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Messages - beauyy

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1
General Questions and Answers / TubeWrapper addon zip file
« on: September 13, 2024, 15:38 »
Dear all,

I cannot download TubeWrapper functionality from addon manager, as our university set a firewall. I am using QuantumATK 2018.06-SP1-1. Is there anyone can share the .zip file of this functionality? 

Thanks very much.

2
General Questions and Answers / output the single-ion anisotropies and anisotropic exchange constants
« on: September 12, 2024, 09:37 »
Dear all,

I am still using QuantumATK 2018. I need to calculate the Curie temperature of some 1D and 2D ferromagnetic materials. According to the Heisenberg model, the anisotropies and anisotropic exchange constants need to be provided. Is there any .py script that can output all these results with DFT+U?

Thanks.

3
General Questions and Answers / carrier doping concentration in 1D nanoribbon
« on: August 31, 2024, 03:24 »
Dear all,

The unit of doping concentration is e/cm3 in QuantumATK.

It is easy to be converted into e per unit, by multiplying with the height, width, and length in 3D materials. But in 1D structures, such as GN nanoribbon, there is a lot of vacuum regions in the vertical and plane direction.

Is it still useful to multiply with the height, width of unit cell, if I want to convert the unit into e/cm in 1D structure. Or should I multiply with the atomic height and he actual width of nanoribbon?

 The height of 1D nanoribbon is atomic scale, I doubt whether the doping concentration (e/cm) will be too low in 1D structure.




4
General Questions and Answers / localized charge setting in complex vdW stacking supercells
« on: May 2, 2023, 06:26 »
Dear all, I need to applied nonzero charge on the sublayer in a vdW stacking supercell. Is it possible to do this operation in QuantumATK 2018.06? Or is there any script to achieve this? 

5
General Questions and Answers / Difficult to converge in spin-polarized two-probe system
« on: December 13, 2022, 13:32 »
Hi all,

I am calculating the zero-bias transmission spectra of two-probe MBHT system. It is very difficult to converge and very low-efficient, even though I have set many computational parameters higher than the guide in https://docs.quantumatk.com/manual/technicalnotes/spin_polarized_negf_convergence_guide/spin_polarized_negf_convergence_guide.html.  To make it converge more quick, I have even reduced the convergence criteria, but still failed to accelerate the calculation. The attachment is my script. 
Is there any method for me to achieve a faster and more reliable convergence? It seems that SGGA  calculation spends too much time. If I choose LSDA, is there any method to achiev a faster and more reliable convergence.

6
General Questions and Answers / Re: error in PDOS calculation
« on: December 8, 2022, 14:04 »
Thanks. You are right.

7
General Questions and Answers / error in PDOS calculation
« on: December 8, 2022, 13:11 »
Dear all,

I built a script to customize the PDOS of a spin-polarized nanoribbon. But an error occurs.
How can I modify the PDOS script to make it run correctly.
The error information is as follows:

Traceback (most recent call last):
  File "/public/home/heyy/ATKJOBS/221208-LGvHMutP/pdos-z-GN-1.py", line 126, in <module>
Traceback (most recent call last):
  File "/public/home/heyy/ATKJOBS/221208-LGvHMutP/pdos-z-GN-1.py", line 126, in <module>
Traceback (most recent call last):
  File "/public/home/heyy/ATKJOBS/221208-LGvHMutP/pdos-z-GN-1.py", line 126, in <module>
    projection_list = Projection(atom=[Carbon], l_quantum_numbers=[1], m_quantum_numbers=[-1, 0, 1], spin=Spin.up)
AttributeError: 'module' object has no attribute 'up'
    projection_list = Projection(atom=[Carbon], l_quantum_numbers=[1], m_quantum_numbers=[-1, 0, 1], spin=Spin.up)
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2

8
General Questions and Answers / LDOS calculation of a spin-polarized bulk in older version
« on: November 30, 2022, 15:45 »
Hi all,

I have read the tutorial: 
http://docs.quantumatk.com/tutorials/tamr_ldos/tamr_ldos.html#stm-simulations-of-tunneling-anisotropic-magneto-resistance-tamr. This is new for QuantumATK S-2021.06.

The script W8_Fe2_Co.py in the tutorial can not run  in 2018 version. Is it possible to modify the script to run in 2018 version? If possible, how can I modify it?

The original script of W8_Fe2_Co.py in 2021 version is:
# -*- coding: utf-8 -*-
# -------------------------------------------------------------
# Bulk Configuration
# -------------------------------------------------------------

angles = [(0,0), (90, 150)]

for (theta, phi) in angles:
    filename = 'W8-Fe2-Co-2x2-theta_{}-phi_{}.hdf5'.format(theta, phi)

    # Set up lattice
    vector_a = [5.482287216117011, 0.0, 0.0]*Angstrom
    vector_b = [-1.827429072039004, 5.168749955904878, 0.0]*Angstrom
    vector_c = [0.0, 0.0, 44.9670510707337]*Angstrom
    lattice = UnitCell(vector_a, vector_b, vector_c)

