Messages

1

General Questions and Answers / can someone help with log file update problem?

« on: April 19, 2025, 17:22 »

Hello, I am trying to optimize some amorphous structures, but the log file would not update.
I am not sure what caused this issue.
I am attaching the log file

the log file won't update and so as hdf5 file

It just stopped at this point
+------------------------------------------------------------------------------+
| Diagonalization solver parallelization report                                |
+------------------------------------------------------------------------------+
| Total number of processes: 240                                               |
| Total number of k-points: 14                                                 |
| Processes per k-point: 18                                                    |
+------------------------------------------------------------------------------+
| Process occupation                                                           |
+------------------------------------------------------------------------------+
| Processes   0 -  17: |=====================================================| |
| Processes  18 -  35: |==========================                           | |
| Processes  36 -  53: |==========================                           | |
| Processes  54 -  71: |==========================                           | |
| Processes  72 -  89: |==========================                           | |
| Processes  90 - 107: |==========================                           | |
| Processes 108 - 125: |==========================                           | |
| Processes 126 - 143: |==========================                           | |
| Processes 144 - 161: |==========================                           | |
| Processes 162 - 179: |==========================                           | |
| Processes 180 - 197: |==========================                           | |
| Processes 198 - 215: |==========================                           | |
| Processes 216 - 233: |==========================                           | |
| Processes 234 - 239: |                                                     | |
+------------------------------------------------------------------------------+
| WARNING: Some processes are idle.                                            |
+------------------------------------------------------------------------------+
|   0 E = -840.065 dE =  1.374980e+01 dH =  1.790209e+00                       |

thank you

2

General Questions and Answers / Langevin MD simulation friction variation

« on: April 9, 2025, 07:53 »

Hello,

I'm currently performing melt-quench molecular dynamics simulations to generate amorphous structures using the Langevin thermostat. In the Langevin method, there's a friction parameter (with a default value of 0.01).

When I use the default value, the system's temperature rapidly rises to unphysically high values like 1e12 K or 1e11 K. However, when I increase the friction coefficient to 0.05 or 0.1, the temperature starts to fluctuate reasonably well around the reservoir temperature.

Still, for some structures, the temperature control is not stable enough. So I'm considering increasing the friction coefficient further to 0.15 or even 0.2.

Here are my questions:

Would increasing the friction coefficient to this extent affect the resulting amorphous structure?

From a theoretical standpoint, how much can I increase the friction coefficient before it starts to significantly affect the dynamics and structural outcomes? Is there a practical or theoretical upper limit?

Kindly waiting for the response.

3

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

« on: March 27, 2025, 15:11 »

Thank you for your response.

I am currently working on training an MTP exclusively for amorphous structures, as there is no corresponding crystalline phase.

I have some questions regarding Step 1 of the standard crystalline training protocol. For training amorphous structures, active learning requires both MTP training and a training set generation function. In this process, MTP training is typically initialized using the random displacement function applied to a crystalline structure.

My question is: Can the crystal random displacement function be used for amorphous structures as well? Or is it strictly applicable to crystalline phases?

I am asking because, in the tutorial (https://docs.quantumatk.com/tutorials/mtp_hfo2/mtp_hfo2.html), the workflow in Step 1 explicitly refers to the "bulk phase." I am a bit confused by the term "crystal" in "crystal training random displacement function" and whether it applies to amorphous systems.

I would appreciate any clarification on this.

4

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

« on: March 17, 2025, 13:44 »

Dear Anders Blom,

Thank you for your kind response.

I have successfully created the GeTe MTP and am now working on incorporating carbon atoms into the GeTe structure using the "defect training set" or "defect formation set".

However, as far as I understand, both methods seem to allow the introduction of only a single interstitial atom. I may be mistaken, but I wanted to check if there is a way to modify this feature to accommodate multiple interstitial atoms.

My goal is to introduce at least three carbon atoms into the GeTe structure. Would it be possible to modify the "Defect" feature to accommodate multiple interstitial atoms? Alternatively, would you advise modifying the atomic coordinates directly in the script?

I would greatly appreciate any guidance you could provide on this matter.

Thank you for your time and assistance.

Best regards,
Changmin

5

General Questions and Answers / Re: Can LCAO calculator srcipt be input in crystal structure prediction script?

« on: March 6, 2025, 20:24 »

Also, I have additional question

I attempted to create an MTP (Machine Learning Interatomic Potential) for GeTe that could be applied to structures with different Ge and Te ratios.

For the ML-FF (Machine Learning Force Field) crystal training, I only used GeTe structures with a 1:1 ratio, as no other compositions were available.

However, for the ML-FF amorphous training, I generated amorphous GeTe structures using Packmol with varying Ge:Te ratios, including 1:1, 1:4, and 23:77, among others.

My question is:
Since I only used 1:1 ratio GeTe for crystal training, while incorporating various Ge:Te ratios for amorphous training, can the resulting MTP still be considered reliable?

I am currently validating the MTP, and the fitted results seem reasonable(figure posted). However, I am still uncertain whether the difference in training data composition could affect the generalization and accuracy of the MTP.

Would this discrepancy impact the reliability of my potential?
Thank you

6

General Questions and Answers / Can LCAO calculator srcipt be input in crystal structure prediction script?

« on: March 6, 2025, 20:02 »

Dear all

Hello, I am trying to make MTP for Carbon-doped Ge(n)Te(m) (n,m are integers).
To start MTP, the tutorial for TiSi MTP indicate to use crystal structure first and then train amorphous.
For amorphous, We can make these structures with packmol, however for crystals, we cannot find structures with C, Te, Ge included.

Therefore I am trying to use crystal structure prediction(i.e. csp). From tutorial, it used forcefield calculator, but I want to use LCAO for more accuracy.
But LCAO requires bulk configuration defined first.
And the script in csp only show elements and the calculator script is prior to elements.
Can someone help me how to revise LCAO for csp?

Thank you

7

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:  27020@165.132.146.214:
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

8

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)?

9

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

10

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

11

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

12

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?

13

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

14

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.

15

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?