Topics

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 / 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

4

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

5

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

6

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?

7

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?

8

General Questions and Answers / Grain Boundary Scattering doping problem

« on: August 18, 2024, 15:30 »

Hi all

I am trying to calculate Silicon grain boundary resistivity through grain boundary generator and grain boundary scattering with doping(5e20) included.

My grain boundary scattering settings are E0=0eV, E1=0eV, point : 1 / K-point density : 7 Angstrom

When calculating Silicon structure with transmission spectrum with E0=0eV, E1=0eV, point : 1, with 5e20 doping, it showed transmission area.

However, boundary scattering transmission did not show transmission area, resulting grain boundary resistivity to infinite.

I want to see the 5e20 doping grain boundary resistivity when E=0eV.  How can I solve this problem?

Thank you

The attached file is the py file with grain boundary scattering

9

General Questions and Answers / p-type, n-type doping, transmission

« on: July 8, 2024, 03:58 »

Hello, I am trying to dope amorphous silicon bulk structure with n, p-type and then try to calculate transmission spectrum, the results shows same.
I calculated same structure and just changed the type of doping.
I attached the py file that I used.

The only difference I made is n and p type doping
external_potential = AtomicCompensationCharge([
    ('doping_0', 2.0207760480856165e-07)
    ]) for n-type and

external_potential = AtomicCompensationCharge([
    ('doping_0', - 2.0207760480856165e-07)
    ]) for p-type

The transmission results appear same, so I attached only 1 figure.
So I was wondering if the results can show same results even if the doping is different

Thank you

10

General Questions and Answers / Radial distribution

« on: June 12, 2024, 06:52 »

I am trying to make radial distribution graph from the quantumatk option :

https://docs.quantumatk.com/manual/Types/RadialDistribution/RadialDistribution.html#radialdistribution-c

When I tried to make graph with the python file example above the link, the calculation was finished but nothing appeared.

How can I solve this problem? Here's the code that I made based on the example link.

Thank you!!

md_trajectory = nlread('216csi_TFMC_1.hdf5')[-1]

rdf = RadialDistribution(md_trajectory,
                         cutoff_radius=3.0*Angstrom,
                         pair_selection=[Silicon, Silicon])

# Get the bin_centers and the histogram of the radial distribution.
distances = rdf.distances().inUnitsOf(Angstrom)
histogram = rdf.data()

# Plot the data using pylab.
import pylab

pylab.plot(distances, histogram, label='Si RDF')
pylab.xlabel('r (Ang)')
pylab.ylabel('g(r)')
pylab.legend()

pylab.show()

11

General Questions and Answers / Questions about MD reservoir temperature and its analysis

« on: June 12, 2024, 06:33 »

Hello.

I am currently simulating amorphous structure of silicon using MD, and also have some questions regarding reservoir temperature.

1. What is exactly reservoir temperature? Can it be understood as starting point?

2. When melting the silicon, is it the right procedure to set the reservoir temperature to 300 or to set reservoir temperature 3000 or more?

3. When checking MD trajectory, the some part of temperature and reservoir temperature are not aligned. For example, in the graph, reservoir temperature shows 300 to 4000K line, while the temperature line only stayed at 300K. How can I interpret this part?

Thank you.

 

12

General Questions and Answers / problems with Hgga_hse06 and MGGA calculation to transmission spectrum

« on: January 17, 2024, 02:55 »

Hello, everyone

Recently I got some serious problems with calculating transmission with mgga.

I calculated transmission for Si in 110 direction by following the example on the quantumATK webpage(https://docs.quantumatk.com/tutorials/transmission_gr_mos2/transmission_gr_mos2.html#mos2).

I expected that the transmission should be 0 for the band gap.
However, I got a non-zero transmission for the energy in the band gap as seen in the attached Transmission vs. Energy plot.
I also calculated the band structure which is also attached in this post. And I could see the band structure calculation shows a clear band gap.
I attached the code that I used.

Please take a look and give me any advices to solve this problem.

Thank you

13

General Questions and Answers / Questions about nlread

« on: January 1, 2024, 05:17 »

Hello, and happy new year everyone.

Recently, I had a Deviceconfiguration that successfully converged with PLDOS. It took more than 10 hours

I wanted to reuse it with transmission spectrum, but since it consumed a lot of time, I was planning to redo it with 'nlread function'.

