41
General Questions and Answers / Re: How to Resolve reservoir temperature Showing 0K in NVT NoserhooverMD Simulation?
« Last post by Anders Blom on January 28, 2025, 01:49 »Can you share the output so we check on that?
Recent Posts
42
Installation and License Questions / Re: QuantumATK error while loading
« Last post by Anders Blom on January 28, 2025, 01:46 »Looks like the settings file has been corrupted somehow, maybe from running an older version at the same time as a newer one (although the error is a bit odd for that).
Anyway, it's quite safe to delete (or rename) the file .quantumatk/main.ini in your home directory to start fresh. You only have to re-add the projects and change any special settings you made in Preferences.
Anyway, it's quite safe to delete (or rename) the file .quantumatk/main.ini in your home directory to start fresh. You only have to re-add the projects and change any special settings you made in Preferences.
43
General Questions and Answers / Re: Can we create MTP with dopant atom included?
« Last post by Anders Blom on January 28, 2025, 01:42 »Didn't notice your follow-up question, sorry.
1. I guess you mean after step 2. Yes, that is a possibility for sure, as long as you start the C atom in many different positions.
2. Yes, and this is true whether you skip 3 or not.
3. Probably, as long as you do step 4. The point of 1+2 is that it's a simpler system, and I prefer to build something complex on something simpler.
1. I guess you mean after step 2. Yes, that is a possibility for sure, as long as you start the C atom in many different positions.
2. Yes, and this is true whether you skip 3 or not.
3. Probably, as long as you do step 4. The point of 1+2 is that it's a simpler system, and I prefer to build something complex on something simpler.
44
Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error
« Last post by aziz.ogutlu on January 28, 2025, 00:49 »Hi filipr,
Thank you for your response.
We are installing almost all desktop packages with singularity definition file like below:
---
dnf -y install libXft libXft-devel libXScrnSaver && \
dnf -y install https://repos.openhpc.community/OpenHPC/2/CentOS_8/x86_64/ohpc-release-2-1.el8.x86_64.rpm && \
dnf -y --enablerepo=powertools install lua-filesystem lua-posix && \
dnf -y install ohpc-filesystem cairo libXext pixman lmod-ohpc && \
dnf -y install mesa-libGL mesa-dri-drivers libglvnd libfabric && \
dnf -y install qt5-qtbase.x86_64 python3-qt5.x86_64 python3-qt5-base.x86_64 lm_sensors-libs && \
---
When we run ld debug and qt debug command on page that you mention, we get these errors:
---
[root@celestia singularity]# singularity shell --cleanenv --env DISPLAY=$DISPLAY --env XDG_SESSION_ID=$XDG_SESSION_ID --network bridge --bind /run/munge:/run/munge --bind /opt/ohpc/pub:/opt/ohpc/pub qatk-2024.09-test.sif
Singularity> LD_DEBUG=files /opt/ohpc/pub/apps/qatk/2024.09/bin/quantumatk > ld_debug.out 2>&1
Singularity> grep -i error ld_debug.out
raise QtBindingsNotFoundError from None
qtpy.QtBindingsNotFoundError: No Qt bindings could be found
Singularity> QT_DEBUG_PLUGINS=3 /opt/ohpc/pub/apps/qatk/2024.09/bin/quantumatk
Traceback (most recent call last):
File "/opt/ohpc/pub/apps/qatk/2024.09/bin/../atkpython/bin/quantumatk", line 8, in <module>
sys.exit(start_quantumatk())
^^^^^^^^^^^^^^^^^^
File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 811, in start_quantumatk
File "zipdir/NL/__init__.py", line 9, in <module>
File "zipdir/NL/GUI/Main/Main.py", line 1, in <module>
File "/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/qtpy/__init__.py", line 259, in <module>
raise QtBindingsNotFoundError from None
qtpy.QtBindingsNotFoundError: No Qt bindings could be found
---
We want to update our systems OS to Rocky Linux 8, it is training for us to run QuantumATK 2024.09 on singularity.
Thank you for your response.
