16
General Questions and Answers / Re: STM image replication
« on: June 26, 2025, 11:12 »
Thanks for the message. But it is not working. May be have to replicate the image manually
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17
General Questions and Answers / Optimization setup check according to a previous study
« on: June 25, 2025, 10:05 »
Dear All, I'm trying to do a geometry optimization of this perovskite. I found a similar relevant settings which describe there system
Previous study
The DFT calculations were performed using the Fireball package. All geometry optimizations and electronic structure analyses were performed using the BLYP exchange-correlation functional with D3 corrections and norm-conserving pseudopotentials with a basis set of optimized numerical atomic-like orbitals. Systems were allowed to relax until the remaining atomic forces reached below 5 × 10−2 eV Å−1. a 2 × 2 unit cell containing 300 atoms. The Brillouin reciprocal zone was sampled by a Monkhorst-Pack grid of 5 × 5 × 1 for the 2 × 2 slab.
Based on above details I have set up the system.
I am using GGA-BLYP functional and Grimme D3 dispersion corrections. A norm-conserving LCAO basis set (analogous to those in PseudoDojo) is used with a 600 eV density mesh cutoff. Occupations were modeled using Fermi–Dirac smearing at 300 K. Brillouin zone integration is performed with a 5×5×1 Monkhorst-Pack grid.
My question is I have selected Norm conserving Pseudo Dojo potential. Is it a good choice ? Do I have to switch to SG15 or FHI. This is a semiconducting material (so I selected Fermi Dirac smearing 300K) with a band gap of 1.5-1.9 eV. Please advice. Thanks
Previous study
The DFT calculations were performed using the Fireball package. All geometry optimizations and electronic structure analyses were performed using the BLYP exchange-correlation functional with D3 corrections and norm-conserving pseudopotentials with a basis set of optimized numerical atomic-like orbitals. Systems were allowed to relax until the remaining atomic forces reached below 5 × 10−2 eV Å−1. a 2 × 2 unit cell containing 300 atoms. The Brillouin reciprocal zone was sampled by a Monkhorst-Pack grid of 5 × 5 × 1 for the 2 × 2 slab.
Based on above details I have set up the system.
I am using GGA-BLYP functional and Grimme D3 dispersion corrections. A norm-conserving LCAO basis set (analogous to those in PseudoDojo) is used with a 600 eV density mesh cutoff. Occupations were modeled using Fermi–Dirac smearing at 300 K. Brillouin zone integration is performed with a 5×5×1 Monkhorst-Pack grid.
My question is I have selected Norm conserving Pseudo Dojo potential. Is it a good choice ? Do I have to switch to SG15 or FHI. This is a semiconducting material (so I selected Fermi Dirac smearing 300K) with a band gap of 1.5-1.9 eV. Please advice. Thanks
18
General Questions and Answers / Re: Making perovskite unit cell for geom optimization using surface cleavage tool
« on: June 25, 2025, 08:56 »
I have attached the snapshot of the unit cell with out replicating in C direction and do surface cleavage. So some of the H atoms are gone in the structure.
19
General Questions and Answers / Making perovskite unit cell for geom optimization using surface cleavage tool
« on: June 25, 2025, 08:44 »
Dear All,
Please advice whether this procedure is correct to make unit cell for the geometry optimization.
To prepare the perovskite slab model for geometry optimization in vacuum, I followed a systematic approach using the Surface Cleavage Tool to ensure structural integrity, particularly for the organic component:
Initial Structure:
I started with the experimental bulk crystal structure of the organic–inorganic hybrid perovskite.
Replication:
To avoid the issue of missing surface atoms (especially hydrogen), I first replicated the bulk structure along the c-axis. This ensured a complete molecular unit at the cleaved surface.
Surface Cleavage:
Using the Surface Cleave tool, I created a (001) surface from the replicated structure. This orientation was selected to expose the desired perovskite layer.
