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1
Scripts, Tutorials and Applications / Re: spatial region extended into the centre region, not calculated during electrode
« Last post by Anders Blom on Yesterday at 20:48 »
Spatial regions are not supposed to be contacts, since they will not be able to conduct hold any current. They are only meant to be used for electrostatic control, like gates. Your source and drain need to be fully atomistic structures which are part of the DFT-NEGF calculation.
2
General Questions and Answers / Re: Information and Capabilities of Pretrained MTPs in Force Field Library for MD
« Last post by Anders Blom on Yesterday at 20:30 »
If you go outside the domain where the potentials are trained you can easily see such effects, yes. Which MTP in particular are you trying to use?
3
Installation and License Questions / Re: Is there any limitation for number of execution of Simulation?
« Last post by Anders Blom on Yesterday at 20:29 »
Yes, there is always a limit, but what it is depends on your license.
4
General Questions and Answers / Missing SK Parameters from Install
« Last post by schintapalli on Yesterday at 20:13 »
Hello,

I am working through the examples found here:

https://docs.quantumatk.com/tutorials/transmission_gr_mos2/transmission_gr_mos2.html.

I am thrown the following error after running the setup:
"NL.ComputerScienceUtilities.Exceptions.NLValueError: The Slater-Koster parameters file Mo-Mo.skf was not found.
The full file path should be: C:\Program Files\QuantumATK\QuantumATK-V-2023.09\share\tightbinding\cp2k\Mo-Mo.skf"

However, I cannot find the Mo-S.skf parameters in the quantumATK install. How can I update the tightbinding/ SK parameter directory?
5
General Questions and Answers / Inelastic current of a molecular junction
« Last post by ml1019 on Yesterday at 13:41 »
Dear All,

I tried to calculate the inelastic current of a molecular junction. However,  the current curve is peculiar. It goes negative and forms a peak before it goes up again. Does anyone have any idea on this negative peak? Would it be a calculation error?

My calculation procedure:
After normal DFT routine, the dynamical matrix is calculated at 0 bias. Due to the lack of computational resources, the dynamical matrix is calculated at gamma point and reused at finite bias calculations. Then I obtain the inelastic current with LOE methods.

Please find attached the I(V) and my inputs.

Thank you for your help.

Best regards,
Ml1019
6
Installation and License Questions / Is there any limitation for number of execution of Simulation?
« Last post by techenthusiast on Yesterday at 11:05 »
Good afternoon,

Is there any limitation for number of  execution of Simulation? Some time its showing licensing error.
Thank You.
7
General Questions and Answers / Information and Capabilities of Pretrained MTPs in Force Field Library for MD
« Last post by msingh96 on May 20, 2024, 18:29 »
Hello QuantumATK users, this is my first post in the forum. I have started using QuantumATK for the MTP functionality it provides as advertised here: https://www.synopsys.com/manufacturing/quantumatk/atomistic-simulation-products/machine-learned-force-fields.html.

One exciting thing I found was the library of pretrained MTPs made available for users: https://docs.quantumatk.com/manual/ForceField.html#pretrained-moment-tensor-potential-mtp-parameter-sets

However I am struggling to use these effectively. I am running into two errors.
1. the nose-hoover thermostats seem to fail/atoms seem to explode for certain interfaces
2. atoms leave simulation regime and MD simulation stalls.

I am wondering if there are any examples or  information about the training data (structures) for these pretrained potentials.

Regards and Thanks, Mayur
8
Scripts, Tutorials and Applications / spatial region extended into the centre region, not calculated during electrode
« Last post by techenthusiast on May 17, 2024, 17:06 »
Good evening, Hope you are doing well. Just to ask :
How to give proper metallic contact to source & drain in quantum atk . It's showing "Spatial regions extending into the electrodes are ignored during the electrode calculation"
Just to ask
:how to avoid or solve  " spatial region extended into the centre region, not calculated during electrode calculation in quantum atk"

Thank you




How to put proper dielectric & metal exactly at the centre region of the device?

Kindly let me know. Thank you.
9
General Questions and Answers / VO2 monoclinic (single crystal) - LCAO: SGGA+U convergence troubles
« Last post by pk364 on May 14, 2024, 16:27 »
Hello!

Since a while, I've been trying to simulate the bandgap of the much celebrated VO2 monoclinic phase (single crystal) using the LCAO calculator with SGGA+U (Hubbard), with PBES functionals and PseudoDojo (ultra) pseudopotentials. I hope to open its bandgap to ~0.6 eV (experimental value), which maybe quite challenging. I have chosen an antiferromagnetic initial configuration with the antiparallel spins on the Vanadium atoms.

