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41
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.
42
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.
43
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!
44
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!

45
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
46
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)

47
Plugin Development / Re: Add-on Controller Not Working
« Last post by Habib on October 26, 2024, 10:16 »
I saw this post and tried, but it didn’t work. Strangely, this add-on is already installed (see the screenshot), but I cannot update it, and it doesn’t appear in the builder. Are there any alternative solutions?
48
General Questions and Answers / Re: configuration for Training set created by random displacement parameters
« Last post by Anders Blom on October 26, 2024, 00:54 »
The algorithm is complex, but these numbers are not going to be exactly obeyed, more of a guidance to the size you want. The are many different combinations of cell distortions and moving atoms going on in the internal machinery to get as good sampling as possible.
49
Plugin Development / Re: Add-on Controller Not Working
« Last post by Anders Blom on October 26, 2024, 00:39 »
Such old versions are not supported anymore. There is another thread on the Forum which the plugin is attached as a standalone zip file
https://forum.quantumatk.com/index.php?topic=12074
Tip: search from the main page of the Forum, you would easily have found this, but when you search on a message page, the results are limited for some reason. Oh and you needed to search for "TubeWrapper", not "Tube Wrapper"
50
Plugin Development / Add-on Controller Not Working
« Last post by Habib on October 25, 2024, 13:42 »
Hi there,

I am using QuantumATK Version Q-2019.12 and was trying to update the add-ons, but I got the following error. I also tried to install just the Tube Wrapper, but received the same error. I checked the forum for similar issues but didn't find a relevant answer.

Here is the error message:

Unable to obtain a list of available add-ons.
Something went wrong in accessing the list of available packages on the repository server. Please check your network connectivity or try again later.

Kind Regards
Habib
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