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General Questions and Answers / Re: Implementing a new Reactive Forcefield
« Last post by AsifShah on Today at 08:46 »Dear Admin,
Is there any update? It is urgent.
Is there any update? It is urgent.
Recent Posts
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General Questions and Answers / Re: Information and Capabilities of Pretrained MTPs in Force Field Library for MD
« Last post by Anders Blom on Yesterday at 19:43 »Yeah MTP can be particularly sensitive to this, forces can diverge in such geometries. We have been experimenting with adding a short-range repulsive potential (ZBL) but it doesn't always work as well as desired. Good that you solved it!
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General Questions and Answers / ChargedPointDefect: interstitial doesn't work / substitutional is fine
« Last post by beomjin on Yesterday at 17:35 »(Final revision: May 31, 2024, 10:30)
Q-ATK Version: V-2023.12-SP1
HPC OS: Rocky Linux 8.7
User: Non-sudoer
Hello, this is my first post on the Q-ATK forum. There might be mistakes in my post, so I appreciate your understanding and any feedback.
I am currently working on the ChargedPointDefect (CPD) module to calculate the charge transition level of defects. I followed the CPD tutorial (https://docs.quantumatk.com/tutorials/charged_point_defect_study_object/charged_point_defect_study_object.html), using Workflows instead of Script Generator as Q-ATK2023 does not support Script Generator.
I successfully obtained results for diamond with a boron substitutional defect (see attached image). However, the ChargedPointDefect module does not work for an interstitial defect. The two .py scripts for substitutional boron and interstitial hydrogen are attached.
Error: Missing 2 required positional arguments: 'supercell_repetitions' and 'charge_state'
In the attached .py scripts, 'supercell_repetitions' defaults to (1x1x1). The 'charge_state' parameter is correctly set in the CPD block, and it works for substitutional boron. However, using the same input scripts for interstitial hydrogen results in an input argument error.
It seems the ChargedPointDefect module works for substitutional defects but not for interstitial defects.
ChatGPT Suggestions:
1. Function Definition and Call Issue: The 'update' method or another method within the ChargedPointDefect class might be calling '_defectSymmetryGroups' without properly passing the required arguments.
2. Incorrect Function Call: Another part of the code might be calling '_defectSymmetryGroups' and missing the necessary arguments.
The 'ChargedPointDefect' library in the QATK.zip file is in .pye format, not .py, so I cannot access its content.
Can someone help me with this error?
Side Question: Does anyone know where the .vnl directory is? I couldn't find it. Some suggest that GUI issues can be solved by removing the ".hdf" file in the ".vnl" directory (https://forum.quantumatk.com/index.php?topic=6335.0).
Thank you in advance.
======================================================================================================
Error message when I open interstitial hydrogen CPD .hdf result file as belows:
Traceback (most recent call last):
File "zipdir/NL/GUI/Tools/Data/DataCatalogWidget.py", line 844, in _onDoubleClicked
File "zipdir/NL/GUI/Tools/Data/DataCatalogWidget.py", line 945, in open
File "/tmp/tmp_xh4zvsfAddOns/ChargedPointDefectAnalyzer/ChargedPointDefectAnalyzerPlugin.py", line 112, in createWidget
File "/tmp/tmp_xh4zvsfAddOns/ChargedPointDefectAnalyzer/ChargedPointDefectAnalyzerWidget.py", line 91, in __init__
File "/tmp/tmp_xh4zvsfAddOns/ChargedPointDefectAnalyzer/DefectCollection.py", line 196, in addDefectCalculations
File "zipdir/NL/Defects/ChargedPointDefects/DefectResultsSummary.py", line 138, in __init__
File "zipdir/NL/Defects/ChargedPointDefects/DefectResultsSummary.py", line 1234, in loadData
File "zipdir/NL/Defects/ChargedPointDefects/DefectResultsSummary.py", line 1268, in loadDataStudy
TypeError: ChargedPointDefect._defectSymmetryGroups() missing 2 required positional arguments: 'supercell_repetitions' and 'charge_state'
Q-ATK Version: V-2023.12-SP1
HPC OS: Rocky Linux 8.7
User: Non-sudoer
Hello, this is my first post on the Q-ATK forum. There might be mistakes in my post, so I appreciate your understanding and any feedback.
I am currently working on the ChargedPointDefect (CPD) module to calculate the charge transition level of defects. I followed the CPD tutorial (https://docs.quantumatk.com/tutorials/charged_point_defect_study_object/charged_point_defect_study_object.html), using Workflows instead of Script Generator as Q-ATK2023 does not support Script Generator.
I successfully obtained results for diamond with a boron substitutional defect (see attached image). However, the ChargedPointDefect module does not work for an interstitial defect. The two .py scripts for substitutional boron and interstitial hydrogen are attached.
Error: Missing 2 required positional arguments: 'supercell_repetitions' and 'charge_state'
In the attached .py scripts, 'supercell_repetitions' defaults to (1x1x1). The 'charge_state' parameter is correctly set in the CPD block, and it works for substitutional boron. However, using the same input scripts for interstitial hydrogen results in an input argument error.
It seems the ChargedPointDefect module works for substitutional defects but not for interstitial defects.
ChatGPT Suggestions:
1. Function Definition and Call Issue: The 'update' method or another method within the ChargedPointDefect class might be calling '_defectSymmetryGroups' without properly passing the required arguments.
2. Incorrect Function Call: Another part of the code might be calling '_defectSymmetryGroups' and missing the necessary arguments.