However, I am unable to converge the calculations and they seem to be oscillating. The density matrix report is as follows:
Code
0 E = -265.535 dE =  1.841101e+02 dH =  1.067618e+00
1 E = -278.785 dE =  1.325025e+01 dH =  5.624259e-01
2 E = -193.078 dE =  8.570705e+01 dH =  1.724710e+02
3 E = -122.926 dE =  7.015169e+01 dH =  3.727634e+01
4 E = -268.054 dE =  1.451278e+02 dH =  3.569472e+01
5 E = -274.404 dE =  6.349619e+00 dH =  6.521554e+01
6 E = -320.104 dE =  4.569986e+01 dH =  3.719561e+01
7 E = -391.865 dE =  7.176161e+01 dH =  3.002920e+01
8 E = -394.076 dE =  2.210358e+00 dH =  3.168863e+01
9 E = -394.507 dE =  4.318557e-01 dH =  2.987522e+01
10 E = -387.011 dE =  7.496348e+00 dH =  2.968226e+01
11 E = -389.401 dE =  2.390098e+00 dH =  3.002361e+01
This goes on forever... until it is artificially stopped by the maximum no. of iterations!

As of now, I have tried to increase the density mesh cut-off and decrease history steps, but they yield no difference. Any suggestions to make this converge would be highly appreciated.

The full script is attached for reference:
Code
# -*- coding: utf-8 -*-
# -------------------------------------------------------------
# Bulk Configuration
# -------------------------------------------------------------

# Set up lattice
lattice = SimpleMonoclinic(5.1836*Angstrom, 5.0504022144*Angstrom, 9.0187*Angstrom, 90.58*Degrees)

# Define elements
elements = [Vanadium, Vanadium, Vanadium, Vanadium, Vanadium, Vanadium,
            Vanadium, Vanadium, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen,
            Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen,
            Oxygen, Oxygen]

# Define coordinates
fractional_coordinates = [[ 0.110304,  0.631185,  0.869553],
                          [ 0.110304,  0.868815,  0.369553],
                          [ 0.889696,  0.131185,  0.630447],
                          [ 0.889696,  0.368815,  0.130447],
                          [ 0.402394,  0.142849,  0.873272],
                          [ 0.402394,  0.357151,  0.373272],
                          [ 0.597606,  0.642849,  0.626728],
                          [ 0.597606,  0.857151,  0.126728],
                          [ 0.150305,  0.171076,  0.484713],
                          [ 0.150305,  0.328924,  0.984713],
                          [ 0.849695,  0.671076,  0.015287],
                          [ 0.849695,  0.828924,  0.515287],
                          [ 0.35536 ,  0.686591,  0.495905],
                          [ 0.35536 ,  0.813409,  0.995905],
                          [ 0.64464 ,  0.186591,  0.004095],
                          [ 0.64464 ,  0.313409,  0.504095],
                          [ 0.112774,  0.545407,  0.27475 ],
                          [ 0.112774,  0.954593,  0.77475 ],
                          [ 0.887226,  0.045407,  0.22525 ],
                          [ 0.887226,  0.454593,  0.72525 ],
                          [ 0.388671,  0.038549,  0.269627],
                          [ 0.388671,  0.461451,  0.769627],
                          [ 0.611329,  0.538549,  0.230373],
                          [ 0.611329,  0.961451,  0.730373]]

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

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Basis Set
#----------------------------------------
oxygen_1s = HydrogenOrbital(
    principal_quantum_number=1,
    angular_momentum=0,
    radial_cutoff_radius=3.89375*Angstrom,
    confinement_start_radius=3.115*Angstrom,
    charge=0.75,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

oxygen_2p = ConfinedOrbital(
    principal_quantum_number=2,
    angular_momentum=1,
    radial_cutoff_radius=4.1953125*Angstrom,
    confinement_start_radius=3.35625*Angstrom,
    additional_charge=0,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

oxygen_2p_0 = HydrogenOrbital(
    principal_quantum_number=2,
    angular_momentum=1,
    radial_cutoff_radius=4.1205078125*Angstrom,
    confinement_start_radius=3.29640625*Angstrom,
    charge=1.8,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

oxygen_2s = ConfinedOrbital(
    principal_quantum_number=2,
    angular_momentum=0,
    radial_cutoff_radius=3.1171875*Angstrom,
    confinement_start_radius=2.49375*Angstrom,
    additional_charge=0,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

oxygen_3d = HydrogenOrbital(
    principal_quantum_number=3,
    angular_momentum=2,
    radial_cutoff_radius=2.8125*Angstrom,
    confinement_start_radius=2.25*Angstrom,
    charge=7.6,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

oxygen_3d_0 = HydrogenOrbital(
    principal_quantum_number=3,
    angular_momentum=2,
    radial_cutoff_radius=3.287109375*Angstrom,
    confinement_start_radius=2.6296875*Angstrom,
    charge=5.6,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

