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Messages - Jahanzaib

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61
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

62
General Questions and Answers / Re: ERROR
« on: December 7, 2022, 14:19 »
Thank you so much.

I will try this script - i hope it will work


63
General Questions and Answers / Re: ERROR
« on: December 6, 2022, 16:29 »
Your point 3rd is not clear to me, Could you please elaborate?

Thank you

64
General Questions and Answers / Re: ERROR
« on: December 6, 2022, 15:04 »
Thank you so much for your detailed response.

Just to add, I have separately optimized stanene, then doing optimization.
but I will follow your guidance and hopefully It starts converging.

Thank you

65
General Questions and Answers / Re: ERROR
« on: December 5, 2022, 12:20 »
Thank you so much for detailed reply.

Actually, I am optimizing cluster on stanene nanoribbon, even 4 days optimization - it's never converged. I am using 1,1,1 k-points in A,B,C direction respectively because there is alot of vaccuum in A and B directions so alot of k-points doesn't have impact on it. I think so?  I have attached .py file. Can you please suggest how to improve it?

66
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?

67
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)

68
General Questions and Answers / Re: Optimization issue
« on: November 28, 2022, 13:55 »
Yes, I tried - I don't know why It's not working

69
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)

70
General Questions and Answers / Re: Error and Role of electron temp
« on: November 1, 2022, 17:59 »
Waiting for the response

71
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?

72
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

73
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

74
General Questions and Answers / Re: Optimization issue
« on: September 29, 2022, 15:04 »
Thank you so much for guiding me. I really appreciate it.

I started with n*m=2*2 then optimized it. After optimization,  I repeat it in the "C direction" to convert it into "device from bulk". I adsorbed the Pd on its surface - to optimized it again to figure out the effect of Pd on stanene nanoribbons in the central regions.

It started with default setting, but it never converged.  However, used 1×1×100 k-point in A,B and C direction respectively but I might change the k point I guess it will effect the simulation too.

Thank you

75
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?

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