Vacuum Addition:
After cleavage, I introduced vacuum spacing on both the top and bottom of the slab to simulate a freestanding perovskite monolayer and eliminate interactions between periodic images.
Layer Isolation:
Finally, I manually removed the excess layers, retaining only a single perovskite unit within the slab. This step ensured that the system represents an isolated slab in vacuum.
⚠️ Note: Direct application of the surface cleavage tool without prior replication caused incomplete surface termination, particularly resulting in missing hydrogen atoms in the organic component. Replication prior to cleavage was therefore essential to obtain a physically realistic and chemically complete slab.
Please advice whether this procedure is correct to make unit cell for the geometry optimization.
To prepare the perovskite slab model for geometry optimization in vacuum, I followed a systematic approach using the Surface Cleavage Tool to ensure structural integrity, particularly for the organic component:
Initial Structure:
I started with the experimental bulk crystal structure of the organic–inorganic hybrid perovskite.
Replication:
To avoid the issue of missing surface atoms (especially hydrogen), I first replicated the bulk structure along the c-axis. This ensured a complete molecular unit at the cleaved surface.
Surface Cleavage:
Using the Surface Cleave tool, I created a (001) surface from the replicated structure. This orientation was selected to expose the desired perovskite layer.
Vacuum Addition:
After cleavage, I introduced vacuum spacing on both the top and bottom of the slab to simulate a freestanding perovskite monolayer and eliminate interactions between periodic images.
Layer Isolation:
Finally, I manually removed the excess layers, retaining only a single perovskite unit within the slab. This step ensured that the system represents an isolated slab in vacuum.
⚠️ Note: Direct application of the surface cleavage tool without prior replication caused incomplete surface termination, particularly resulting in missing hydrogen atoms in the organic component. Replication prior to cleavage was therefore essential to obtain a physically realistic and chemically complete slab.
20
General Questions and Answers / Re: Request for Feedback on Spin Transport System Setup
« on: June 25, 2025, 08:28 »
Thank you for the detailed explanation. So I guess here the perovskite also I should start with the Bulk optimization right?
21
General Questions and Answers / Re: Request for Feedback on Spin Transport System Setup
« on: June 23, 2025, 08:51 »
hi, Thank you very much and now I understand what you meant. I think I misunderstood the procedure. Now I'm in the process of optimizing the Ni (111) and Au (111) separately. I will optimize the perovskite as well before making the electrode structures. In this optimization procedure i have not select the cell length optimization. Please see the attached script. Please correct me if that is wrong.
Thanks
GN
Thanks
GN
22
General Questions and Answers / Re: Request for Feedback on Spin Transport System Setup
« on: June 23, 2025, 07:14 »
Hi,
Thank you very much for your comments.
I will first do the optimization of the electrodes before making the system using interface builder. I have a concern on adding vacuum on z direction. I made this system following https://docs.quantumatk.com/tutorials/fe_mgo_fe/fe_mgo_fe.html tutorial. However they have not included a vacuum slab. Please explain this to me.
Thanks
GN
Thank you very much for your comments.
I will first do the optimization of the electrodes before making the system using interface builder. I have a concern on adding vacuum on z direction. I made this system following https://docs.quantumatk.com/tutorials/fe_mgo_fe/fe_mgo_fe.html tutorial. However they have not included a vacuum slab. Please explain this to me.
Thanks
GN
23
General Questions and Answers / Request for Feedback on Spin Transport System Setup
« on: June 20, 2025, 09:40 »
Dear All,
I am currently setting up a system to study spin transport using an organic-inorganic perovskite structure. The electrodes I am using are Ni (for spin injection) and Au.
After reviewing some relevant tutorials and incorporating suggestions from earlier discussions, I have outlined the following proposed steps for the study:
Optimize the device configuration
Extend the electrode lengths as needed
Perform the spin transport calculation
I have already prepared the geometry optimization script for the initial step. As a preliminary test (Test 1), I have assigned spin polarization as follows: Ni with spin-up, and perovskite and Au with zero spin, based on discussions with our experimental collaborators.