The 'ChargedPointDefect' library in the QATK.zip file is in .pye format, not .py, so I cannot access its content.
Can someone help me with this error?
Side Question: Does anyone know where the .vnl directory is? I couldn't find it. Some suggest that GUI issues can be solved by removing the ".hdf" file in the ".vnl" directory (https://forum.quantumatk.com/index.php?topic=6335.0).
Thank you in advance.
======================================================================================================
Error message when I open interstitial hydrogen CPD .hdf result file as belows:
Traceback (most recent call last):
File "zipdir/NL/GUI/Tools/Data/DataCatalogWidget.py", line 844, in _onDoubleClicked
File "zipdir/NL/GUI/Tools/Data/DataCatalogWidget.py", line 945, in open
File "/tmp/tmp_xh4zvsfAddOns/ChargedPointDefectAnalyzer/ChargedPointDefectAnalyzerPlugin.py", line 112, in createWidget
File "/tmp/tmp_xh4zvsfAddOns/ChargedPointDefectAnalyzer/ChargedPointDefectAnalyzerWidget.py", line 91, in __init__
File "/tmp/tmp_xh4zvsfAddOns/ChargedPointDefectAnalyzer/DefectCollection.py", line 196, in addDefectCalculations
File "zipdir/NL/Defects/ChargedPointDefects/DefectResultsSummary.py", line 138, in __init__
File "zipdir/NL/Defects/ChargedPointDefects/DefectResultsSummary.py", line 1234, in loadData
File "zipdir/NL/Defects/ChargedPointDefects/DefectResultsSummary.py", line 1268, in loadDataStudy
TypeError: ChargedPointDefect._defectSymmetryGroups() missing 2 required positional arguments: 'supercell_repetitions' and 'charge_state'
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General Questions and Answers / Re: Information and Capabilities of Pretrained MTPs in Force Field Library for MD
« Last post by msingh96 on May 29, 2024, 17:35 »Hello. I think I figured it out. the distance between surfaces in the initial geometry was too close, causing large forces to explode and break most structures.
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General Questions and Answers / Re: Information and Capabilities of Pretrained MTPs in Force Field Library for MD
« Last post by msingh96 on May 27, 2024, 22:56 »Hi Anders, I've been trying to figure this out on my own before posting again.
I am trying to use the Si/TiSi2 potential for MD simulations. I have had modest success with small structures, but the most frequent error is atoms leaving the simulation cell. this error causes the MD simulation to stall and get stuck. my instinct is an issue with the structures I provided, I used the interface builder to make an initial structure with Si [100] surface and TiSi[001] surface but I have to manually modify the distance between the surfaces using shift surface. I want to equilibrate the surface distance suing NPT but that's not working either.
Are there any example geometries from the training data for this potential to see where I'm going wrong?
I am trying to use the Si/TiSi2 potential for MD simulations. I have had modest success with small structures, but the most frequent error is atoms leaving the simulation cell. this error causes the MD simulation to stall and get stuck. my instinct is an issue with the structures I provided, I used the interface builder to make an initial structure with Si [100] surface and TiSi[001] surface but I have to manually modify the distance between the surfaces using shift surface. I want to equilibrate the surface distance suing NPT but that's not working either.
Are there any example geometries from the training data for this potential to see where I'm going wrong?
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Installation and License Questions / Re: Is there any limitation for number of execution of Simulation?
« Last post by Anders Blom on May 24, 2024, 18:30 »Could be. Finished just means the job is not running any more, but the Job Manager does not know anything about possible errors that arose.
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Installation and License Questions / Re: Is there any limitation for number of execution of Simulation?
« Last post by techenthusiast on May 24, 2024, 08:55 »Also there is a small doubt: Sometimes its showing Job status as "finished" even ongoing execution for example ("Executing task - 7/20") . Without throwing any error. Its similar to this?
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Scripts, Tutorials and Applications / Re: spatial region extended into the centre region, not calculated during electrode
« Last post by techenthusiast on May 24, 2024, 05:53 »Thank You for your kind advise. The system is a metallic wrap around gate across the central region (Channel).
Like this (Device_setup.py) -https://docs.quantumatk.com/manual/Types/IVCharacteristics/IVCharacteristics.html#usage-example
For tutorial I was following this (Top & bottom metallic box gate) -https://docs.quantumatk.com/tutorials/ivcharacteristics/ivcharacteristics.html
That's why probably I was bit confused regarding the approach -whether it is same or not for both the cases.
Thank you once again.
Like this (Device_setup.py) -https://docs.quantumatk.com/manual/Types/IVCharacteristics/IVCharacteristics.html#usage-example
For tutorial I was following this (Top & bottom metallic box gate) -https://docs.quantumatk.com/tutorials/ivcharacteristics/ivcharacteristics.html
That's why probably I was bit confused regarding the approach -whether it is same or not for both the cases.
Thank you once again.
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Scripts, Tutorials and Applications / Re: spatial region extended into the centre region, not calculated during electrode
« Last post by Anders Blom on May 24, 2024, 00:58 »The IVCharacteristics framework is handy since it is restartable and provides a nice way to loop over all bias values and gate voltages. If you have multiple gates or a more complex system I recommend just running individual simulations or a script with a loop over values, and then collect the results in the end.
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General Questions and Answers / Re: Missing SK Parameters from Install
« Last post by Anders Blom on May 24, 2024, 00:56 »Yeah sorry, we removed this model because it was not giving good results. We forgot to update the tutorial. You will have to run with DFT instead, you can use the smallest basis set FHI/SingleZeta to get fast results, probably similar accuracy as DFTB.