Messages

16

General Questions and Answers / MTP force-field license problem and colum key duplicate error

« on: February 20, 2025, 05:38 »

Hello, I am trying to calculate GeTe MTP first based on the question in " https://forum.quantumatk.com/index.php?topic=12445.msg42955#new "

At first, the MTP training worked well, but after a few hours the error occurred
License Error: Unable to obtain a required license for the
requested license feature. It could mean there are no valid
licenses left, a problem with the connection to the license
server, or the license file does not contain the requested feature.
See below for more details.

Licensed number of users already reached.
Feature:       qatk_forcefield
License path:  [email protected]:
FlexNet Licensing error:-4,234

And I tried to recalculate it again and the other error occurred.

node01
Thu Feb 20 11:26:21 KST 2025
Traceback (most recent call last):
  File "/home/synopsys/quantumatk/W-2024.09/bin/../atkpython/bin/atkpython", line 8, in <module>
Traceback (most recent call last):
  File "/home/synopsys/quantumatk/W-2024.09/bin/../atkpython/bin/atkpython", line 8, in <module>
    sys.exit(__run_atkpython())
    sys.exit(__run_atkpython())
             ^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 803, in __run_atkpython
             ^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 803, in __run_atkpython
  File "gete_mtp.py", line 338, in <module>
  File "gete_mtp.py", line 338, in <module>
    training__set__table.addInstanceColumn(key='training_set', types=TrainingSet)
  File "zipdir/NL/ComputerScienceUtilities/Table/Columns.py", line 2269, in addInstanceColumn
    training__set__table.addInstanceColumn(key='training_set', types=TrainingSet)
  File "zipdir/NL/ComputerScienceUtilities/Table/Columns.py", line 2269, in addInstanceColumn
  File "zipdir/NL/ComputerScienceUtilities/Table/Columns.py", line 2301, in addColumn
NL.ComputerScienceUtilities.Exceptions.NLValueError: The column key, training_set, is already used in the table. Duplicate keys are not allowed.
  File "zipdir/NL/ComputerScienceUtilities/Table/Columns.py", line 2301, in addColumn
NL.ComputerScienceUtilities.Exceptions.NLValueError: The column key, training_set, is already used in the table. Duplicate keys are not allowed.
Traceback (most recent call last):
  File "/home/synopsys/quantumatk/W-2024.09/bin/../atkpython/bin/atkpython", line 8, in <module>
Abort(1) on node 3 (rank 3 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
Abort(1) on node 12 (rank 12 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 12
    sys.exit(__run_atkpython())
             ^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 803, in __run_atkpython

I tried to find some answers to this "Duplicate keys are not allowed" error from atk forum but I couldn't find any.

Can anyone help me with this issue?

I attached the py file that I used bellow.

Thank you

17

General Questions and Answers / Re: Can we create MTP with dopant atom included?

« on: February 19, 2025, 20:43 »

Oh, and other question regarding to previous ones, if I were to investigate amorphous structure only, then can I skip step 1(crystal mtp) and go straight to step 2(amorphous mtp)?

18

General Questions and Answers / Re: Can we create MTP with dopant atom included?

« on: February 19, 2025, 07:45 »

Thank you for your reply.

Again, I have some other questions related to previous ones.

1. I want to train crystal GeTe with ratio 1:3 for Ge and Te each. However, from materials project, there was no Ge1Te3 crystal structures. So can I just use GeTe instead for MTP training to get Ge1Te3 MTP?

2. From your answer about putting C atom into GeTe, can I just use amorphous C doped GeTe with packmol as initial training set and skip step 1, 2(only getting GeTe MTP) ? I am little bit confused that why should I create only GeTe MTP first before training atom-doped GeTe.

Thank you

19

General Questions and Answers / Can anyone help me with convergence error problems?

« on: February 7, 2025, 13:52 »

Hello, I am trying to calculate transmission spectrum at 0 eV with Silicon/Silicide contact with different doping concentration(5e19,1e20,5e20,1e21)

I tried to converge the LCAO calculator but the device would not converge.

I changed density mesh cutoff, device algorithm(neutral atom, equivalent bulk etc..), contour parameter(ozaki point) for about a week with same structure, but nothing would work.

