Topics

1

General Questions and Answers / LCAO basis set used for initialisation and projection in PlaneWave caclulator

« on: August 9, 2020, 03:12 »

I am using plane wave calculator for optimising my structure but in Pseudopotential->Basis Set in the plane wave calculator it is showing  "The LCAO basis set is used for initialization and projection". Why is it so, shouldn't it be plane wave basis set instead? I have attached a screenshot for the same.

2

General Questions and Answers / Adding DFT-D2 in planewave calculators

« on: August 9, 2020, 01:36 »

Hello I want to use incorporate van-der-waals correction (grimme-dft d2) in my gas adsorption studies by that option isn't coming when I am using planewave calculator. I have attached screenshot of the calculators. It is showing in case of using LCAO calculators.

3

General Questions and Answers / Periodic Boundary Conditions

« on: July 25, 2020, 08:53 »

I am working on a 2D material. How do I incorporate the periodic boundary conditions when trying to relax the structure and perform other caclulations? I saw in one of the tabs for Poisson Solver that there was written periodic boundary conditions as shown in picture 1 and picture 2.
When changing the solver type to FFT I could not modify anything in the dropdowns for Boundary Condition and when selecting conjugate gradient I am only getting Dirichlet and Periodic options.
So I want to ask
1. How to select periodic boundary conditions?
2. To prevent periodic interaction between repeating layers in c-direction we add a vacuum spacing so, instead of that could we use a different boundary condition which might help us to decrease the vacuum spacing and save us some time computationally?

4

General Questions and Answers / Trouble with density mesh cutoff

« on: July 24, 2020, 23:10 »

In this paper, the Dol3 package with the density functional theory (DFT) was used to calculate the energy parameters and the electronic properties of the simulation models. Moreover, the Perdew-Burke-Ernzerhof (PBE) functional was selected to treat the exchange correla-tion energy [21]. The calculation accuracy of energy, force and displacement were set to 1 × 10⁻⁵ Ha, 2 × 10⁻³ Ha/Å, and 5 × 10⁻³
Ha/Å, respectively. As the default setting, the Double numerical plus polarization (DNP) was selected for further calculation. The semi-core pseudopotential (DSPP) was applied for core electrons calculation due to its relativistic effects [22–24]. The k point of the Brillouin zone integration was 5 × 5 × 1, and the self-consistent (SCF) field tolerance was set to 1 × 10⁻⁶ Ha in this study. In addition, in order to accelerate the convergence of SCF charge density, the direct inversion of iterative subspace (DIIS) size was set to 6 [25–27]. The influence of spin-polarization can be ignored in the study. A 4 × 4 × 1 MoS2 monolayer supercell was built. The vacuum distance was set to 20 Å in order to avoid the interactions between adjacent layers. The lattice parameter of MoS2 monolayer obtained by optimization calculation is 3.18 Å, which matches well with the theoretical and the experimental values (3.18 Å; 3.20 Å) obtained from the previous studies [28–30]. In addition, one Au or Ag atom bonds with three S atoms on the upper surface of MoS2 monolayer to form the doped MoS2 monolayer.

This is an excerpt from this paper https://www.sciencedirect.com/science/article/pii/S1386947719301262
(1) I am not able to understand what is the density functional value selected here.
(2) Where the force and displacement value mentioned above, do they stand for force tolerance and maximum step size?
(3) What does SCF field tolerance represents?

5

General Questions and Answers / Change in space group

« on: July 2, 2020, 04:58 »

I want to create an MoS2 monolayer (4x4x1) supercell but when I delete the extra layer after adding molybdenite the space group changes from p63/mmc to p6m2. I want to retain the p63/mmc space group. How can I do that?

6

General Questions and Answers / Modifying bands above and below fermi level for Bandstructure and DOS

« on: June 28, 2020, 21:48 »

We can modify number of bands to be selected for above fermi level using "bands_above_fermi_level" . Can use to select total number of bands to be selected for below fermi level?
I just want to select the bands near the fermi level for bandstructure calculation. I don't need the so many bands so I want to limit the total number of bands to 40. How can I do it?