oxygen_3p = HydrogenOrbital(
    principal_quantum_number=3,
    angular_momentum=1,
    radial_cutoff_radius=3.071875*Angstrom,
    confinement_start_radius=2.4575*Angstrom,
    charge=6.2,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

oxygen_3s = HydrogenOrbital(
    principal_quantum_number=3,
    angular_momentum=0,
    radial_cutoff_radius=3.55625*Angstrom,
    confinement_start_radius=2.845*Angstrom,
    charge=6.4,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

oxygen_4f = HydrogenOrbital(
    principal_quantum_number=4,
    angular_momentum=3,
    radial_cutoff_radius=2.78125*Angstrom,
    confinement_start_radius=2.225*Angstrom,
    charge=11.6,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

oxygen_5g = HydrogenOrbital(
    principal_quantum_number=5,
    angular_momentum=4,
    radial_cutoff_radius=2.57421875*Angstrom,
    confinement_start_radius=2.059375*Angstrom,
    charge=17.6,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

OxygenBasis = BasisSet(
    element=PeriodicTable.Oxygen,
    orbitals=[oxygen_2s, oxygen_2p, oxygen_2p_0, oxygen_3d, oxygen_3s, oxygen_4f, oxygen_3p, oxygen_3d_0, oxygen_5g, oxygen_1s],
    occupations=[3.5, 3.5, 2.0, -0.5, -0.5, -2.0, 0.0, 0.0, 0.0, 0.0],
    hubbard_u=[0.0, 0.95, 0.95, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]*eV,
    dft_half_parameters=Automatic,
    filling_method=SphericalSymmetric,
    onsite_spin_orbit_split=[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]*eV,
    pseudopotential=NormConservingPseudoPotential("normconserving/pseudodojo/gga/stringent/08_O.upf", local_potential_cutoff_threshold=1e-06*Hartree, local_potential_cutoff_radius=6.0*Bohr),
    )

vanadium_1s = HydrogenOrbital(
    principal_quantum_number=1,
    angular_momentum=0,
    radial_cutoff_radius=3.653125*Angstrom,
    confinement_start_radius=2.9225*Angstrom,
    charge=0.6,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

vanadium_3d = ConfinedOrbital(
    principal_quantum_number=3,
    angular_momentum=2,
    radial_cutoff_radius=3.46875*Angstrom,
    confinement_start_radius=2.775*Angstrom,
    additional_charge=0,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

vanadium_3d_0 = HydrogenOrbital(
    principal_quantum_number=3,
    angular_momentum=2,
    radial_cutoff_radius=4.348828125*Angstrom,
    confinement_start_radius=3.4790625*Angstrom,
    charge=3,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

vanadium_3d_1 = HydrogenOrbital(
    principal_quantum_number=3,
    angular_momentum=2,
    radial_cutoff_radius=2.94140625*Angstrom,
    confinement_start_radius=2.353125*Angstrom,
    charge=5.4,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

vanadium_3p = ConfinedOrbital(
    principal_quantum_number=3,
    angular_momentum=1,
    radial_cutoff_radius=2.8359375*Angstrom,
    confinement_start_radius=2.26875*Angstrom,
    additional_charge=0,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

vanadium_3s = ConfinedOrbital(
    principal_quantum_number=3,
    angular_momentum=0,
    radial_cutoff_radius=2.6171875*Angstrom,
    confinement_start_radius=2.09375*Angstrom,
    additional_charge=0,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

vanadium_4d = HydrogenOrbital(
    principal_quantum_number=4,
    angular_momentum=2,
    radial_cutoff_radius=4.412109375*Angstrom,
    confinement_start_radius=3.5296875*Angstrom,
    charge=7,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

vanadium_4f = HydrogenOrbital(
    principal_quantum_number=4,
    angular_momentum=3,
    radial_cutoff_radius=3.8875*Angstrom,
    confinement_start_radius=3.11*Angstrom,
    charge=9,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

vanadium_4f_0 = HydrogenOrbital(
    principal_quantum_number=4,
    angular_momentum=3,
    radial_cutoff_radius=2.3515625*Angstrom,
    confinement_start_radius=1.88125*Angstrom,
    charge=11.2,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

vanadium_4p = ConfinedOrbital(
    principal_quantum_number=4,
    angular_momentum=1,
    radial_cutoff_radius=2.545703125*Angstrom,
    confinement_start_radius=2.0365625*Angstrom,
    additional_charge=2,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

vanadium_4p_0 = HydrogenOrbital(
    principal_quantum_number=4,
    angular_momentum=1,
    radial_cutoff_radius=4.79296875*Angstrom,
    confinement_start_radius=3.834375*Angstrom,
    charge=5.6,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

