Show Posts

This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.


Messages - Habib

Pages: [1] 2
1
General Questions and Answers / Re: Why the adsorption is on substrate ?
« on: December 24, 2024, 06:31 »
Dear Khariah,

In case of just one H2O molecule (as i can see from your pictures), I suggest selecting the H2O molecule by first clicking on the O atom. Then, press the Control (Ctrl) button and click on the H (hydrogen) atoms. Once the two H atoms and the O atom of H2O are all selected, use the up or down arrow keys on your keyboard to move them accordingly. You can move them to your desired position.

Kind Regards
Habib

2
General Questions and Answers / Request for Assistance: Converting MoS2 Structure into Onion Shape
« on: December 23, 2024, 19:41 »
Dear colleagues,
I am currently working on creating an onion-shaped model of MoS2. Unfortunately, I am using an outdated version of QuantumATK (2019) that lacks the TubeWrapper addon, which cannot be installed in this version. We have requested the latest version of QuantumATK and expect to have access by late January or February 2025.
In the meantime, could anyone with the necessary expertise and time help convert the attached MoS2 structure into a spherical shape (with diameter of 12 or 15Å) and send me the file? Just a simple spherical ball of MoS2 (single layer) will be more than enough. Or any other suggestions and recommendations?

Your assistance would be greatly appreciated.
Kind Regards
Habib

3
General Questions and Answers / Re: Elastic Constants at higher Temperature
« on: November 25, 2024, 12:36 »
Hi Anders,
Yes, Thermal study is the exciting new application areas, In the current project we aim to predict a high-entropy alloy with exceptional hardness and stability at elevated temperatures. While DFT simulations at 0 K are straightforward for calculating elastic constants and hardness, but high-temperature case is challenging, especially with the limitations of available forcefields. I hope with updated QuantumATK, it might help.
However, there are many reports where they reported temperature effect either approximate or use reliable theoretical models https://iopscience.iop.org/article/10.1088/0953-8984/22/22/225404. Additionally, some open source programs like Gibbs (thermal effects within the quasi-harmonic Debye model) is also reported.

It would be fantastic if future QuantumATK updates could include:
Temperature-dependent effects in DFT.
Hardness prediction.
COHP and pCOHP analyses.

4
General Questions and Answers / Re: Elastic Constants at higher Temperature
« on: November 22, 2024, 17:46 »
Hi Anders,

Many thanks for your time.
Yes, I completely agree that the approach of selecting several MD images, calculating their average, and then comparing them is very time-consuming.
This time, I extended the model size to approximately 6 nm along the c-direction and repeated the calculations at 0 K, 300 K, 1500K, and 2000K using the same method. However, I got similar results for all different Temperatures. The scripts are attached. I think this could be due to the limitations of the forcefield. I am further increasing the size of the system to give it another try; let's see.
+------------------------------------------------------------------------------+
| Elastic Constants in GPa                                                     |
+------------------------------------------------------------------------------+
|   363.46      35.09      35.07       0.01      -0.00      -0.01              |
|              363.46      35.08       0.00      -0.02      -0.02              |
|                         363.46      -0.01      -0.01       0.01              |
|                                     50.53      -0.01      -0.01              |
|                                                50.52       0.01              |
|                                                           50.52              |
+------------------------------------------------------------------------------+

+------------------------------------------------------------------------------+
| Material properties calculated from the elastic constants:                   |
+------------------------------------------------------------------------------+
| Moduli in units of GPa:                                                      |
+------------------------------------------------------------------------------+
|                 Reuss     Voigt     Hill                                     |
+------------------------------------------------------------------------------+
| Bulk modulus:   144.5405  144.5405  144.5405                                 |
| Shear modulus:   69.8703   95.9892   82.9298                                 |
+------------------------------------------------------------------------------+
|                     X         Y         Z                                    |
| Young's modulus:   357.2838  357.2880  357.2832                              |
+------------------------------------------------------------------------------+

It seems the current forcefield calculations may not be well-suited for my system, as my system is composed of high-entropy alloys (Ti, Zr, Nb, Hf, Ta, etc).
On the other hand, simulating the dynamical matrix with DFT is very time-consuming, even for small systems. Is there any way to compute a reasonable dynamical matrix using DFT with reduced computational time?
Regarding the use of MACE or M3GNet neural network potentials, I currently don’t have access to them because I am using the 2019 version of QuantumATK. However, we have ordered the latest version through the Microelectronics Centre (STFC), although the process is taking some time. Once I gain access to the updated version, I will certainly explore these methods as well.

