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11
General Questions and Answers / Missing SK Parameters from Install
« Last post by schintapalli on May 21, 2024, 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?
12
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
13
Good afternoon,

Is there any limitation for number of  execution of Simulation? Some time its showing licensing error.
Thank You.
14
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
15
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.
16
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

17
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.
18
General Questions and Answers / Re: Orbital coefficients
« Last post by lohy on May 13, 2024, 08:38 »
Wonderful thank you!  - you had a great idea 10 years ago  :)

Just to be sure, the script "only" needs the configuration and the energy state of the molecule I am interested in? and then I can choose which atoms I want to project on? where you have e.g. 0, can I then have a list or do I need to have a line for each atom in the molecule?
19
How to get/plot the loss function for the training/testing set of the moment tensor potential, i.e., variation in the error with respect to the number of epochs.
20
General Questions and Answers / Re: Random Swap of Elements
« Last post by Anders Blom on May 10, 2024, 00:17 »
Python coding...
You can easily access the elements in a structure with configuration.elements(), that gives a list of the elements, you can then use the random.random() function to pick indices in a relevant way, replace an element and then put it back into the configuration with the secret method configuration._changeAtoms(elements=new_elements).

Or you can just remake the configuration from it's old parts:
new_configuration = BulkConfiguration(old_configuration.bravaisLattice(), new_elements, old_configuration.cartesianCoordinates())
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