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General Questions and Answers / Re: Module "calculatePlasmaFrequency"
« on: April 8, 2025, 09:06 »
The function returns the plasma frequency, i.e. the square root of the expression in the documentation.
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2
Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error
« on: March 6, 2025, 10:15 »
We have not looked into this yet, and it might take quite some time (months+) before it will happen, so if you need an urgent solution I recommend that you look for alternative ways to run QuantumATK. I have filed a ticket in our bug reporting system, so that the issue is not forgotten.
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General Questions and Answers / Re: I need help on bader charge analysis
« on: February 24, 2025, 17:35 »
You should use the PAW method instead of normconserving pseudopotentials. See also documentation and notes in the manual: https://docs.quantumatk.com/manual/Types/BaderCharges/BaderCharges.html
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Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error
« on: January 28, 2025, 15:37 »
Hmm it seems to be something different than just missing system libraries - probably some deeper problem related to how these containers work. I don't have a solution for you right now - we will have to try to get our hands on our own singularity container and that can take a while.
I suggest that you install QuantumATK on bare metal or in a VM. Do note that QuantumATK ships all needed dependencies and does not require that the cluster has anything installed as long as it lives up to our stated requirements, most notably a Linux distro that has glibc version 2.28 or newer (no RHEL/CentOS 7). For that reason there is little utility in using containers for QuantumATK.
I suggest that you install QuantumATK on bare metal or in a VM. Do note that QuantumATK ships all needed dependencies and does not require that the cluster has anything installed as long as it lives up to our stated requirements, most notably a Linux distro that has glibc version 2.28 or newer (no RHEL/CentOS 7). For that reason there is little utility in using containers for QuantumATK.
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Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error
« on: January 28, 2025, 12:59 »
Is the file 'libQt5Core.so.5' in the directory '/opt/ohpc/pub/apps/qatk/2024.09/lib'? i.e. does the symlink ''/opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so.5' exist and point to the file '/opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so.5.15.14'?
If it exists, what it the output of 'ldd /opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so.5.15.14'?
If it exists, what it the output of 'ldd /opt/ohpc/pub/apps/qatk/2024.09/lib/libQt5Core.so.5.15.14'?
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Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error
« on: January 28, 2025, 11:48 »
Hmm, try to run
Code
/opt/ohpc/pub/apps/qatk/2024.09/atkpython/bin/python -c "from PyQt5 import QtCore"
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Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error
« on: January 28, 2025, 09:54 »
Ok, as you can see the error comes from within the loading of the 'QtPy' Python package in the file (which you can open yourself to see): "/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/qtpy/__init__.py" on line 259. It appears that QtPy tries to load PySide but fails. QuantumATK uses PyQt5, not PySide. So something causes it to try to load PySide instead. This can either be because an environment variable 'QT_API' is set or because PyQt5 cannot be loaded for some reason (most likely missing system libraries).
So first check if there's an environment variable 'QT_API' set before running 'quantumatk'? If there is, be sure to unset this before running quantumatk: 'unset QT_API'.
If there's no such variable, try to run: `/opt/ohpc/pub/apps/qatk/2024.09/bin/atkpython -c "from PyQt5 import QtCore"' and see what comes out. If it fail, but doesn't mention any reason, try to run:
and then grep for errors in the generated file 'pyqt5_ld_debug.out'.
So first check if there's an environment variable 'QT_API' set before running 'quantumatk'? If there is, be sure to unset this before running quantumatk: 'unset QT_API'.
If there's no such variable, try to run: `/opt/ohpc/pub/apps/qatk/2024.09/bin/atkpython -c "from PyQt5 import QtCore"' and see what comes out. If it fail, but doesn't mention any reason, try to run:
Code
LD_DEBUG=files /opt/ohpc/pub/apps/qatk/2024.09/bin/atkpython -c "from PyQt5 import QtCore" > pyqt5_ld_debug.out 2>&1
and then grep for errors in the generated file 'pyqt5_ld_debug.out'.