5
General Questions and Answers / Re: Elastic Constants at higher Temperature
« on: November 21, 2024, 22:23 »
Hi Anders,

Thanks for the corrections, but still the results are not convincing, i am trying my best let see.

I have another idea regarding the simulation of elastic constants at different temperatures using a combination of DFT and MD simulations (maybe i am completely wrong). 
How about this approach: 
1. First, optimize the model using DFT. 
2. Then, use the DFT-optimized model for MD simulations at the desired temperature (e.g., heat up to 1500 K or any Temperature) with the NPT ensemble. 
3. Finally, take the last snapshot of the MD-simulated model (at the desired temperature) and calculate the elastic constants using DFT again, without further optimization. 

6
General Questions and Answers / Re: Elastic Constants at higher Temperature
« on: November 21, 2024, 12:44 »
Hi Anders,

I followed your method and calculated the Elastic Constants of ZrC at three different temperatures (0 K, 300 K, and 1500 K) using the provided forcefield in QuantumATK (ReaxFF_CHONSiPtZrYBaTi_2013). Since these are very fast calculations, I also computed the Dynamical Matrix for all of them. However, I got similar results for all of these three temperatures.


+------------------------------------------------------------------------------+
| Elastic Constants in GPa                                                     |
+------------------------------------------------------------------------------+
|   402.38     101.43     101.43       0.00       0.00       0.00              |
|              402.38     101.43       0.00       0.00       0.00              |
|                         402.38       0.00       0.00       0.00              |
|                                    192.39       0.00       0.00              |
|                                               192.39       0.00              |
|                                                          192.39              |
+------------------------------------------------------------------------------+

The scripts of these three cases are attached. Could you please review them and let me know where I am making mistakes?

Kind regards,
Habib

7
General Questions and Answers / Re: Band Structure
« on: November 11, 2024, 15:28 »
Hi Jahanzaib,

Yes, you can change the colour by clicking on the plot editor. From there, select the bands you’re interested in and choose your preferred colour and line width. Please see the attached screenshot for reference.

I’m using QuantumATK 2019.12, but I’m confident there’s a similar option in the new version as well.
cannot help with the python code, but I use the GUI for combining BS and DOS etc.

Kind Regards
Habib

8
Plugin Development / Re: Add-on Controller Not Working
« 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?

9
Plugin Development / Add-on Controller Not Working
« 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

10
General Questions and Answers / Re: Elastic Constants at higher Temperature
« on: July 30, 2024, 19:07 »
Hi Anders,
Many thanks for the detailed response. I agree with you that it has the potential to be a good article. I will try that approach and get back to you if I encounter any serious issues.

11
General Questions and Answers / Elastic Constants at higher Temperature
« on: June 26, 2024, 14:44 »
Hi there,

I'm currently working on simulating the Elastic Constants of TiN, as attached, at various temperatures ranging from 0 K to 1500 K. DFT simulations allow us to calculate these constants only at 0 K. There are several approximations available to estimate the Elastic Constants at elevated temperatures https://doi.org/10.1016/j.tsf.2021.138872. I am using QuantumATK Q-2019.12. Could you please provide guidance, scripts, or options within QuantumATK that could assist me in simulating the Elastic Constants of crystal materials at different temperatures?

Elastic constants of TiN unit cell at 0K
+------------------------------------------------------------------------------+
| Elastic Constants in GPa                                                     |
+------------------------------------------------------------------------------+
|   523.42     136.72     136.72       0.00       0.00       0.00              |
|              523.42     136.72       0.00       0.00       0.00              |
|                         523.42       0.00       0.00       0.00              |
|                                    138.84       0.00       0.00              |
|                                               138.84       0.00              |
|                                                          138.84              |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Material properties calculated from the elastic constants:                   |
+------------------------------------------------------------------------------+
| Moduli in units of GPa:                                                      |
+------------------------------------------------------------------------------+
|                 Reuss     Voigt     Hill                                     |
+------------------------------------------------------------------------------+
| Bulk modulus:   265.6166  265.6166  265.6166                                 |
| Shear modulus:  156.4882  160.6448  158.5665                                 |
+------------------------------------------------------------------------------+
|                     X         Y         Z                                    |
| Young's modulus:   466.7859  466.7859  466.7859                              |
+------------------------------------------------------------------------------+
|                     XY        XZ         YZ                                  |
| Poisson ratios:      0.2071    0.2071    0.2071                              |
|                     YX        ZX         ZY                                  |
|                      0.2071    0.2071    0.2071                              |
+------------------------------------------------------------------------------+




12
General Questions and Answers / Re: Simulation of COHP and pCOHP
« on: January 7, 2024, 22:15 »
Hi Anders,

Thanks for your reply.
I have been attempting to simulate the five 3d orbitals of Fe in LaFeO3—namely, dxy, dxz, dyz, dx2-dy2, and dz2—through spin-polarized DFT+U simulations. I utilized PDOS with the "projections=ProjectOnOrbitalsByElement" setting, and it worked well, producing the DOS of the mentioned orbitals in one spin (refer to the attached file). However, I require both spin-up and spin-down positions. Can you help me to simulate the DOS in both spin?