Here is my code

# DeviceConfiguration
Device_configuration = nlread('Si80_111_5e19_4040.hdf5',DeviceConfiguration_0)[0]

#Choose the first configuration in the list
Device_configuration = Device_configuration_list[0]

# %% Set Calculator

Device_configuration.setCalculator(calculator)

Device_configuration.update()

nlsave('Si80_111_5e19_5050trans.hdf5', Device_configuration)

# %% TransmissionSpectrum

kpoints = MonkhorstPackGrid(
    na=50,
    nb=50,
    nc=1,
    symmetries=[
        ([[ 1., 0., 0.],
          [ 0., 1., 0.],
          [ 0., 0., 1.]], [ 0., 0., 0.]),
        ([[-1., 0., 0.],
          [ 0.,-1., 0.],
          [ 0., 0.,-1.]], [ 0., 0., 0.]),
    ],
    force_timereversal=True,
    k_point_shift=None,
    shift_to_gamma=[True, True, True]
)

self_energy_calculator = RecursionSelfEnergy(
    storage_strategy=NoStorage()
)

device_transmission_method = GreensFunction(
    processes_per_contour_point=1,
    )

transmission_spectrum = TransmissionSpectrum(
    configuration=Device_configuration,
    energies=numpy.linspace(0.0, 0.0, 1)*eV,
    kpoints=kpoints,
    kpoints_weights=None,
    self_energy_calculator=self_energy_calculator,
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    device_transmission_method=device_transmission_method,
    enforce_zero_in_band_gap=True
)
nlsave('Si80_111_5e19_5050trans.hdf5', transmission_spectrum)

However when I ran the calculation nothing appeared on the log file, and the calculation did not run.

Could somebody please help me with how to use 'nlread' properly?

Thank you.

14

General Questions and Answers / mpirun hostfile rank allocate error

« on: December 11, 2023, 03:20 »

Dear Expert
Hello, I am currently having some problems when running mpi.

My hostfile is dirac1, dirac2... dirac8 and each one contains max. 20 mpi nodes.

I named each hostfile as dirac1=hf1, dirac2=hf2, dirac3+dirac4=hf34

I works well when I run just one hostfile, the calculation runs properly.

However, when the I run hostfiles more than 2 (for example, hf34=dirac3 and 4) the log file only shows blank space, although the terminal, shows that the process is working properly.

Also while allocating mpi, I make hostfile through terminal

vi hf34
dirac3:15
dirac4:15
:wq

and when I run the calculation
mpirun -n hf34 -p 30 home/edrl_04/Desktop/quantum23ver/quantumatk/V-2023.09/bin/atkpython opt_device_conf_110_5e20.py > opt_device_conf_110_5e20.log &

the process allocate as dirac3:20 and dirac4:10 although I already set their process as 15 each. And the log file shows nothing.

I am using 23.9 version of quantum atk and my intel mpi verison is 21.10 version

Is there anything that I can do to fix this 2 major problems?
Thank you for reading the questions.

15

General Questions and Answers / Device calculation error at 2022.12-U-atk

« on: November 8, 2023, 02:51 »

Hello, my name is changmin Lim and I am currently using Quantum-atk 2022.12-U version

Recently when I was calculating device I ran into unknown error.

Traceback (most recent call last):
  File "zipdir/NL/GUI/Tools/Data/DataCatalogWidget.py", line 793, in _onDoubleClicked
  File "zipdir/NL/GUI/Tools/Data/DataCatalogWidget.py", line 896, in open
  File "zipdir/NL/GUI/Tools/Data/DataCatalogWidget.py", line 896, in <listcomp>
  File "zipdir/NL/GUI/Tools/Data/ToolAnalysisPlugins.py", line 214, in createWidget
  File "zipdir/NL/GUI/Tools/Tool.py", line 960, in dropEvent
  File "zipdir/NL/GUI/DnD/DropExtractor.py", line 618, in extract
  File "zipdir/NL/GUI/DnD/DropExtractor.py", line 248, in mimeDataTextsFromInstances
  File "zipdir/NL/IO/NLPrint.py", line 70, in nlprint
  File "zipdir/NL/Study/Study.py", line 939, in nlprint
  File "zipdir/NL/Study/OptimizeDeviceConfiguration.py", line 514, in _nlprint
  File "zipdir/NL/Study/OptimizeDeviceConfiguration.py", line 463, in result
  File "zipdir/NL/Study/Study.py", line 620, in _results
  File "zipdir/NL/Study/Study.py", line 587, in _tasks
  File "zipdir/NL/Study/Study.py", line 510, in _workflow
NL.ComputerScienceUtilities.Exceptions.NLValueError: The study object workflow not available on a lightweight instance. To access the workflow read the study object as a heavyweight instance.


I tried to search heavyweight and lightweight on qna, but nothing was found.

also, I tried to find txt files that showed on error, but I could not find the error line as well.

Can anyone help me with this error?
Thank you