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Topics - Jahanzaib

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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 / 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

3
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.

4
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

5
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

6
General Questions and Answers / Software
« on: December 14, 2022, 02:41 »
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?

How to calculate integrated DOS in quantumatk? or how to get an idea of molecular orbitals in bulk and device configurations?

Thank you

7
General Questions and Answers / Convergences error
« on: December 4, 2022, 03:26 »
Hello
The energy and Hamiltonian differences dE and dH should decrease steadily towards the specified tolerance. If it's not doing the same what could be the possible error in the job. Should Poisson solver needs to be changed or the geometry should be changed?

8
General Questions and Answers / ERROR
« on: November 29, 2022, 16:29 »
Respected Experts,
I have attached the input and I found this error. Can someone please suggest me what's the issue

Convergence Report                                                           |
+------------------------------------------------------------------------------+
|                                                                              |
| SCF Tolerance: 1.00000e-04                                                   |
| Maximum number of steps: 100                                                 |
|                                                                              |
| Convergence Criteria:                                                        |
|                                                                              |
|  * Label: dE                                                                 |
|    Description: Band Energy Absolute Difference (Hartree)                    |
|    Value: 1.57915e-01 (Tolerance not reached)                                |
|                                                                              |
|  * Label: dH                                                                 |
|    Description: Maximum Norm of Hamiltonian Difference (Hartree)             |
|    Value: 9.84124e-04 (Tolerance not reached)

9
General Questions and Answers / Optimization issue
« on: November 26, 2022, 23:57 »
Hello,
I am optimizing the stanene nanoribbon and cluster on it surface, but even 3,4 days it's not converging. I have attached the input file - Can some one guide me what would be the issue due to which it's not converging even after 3,4 days?

# -*- coding: utf-8 -*-
# -------------------------------------------------------------
# Bulk Configuration
# -------------------------------------------------------------

# Set up lattice
vector_a = [87.7884, 0.0, 0.0]*Angstrom
vector_b = [0.0, 175.0, 0.0]*Angstrom
vector_c = [0.0, 0.0, 32.51127454211999]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
elements = [Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin,
            Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin,
            Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin,
            Tin, Hydrogen, Hydrogen, Hydrogen, Hydrogen, Hydrogen, Hydrogen,
            Hydrogen, Hydrogen, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin,
            Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin,
            Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin,
            Tin, Tin, Tin, Tin, Tin, Hydrogen, Hydrogen, Hydrogen, Hydrogen,
            Hydrogen, Hydrogen, Hydrogen, Hydrogen, Tin, Tin, Tin, Tin, Tin,
            Tin, Tin, Tin, Tin, Iron, Iron, Tin, Tin, Tin, Tin, Tin, Tin, Tin,
            Tin, Tin, Iron]