13
General Questions and Answers / Re: VASP Band Structure Projection onto Specific Atomic Orbitals
« on: January 1, 2024, 22:40 »
Hi There,

I guess yes, use fat band structure simulations. Watch this very useful short video :)
 https://www.google.com/search?client=opera&q=fat+band+structure+quantumatk&sourceid=opera&ie=UTF-8&oe=UTF-8#fpstate=ive&vld=cid:92ce9bad,vid:CEVBYtZkbbM,st:0

Kind Regards
Habib

14
General Questions and Answers / Re: DOS of five d orbitals dxy, dxz, dyz, dx2-dy2, and dz2
« on: December 20, 2023, 15:49 »
Dear Admin and Colleagues,

I have been attempting to simulate the five 3d orbitals of Fe in LaFeO3—namely, dxy, dxz, dyz, dx2-dy2, and dz2—through spin-polarized DFT+U simulations. I utilized PDOS with the "projections=ProjectOnOrbitalsByElement" setting, and it worked well, producing the DOS of the mentioned orbitals in one spin (refer to the attached file). However, I require both spin-up and spin-down positions. Can you help me to simulate the DOS in both spin?

Additionally, I tried manually adding sub-orbitals for the Fe 3d orbitals in the script (as shown below), but encountered an error as the software does not recognize the azimuthal quantum number.

# Basis Set
#----------------------------------------
iron_3d_dxy = ConfinedOrbital(
    principal_quantum_number=3,
    angular_momentum=2,
    azimuthal_quantum_number=0,
    radial_cutoff_radius=7.117*Bohr,
    confinement_start_radius=5.117*Bohr,
    additional_charge=0,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
)

iron_3d_dxz = ConfinedOrbital(
    principal_quantum_number=3,
    angular_momentum=2,
    azimuthal_quantum_number=1,
    radial_cutoff_radius=7.117*Bohr,
    confinement_start_radius=5.117*Bohr,
    additional_charge=0,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
)

iron_3d_dyz = ConfinedOrbital(
    principal_quantum_number=3,
    angular_momentum=2,
    azimuthal_quantum_number=2,
    radial_cutoff_radius=7.117*Bohr,
    confinement_start_radius=5.117*Bohr,
    additional_charge=0,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
)

iron_3d_dx2_y2 = ConfinedOrbital(
    principal_quantum_number=3,
    angular_momentum=2,
    azimuthal_quantum_number=3,
    radial_cutoff_radius=7.117*Bohr,
    confinement_start_radius=5.117*Bohr,
    additional_charge=0,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
)

iron_3d_dz2 = ConfinedOrbital(
    principal_quantum_number=3,
    angular_momentum=2,
    azimuthal_quantum_number=4,
    radial_cutoff_radius=7.117*Bohr,
    confinement_start_radius=5.117*Bohr,
    additional_charge=0,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
)

iron_4f = ConfinedOrbital(
    principal_quantum_number=4,
    angular_momentum=3,
    radial_cutoff_radius=3.337*Bohr,
    confinement_start_radius=1.337*Bohr,
    additional_charge=0.013,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
)

IronBasis = BasisSet(
    element=PeriodicTable.Iron,
    orbitals=[iron_3s, iron_3p, iron_3d_dxy, iron_3d_dxz, iron_3d_dyz, iron_3d_dx2_y2, iron_3d_dz2, iron_4p, iron_4s_0, iron_4f],
    occupations=[2.0, 6.0, 6.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
    hubbard_u=[0.0, 0.0, 5.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]*eV,
    dft_half_parameters=Automatic,
    filling_method=SphericalSymmetric,
    onsite_spin_orbit_split=[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]*eV,
    pseudopotential=NormConservingPseudoPotential("normconserving/26FE.16.GGAPBE.zip"),

15
General Questions and Answers / Re: DOS of five d orbitals
« on: December 18, 2023, 12:27 »
Thanks, Jahanzaib. I will try this, and it looks like it will work. At the moment, I solved this issue with VASP, as I needed the COHP and pCOHP, so I used the same file.

Pages: [1] 2