Messages

1

General Questions and Answers / Medium basis set for PseudoDojo Pseudopotentials

« on: March 26, 2023, 16:50 »

Hello Expert.

I am interested to understand the medium basis set for PseudoDojo Pseudopotentials. What is medium basis set ? I studied but I am confused. Could any one guide me about "medium basis set for Pseudo Dojo Pseudopetential?

2

General Questions and Answers / Re: Molecular Energy Spectrum

« on: March 14, 2023, 03:08 »

Thank you Prof. Blom for your response.

I have computed transmission spectra(TS) and DDOS, so I want to compare which peak in TS is associated with which energy level and similar for DDOS? I have already calculated the MPSH for that but could not figure it ?

I also followed the tutorial of Molecular devices (https://docs.quantumatk.com/tutorials/molecular_device/molecular_device.html) but I couldn't figure out

- when MPSH with Atom indices (37,38,39,40,41,42,43,44,45,46) are computed and in next step why quantum number 13, 14, 15, 16 were chosen?

3

General Questions and Answers / Re: Molecular Energy Spectrum

« on: March 10, 2023, 16:05 »

This is MES for fe orbital, and I don't have an idea - how to interpret this. I have already attached output of this in previous message. Guide me

4

General Questions and Answers / Molecular Energy Spectrum

« on: March 9, 2023, 02:58 »

I've attached the output file for my system - Fe on the surface of nanoribbons. In output, I have energies with occupation and spinup/down.

I'm interested in plot MO diagram. Is there a way in quantumatk or I need to used python or any other way. Please guide me

5

General Questions and Answers / Re: PDDOS

« on: March 3, 2023, 15:11 »

Thank you so much.
I really appreciate your effect and support.

6

General Questions and Answers / Re: PDDOS

« on: March 2, 2023, 14:59 »

Thank you so much for your detailed response and guidance. I really appreciate your effort.

     - I successfully generated the PDOS using the script I wrote myself, after removing errors. I just checked the method you mentioned to export data and plot PDOS in excel. So, it works for me
    - Similarly, for transmission spectrum, is it possible to explore peak that which peak is associated with atom?

  - Would it be possible for you to share your complete python script which you wrote, I can compare it with mine and figure it out where I was doing wrong.


Thank you

7

General Questions and Answers / Re: PDDOS

« on: March 1, 2023, 12:39 »

Please find the attached .hdf5 file. There is no error in .hdf5 files but the main issue is that I got the PDOS for whole system rather than "Fe" atom with spin-up and spin-down which I am interested.

   - While using DOS analyzer, I put 101 for Fe, and got PDOS with spin UP/Down but there is not way to save this ( not interested to save it using snip tool) - I want its value so I can use excel or other program to plot PDOS of Fe.

8

General Questions and Answers / Re: PDDOS

« on: March 1, 2023, 02:32 »

Dear Dr. Blom
I have already attempted to use the method you suggested in our previous correspondence, but I encountered a problem: the resulting PDOS shows contributions from the entire system, rather than just the "Fe" atom with spin-up and spin-down which I am interested in. I have attached the .py file - if you have a look into it and suggested me what's wrong in it.

In addition to previous .py files, I made the changes given below, but still got error

# -------------------------------------------------------------
# Device Density Of States
# -------------------------------------------------------------
# Define the k-points grid
kpoint_grid = MonkhorstPackGrid()

# Define a projection on all orbitals
p1 = Projection()

# Define a projection on spin up of Iron
p2 = Projection(spin=Spin.Up, atoms=[Iron]) + Projection(spin=Spin.Down, atoms=[Iron])

# Create the DeviceDensityofStates object
device_density_of_states = DeviceDensityOfStates(
    configuration=configuration,
    energies=numpy.linspace(-3,3,101)*eV,
    kpoints=kpoint_grid,
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    self_energy_calculator=RecursionSelfEnergy(storage_strategy=NoStorage()),
    )

# Evaluate the device density of states with the projection list
result = device_density_of_states.evaluate(projection=p2)

# Print the results using nlprint()
nlsave('Dos.hdf5', device_density_of_states)
nlprint(result)

9

General Questions and Answers / Re: A issue when Generating A Moment Tensor Potential

« on: February 24, 2023, 12:51 »

The code is trying to access the last element in the list using the index -1, but the list appears to be empty or have no elements.  This could be caused by a number of reasons, such as the file not existing in the specified path, incorrect file path or filename, or issues with file permissions.

10

General Questions and Answers / Re: PDDOS

« on: February 23, 2023, 17:24 »

In PDDOS, I projected the Fe on the nanoribbons but when I mentioned spinUpDown in projectionlist - it shows error (TypeError: __init__() got an unexpected keyword argument 'spin'
). Can any one guide me how to or where to put spin argument in the input so I can get PDDOS of Fe with SPIN UP AND SPIN DOWN.

Thank you

# Define the k-points grid
kpoint_grid = MonkhorstPackGrid()

# Create the DeviceDensityofStates object
device_density_of_states = DeviceDensityOfStates(
    configuration=configuration,
    energies=numpy.linspace(-3,3,101)*eV,
    kpoints=kpoint_grid,
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    self_energy_calculator=RecursionSelfEnergy(storage_strategy=NoStorage()),
    )

# Define the projection list
projection_list = ProjectionList(atoms=[101], elements=[Iron], angular_momenta=[2], spin=UpDownProjection)

nlprint(result)
nlsave('P-S-UD.hdf5', results)

11

General Questions and Answers / Re: PDDOS

« on: February 15, 2023, 17:45 »

Any one please guide me?

12

General Questions and Answers / PDDOS

« on: February 14, 2023, 20:03 »

kpoint_grid = MonkhorstPackGrid()

device_density_of_states = DeviceDensityOfStates(
    configuration=device_configuration,
    energies=numpy.linspace(-3,3,101)*eV,
    kpoints=kpoint_grid,
    projection_list=ProjectionList(atoms=[95, 111, 118], elements=[Iron], angular_momenta=[2]),
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    self_energy_calculator=RecursionSelfEnergy(storage_strategy=NoStorage()),
    )
I tried to adjust the input file and add line of "Projection list" but it's not working. Basically, i have three iron in cluster which is adsorbed on nanoribbons. I just want to know the PDOS of each Iron with d-orbitals only. Can someone plz suggest what's wrong in it.

13

General Questions and Answers / Re: PDOS for orbital spin up and spin down

« on: February 7, 2023, 00:35 »

Thank you so much. I will try this technique.

14

General Questions and Answers / Re: PDOS for orbital spin up and spin down

« on: February 4, 2023, 00:45 »

Thank you so much Dr. Blom. I truly appreciate the time and energy you have invested in helping the students.

I tried this for my system and it's working fine.

Can you please guide me how to improve python skill in computational chemistry as I know python very well but while writing script - I never succeeded.

 

15

General Questions and Answers / Re: PDOS for orbital spin up and spin down

« on: January 31, 2023, 22:49 »

Thank you so much for guiding.
I tried but it showed combined projection not separate spin up and spin down.

I think I couldn't explained my query well. Sorry for that.

I have already calculated "Projection on shell by elements" which showed "sum of spin" of each orbital but I am interested to find out spin up and down separately of each orbital (p and d). How could I can adjust input? Can you please guide me?