Messages

1

General Questions and Answers / Re: ComplexMatrix error in fatbandstructure calculation

« on: December 5, 2023, 04:51 »

Thank you , and I attached the python file of my code.

Thank you again in advance for checking out.

2

General Questions and Answers / Re: ComplexMatrix error in fatbandstructure calculation

« on: December 4, 2023, 05:45 »

Thank you for your reply.

I am using the 2022-12 version of quantumATK, and below is my input python file.

# %% MoS2_WTe2_60degree_ortho_pointcheck

[atomic configuration ... info is deleted because of the character limitation]

# %% Set LCAOCalculator_DFT_D3_Neu_Dir_higher_cutoff_density_new

# %% LCAOCalculator

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

correction_extension = GrimmeDFTD3(
    maximum_neighbour_distance=60.0*Angstrom,
    exchange_correlation=exchange_correlation
)

k_point_sampling = MonkhorstPackGrid(
    na=2,
    nb=1,
    nc=1
)

numerical_accuracy_parameters = NumericalAccuracyParameters(
    k_point_sampling=k_point_sampling
)

poisson_solver = FastFourier2DSolver(
    boundary_conditions=[
        [PeriodicBoundaryCondition(), PeriodicBoundaryCondition()],
        [PeriodicBoundaryCondition(), PeriodicBoundaryCondition()],
        [NeumannBoundaryCondition(), DirichletBoundaryCondition()]
    ]
)

checkpoint_handler = NoCheckpointHandler

calculator = LCAOCalculator(
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=numerical_accuracy_parameters,
    poisson_solver=poisson_solver,
    checkpoint_handler=checkpoint_handler,
    correction_extension=correction_extension
)


# %% Set Calculator

mos2_wte2_60degree_ortho_pointcheck.setCalculator(calculator)

mos2_wte2_60degree_ortho_pointcheck.update()

nlsave('MoS2_WTe2_60degree_ortho_pointcheck_results.hdf5', mos2_wte2_60degree_ortho_pointcheck)


# %% ChemicalPotential

chemical_potential = ChemicalPotential(
    configuration=mos2_wte2_60degree_ortho_pointcheck
)
nlsave('MoS2_WTe2_60degree_ortho_pointcheck_results.hdf5', chemical_potential)


# %% ProjectedDensityOfStates_elements

kpoints = MonkhorstPackGrid(
    na=3,
    nb=2,
    nc=1
)

projected_density_of_states = ProjectedDensityOfStates(
    configuration=mos2_wte2_60degree_ortho_pointcheck,
    kpoints=kpoints,
    projections=ProjectOnElements,
    energies=numpy.linspace(-4.0, 4.0, 801)*eV,
    spectrum_method=GaussianBroadening(
        broadening=0.01*eV
    )
)
nlsave('MoS2_WTe2_60degree_ortho_pointcheck_results.hdf5', projected_density_of_states)


# %% FatBandstructure_elements

fat_bandstructure = FatBandstructure(
    configuration=mos2_wte2_60degree_ortho_pointcheck,
    route=('G', 'Y', 'C', 'X', 'G', 'C'),
    points_per_segment=100,
    projections=ProjectOnElements
)
nlsave('MoS2_WTe2_60degree_ortho_pointcheck_results.hdf5', fat_bandstructure)




Thank you in advance.

3

General Questions and Answers / Re: How can I set a specific atom to an anion or a cation?

« on: December 3, 2023, 10:16 »

Thank you for your reply.

I am trying to do DFT calculation, but I think in my system the slight charge difference induced by charge transfer is not that important.

Now I am using 2022.12 version of quantumATK, and in Builder > Coordinate Tools > Partial Charges section, I can find that there are three parts that I can define.

1. Set Partial Charges (e)
2. Total Charge (e)
3. Scale Charges

I was thinking of setting the partial charge (which is 1. above), but I am not sure about the scale charges (which is 3. above).
Is it okay if I just set the scale charge by the reference ionic scale (ionic radius)?

Thank you again in advance.

4

General Questions and Answers / How can I set a specific atom to an anion or a cation?

« on: November 26, 2023, 11:50 »

Using the bulk configuration, I want to add an anion or a cation with the builder.

Is setting the partial charge by selecting the wanted atom correct for transforming the atom to ion?

For example, I add Fluorine in my structure and want to transform it into -1 charged Fluorine ion.
Can I do that by selecting the Fluorine atom and change the 'Set Partial Charges' to minus 1, in the "Coordinate Tools > Partial Charges"?

5

General Questions and Answers / ComplexMatrix error in fatbandstructure calculation

« on: November 22, 2023, 07:15 »

Hi, I am trying to calculate the fatbandstructure of a heterostructure which includes two different 2D layers.

The system has about 700 atoms including the ghost atoms, since we are trying to estimate the workfunction (or Fermi level) more accurately.

Anyway, the calculator I have set was chemical potential, projected density of states, and fatbandstructure.
The rest of the calculations are completed, but I got the following error sign...

   File "/home/JW/quantumatk/MoS2-WTe2/vdW_study_without_zdirection_constant/Output/MoS2_WTe2_60degree_ortho_pointcheck_results_231121_h51vapb4/MoS2_WTe2_60degree_ortho_pointcheck_results.py", line 1041, in <module>
    fat_bandstructure = FatBandstructure(
  File "zipdir/NL/Analysis/FatBandstructure.py", line 207, in __init__
  File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/Analysis/Projections.py", line 170, in calculateEigenvaluesAndProjectionWeights
  File "zipdir/NL/ComputerScienceUtilities/ParallelTools/StaticTaskScheduler.py", line 229, in run
  File "zipdir/NL/ComputerScienceUtilities/ParallelTools/StaticTaskScheduler.py", line 282, in __runInParallelMode
  File "zipdir/NL/ComputerScienceUtilities/ParallelTools/StaticTaskScheduler.py", line 304, in __performTask
  File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/Analysis/Projections.py", line 155, in kPointTask
  File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/Analysis/Projections.py", line 449, in calculateProjectionWeightsAndEigenvalues
TypeError: unsupported operand type(s) for *: 'ComplexMatrix' and 'ComplexMatrix'
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 35


Has anyone seen this kind of error? Help me, please