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Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error
« on: January 27, 2025, 11:20 »
It could be that the Rocky Linux Singularity image is rather minimal and does not come by default with basic libraries for graphics applications (X window system). Our installation guide and system requirements assumes a default consumer Linux distribution.
It might be that you have to install some X related system libraries, check out: https://docs.quantumatk.com/intro/installation/technical_hardware.html#distribution-specific-installation-steps and https://docs.quantumatk.com/faq/faq_technical_hardware_for_v2023_12.html#distribution-specific-installation-steps
If installing the mentioned libraries (libxcb-xinerama0 and perhaps libXScrnSaver) does not fix it, you can check if more libraries are missing by running
then look in the generated file 'ld_debug.out' for errors, e.g. 'grep -i error ld_debug.out' and see if it fails to find any .so files. If it does, then find out what system packages (typically some X/xcb related ones) are missing and install those. You can look for which packages that ship library files here: https://pkgs.org/ (filter by Rocky8 and x86_64)
If you cannot install/use graphical applications in the Singularity container, you need to create a container that allows for this. We do not officially support Singularity containers, but we hope to get some time to look into this if this becomes a frequent user request.
It might be that you have to install some X related system libraries, check out: https://docs.quantumatk.com/intro/installation/technical_hardware.html#distribution-specific-installation-steps and https://docs.quantumatk.com/faq/faq_technical_hardware_for_v2023_12.html#distribution-specific-installation-steps
If installing the mentioned libraries (libxcb-xinerama0 and perhaps libXScrnSaver) does not fix it, you can check if more libraries are missing by running
Code
$> LD_DEBUG=files path/to/quantumatk > ld_debug.out 2>&1
then look in the generated file 'ld_debug.out' for errors, e.g. 'grep -i error ld_debug.out' and see if it fails to find any .so files. If it does, then find out what system packages (typically some X/xcb related ones) are missing and install those. You can look for which packages that ship library files here: https://pkgs.org/ (filter by Rocky8 and x86_64)
If you cannot install/use graphical applications in the Singularity container, you need to create a container that allows for this. We do not officially support Singularity containers, but we hope to get some time to look into this if this becomes a frequent user request.
9
Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error
« on: January 23, 2025, 14:02 »
Hi Aziz,
QuantumATK ships it's own version of Qt and PyQt - it does not depend, nor use the one installed on the system. When you say "But this time we get PyQt5 mismatch error with atkpython" what do you mean by this? How do you get this error? How do you attempt to run atkpython or quantumatk? And what is the full error message? (please copy and paste verbatim)
QuantumATK ships it's own version of Qt and PyQt - it does not depend, nor use the one installed on the system. When you say "But this time we get PyQt5 mismatch error with atkpython" what do you mean by this? How do you get this error? How do you attempt to run atkpython or quantumatk? And what is the full error message? (please copy and paste verbatim)
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General Questions and Answers / Re: linear response optimization of Hubbard U value for non-metallic kagome graphene
« on: January 13, 2025, 13:49 »
Not in 2018.06, but in the newest version 2024.09 you can calculate U from linear response: https://docs.quantumatk.com/manual/Types/calculateFiniteDifferenceLinearResponseHubbardU/calculateFiniteDifferenceLinearResponseHubbardU.html
11
General Questions and Answers / Re: Job suddenly stop and Segmentation fault
« on: December 16, 2024, 11:48 »
Hi again,
I can confirm that I can reproduce a segmentation fault with your script in v2023.12. My suspicion was that it was the same bug as we've seen in some transmission calculations with the same version when using threading, which are due to a bug in Intel MKL. We've made a fix for this in v2024.09-SP1 which has just been released (see forum post https://forum.quantumatk.com/index.php?topic=12114.msg41940#new) and indeed with that version I no longer get the segfault.
Try to install the new v2024.09-SP1 version and see if that fixes the issue. Otherwise you may be able to work around the problem by not using OpenMP threads by setting OMP_NUM_THREADS=1 - but notice that this increases the memory requirements.