    # Define elements
    elements = [Tungsten, Tungsten, Tungsten, Tungsten, Tungsten, Tungsten,
                Tungsten, Tungsten, Tungsten, Tungsten, Tungsten, Tungsten,
                Tungsten, Tungsten, Tungsten, Tungsten, Tungsten, Tungsten,
                Tungsten, Tungsten, Tungsten, Tungsten, Tungsten, Tungsten,
                Tungsten, Tungsten, Tungsten, Tungsten, Tungsten, Tungsten,
                Tungsten, Tungsten, Iron, Iron, Iron, Iron, Iron, Iron, Iron, Iron,
                Cobalt]

    # Define coordinates
    fractional_coordinates = [[ 0.25          ,  0.25          ,  0.30118631364 ],
                              [ 0.25          ,  0.75          ,  0.301186278457],
                              [ 0.75          ,  0.25          ,  0.301186278457],
                              [ 0.75          ,  0.75          ,  0.301186242332],
                              [-0.000000998907, -0.000000998907,  0.350454016187],
                              [-0.000000503015,  0.500000503015,  0.350454015157],
                              [ 0.500000503015, -0.000000503015,  0.350454015157],
                              [ 0.500000998907,  0.500000998907,  0.350454016187],
                              [ 0.25          ,  0.25          ,  0.400260701577],
                              [ 0.25          ,  0.75          ,  0.400261649879],
                              [ 0.75          ,  0.25          ,  0.400261649879],
                              [ 0.75          ,  0.75          ,  0.400262571411],
                              [ 0.000013667016,  0.000013667016,  0.450062461809],
                              [ 0.000006758676,  0.499993241324,  0.450062741191],
                              [ 0.499993241324,  0.000006758676,  0.450062741191],
                              [ 0.499986332984,  0.499986332984,  0.450062461809],
                              [ 0.25          ,  0.25          ,  0.499890596355],
                              [ 0.25          ,  0.75          ,  0.49988412114 ],
                              [ 0.75          ,  0.25          ,  0.49988412114 ],
                              [ 0.75          ,  0.75          ,  0.499873815331],
                              [-0.000133552734, -0.000133552734,  0.54969793658 ],
                              [-0.000065862576,  0.500065862576,  0.549705930495],
                              [ 0.500065862576, -0.000065862576,  0.549705930495],
                              [ 0.500133552734,  0.500133552734,  0.54969793658 ],
                              [ 0.25          ,  0.25          ,  0.599373131644],
                              [ 0.25          ,  0.75          ,  0.599538357583],
                              [ 0.75          ,  0.25          ,  0.599538357583],
                              [ 0.75          ,  0.75          ,  0.599633530735],
                              [ 0.003412645763,  0.003412645763,  0.649063001825],
                              [-0.000133957938,  0.500133957938,  0.649263802117],
                              [ 0.500133957938, -0.000133957938,  0.649263802117],
                              [ 0.496587354237,  0.496587354237,  0.649063001825],
                              [ 0.25          ,  0.25          ,  0.696649707841],
                              [ 0.25          ,  0.75          ,  0.694517503389],
                              [ 0.75          ,  0.25          ,  0.694517503389],
                              [ 0.75          ,  0.75          ,  0.691660105602],
                              [-0.043518053127, -0.043518053127,  0.734575517354],
                              [ 0.012602780483,  0.487397219517,  0.735779056149],
                              [ 0.487397219517,  0.012602780483,  0.735779056149],
                              [ 0.543518053127,  0.543518053127,  0.734575517354],
                              [ 0.25          ,  0.25          ,  0.763611260037]]

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

    # Add tags
    bulk_configuration.addTags('molecule0_Co', [40])
    bulk_configuration.addTags('substrate',    [ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12,
                                                13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
                                                26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,
                                                39])

    # -------------------------------------------------------------
    # Calculator
    # -------------------------------------------------------------
    #----------------------------------------
    # Basis Set
    #----------------------------------------
    basis_set = [
        BasisGGAPseudoDojoSO.Iron_Medium,
        BasisGGAPseudoDojoSO.Cobalt_Medium,
        BasisGGAPseudoDojoSO.Tungsten_Medium,
        ]

    #----------------------------------------
    # Exchange-Correlation
    #----------------------------------------
    exchange_correlation = SOGGA.PBE

    k_point_sampling = KpointDensity(
        density_a=7.0*Angstrom,
        density_c=0.0*Angstrom,
        force_timereversal=False,
        )
    numerical_accuracy_parameters = NumericalAccuracyParameters(
        density_mesh_cutoff=120.0*Hartree,
        k_point_sampling=k_point_sampling,
        )

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

    bulk_configuration.setCalculator(calculator)

    # -------------------------------------------------------------
    # Initial State
    # -------------------------------------------------------------
    scaled_spins = [(i, 1.0, theta*Degrees, phi*Degrees) for i in range(len(bulk_configuration))]

    initial_spin = InitialSpin(scaled_spins=scaled_spins)

    bulk_configuration.setCalculator(
        calculator,
        initial_spin=initial_spin,
    )
    bulk_configuration.update()
    nlsave(filename, bulk_configuration)
    nlprint(bulk_configuration)