# Define coordinates
fractional_coordinates = [[ 0.545001091377,  0.439667441783,  0.008394265003],
                          [ 0.545001091377,  0.439667441783,  0.258394265003],
                          [ 0.545001091377,  0.439667441783,  0.508394265003],
                          [ 0.545001091377,  0.439667441783,  0.758394265003],
                          [ 0.545001091377,  0.466482059909,  0.008394265003],
                          [ 0.545001091377,  0.466482059909,  0.258394265003],
                          [ 0.545001091377,  0.466482059909,  0.508394265003],
                          [ 0.545001091377,  0.466482059909,  0.758394265003],
                          [ 0.545001091377,  0.493296678034,  0.008394265003],
                          [ 0.545001091377,  0.493296678034,  0.258394265003],
                          [ 0.545001091377,  0.493296678034,  0.508394265003],
                          [ 0.545001091377,  0.493296678034,  0.758394265003],
                          [ 0.545001091377,  0.520111296159,  0.008394265003],
                          [ 0.545001091377,  0.520111296159,  0.258394265003],
                          [ 0.545001091377,  0.520111296159,  0.508394265003],
                          [ 0.545001091377,  0.520111296159,  0.758394265003],
                          [ 0.545001091377,  0.546925914284,  0.008394265003],
                          [ 0.545001091377,  0.546925914284,  0.258394265003],
                          [ 0.545001091377,  0.546925914284,  0.508394265003],
                          [ 0.545001091377,  0.546925914284,  0.758394265003],
                          [ 0.534447034618,  0.439666890916,  0.091815649394],
                          [ 0.534447034618,  0.439666890916,  0.341815649394],
                          [ 0.534447034618,  0.439666890916,  0.591815649394],
                          [ 0.534447034618,  0.439666890916,  0.841815649394],
                          [ 0.534447034618,  0.466481509041,  0.091815649394],
                          [ 0.534447034618,  0.466481509041,  0.341815649394],
                          [ 0.534447034618,  0.466481509041,  0.591815649394],
                          [ 0.534447034618,  0.466481509041,  0.841815649394],
                          [ 0.534447034618,  0.520110745291,  0.091815649394],
                          [ 0.534447034618,  0.520110745291,  0.341815649394],
                          [ 0.534447034618,  0.520110745291,  0.591815649394],
                          [ 0.534447034618,  0.520110745291,  0.841815649394],
                          [ 0.534447034618,  0.546925363416,  0.091815649394],
                          [ 0.534447034618,  0.546925363416,  0.341815649394],
                          [ 0.534447034618,  0.546925363416,  0.591815649394],
                          [ 0.534447034618,  0.546925363416,  0.841815649394],
                          [ 0.534447034618,  0.493296127166,  0.091815649395],
                          [ 0.534447034618,  0.493296127166,  0.341815649395],
                          [ 0.534447034618,  0.493296127166,  0.591815649395],
                          [ 0.534447034618,  0.493296127166,  0.841815649395],
                          [ 0.538725180092,  0.568336949088,  0.108590434607],
                          [ 0.538725180092,  0.568336949088,  0.358590434607],
                          [ 0.538725180092,  0.568336949088,  0.608590434607],
                          [ 0.538725180092,  0.568336949088,  0.858590434607],
                          [ 0.540784511345,  0.431663050912,  0.116665156977],
                          [ 0.540784511345,  0.431663050912,  0.366665156977],
                          [ 0.540784511345,  0.431663050912,  0.616665156977],
                          [ 0.540784511345,  0.431663050912,  0.866665156977],
                          [ 0.545062656885,  0.533518490939,  0.133439941882],
                          [ 0.545062656885,  0.533518490939,  0.383439941882],
                          [ 0.545062656885,  0.533518490939,  0.633439941882],
                          [ 0.545062656885,  0.533518490939,  0.883439941882],
                          [ 0.545062656885,  0.453074636564,  0.133439941882],
                          [ 0.545062656885,  0.453074636564,  0.383439941882],
                          [ 0.545062656885,  0.453074636564,  0.633439941882],
                          [ 0.545062656885,  0.453074636564,  0.883439941882],
                          [ 0.545062656885,  0.479889254689,  0.133439941882],
                          [ 0.545062656885,  0.479889254689,  0.383439941882],
                          [ 0.545062656885,  0.479889254689,  0.633439941882],
                          [ 0.545062656885,  0.479889254689,  0.883439941882],
                          [ 0.545062656885,  0.506703872814,  0.133439941882],
                          [ 0.545062656885,  0.506703872814,  0.383439941882],
                          [ 0.545062656885,  0.506703872814,  0.633439941882],
                          [ 0.545062656885,  0.506703872814,  0.883439941882],
                          [ 0.545062656885,  0.560333109065,  0.133439941882],
                          [ 0.545062656885,  0.560333109065,  0.383439941882],
                          [ 0.545062656885,  0.560333109065,  0.633439941882],
                          [ 0.545062656885,  0.560333109065,  0.883439941882],
                          [ 0.534391508784,  0.453074334526,  0.216743534207],
                          [ 0.534391508784,  0.453074334526,  0.466743534207],
                          [ 0.534391508784,  0.453074334526,  0.716743534207],
                          [ 0.534391508784,  0.453074334526,  0.966743534207],
                          [ 0.534391508784,  0.479888952651,  0.216743534207],
                          [ 0.534391508784,  0.479888952651,  0.466743534207],
                          [ 0.534391508784,  0.479888952651,  0.716743534207],
                          [ 0.534391508784,  0.479888952651,  0.966743534207],
                          [ 0.534391508784,  0.506703570776,  0.216743534207],
                          [ 0.534391508784,  0.506703570776,  0.466743534207],
                          [ 0.534391508784,  0.506703570776,  0.716743534207],
                          [ 0.534391508784,  0.506703570776,  0.966743534207],
                          [ 0.534391508784,  0.533518188901,  0.216743534207],
                          [ 0.534391508784,  0.533518188901,  0.466743534207],
                          [ 0.534391508784,  0.533518188901,  0.716743534207],
                          [ 0.534391508784,  0.533518188901,  0.966743534207],
                          [ 0.534391508784,  0.560332807026,  0.216743534207],
                          [ 0.534391508784,  0.560332807026,  0.466743534207],
                          [ 0.534391508784,  0.560332807026,  0.716743534207],
                          [ 0.534391508784,  0.560332807026,  0.966743534207],
                          [ 0.538668007478,  0.431664087298,  0.233532064004],
                          [ 0.538668007478,  0.431664087298,  0.483532064004],
                          [ 0.538668007478,  0.431664087298,  0.733532064004],
                          [ 0.538668007478,  0.431664087298,  0.983532064004],
                          [ 0.540724592801,  0.56833616151 ,  0.241605734997],
                          [ 0.540724592801,  0.56833616151 ,  0.491605734997],
                          [ 0.540724592801,  0.56833616151 ,  0.741605734997],
                          [ 0.540724592801,  0.56833616151 ,  0.991605734997],
                          [ 0.481191360607,  0.490116494889,  0.433668563691],
                          [ 0.454937343115,  0.51128640202 ,  0.559207748975],
                          [ 0.457765726314,  0.510467556028,  0.433668031845],
                          [ 0.481191138358,  0.493838475594,  0.326063421612],
                          [ 0.457767592128,  0.496900652858,  0.510787308269],
                          [ 0.454940306488,  0.496082029735,  0.38524772928 ],
                          [ 0.498185776347,  0.50860527515 ,  0.326062205358],
                          [ 0.46419187606 ,  0.508606614722,  0.326063035667],
                          [ 0.481187018047,  0.518888042359,  0.385245850884],
                          [ 0.481189107277,  0.503683181452,  0.472227097958],
                          [ 0.481189352698,  0.503683318637,  0.398966408015],
                          [ 0.481186853947,  0.517249868015,  0.510785632225],
                          [ 0.507440871439,  0.496079960885,  0.385246446941],
                          [ 0.50461248824 ,  0.496898806876,  0.510786164071],
                          [ 0.481187076197,  0.51352788731 ,  0.618390774304],
                          [ 0.504610622426,  0.510465710046,  0.433666887647],
                          [ 0.507437908066,  0.511284333169,  0.559206466636],
                          [ 0.464192438208,  0.498761087755,  0.618391990558],
                          [ 0.498186338494,  0.498759748182,  0.618391160249],
                          [ 0.481191196508,  0.488478320545,  0.559208345032],
                          [ 0.481188861857,  0.503683044267,  0.545487787901]]