We are installing almost all desktop packages with singularity definition file like below:
---
dnf -y install libXft libXft-devel libXScrnSaver && \
dnf -y install https://repos.openhpc.community/OpenHPC/2/CentOS_8/x86_64/ohpc-release-2-1.el8.x86_64.rpm && \
dnf -y --enablerepo=powertools install lua-filesystem lua-posix && \
dnf -y install ohpc-filesystem cairo libXext pixman lmod-ohpc && \
dnf -y install mesa-libGL mesa-dri-drivers libglvnd libfabric && \
dnf -y install qt5-qtbase.x86_64 python3-qt5.x86_64 python3-qt5-base.x86_64 lm_sensors-libs && \
---
When we run ld debug and qt debug command on page that you mention, we get these errors:
---
[root@celestia singularity]# singularity shell --cleanenv --env DISPLAY=$DISPLAY --env XDG_SESSION_ID=$XDG_SESSION_ID --network bridge --bind /run/munge:/run/munge --bind /opt/ohpc/pub:/opt/ohpc/pub qatk-2024.09-test.sif
Singularity> LD_DEBUG=files /opt/ohpc/pub/apps/qatk/2024.09/bin/quantumatk > ld_debug.out 2>&1
Singularity> grep -i error ld_debug.out
raise QtBindingsNotFoundError from None
qtpy.QtBindingsNotFoundError: No Qt bindings could be found
Singularity> QT_DEBUG_PLUGINS=3 /opt/ohpc/pub/apps/qatk/2024.09/bin/quantumatk
Traceback (most recent call last):
File "/opt/ohpc/pub/apps/qatk/2024.09/bin/../atkpython/bin/quantumatk", line 8, in <module>
sys.exit(start_quantumatk())
^^^^^^^^^^^^^^^^^^
File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 811, in start_quantumatk
File "zipdir/NL/__init__.py", line 9, in <module>
File "zipdir/NL/GUI/Main/Main.py", line 1, in <module>
File "/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/qtpy/__init__.py", line 259, in <module>
raise QtBindingsNotFoundError from None
qtpy.QtBindingsNotFoundError: No Qt bindings could be found
---
We want to update our systems OS to Rocky Linux 8, it is training for us to run QuantumATK 2024.09 on singularity.
45
Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error
« Last post by filipr 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
$> LD_DEBUG=files path/to/quantumatk > ld_debug.out 2>&1
then look in the generated file 'ld_debug.out' for errors, e.g. 'grep -i error ld_debug.out' and see if it fails to find any .so files. If it does, then find out what system packages (typically some X/xcb related ones) are missing and install those. You can look for which packages that ship library files here: https://pkgs.org/ (filter by Rocky8 and x86_64)
If you cannot install/use graphical applications in the Singularity container, you need to create a container that allows for this. We do not officially support Singularity containers, but we hope to get some time to look into this if this becomes a frequent user request.
46
Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error
« Last post by aziz.ogutlu on January 23, 2025, 14:47 »Hi filipr,
We run quantumatk command inside the singularity container like this:
---
[root@celestia singularity]# singularity shell --cleanenv --env DISPLAY=$DISPLAY --env XDG_SESSION_ID=$XDG_SESSION_ID --network bridge --bind /run/munge:/run/munge --bind /opt/ohpc/pub:/opt/ohpc/pub qatk-2024.09-test.sif
Singularity> quantumatk
Traceback (most recent call last):
File "/opt/ohpc/pub/apps/qatk/2024.09/bin/../atkpython/bin/quantumatk", line 8, in <module>
sys.exit(start_quantumatk())
^^^^^^^^^^^^^^^^^^
File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 811, in start_quantumatk
File "zipdir/NL/__init__.py", line 9, in <module>
File "zipdir/NL/GUI/Main/Main.py", line 1, in <module>
File "/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/qtpy/__init__.py", line 259, in <module>
raise QtBindingsNotFoundError from None
qtpy.QtBindingsNotFoundError: No Qt bindings could be found
---
We run quantumatk command inside the singularity container like this:
---
[root@celestia singularity]# singularity shell --cleanenv --env DISPLAY=$DISPLAY --env XDG_SESSION_ID=$XDG_SESSION_ID --network bridge --bind /run/munge:/run/munge --bind /opt/ohpc/pub:/opt/ohpc/pub qatk-2024.09-test.sif
