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31
General Questions and Answers / Re: Band Structure
« Last post by Anders Blom on October 31, 2024, 20:23 »
You can always extract the eigenvalues and k-points using the evaluate() and kpoints() methods on the band structure object (see https://docs.quantumatk.com/manual/Types/Bandstructure/Bandstructure.html), but recreating the plot with correct horizontal axis etc is quite complex, esp. when you have a non-trivial path in the Brillouin zone.
32
General Questions and Answers / Re: How to build a MTJ device with different oxide 'stack'?
« Last post by prayash on October 31, 2024, 19:31 »
Quote from: bikash on April  6, 2017, 09:17
I wish to build a MTJ device for certain simulation and tried using the existing plugin of Fe-MgO but I couldn't build one with a different oxide 'stack' as only single oxide layer was possible. How do I replace the oxide with a oxide 'stack' of different combination.
Hi, I am creating a multilayer stack (CoMgOFeMnCo) using the interface plugin. I need to do the electron transport calculation of this device. However, to create an electrode I need to cleave the surface. When I cleave the surface in 100 miller index, the electrodes are applied in the X direction, but I need it in Z. If I cleave the surface in 001 miller index, the surface is cleaved correctly, but I cannot put anything in the electrode box, and no electrode is generated.
Is there anything I can do to solve this problem?
Sorry if the question is dumb, I am new in this field.
33
General Questions and Answers / Re: Job suddenly stop and Segmentation fault
« Last post by dmicje12 on October 31, 2024, 05:06 »
OK
I would try lowering the MPI
Thanks for the reply!

 
34
General Questions and Answers / Re: Band Structure
« Last post by Jahanzaib on October 31, 2024, 00:53 »
Thank you so much. Is there a way to extract BS using python code?
35
General Questions and Answers / Re: Band Structure
« Last post by Anders Blom on October 30, 2024, 21:26 »
The easiest way to plot bands and DOS next to each other is in the GUI. You can drag and drop one of the plots onto the other to combine them.
36
General Questions and Answers / Re: Job suddenly stop and Segmentation fault
« Last post by Anders Blom on October 30, 2024, 20:20 »
Hard to say without any input script. Also, if you run very many parallel processes on the same node, you can still use quite a lot of memory. In 95% of all cases, this error means out of memory.
37
General Questions and Answers / Band Structure
« Last post by Jahanzaib on October 30, 2024, 15:41 »
Dear Expert,

I have attached my band structure plot, and I would like to recreate this plot using "atkpython." Is there a way to extract the necessary information using a script?

Additionally, I already have a script for the density of states of the same system, and I was wondering if it would be possible to plot both BS and DOS side by side.

Thank you!
38
General Questions and Answers / Job suddenly stop and Segmentation fault
« Last post by dmicje12 on October 30, 2024, 09:55 »
Hi everyone,
My JOB has encountered Segmentation fault frequently recently.
I'm pretty sure there is enough ram during the calculation,
When doing SCF operation, the first few steps can be calculated stably, but it will stop when calculating the Calculating Density Matrix at a certain step.
The log file look like this at the end:
+------------------------------------------------------------------------------+
| Total Density Report                    DM           DD           dQ         |
+------------------------------------------------------------------------------+
| Left Electrode Extension            64.85281    -25.14719    -25.14719       |
| Right Electrode Extension           64.42974    -25.57026    -25.57026       |
| Central Region                    1532.77422    -33.22578    -33.22578       |
+------------------------------------------------------------------------------+
|  15 E = -509.293 dE =  2.042577e+00 dH =  4.867394e-01                       |
+------------------------------------------------------------------------------+

                            |--------------------------------------------------|
Calculating Density Matrix : ===========================

mobaxterm will display:
===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 58 PID 27109 RUNNING AT 512.lab.nycu.edu.tw
=   KILLED BY SIGNAL: 9 (Killed)
===================================================================================

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 59 PID 27123 RUNNING AT 512.lab.nycu.edu.tw
=   KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================
My ATK version is 2023.12-sp1 and operating system is CentOS 8
I only calculate the system of 240 atoms-noncollinear-FHI-DZP basis
I want to know how to solve the problem, or why the problem occurs.
Thanks!

39
General Questions and Answers / Simulate edge behavior of 2D MoS2 flake
« Last post by cam on October 30, 2024, 08:08 »
Dear all,

I am studying the effect of passivation and functionalisation of 2D MoS2. Since this mainly occurs at the edge sites (due to the greater presence of dangling bonds), I would like to terminate the material in the basal plane direction and introduce my functional groups. I initially wanted to add vacuum in the A/B direction. However, I am running into issues due to the distortion of the unit cell (no longer hexagonal, which distorts the Brillouin zone).

Would anyone have any suggestions? I found reports in literature, but I don't know whether this is feasible using Quantum ATK. Any help would be appreciated!

Kindly
40
General Questions and Answers / Difference in bulk properties for repeated cell
« Last post by cam on October 30, 2024, 07:33 »
Dear all,

I am trying to perform DFT calculation on MoS2 to study the effects of passivation, defects, number of layer, etc on the material properties. For this, I used the molybdenite unit cell from the database.

To introduce vacancies in my lattice, I repeated the unit cell 2 times in A and B. Before introducing defects, I ran a control simulation which consisted of the cell repeated twice in A and B under the same parameters (hGGA, PseudoDojo (medium)) (to preserve the hexagonal lattice structure). However, I obtain different band structures for these two input files with different bandgap values. Would anyone be able to advise me on how to minimise this variation?