# Set up configuration
bulk_configuration = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = SGGA.PBE

numerical_accuracy_parameters = NumericalAccuracyParameters(
    density_mesh_cutoff=85.0*Hartree,
    occupation_method=FermiDirac(0.01*eV),
    )

calculator = LCAOCalculator(
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=numerical_accuracy_parameters,
    )

bulk_configuration.setCalculator(calculator)
nlprint(bulk_configuration)
bulk_configuration.update()
nlsave('C-Pre.hdf5', bulk_configuration)

# -------------------------------------------------------------
# Optimize Geometry
# -------------------------------------------------------------

constraints = [FixStrain(x=False, y=False, z=True)]

bulk_configuration = OptimizeGeometry(
    bulk_configuration,
    max_forces=0.05*eV/Ang,
    max_stress=0.1*GPa,
    max_steps=200,
    max_step_length=0.2*Ang,
    constraints=constraints,
    trajectory_filename='C-Pre_trajectory.hdf5',
    trajectory_interval=5.0*Minute,
    restart_strategy=RestartFromTrajectory(),
    optimizer_method=LBFGS(),
    enable_optimization_stop_file=True,
)
nlsave('C-Pre.hdf5', bulk_configuration)
nlprint(bulk_configuration)

10
General Questions and Answers / Error and Role of electron temp
« on: October 28, 2022, 00:22 »
Hello, I have been encountering this issue again and again but couldn't figure it out.

# The computed multigrid residual is greater than the required accuracy.       
# Computed residual :   1.48902e-12                                           
# Required accuracy :   1.00000e-12 

I also want to know "What is role of electron temperature in device calculation?  It's 300K by default but if the temperature is increased - does it plays significance role in convergence or it's role is different?

11
General Questions and Answers / Hydrogen passivation
« on: October 15, 2022, 14:44 »
I want to know the role of hydrogen passivation in device configuration.
I am using stanane nanoribbons so at the top and botton in B direction, If I or I don't passivate hydrogen will it effect the optimization?

Thank you

12
General Questions and Answers / Error in device
« on: October 8, 2022, 15:48 »
Hello to all,

After optimizing the central region separtely, I took the cartesain co-ordinate of optimized geometry and form a device. Left and right electrode are also optimized. But i found this error, i tried alot to figure this out but I couldn't. What could be the possible solution?

An electrode-like region in the central-region in a two-probe system may not contain atoms not
present in the corresponding electrode. The repeated left electrode has 14 atoms defined, while the
left electrode-like region in the central-region contains 28 atoms. The electrode-like region is
expected to be the left electrode repeated (1, 1, 1) times along (a, b, c) according to the given
equivalent_electrode_length and transverse_electrode_repetitions.

Thank you

13
General Questions and Answers / Role of electron temperature in device calculation
« on: September 27, 2022, 16:58 »
I am doing device calculation and the left and right electron temperature is 300K by default, so this temperature gives poor convergences so I can't find out the role of electron temperature in device calculation. Can anyone guide me a bit?

14
General Questions and Answers / Optimization issue
« on: September 21, 2022, 00:47 »
I have been facing alot of problem while optimizing the device calculations. It takes even a week but it didn't converged. Here in, I attached the input file. May be there is an issue in the input file. Can some suggest me ?
I have attached the pdf file for my input. Can someone look into it and suggested me what's wrong in it due to which I am unable to get result for optimized geometry and Device optimized geometry.

15
General Questions and Answers / Transmission spectra vs k-points
« on: August 30, 2022, 12:28 »
I am doing research in 1-D stanene nanoribbon for device calculation and interested to optimize the Pd on it.
I want to know what is the role of k-point in transmission spectra of 1-D stanene nanoribbons, I have chosen 1×1 and 9×9 k-points but couldn't get the desired results for transmission spectra.

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