    # -------------------------------------------------------------
    # Local Density Of States
    # -------------------------------------------------------------
    kpoints = KpointDensity(
        density_a=17.0*Angstrom,
        density_c=0.0*Angstrom,
        force_timereversal=False,
        )

    local_density_of_states = LocalDensityOfStates(
        configuration=bulk_configuration,
        kpoints=kpoints,
        energies=numpy.linspace(-0.2, 0.8, 41)*eV,
        band_indices=All,
        energy_zero_parameter=FermiLevel,
        spectrum_method=GaussianBroadening(0.025*eV),
        density_mesh_cutoff=30*Hartree,
        )
    nlsave(filename, local_density_of_states)

    # -------------------------------------------------------------
    # Mulliken Population
    # -------------------------------------------------------------
    mulliken_population = MullikenPopulation(bulk_configuration)
    nlsave(filename, mulliken_population)
    nlprint(mulliken_population)



9
Installation and License Questions / Re: Job manager failed on Win10
« on: September 15, 2022, 06:10 »
I've tried as your guide. The job manager setting is removed. But if I want to send job on remote, the same remote setting should be saved in job manager. Then the software still quits again. Is there any method to solve this problem in this old version?

10
Installation and License Questions / Job manager failed on Win10
« on: September 9, 2022, 06:01 »
I installed QuantumATK 2018.06 on Win10 professional. All structures can not be shown in Builder and Viewer. They can only be shown in low-performance mode. When I enlarged the GUI, the buttons on the top were out of the screen and thus hard to be rescaled. The largest problen is: When I opened Job manager, the software quited immediately.   On Win7, everything goes well. What is the problem? How can I deal with it?

11
General Questions and Answers / Re: Is it possible to calculate the PLDOS at a definite bias from the I-V curve?
« on: November 3, 2021, 08:39 »
I have run this script
m = nlread("pldos-Sn4S8-1e19-n-Vds0.64V-Vg-1.0V.hdf5", MullikenPopulation)[0]       
print(m.atomicCharge().sum())                                                           
                                                                                                                                                                           
Then, there appeared an error message as IndexError: list index out of range.
The script for calculating MullikenPopulation is as follows:
# -*- coding: utf-8 -*-                                               
# -------------------------------------------------------------       
# Analysis from File                                                 
# -------------------------------------------------------------       
filename = u'pldos-Sn4S8-1e19-n-Vds0.64V-Vg-1.0V.hdf5'               
                                                                     
iv_characteristics = IVCharacteristics(                               
    configuration=nlread(filename, object_id='DeviceConfiguration_0')[
    filename=filename,                                               
    object_id='iv-Sn4S8-1e19-n',                                     
    gate_regions=[0, 1],                                             
    gate_source_voltages= -1.0 * Volt,                               
    drain_source_voltages= 0.64 * Volt,                               
    log_filename_prefix=LogToStdOut,                                 
    number_of_processes_per_task=12,                                 
)                                                                     
                                                                     
iv_characteristics.addAnalysis(                                       
    -1.0 * Volt, 0.64 * Volt, MullikenPopulation)                     
iv_characteristics.addProjectedLocalDensityOfStates(                 
    -1.0 *Volt, 0.64 * Volt)                                         
iv_characteristics.update()   

How can I modify the script?

The attached view of MullikenPopulation indicates the .hdf5 does contain the MullikenPopulation data.                                     

12
General Questions and Answers / Re: Is it possible to calculate the PLDOS at a definite bias from the I-V curve?
« on: November 2, 2021, 06:17 »
Yes, I can see the view of Mulliken Population according to your instruction. Then, how can I get a total charge of the device at a definite Vds and Vg from it, even though it is very rough. Is it possible to get a .txt file , like the Mulliken Population of a bulk structure. I need this data to further evaluate the device performance of a FET. 

13
General Questions and Answers / Re: Is it possible to calculate the PLDOS at a definite bias from the I-V curve?
« on: November 1, 2021, 13:09 »
Thanks very much. I have known the reason for this error. I still have another question. The calculation of Mulliken Population is finished.  But I don't kown how to read the data. I know the way to read PLDOS is similar to transmission spectra.  But I can't find Milliken Population at the same place.

14
General Questions and Answers / Re: Is it possible to calculate the PLDOS at a definite bias from the I-V curve?
« on: October 29, 2021, 05:39 »
Thank you. But when I calculated the PLDOS and Mulliken charge from the IV characteristics, it always terminated with exit code 139. Even though I recalcuated the IV characteristics with PLDOS and Mulliken charge from the device, the same problem still existed. This error occured after the PLDOS and Mulliken charge calculations were finished. I guess it is not because of the out of memory. How can I solve this problem?
The script is attached.

15
General Questions and Answers / Is it possible to calculate the PLDOS at a definite bias from the I-V curve?
« on: October 21, 2021, 06:50 »
 In the calculation of Ids-Vg curve, I forgot to analyze the PLDOS. Can I get the PLDOS at a definite Vg from the  Ids-Vg curve results? If possible, how can I do that? Is there any guideline?

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