I tried to solve this problem on my own, but after spending a week with same structure, I realized it was beyond my beyond my capabilities.
Therefore, I have decided to seek assistance.

I am wondering if I am making a mistake or the structure is not properly optimized(0.02eV/A, optimize length : 10A). (I attached txt file of the calculation information)

Can anyone could give me some tips regarding with convergence problem?

When I check the log file, for some reason, the convergence energy suddenly changed to higher value. (40E~42E)

26 E = -940.453 dE =  3.211179e-01 dH =  8.870016e-01                       |
|  27 E = -942.197 dE =  1.744240e+00 dH =  8.995829e-01                       |
|  28 E =  -941.24 dE =  9.571292e-01 dH =  7.565638e-01                       |
|  29 E = -942.876 dE =  1.635776e+00 dH =  8.258672e-01                       |
|  30 E = -943.925 dE =  1.048822e+00 dH =  8.581108e-01                       |
|  31 E =  -944.33 dE =  4.050945e-01 dH =  9.593208e-01                       |
|  32 E = -942.058 dE =  2.272090e+00 dH =  8.716657e-01                       |
|  33 E = -942.011 dE =  4.704906e-02 dH =  8.909611e-01                       |
|  34 E = -941.766 dE =  2.451188e-01 dH =  7.616103e-01                       |
|  35 E = -942.428 dE =  6.625315e-01 dH =  7.147292e-01                       |
|  36 E = -942.211 dE =  2.172081e-01 dH =  6.725936e-01                       |
|  37 E = -942.583 dE =  3.722324e-01 dH =  6.988655e-01                       |
|  38 E = -942.315 dE =  2.688179e-01 dH =  7.281209e-01                       |
|  39 E = -946.068 dE =  3.753141e+00 dH =  7.930580e-01                       |
|  40 E = -944.435 dE =  1.633055e+00 dH =  6.637546e-01                       |
|  41 E =  -961.58 dE =  1.714573e+01 dH =  2.050847e+00                       |
|  42 E = -2420.58 dE =  1.458995e+03 dH =  8.792229e+01                       |
|  43 E = -2558.35 dE =  1.377787e+02 dH =  9.421465e+01                       |
|  44 E = -2414.11 dE =  1.442476e+02 dH =  8.872245e+01                       |
|  45 E = -1620.06 dE =  7.940496e+02 dH =  5.332355e+01                       |
|  46 E = -1685.53 dE =  6.547581e+01 dH =  5.754290e+01                       |
|  47 E = -2391.43 dE =  7.058958e+02 dH =  9.732136e+01                       |
|  48 E = -2297.45 dE =  9.397452e+01 dH =  9.073635e+01                       |
 

Thank you for reading the question

20

General Questions and Answers / Re: Question of : interface builder -> surface cell -> Some matches are degenerate?

« on: February 3, 2025, 09:47 »

Sorry for the late reply, I attached the structure information by .py files

21

General Questions and Answers / Can we create MTP with dopant atom included?

« on: January 16, 2025, 06:10 »

Hello, I have some questions regarding MTP training with dopant atom attached.

We are planning to put carbon dopant in GeTe amorphous structure with different doping density.

However, since there are no force field related to C, Ge, Te, we decided to create MTP.

Here is the question, to create MTP, as far as I know, making initial training set is essential.

But since there are no initial training set regarding to different carbon doping density in GeTe, I wonder how should we proceed with the first step of creating MTP.

Is there any tips for it?

22

General Questions and Answers / Re: Question of : interface builder -> surface cell -> Some matches are degenerate?

« on: January 16, 2025, 04:01 »

Oh, I accidently forget to input more information.

I used the latest version of ATK and I optimized primitive cell of Si and Mo at 0.02eV/A tolerance.

Then I cleaved each with 110 and 001

23

General Questions and Answers / Re: Question of : interface builder -> surface cell -> Some matches are degenerate?

« on: January 14, 2025, 13:29 »

Dear Anders Blom

I created the interface with silicon and Molybdenium with the orientation of Si=(110)/Mo=(001)
I attached the pictures that I saw.

The sentence  "Some matches are degenerate" turns into red.

There were no signs of errors after I created the structure, but I still have some concerns regarding this issue.

24

General Questions and Answers / Question of : interface builder -> surface cell -> Some matches are degenerate?

