetic Monte Carlo (AKMC) calculation and the output file which is the log file. The saddle search stopped after 69th saddle search and apparently, there were no new state discovered after this.

This is the error message shown in the log file:

  Traceback (most recent call last):
    File "zipdir/NL/ComputerScienceUtilities/ParallelTools/DynamicTaskScheduler.py", line 427, in __runInParallelModeAsDelegator
    File "zipdir/NL/Dynamics/AdaptiveKineticMonteCarlo.py", line 1313, in schedulerCode
    File "zipdir/NL/Dynamics/AdaptiveKineticMonteCarlo.py", line 840, in search
    File "zipdir/NL/ComputerScienceUtilities/ParallelTools/DynamicTaskScheduler.py", line 793, in waitAnyTaskFinished
    File "zipdir/NL/ComputerScienceUtilities/ParallelTools/DynamicTaskScheduler.py", line 1120, in __monitorTasks
    File "Request.pyx", line 47, in mpi4py.MPI.Request.Test (src/mpi4py.MPI.c:50413)
  mpi4py.MPI.Exception: Unknown error class, error stack:
  PMPI_Test(189)........................: MPI_Test(request=0x1529336f4f70, flag=0x7ffca46265c8, status=0x1) failed
  MPIR_Test_impl(67)....................: fail failed
  MPIDU_Complete_posted_with_error(1710): Process failed

Can anyone guide me through this error and explain why this error message showed up? Thank you!

13

Scripts, Tutorials and Applications / Question about Boron diffusion in bulk silicon tutorial

« on: July 6, 2023, 09:13 »

Hello,

I was looking at tutorial titled "Boron diffusion in bulk silicon" (link = "https://docs.quantumatk.com/tutorials/boron_diffusion_in_si/boron_diffusion_in_si.html" ) to perform Adaptive Kinetic Monte Carlo (AKMC) simulation. I realized that silicon was initially geometrically optimized but with the two atoms (which is all the atoms there is in the primitive cell) fixed. Does performing a geometry optimization calculation with all the atoms fixed have any meaningful purpose? I didn't understand why the Silicon atoms were fixed here.

Thanks.

+++ This was a bad question, lattice vectors were unfixed. Problem solved.