I would appreciate it if someone could kindly review my parameter selections and let me know if they are appropriate for this system.
Thank you very much for your support.
Best regards,
GN
I am currently setting up a system to study spin transport using an organic-inorganic perovskite structure. The electrodes I am using are Ni (for spin injection) and Au.
After reviewing some relevant tutorials and incorporating suggestions from earlier discussions, I have outlined the following proposed steps for the study:
Optimize the device configuration
Extend the electrode lengths as needed
Perform the spin transport calculation
I have already prepared the geometry optimization script for the initial step. As a preliminary test (Test 1), I have assigned spin polarization as follows: Ni with spin-up, and perovskite and Au with zero spin, based on discussions with our experimental collaborators.
I would appreciate it if someone could kindly review my parameter selections and let me know if they are appropriate for this system.
Thank you very much for your support.
Best regards,
GN
24
General Questions and Answers / Re: Setting up the system for a Spin transport study
« on: June 20, 2025, 07:03 »
Thank you
25
General Questions and Answers / Re: Setting up the system for a Spin transport study
« on: June 7, 2025, 10:58 »
how long electrode length should someone use? In generally .... Thanks
26
Scripts, Tutorials and Applications / Re: Question on Transport calculations with QuantumATK
« on: June 7, 2025, 10:43 »
Thanks for the message !!!
27
General Questions and Answers / Setting up the system for a Spin transport study
« on: June 6, 2025, 09:11 »
Dear All,
I have setup a system for a Spin transport study. Perovskite is sandwiched between Ni And Au
Ni is injecting spin from the top and gold is for collecting from the bottom. I made the structure following multilayers structure and then made the device. Can someone please check this structure whether it is correctly assembled. I have attached two python scripts for the geometry
Thanks
Gayani
I have setup a system for a Spin transport study. Perovskite is sandwiched between Ni And Au
Ni is injecting spin from the top and gold is for collecting from the bottom. I made the structure following multilayers structure and then made the device. Can someone please check this structure whether it is correctly assembled. I have attached two python scripts for the geometry
Thanks
Gayani
28
General Questions and Answers / STM image replication
« on: June 5, 2025, 10:24 »
Dear All,
I got an STM image using LDOS (pls see the attachment). My question is I want to replicate this image in x and y direction.
Can someone advise me how to do this.
Thanks
GN
I got an STM image using LDOS (pls see the attachment). My question is I want to replicate this image in x and y direction.
Can someone advise me how to do this.
Thanks
GN
29
Scripts, Tutorials and Applications / Question on Transport calculations with QuantumATK
« on: June 5, 2025, 05:34 »
Dear All,
My version is W-2024.09-SP1
I want to study spin current through a Perovskite materials
As a startup I'm doing some tutorials.
https://docs.quantumatk.com/tutorials/atk_transport_calculations/atk_transport_calculations.html#atk-transport-calculations
So the defined Calculator ATK-Slator Koster cannot be found in my menu. Can you please advise me on how to proceed with this. I want to start from the very beginning since this is the first time that I'm doing this type of a calculation.
Thanks
GN
My version is W-2024.09-SP1
I want to study spin current through a Perovskite materials
As a startup I'm doing some tutorials.
https://docs.quantumatk.com/tutorials/atk_transport_calculations/atk_transport_calculations.html#atk-transport-calculations
So the defined Calculator ATK-Slator Koster cannot be found in my menu. Can you please advise me on how to proceed with this. I want to start from the very beginning since this is the first time that I'm doing this type of a calculation.
Thanks
GN
30
General Questions and Answers / AFM images
« on: June 3, 2025, 07:23 »
Dear All,
I need to obtain AFM images
1. I have seen AFM Cantilever Tip in the Builders. Can I use this?
2. Is there a tutorial or example I can refer?
Thanks
GN
I need to obtain AFM images
1. I have seen AFM Cantilever Tip in the Builders. Can I use this?
2. Is there a tutorial or example I can refer?
Thanks
GN