Messages

1

General Questions and Answers / Transport properties for Optimized Structures

« on: August 14, 2025, 14:35 »

Hello everyone,

I’m facing an issue when trying to convert a bulk structure into a device for transport property calculations. I can successfully perform the bulk-to-device conversion for the original (unoptimized) structures. I want to apply pressure on the material and calculate the transport properties which is an available feature in the "Optimize Geometry" block. However, after geometry optimization, I’m unable to convert the optimized structure into a device.

Could you please explain why this happens and how I can convert the optimized structure into a device?

Note:     Ori.png: Original structure>Surface Cleave (Thickness=5)>Device from Bulk
Optgeom1.png: Optimized Structure>Surface Cleave
Optgeom2.png: Surface Cleave (of Optimized structure)>Device from Bulk

Additionally, I’d like to know how to calculate the transport properties of amorphous materials, and what would be an maximum number of atoms to use for such calculations.

Thanks in advance for your help!

2

General Questions and Answers / Re: WYCKOFF POSITIONS FROM CRYSTAL STRUCTURE PREDICTION SCRIPTOR

« on: August 14, 2025, 09:19 »

Thank you for providing the solution. It was really useful.

3

Links to Resources and Publications / Re: Paper from 2024 ("Device from bulk" inactive in GUI)

« on: August 14, 2025, 09:14 »

Dear Anders Blom,
Thank you for your response. I found your advice very insightful. However, I am not entirely sure how to set the electrode direction (C) so that it is perpendicular to the two AB directions. Could you please elaborate on this procedure?


Thank you once again.

4

General Questions and Answers / Re: WYCKOFF POSITIONS FROM CRYSTAL STRUCTURE PREDICTION SCRIPTOR

« on: August 12, 2025, 19:14 »

The simulation was brief, and the code is shown below
# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------

potentialSet = Pedone_2006Fe2()
calculator = TremoloXCalculator(parameters=potentialSet)
calculator.setVerletListsDelta(0.25*Angstrom)

# -------------------------------------------------------------
# Elements
# -------------------------------------------------------------

elements = [Oxygen, Oxygen, Oxygen, Oxygen, Titanium, Titanium]

# -------------------------------------------------------------
# Random Number Generator
# -------------------------------------------------------------

rng = numpy.random.RandomState()

# -------------------------------------------------------------
# Initial Population
# -------------------------------------------------------------

initial_population = generateInitialPopulation(
    elements=elements,
    population_size=10,
    calculator=calculator,
    volume=51.57*Angstrom**3,
    max_forces=0.01*eV/Angstrom,
    max_stress=0.1*GPa,
    max_steps=1000,
    max_step_length=0.2*Angstrom,
    external_pressure=0.0*GPa,
    rng=rng,
    log_filename_prefix="initial_population_",
    )

# -------------------------------------------------------------
# Crystal Structure Prediction
# -------------------------------------------------------------

crystal_structure_prediction = CrystalStructurePrediction(
    initial_population,
    number_of_generations=20,
    selection_pressure=2.0,
    number_of_elites=10,
    number_to_promote=4,
    heredity_probability=50.0,
    permutation_probability=20.0,
    mutation_probability=30.0,
    sigma_lattice=0.7,
    max_forces=0.01*eV/Angstrom,
    max_stress=0.1*GPa,
    max_steps=1000,
    max_step_length=0.2*Angstrom,
    external_pressure=0.0*GPa,
    rng=rng,
    write_population=True,
    log_filename_prefix="generation_",
    )

5

Links to Resources and Publications / Paper from 2024 ("Device from bulk" inactive in GUI)

« on: August 11, 2025, 14:12 »

Hi all,

I’m trying to calculate the thermal properties of Bi₂Te₃ (space group R3m) following the methodology from a paper (https://doi.org/10.1016/j.scriptamat.2024.115991). I was able to successfully compute the density of states (DOS) for the bulk structure.

However, I’m having trouble creating a device configuration from the bulk structure. The “Device from Bulk” option in the GUI is grayed out (inactive), so I can’t define electrodes.

Could anyone explain why this option might be unavailable, and how I should proceed to set up a device model from the bulk structure?

Thanks in advance!

6

General Questions and Answers / Re: WYCKOFF POSITIONS FROM CRYSTAL STRUCTURE PREDICTION SCRIPTOR

« on: August 5, 2025, 13:58 »

Dear Anders Blom,

Thank you for your response. However, upon clicking the "Unpack" option, I encountered the following error:

'numpy.float64' object has no attribute 'inUnitsOf'

I would appreciate your guidance on how to resolve this issue.