Singularity> quantumatk
Traceback (most recent call last):
File "/opt/ohpc/pub/apps/qatk/2024.09/bin/../atkpython/bin/quantumatk", line 8, in <module>
sys.exit(start_quantumatk())
^^^^^^^^^^^^^^^^^^
File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 811, in start_quantumatk
File "zipdir/NL/__init__.py", line 9, in <module>
File "zipdir/NL/GUI/Main/Main.py", line 1, in <module>
File "/opt/ohpc/pub/apps/qatk/2024.09/atkpython/lib/python3.11/site-packages/qtpy/__init__.py", line 259, in <module>
raise QtBindingsNotFoundError from None
qtpy.QtBindingsNotFoundError: No Qt bindings could be found
---
47
Installation and License Questions / Re: QuantumATK 2024.09 PyQt5 error
« Last post by filipr 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)
48
Installation and License Questions / QuantumATK 2024.09 PyQt5 error
« Last post by aziz.ogutlu on January 23, 2025, 09:53 »Hi there all,
We are trying to install QuantumATK 2024.09 (also SP1) on Centos 7.9 HPC system. It's giving glibc 2.28 error because centos 7.9 supports 2.17 version max. Then we try to install on singularity image with Rocky Linux 8. But this time we get PyQt5 mismatch error with atkpython (which is 5.15.12 and it is only for macos on pypi.org) and system wide. Do you have PyQt5 5.15.12 downloadable version for x64 linux system? Also do you have any suggestion for using QuantumATK 2024.09 on our HPC system?
Best regards,
Aziz
We are trying to install QuantumATK 2024.09 (also SP1) on Centos 7.9 HPC system. It's giving glibc 2.28 error because centos 7.9 supports 2.17 version max. Then we try to install on singularity image with Rocky Linux 8. But this time we get PyQt5 mismatch error with atkpython (which is 5.15.12 and it is only for macos on pypi.org) and system wide. Do you have PyQt5 5.15.12 downloadable version for x64 linux system? Also do you have any suggestion for using QuantumATK 2024.09 on our HPC system?
Best regards,
Aziz
49
General Questions and Answers / How to extract the equivalent molecules concentration ?
« Last post by khariyahA on January 21, 2025, 20:07 »Dear Sir,
I am studying gas sensing effect on graphene. I watch video tutorial as this link ..https://www.youtube.com/watch?v=BeDbeDztQeY&t=98s ...I am seeking help from expert to guide on how to extract the equivalent molecules concentration as demonstrated in this video.
Thank you
I am studying gas sensing effect on graphene. I watch video tutorial as this link ..https://www.youtube.com/watch?v=BeDbeDztQeY&t=98s ...I am seeking help from expert to guide on how to extract the equivalent molecules concentration as demonstrated in this video.
Thank you
50
General Questions and Answers / Re: How to extract effective potential and J from IVCharacteristics block?
« Last post by dmicje12 on January 21, 2025, 05:06 »Hi everyone, I really want to know how to extract data from ivc. This is urgent because the deadline is approaching. I will try any method as long as I can get the J and effective potential of ivc and the converged device_configuration.
===========================================
Thanks, I found a solution!
Using Ulrik G. Vej-Hansen's suggestion
"
ivc = nlread(filename, IVCharacteristics)[0]
pldos = ivc.results(0.0*Volt, 0.0*Volt, result_types=[ProjectedLocalDensityOfStates])[0]
pldos.nlprint()
"
Change "pldos.nlprint()" to "nlsave('test.hdf5',pldos)" to extract the calculation results in IVCharacteristics
It is recommended that you add this method back to the IVCharacteristics manual.
===========================================
Thanks, I found a solution!
Using Ulrik G. Vej-Hansen's suggestion
"
ivc = nlread(filename, IVCharacteristics)[0]
pldos = ivc.results(0.0*Volt, 0.0*Volt, result_types=[ProjectedLocalDensityOfStates])[0]
pldos.nlprint()
"
Change "pldos.nlprint()" to "nlsave('test.hdf5',pldos)" to extract the calculation results in IVCharacteristics
It is recommended that you add this method back to the IVCharacteristics manual.