7

General Questions and Answers / Comparing DOS contribution from various orbitals

« on: June 22, 2020, 22:16 »

I want to know that can we compare the contribution of various oritals to DOS. I checked that we can see the s, p, d,f contributions in DOS analyzer however if I want to differentiate between the contribution from s, p, d and f respectively. How to do that?

8

General Questions and Answers / Making a Device for MoS2

« on: March 23, 2020, 00:08 »

I am having a confusion regarding making a device using MoS2 as when I am clicking device from bulk it is showing no electron on the left electrode side.
However when I swap the axes the option for "device" is not showing either.
What change should I make?

9

General Questions and Answers / Boundary Conditions

« on: February 27, 2020, 06:48 »

Well I am trying to study a monolayer system and I want to incorporate periodicity in x and y direction which I am doing in Poisson Solver (using [Parallel] Conjugate Gradient).
However for the C direction I am getting these options - Periodic, Dirichlet, Neumann, Monopole
Which one should I select for top (C) and bottom (C), if  I do not want it to be periodic in that direction

10

General Questions and Answers / Incorporating Van der waal forces

« on: February 26, 2020, 07:31 »

Do we have to use DFT-D2 after performing geometry optimization for a particular structure or can we use it later for energy calculation?

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General Questions and Answers / Performing physisorption

« on: February 26, 2020, 07:27 »

Is there a way to differently perform or distinguish whether a particular adsorption is physisorption or chemisorption?

12

General Questions and Answers / Problem in brillouin zone viewer

« on: February 19, 2020, 05:42 »

Here in quantum atk I found that there are no K or M points for selecting a high symmetry brillouin zone route for sampling bandstructure whereas in literature it is usually reported that direct band gap for MoS2 is found at K-point.
So are the naming of the points been changed in quantum atk?
I have attached the image for brillouin zone of mos2 as seen in quantum atk brillouin zone viewer.

13

General Questions and Answers / Error in device formation using bulk

« on: February 11, 2020, 10:13 »

I was trying to make a device however I got this error. I am unable to understand what went wrong because it is working fine with other structures.

Traceback (most recent call last):
  File "zipdir\NL\GUI\Plugin\PanelBar\PanelView.py", line 256, in itemClicked
  File "zipdir\NL\GUI\Tools\Builder\PanelBar.py", line 52, in widget
  File "C:\Program Files\QuantumATK\QuantumATK-Q-2019.12\Lib\site-packages\AddOns\DevicePackage\CreateDeviceFromBulkPlugin.py", line 55, in widget
    self._widget = CreateDeviceFromBulkWidget(configuration, stash=self.stash(), device_type=DeviceConfiguration)
  File "C:\Program Files\QuantumATK\QuantumATK-Q-2019.12\Lib\site-packages\AddOns\DevicePackage\CreateDeviceFromBulkWidget.py", line 60, in __init__
    self._control = CreateDeviceFromBulkControlWidget(bulk_configuration, device_type)
  File "C:\Program Files\QuantumATK\QuantumATK-Q-2019.12\Lib\site-packages\AddOns\DevicePackage\CreateDeviceFromBulkWidget.py", line 150, in __init__
    self.setCentralRegion(bulk_configuration)
  File "C:\Program Files\QuantumATK\QuantumATK-Q-2019.12\Lib\site-packages\AddOns\DevicePackage\CreateDeviceFromBulkWidget.py", line 245, in setCentralRegion
    enable_transverse_electrode_repetitions=self.useTransverse(),
  File "zipdir\NL\CommonConcepts\Configurations\DeviceFromBulk.py", line 882, in deviceFromBulk
NL.ComputerScienceUtilities.Exceptions.NLValueError: The sum of the lengths of the electrodes may not exceed the length of the central region.

14

General Questions and Answers / Convergence of simulation

« on: February 4, 2020, 06:47 »

1. Is there some way to understand whether running a particular script will lead to convergence without first running the geometry optimization.

2. How to do a convergence analysis to understand best which parameter set will be best suited for faster convergence.

3. Could you suggest some resource and ways to speed up a simulation (links to related articles will be helpful in understanding them in detail)

15

General Questions and Answers / Bader Charge Analysis

« on: January 3, 2020, 09:22 »

Is there a tutorial on bader charge analysis? Which block should I select in the analysis in scripter to  implement it in quantum atk?