I can confirm that I can reproduce a segmentation fault with your script in v2023.12. My suspicion was that it was the same bug as we've seen in some transmission calculations with the same version when using threading, which are due to a bug in Intel MKL. We've made a fix for this in v2024.09-SP1 which has just been released (see forum post https://forum.quantumatk.com/index.php?topic=12114.msg41940#new) and indeed with that version I no longer get the segfault.
Try to install the new v2024.09-SP1 version and see if that fixes the issue. Otherwise you may be able to work around the problem by not using OpenMP threads by setting OMP_NUM_THREADS=1 - but notice that this increases the memory requirements.
12
General Questions and Answers / Re: Job suddenly stop and Segmentation fault
« on: December 9, 2024, 10:41 »
Hi djicje12,
Do you have possibility of sending us the full script including the atomic configuration as well as how you run it, i.e. how many MPI processes and threads you use? In order for us to look into this we need to be able to reproduce the error.
Thanks,
Filip
Do you have possibility of sending us the full script including the atomic configuration as well as how you run it, i.e. how many MPI processes and threads you use? In order for us to look into this we need to be able to reproduce the error.
Thanks,
Filip
13
Installation and License Questions / Re: Error opening qATK on cluster
« 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
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
14
Installation and License Questions / Re: Error in open quantumatk
« on: September 25, 2024, 17:12 »
Does the executable file /user/cad/synopsys/qatk/2023.12/quantumatk/V-2023.12/atkpython/bin/python3.11 exist? Probably not - most likely you moved the installation of QuantumATK to a different folder: you are trying to run it from the directory /usr/cad/synopsys/qatk/cur (notice even how it's /usr/.. and not /user/...).
You can't move a QuantumATK installation as the launcher scripts (quantumatk and atkpython) hardcode the path to the shipped python executable. So if you moved the QuantumATK installation, either move it back, or delete it and reinstall.
No, QuantumATK is self-contained: it doesn't require any (much) installed software and certainly doesn't depend on other Python installations on the system. It ships its own custom Python interpreter and you can use both side by side without problems (as long as you are careful). For more info see: https://docs.quantumatk.com/manual/Python.html#command-line-usage-with-qatk-shell-environments
You can't move a QuantumATK installation as the launcher scripts (quantumatk and atkpython) hardcode the path to the shipped python executable. So if you moved the QuantumATK installation, either move it back, or delete it and reinstall.
Quote
So,Need I upgrade the python version?
No, QuantumATK is self-contained: it doesn't require any (much) installed software and certainly doesn't depend on other Python installations on the system. It ships its own custom Python interpreter and you can use both side by side without problems (as long as you are careful). For more info see: https://docs.quantumatk.com/manual/Python.html#command-line-usage-with-qatk-shell-environments
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General Questions and Answers / Re: Brodening in LCAO calculator
« on: September 24, 2024, 15:59 »
If you look at the second formula in the documentation (how the density is calculated) you will see that it involves an integral over the Brillouin zone. This is turned into a numerical integral, a.k.a. sum weighted by the k-grid volume element dk = Δkx Δky Δkz. The broadening should be chosen proportional to this value. If your system is long along one dimension then the Δk will be small along that direction given a constant k-point density as the Brillouin zone is inversely proportional to the length along that direction: for a cell with perpendicular lattice vectors you have Δk = 2π/(LN), where L is the length of the cell along that direction and N is the number of k-points. If you keep only one k-point along the C direction then the broadening should be proportional to Δkx Δky = (2π)2/(Lx Nx Ly Ny)
As a rule of thumb you can use a broadening of 1000K for metals and 100K for semiconductors and if the metal has a hard time converging you can either 1) increase the k-point sampling (expensive) or 2) increase the broadening (cheap, but reduces quality of results due to artificial smearing)
As a rule of thumb you can use a broadening of 1000K for metals and 100K for semiconductors and if the metal has a hard time converging you can either 1) increase the k-point sampling (expensive) or 2) increase the broadening (cheap, but reduces quality of results due to artificial smearing)