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Messages - dmicje12

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1
Hello, the calculation of negative bias voltage is similar. ATK will read 0V and then calculate -0.1V. It will read 0V&-0.1V and calculate 0.2V and keep calculating.

2
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.

3
Thanks for reply!
Yes,my hdf5 file format is indeed different bias analysis saved in one file, as shown in the attached picture.
Is there any way to split this hdf5 file into multiple hdf5 files, each hdf5 file has only one bias calculation result?
Or what settings should be made before calculation so that each bias calculation result can be saved as a separate HDF5 file?
I think IVCharacteristics is a simple and practical block. Its automatic reading of initial state function is really convenient, but I am very troubled that I cannot read the SCF convergence results and analysis.
=============================================================================================
Hello, I have a small question.
I unpacked IVCharacteristics and exported one of the objects into an hdf5 file, as shown in Figure 2.
I clicked it but nothing happened and no file was exported as hdf5 file. Is this normal?
Thanks!



4
Thanks for reply!
There is some questions:
===============================================================================================================
1.I tried the "nlinspect" method in your reply
The generated file is shown in Attachment 1. I cannot tell which object has the effective potential or current density at which voltage point. Is there any way to help me parse this data?
===============================================================================================================
2.What does object_id mean?
When I unpack IVCharacteristics,I can see the "type" and "name" of the calculation result.
For example, if I want to read the Current density of Gate -1 Volt, Drain -0.05 Volt, I use the following command:
Code
file_data = nlread("file.hdf5",CurrentDensity,object_id="Gate -1 Volt, Drain -0.05 Volt")[-1]

It will display "IndexError: list index out of range" as shown in Attachment 2
===============================================================================================================

3.Is there no way to extract the effective potential and current density calculated using IVCharacteristics addAnalysis method?
The effective potential and current density I mentioned in this article are calculated using the IVCharacteristics addAnalysis method, as shown in the attached figure.
======================================================================================================================

Thanks again for your reply!

5
I really need help
I tried a lot of command writing methods but couldn't read it.
I've searched all over the GUI interface and still can't find a way to read it.
Thanks!
=====================================
A very serious problem occurred
I was trying to read hdf5 data and suddenly I couldn’t read it.
Please tell me how to solve this problem

6
Hello, everyone!

I used the IVCharacteristics function to calculate the effective potential at many different voltage points.
Now, I want to extract the effective potential and current density data at a specific voltage point for further processing.
However, I'm not sure which command I should use to extract the data.

Could anyone help me with this?
Thank you all!

Based on my current understanding,
if the HDF5 file only contains device_configuration and effective potential,
this type of command can be used to read the data:
veff1 = nlread('result.hdf5', EffectivePotential)[0]
However, I am still unsure about the reading format for IVCharacteristics.

There are additional questions
Is there a way to read these device_configurations from IVCharacteristics and use them to calculate other physical quantities?
Thank you all!
=========================================
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.




7
Thanks for your reply!
This is exactly what i need!

8
I'd like to know the commands for converting 'atkpython' files to CIF or POSCAR. Thank you everyone.

9
Hello everyone
Because I need to make some changes to the structure and save it as a new structure, and the new structure must be in the form of a cif file.
So is there any way to convert the structure in atkpython form into cif file form using command line or python syntax?
Thanks!

10
Hello, my ATK version is 2023.12-sp1, the operating system is ubuntu24.04 LTS, I have 96 cores and 192 threads(epyc 7k62),
I use 32MPI, 6 threads to calculate,
the memory usage does not exceed the maximum memory(512G),
strangely, my friend uses the 20-core Xeon-e5 series and CentOS version 7.9 and ATK 2022.12 version, and there is no sudden stop of the job when calculating similar structures. (20MPI and threads setting is automatic)
Then I have another machine that is being calculated. Its configuration is xeon 4514y with CentOS 7.9 installed and ATK version 2023.12. When calculating the same structure, the job will suddenly stop. (32MPI and 2 threads)
If you need more information please remind me.
Thanks!
p.s. I will use all threads when calculating. I wonder if this will affect the stability of the calculation?

11
Thanks for reply!
I am the only user of the server
If the license server cannot be connected due to network instability, will jobs suddenly stop?
But I remember that when encountering network conditions before, , the word "heartbeat" would appear in the log file.
Finally, I hope ATK can add the function of automatic restarting calculation, because I encountered many times that jobs suddenly stopped while I was sleeping, which was very frustrating.
Anyway, thank you very much for the help!
Thanks!




12
Hello!
My jobs suddenly crashed again
When I use the "coredumpctl list" command, the following line appears:
Fri 2024-12-06 15:38:51 CST  396269 1000 1000 SIGSEGV present  /cad/synopsys/qatk/2023.12-sp1/atkpython/bin/python3.11   1.0G
Then I used "gdb /cad/synopsys/qatk/2023.12-sp1/atkpython/bin/python3.11 core"
It appears in the following line:
gdb: symbol lookup error: /lib/x86_64-linux-gnu/libpython3.12.so.1.0: undefined symbol: XML_SetReparseDeferralEnabled

I'm pretty sure the ram is enough during the calculation
My server has 500g of ram. The peak ram usage during calculation is about 200g.
Sometimes the calculation can be stable for 2 to 3 days, but sometimes the calculation stops after 4 hours.
I still don't know why jobs stopped suddenly.
Attached is my script below
Thanks!


13
Thanks for reply!
but,I still don’t understand
1.
I added configuration = nlread("file.hdf5", DeviceConfiguration)[-1] to the script.
If the metallic region in the DeviceConfiguration of file.hdf5 is at 0V, does that mean the calculated Veff result will be the "effective potential of the metallic region at 0V"?
But if I want to use the "DeviceConfiguration of the metallic region at 0V" as the initial state for calculating the "effective potential of the metallic region at -1V," is that possible?
2.
Also, where exactly should configuration = nlread("file.hdf5", DeviceConfiguration)[-1] be added in the script?
I tried adding it to both DeviceLCAOCalculator and DeviceConfiguration, but neither worked.
Thanks!
=======================================================
Thanks!
I already know how to import the initial state!

Just place the following:
job.setCalculator(
    calculator=calculator, initial_state=nlread("file.hdf5", DeviceConfiguration)[0]
)
before job.update()


14
Thanks for reply!
I have a few questions:
1.How do I use the nlread command?
potential_calculate = nlread(
    'iv_calculate.hdf5',
    DeviceConfiguration_0
)
Should I replace the DeviceConfiguration part of the original script with the text above?

2.Is there a strict requirement for reading DeviceConfiguration_0? For example, if I want to calculate the effective potential of gate (metallic region) at -1V, do I necessarily need to read the DeviceConfiguration at gate (metallic region) -1V? If I read DeviceConfiguration at gate (metallic region) 0V, will it restart the calculation, or will it take this converged state as the initial state and continue from there?

Thank you!

15
Hello everyone!

Currently, I need to calculate three properties: IV characteristics, current density, and effective potential.
Each time, I have to restart the SCF calculation from scratch.

I would like to ask: is it possible to use the electron density obtained from the IV characteristics calculation for the effective potential calculation?
Would it work if I directly use nlread to read the HDF5 file generated from the IV characteristics?

Or are there other ways to improve the efficiency?

Thank you all!

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