« on: January 5, 2025, 11:09 »

Hello, I am trying to match some surface with interface builder.

There are a lot of surface cell that I could choose, however for some samples, the sentence "Some matches are degenerate" turns into red and show the degenerate match groups.

Could anyone please tell me what this means? and could it affect the calculation results?

Also how can I solve this degenerate issue?

25

General Questions and Answers / Re: Grain Boundary Scattering doping problem

« on: October 17, 2024, 06:46 »

Dear Anders Blom

Thank you for your advice.
I have some questions and a new issue while calculating the grain boundary.

1. From your reply, at number 6,7 is there a reason to calculate the total energy of relaxed structure? Can I just run over to 8,9 instead without calculating total energy?

2. I calculated a structure with 1e21 doping tag attached, and grain boundary scattering actually worked. But only for this structure. I tried other structures and they gave infinite resistance results.
I attached the py, log file and screenshot of the 1e21 doping structure results. As you can see, I calculated the grain boundary scattering with 1e21 doping and 0eV. But the calculation was successful.  Hope this might help.

26

General Questions and Answers / Re: Grain Boundary Scattering doping problem

« on: October 4, 2024, 09:37 »

Thank you for your answer. But I am little bit confused with your answer about "put together the workflow yourself".

Does it mean that I have to used the analysis in workflows part?

Also, would it be little bit more probable if I use the nlread settings of doped structure in SMW import?

For example, the grain boundary scattering needs optimization of the structure in advance, so what I am planning is
1. optimize the structure.
2. Put the structure into the builder and dope it with 1e21 or 5e20.
3. Than using the nlread setting from python

I posted the python file that I mentioned above.
Would it be better if I can arranged the code like that?

Thank you.

27

General Questions and Answers / Re: Grain Boundary Scattering doping problem

« on: September 21, 2024, 08:55 »

Thank you for your help!!

I posted the py file of 5e20 and 1e21 doping polycrystal structure!!

I hope this will help to solve the problem!!

28

General Questions and Answers / Re: Grain Boundary Scattering doping problem

« on: September 20, 2024, 05:05 »

I think there is some error occurred while uploading hdf5 file. So I uploaded log files first.

For hdf5 file, I uploaded the files as py output files.

The file attached in this reply is hdf5 files

Thank you

29

General Questions and Answers / Re: Grain Boundary Scattering doping problem

« on: September 20, 2024, 05:00 »

Thank you for the tips!

I am sending the log and hdf5 file for 5e20, and 1e21 doping respectively. You can see the doping concentration in the title of the file.
I used GGA.PBE at 5e20 and MGGA.R2SCAN at 1e21.

I will also try to find some ways to solve the issue.

Thank you

30

General Questions and Answers / Re: Grain Boundary Scattering doping problem

« on: September 2, 2024, 15:23 »

Thank you for your reply.
For more doping for the Silicon however, 1e21 didn't work as well. From the band structure of the silicon at 5e20 doping, conduction bands go 0.145 eV below fermi energy level, which can make transmission spectrum. These doping (1e20, 5e20, 1e21) transmission spectrum went well with bulk silicon(not poly-silicon), but didn't meet the expectation at grain boundary scattering.

Should I just adjust the energy point at transmission parameter in grain boundary scattering instead of doping?
Since doping changes the fermi level in bandgap, I assume that adjusting fermi energy level point in transmission parameter would make similar results.

And another thing is that the calculation keeps show that it does not support HSE06 for grain boundary scattering.
I am posting a error code below.

File "zipdir/SentaurusMaterialsWorkbench/GrainBoundaryScattering/GrainBoundaryScattering.py", line 488, in __init__
                                ^^^^^^^^^^^^^^^^^^^^^^^^
  File "zipdir/SentaurusMaterialsWorkbench/GrainBoundaryScattering/GrainBoundaryScattering.py", line 488, in __init__
NL.ComputerScienceUtilities.Exceptions.NLValueError: GrainBoundaryScattering is not supported for HSE06.
NL.ComputerScienceUtilities.Exceptions.NLValueError: GrainBoundaryScattering is not supported for HSE06.
NL.ComputerScienceUtilities.Exceptions.NLValueError: GrainBoundaryScattering is not supported for HSE06.
                                ^^^^^^^^^^^^^^^^^^^^^^^^
Thank you!