vanadium_4s = ConfinedOrbital(
    principal_quantum_number=4,
    angular_momentum=0,
    radial_cutoff_radius=3.615625*Angstrom,
    confinement_start_radius=2.8925*Angstrom,
    additional_charge=0,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

vanadium_4s_0 = ConfinedOrbital(
    principal_quantum_number=4,
    angular_momentum=0,
    radial_cutoff_radius=2.305078125*Angstrom,
    confinement_start_radius=1.8440625*Angstrom,
    additional_charge=2,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

vanadium_5f = HydrogenOrbital(
    principal_quantum_number=5,
    angular_momentum=3,
    radial_cutoff_radius=3.48046875*Angstrom,
    confinement_start_radius=2.784375*Angstrom,
    charge=11.2,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

vanadium_5g = HydrogenOrbital(
    principal_quantum_number=5,
    angular_momentum=4,
    radial_cutoff_radius=2.73828125*Angstrom,
    confinement_start_radius=2.190625*Angstrom,
    charge=12.8,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

vanadium_5g_0 = HydrogenOrbital(
    principal_quantum_number=5,
    angular_momentum=4,
    radial_cutoff_radius=2.70703125*Angstrom,
    confinement_start_radius=2.165625*Angstrom,
    charge=14,
    confinement_strength=12.5*Hartree,
    confinement_power=2,
    radial_step_size=0.001*Bohr,
    )

VanadiumBasis = BasisSet(
    element=PeriodicTable.Vanadium,
    orbitals=[vanadium_3s, vanadium_3p, vanadium_4s, vanadium_3d, vanadium_4f, vanadium_3d_0, vanadium_4p, vanadium_5g, vanadium_4s_0, vanadium_3d_1, vanadium_5f, vanadium_4d, vanadium_4f_0, vanadium_4p_0, vanadium_5g_0, vanadium_1s],
    occupations=[2.0, 5.5, 5.0, 4.0, -3.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
    hubbard_u=[0.0, 0.0, 0.0, 5.2, 0.0, 5.2, 0.0, 0.0, 0.0, 5.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]*eV,
    dft_half_parameters=Automatic,
    filling_method=SphericalSymmetric,
    onsite_spin_orbit_split=[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]*eV,
    pseudopotential=NormConservingPseudoPotential("normconserving/pseudodojo/gga/standard/23_V.upf", local_potential_cutoff_threshold=1e-06*Hartree, local_potential_cutoff_radius=6.0*Bohr),
    )

basis_set = [
    OxygenBasis,
    VanadiumBasis,
    ]

#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = SGGAU.PBES

k_point_sampling = KpointDensity(
    density_a=4.0*Angstrom,
    )
numerical_accuracy_parameters = NumericalAccuracyParameters(
    density_mesh_cutoff=200.0*Hartree,
    k_point_sampling=k_point_sampling,
    )

iteration_control_parameters = IterationControlParameters(
    number_of_history_steps=15,
    )

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

bulk_configuration.setCalculator(calculator)

# -------------------------------------------------------------
# Initial State
# -------------------------------------------------------------
scaled_spins = [
    1.0,
    1.0,
    1.0,
    1.0,
    -1.0,
    -1.0,
    -1.0,
    -1.0,
    0.0,
    0.0,
    0.0,
    0.0,
    0.0,
    0.0,
    0.0,
    0.0,
    0.0,
    0.0,
    0.0,
    0.0,
    0.0,
    0.0,
    0.0,
    0.0,
]
initial_spin = InitialSpin(scaled_spins=scaled_spins)

bulk_configuration.setCalculator(
    calculator,
    initial_spin=initial_spin,
)
bulk_configuration.update()
nlsave('E:/Praful/20240503/VO2 Monoclinic script LCAO test.hdf5', bulk_configuration)
nlprint(bulk_configuration)

# -------------------------------------------------------------
# Bandstructure
# -------------------------------------------------------------
bandstructure = Bandstructure(
    configuration=bulk_configuration,
    route=['G', 'Y', 'C', 'Z', 'E', 'A', 'G', 'B', 'D', 'Z', 'G'],
    points_per_segment=20,
    bands_above_fermi_level=30,
    method=Full,
    )
nlsave('E:/Praful/20240503/VO2 Monoclinic script LCAO test.hdf5', bandstructure)


Kind regards,
Praful

10
General Questions and Answers / Re: Orbital coefficients
« Last post by Anders Blom on May 13, 2024, 20:17 »
It just need to have converged the molecular calculation. You can project on individual atoms (the example shows projection on N, H, H, H through the numbers 0,1,2,3.) or a collection of atoms by giving more than one index in the list.
Pages: [1] 2 3 ... 10