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1
Installation and License Questions / License error _ Kindly Advise_Reg
« Last post by techenthusiast on Today at 11:24 »
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See below for more details.

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License configuration (environment variables):
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For assistance on resolving this matter, there are several options:
2
General Questions and Answers / VO2 monoclinic (single crystal) - LCAO: SGGA+U convergence troubles
« Last post by pk364 on Yesterday at 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

3
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.
4
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?
5
General Questions and Answers / Loss function of the training/testing set
« Last post by aknair on May 10, 2024, 22:16 »
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.
6
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())
7
General Questions and Answers / Re: Orbital coefficients
« Last post by Anders Blom on May 9, 2024, 21:42 »
Lucky for you I actually wrote a script to do this about 10 years ago, but nobody seemed to need the functionality so we never made it a feature in the software.

The usage is pretty obvious; the return is a list (one entry per eigenstate) of arrays, which contain the "contributions" (projections) onto the angular momenta s, p, d, and f.

I tested with NH3 from the example in the manual (https://docs.quantumatk.com/manual/Types/ElectronDensity/ElectronDensity.html) and the run this slightly clumsy code

Code: python
from PartialNorm import getPartialNorms
molecule = nlread("nh3.hdf5", MoleculeConfiguration)[0]
# HOMO state is 3
ix = 3
partial_norms = getPartialNorms(molecule, projection_atoms=[0])
print(partial_norms[ix])
partial_norms = getPartialNorms(molecule, projection_atoms=[1])
print(partial_norms[ix])
partial_norms = getPartialNorms(molecule, projection_atoms=[2])
print(partial_norms[ix])
partial_norms = getPartialNorms(molecule, projection_atoms=[3])
print(partial_norms[ix])

We can then see that the HOMO level derives almost 90% from Nitrogen (mostly p-states), but if we change to ix=4 we note that LUMO has a lot more H contributions (and the LUMO state is, as expected, dominated by s-states). Hopefully this is helpful for the analysis of your molecule too.

This function can be used for a lot of other cool things, like mapping out where s and p states dominate in the band structure of GaAs (RGB color scale mapped from spd contributions) as in the attached picture!
8
General Questions and Answers / Re: Can't find builder(bulk, selection, device etc.) tools on the right
« Last post by Anders Blom on May 9, 2024, 20:32 »
Yes the same trick should work
9
General Questions and Answers / Re: Building type 1, 2, 3 quaternary heusler alloy
« Last post by Anders Blom on May 9, 2024, 20:32 »
Yeah that should be enough. Are these DOS lines at very low energy or around the Fermi level? Really hard to provide any help without the actual input and output...
10
General Questions and Answers / Re: Unit trouble dipole moments
« Last post by Anders Blom on May 9, 2024, 20:30 »
I don't think there should be any confusion about units? It prints
X Y Z of dipole: [ 7.50489746e-07 -5.50684384e-05  6.86097535e-01] Bohr**4*e
to the file, and if you had printed the magnitude as you perhaps intended (you write m1 to the file) it would have shown
0.686097536725 Bohr**4*e

(The numbers are not your numbers as I don't have your molecule, I just use NH3 as an example)

Oh, I see you still use the old wrong script from the manual. You need to remove * length_unit**3 from the line defining dV
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