Messages

46

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

47

General Questions and Answers / Re: PDDOS

« on: March 3, 2023, 15:11 »

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

48

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

49

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.

50

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)

51

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.

52

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)

53

General Questions and Answers / Re: PDDOS

« on: February 15, 2023, 17:45 »

Any one please guide me?

54

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.

55

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.

56

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.

 

57

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?

58

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

« on: January 31, 2023, 17:07 »

Hello expert,

I have calculated the sum of spin for orbitals but I am interested to separately calculated the spin up and spin down for each orbital.

kpoint_grid = MonkhorstPackGrid()

projected_density_of_states = ProjectedDensityOfStates(
    configuration=configuration,
    kpoints=kpoint_grid,
    projections=ProjectOnShellsByElement,
     spin_up = spin.evaluate(spin=Spin.Up)
       spin_dn = spin.evaluate(spin=Spin.Down)
    energies=numpy.linspace(-2, 2, 401)*eV,
    energy_zero_parameter=FermiLevel,
    bands_above_fermi_level=All,
    spectrum_method=GaussianBroadening(0.01*eV),
)

It's not working - can you please suggest me what's wrong in here

59

General Questions and Answers / Re: Integrated DOS and molecular orbital in quantumatk

« on: January 18, 2023, 21:44 »

Thank you so much for your detailed response.
I was interested for integrated DOS over energy - I successfully did that.

Need you expert view point for my system.

I have six width long nanoribbons long C direction as shown in figure. I just pick it randomly but I want to know what kind of analysis i should do to verify that this 6 width long nanoribbons is fine - similarly how I can do analysis that these 4 layers are also fine?

I haven't figure it out how long the nanoribbons should be? how many layers are needed?

Need your expert point of view on it.

Thank you

60

General Questions and Answers / Integrated DOS and molecular orbital in quantumatk

« on: January 10, 2023, 12:36 »

Hello
I have quick question: for bulk configuration - NonuniformGridConjugateGradientSolver and fast fourier solver are the best. I am having a system where I am using stanene nanoribbons and cluster on it (bulk configuration). How to choose Solver in this case?

1. Is there a way for COOP or OPDOS analysis in quantumatk?
2. How to calculate integrated DOS in quantumatk? or how to get an idea of molecular orbitals in bulk and device configurations?

Thank you