Otherwise, I am using the 2021 version. How do I adjust the percentage of vacancies without changing the number of repeated unit cells?
Code
# -*- coding: utf-8 -*-
# -------------------------------------------------------------
# Bulk Configuration
# -------------------------------------------------------------
 
# Set up lattice
lattice = Hexagonal(3.1604*Angstrom, 12.295*Angstrom)
 
# Define elements
elements = [Molybdenum, Molybdenum, Sulfur, Sulfur, Sulfur, Sulfur]
 
# Define coordinates
fractional_coordinates = [[ 0.333333333333,  0.666666666667,  0.25          ],
                          [ 0.666666666667,  0.333333333333,  0.75          ],
                          [ 0.333333333333,  0.666666666667,  0.621         ],
                          [ 0.666666666667,  0.333333333333,  0.121         ],
                          [ 0.333333333333,  0.666666666667,  0.879         ],
                          [ 0.666666666667,  0.333333333333,  0.379         ]]
 
# Set up configuration
bulk_configuration = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )
 
# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = HybridGGA.HSE06
 
k_point_sampling = KpointDensity(
    density_a=4.0*Angstrom,
    )
numerical_accuracy_parameters = NumericalAccuracyParameters(
    density_mesh_cutoff=55.0*Hartree,
    k_point_sampling=k_point_sampling,
    occupation_method=FermiDirac(300.0*Kelvin*boltzmann_constant),
    )
 
calculator = LCAOCalculator(
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=numerical_accuracy_parameters,
    )
 
bulk_configuration.setCalculator(calculator)
nlprint(bulk_configuration)
bulk_configuration.update()
nlsave('Molybdenite.hdf5', bulk_configuration)
 
# -------------------------------------------------------------
# Bandstructure
# -------------------------------------------------------------
bandstructure = Bandstructure(
    configuration=bulk_configuration,
    route=['G', 'M', 'L', 'A', 'G', 'K', 'H', 'A'],
    points_per_segment=20,
    bands_above_fermi_level=All,
    method=Full,
    )
nlsave('Molybdenite.hdf5', bandstructure)


Repeated band:
Code
# -*- coding: utf-8 -*-
# -------------------------------------------------------------
# Bulk Configuration
# -------------------------------------------------------------
 
# Set up lattice
lattice = Hexagonal(6.3208*Angstrom, 12.295*Angstrom)
 
# Define elements
elements = [Molybdenum, Molybdenum, Molybdenum, Molybdenum, Molybdenum,
            Molybdenum, Molybdenum, Molybdenum, Sulfur, Sulfur, Sulfur, Sulfur,
            Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Sulfur, Sulfur,
            Sulfur, Sulfur, Sulfur, Sulfur]
 
# Define coordinates
fractional_coordinates = [[ 0.166666666667,  0.333333333333,  0.25          ],
                          [ 0.166666666667,  0.833333333333,  0.25          ],
                          [ 0.666666666667,  0.333333333333,  0.25          ],
                          [ 0.666666666667,  0.833333333333,  0.25          ],
                          [ 0.333333333333,  0.166666666667,  0.75          ],
                          [ 0.333333333333,  0.666666666667,  0.75          ],
                          [ 0.833333333333,  0.166666666667,  0.75          ],
                          [ 0.833333333333,  0.666666666667,  0.75          ],
                          [ 0.166666666667,  0.333333333333,  0.621         ],
                          [ 0.166666666667,  0.833333333333,  0.621         ],
                          [ 0.666666666667,  0.333333333333,  0.621         ],
                          [ 0.666666666667,  0.833333333333,  0.621         ],
                          [ 0.333333333333,  0.166666666667,  0.121         ],
                          [ 0.333333333333,  0.666666666667,  0.121         ],
                          [ 0.833333333333,  0.166666666667,  0.121         ],
                          [ 0.833333333333,  0.666666666667,  0.121         ],
                          [ 0.166666666667,  0.333333333333,  0.879         ],
                          [ 0.166666666667,  0.833333333333,  0.879         ],
                          [ 0.666666666667,  0.333333333333,  0.879         ],
                          [ 0.666666666667,  0.833333333333,  0.879         ],
                          [ 0.333333333333,  0.166666666667,  0.379         ],
                          [ 0.333333333333,  0.666666666667,  0.379         ],
                          [ 0.833333333333,  0.166666666667,  0.379         ],
                          [ 0.833333333333,  0.666666666667,  0.379         ]]
 
# Set up configuration
bulk_configuration = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )
 
# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = HybridGGA.HSE06
 
k_point_sampling = KpointDensity(
    density_a=4.0*Angstrom,
    )
numerical_accuracy_parameters = NumericalAccuracyParameters(
    density_mesh_cutoff=55.0*Hartree,
    k_point_sampling=k_point_sampling,
    occupation_method=FermiDirac(300.0*Kelvin*boltzmann_constant),
    )
 
calculator = LCAOCalculator(
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=numerical_accuracy_parameters,
    )
 
bulk_configuration.setCalculator(calculator)
nlprint(bulk_configuration)
bulk_configuration.update()
nlsave('MoS2_bulk_control.hdf5', bulk_configuration)
 
# -------------------------------------------------------------
# Bandstructure
# -------------------------------------------------------------
bandstructure = Bandstructure(
    configuration=bulk_configuration,
    route=['G', 'M', 'L', 'A', 'G', 'K', 'H', 'A'],
    points_per_segment=20,
    bands_above_fermi_level=All,
    method=Full,
    )
nlsave('MoS2_bulk_control.hdf5', bandstructure)

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