7

General Questions and Answers / CALCULATED CARRIER CONCENTRATION

« on: August 4, 2025, 14:06 »

Greetings,
I am currently facing an issue while attempting to simulate carrier concentration—specifically, the function "carrier_conc" is not recognized. My objective is to compute carrier concentration as a function of chemical potential.

Could you please guide me on how to correctly perform these simulations?

Here is the code I am using:


# %% BulkConfiguration_0 (1)

# Set up lattice
vector_a = [3.950731, 0.0, 0.0]*Angstrom
vector_b = [0.0, 3.950731, 0.0]*Angstrom
vector_c = [0.0, 0.0, 3.950731]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
elements = [Titanium, Tin, Oxygen, Oxygen, Oxygen]

# Define coordinates
fractional_coordinates = [[ 0.5,  0.5,  0.5],
                          [ 0. ,  0. ,  0. ],
                          [ 0. ,  0.5,  0.5],
                          [ 0.5,  0.5,  0. ],
                          [ 0.5,  0. ,  0.5]]

# Set up configuration
bulkconfiguration_0_1 = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )

bulkconfiguration_0_1_name = "bulkconfiguration_0_1"


# %% Set LCAOCalculator

# %% LCAOCalculator

k_point_sampling = KpointDensity(
    density_a=4.0 * Angstrom, density_b=4.0 * Angstrom, density_c=4.0 * Angstrom
)

numerical_accuracy_parameters = NumericalAccuracyParameters(
    k_point_sampling=k_point_sampling
)

calculator = LCAOCalculator(
    numerical_accuracy_parameters=numerical_accuracy_parameters,
    checkpoint_handler=NoCheckpointHandler,
)


# %% Set Calculator

bulkconfiguration_0_1.setCalculator(calculator)

bulkconfiguration_0_1.update()

nlsave('BulkConfiguration_0_1_results.hdf5', bulkconfiguration_0_1)


# %% DensityOfStates

density_of_states = DensityOfStates(configuration=bulkconfiguration_0_1)
carrier_conc=calculateCarrierConcentration(contribution=Electron,fermi_shift=None,temperature=None)
nlsave('BulkConfiguration_0_1_results.hdf5', density_of_states)
nlsave('BulkConfiguration_0_1_results.hdf5', carrier_conc)


Thank you in advance for your support.

8

General Questions and Answers / Re: WYCKOFF POSITIONS FROM CRYSTAL STRUCTURE PREDICTION SCRIPTOR

« on: August 1, 2025, 06:08 »

By "output," I’m referring to the structure displayed in the Builder. However, when I click on the HDF5 file, there is no option such as "Create" or "Open in Builder." Although I can view the structure using the "Viewer" and access structural details, I’m unable to export or send the structure directly to the Builder for further modification.

9

General Questions and Answers / WYCKOFF POSITIONS FROM CRYSTAL STRUCTURE PREDICTION SCRIPTOR

« on: July 31, 2025, 09:59 »

Dear Experts,
I need your assistance regarding the output of a crystal structure prediction script. I want to create a structure for a material and have been following the crystal structure prediction tutorial. However, I noticed that the output does not include structural details such as the Wyckoff positions or lattice parameters (a, b, c, and angles α, β, γ).

How can I extract these details from the predicted structures?

10

General Questions and Answers / Boltzman Transport Calculations

« on: July 22, 2025, 12:52 »

I am currently working on the following research paper: https://www.mdpi.com/2073-4352/12/9/1317, and I am seeking guidance on using Boltzmann transport theory to calculate the Seebeck coefficient and thermal conductivity.

Specifically, I am having difficulty understanding how to compute the Seebeck and Hall coefficients as functions of chemical potential. I would greatly appreciate your insights or any relevant references that could help clarify this process.

11

General Questions and Answers / Re: Optimized geometry configuration is not visible

« on: April 29, 2025, 12:51 »

Thank you!

12

General Questions and Answers / Re: Documentation example is not working

« on: April 29, 2025, 12:50 »

Yes after trying this *elementary_charge, the error popping up with the elastic Constants saying an unexpected keyword argument 'scf_restart_step_length'. i tried after removing the line 'scf_restart_step_length=0.1*Angstrom' from the elastic constants. The simulation finishes but now resultant structure (.hdf5) was not generated. What would be the issue?

13

General Questions and Answers / Optimized geometry configuration is not visible

« on: April 28, 2025, 14:51 »

Hi everyone, I'm facing an error after running a Molecular Dynamics simulation that involves the following steps- Heating, quenching and geometry optimization. The simulation finishes successfully. However, when I try to open the optimized geometry in the Builder, the screen appears blank and no structure is visible. But i get to see the configuration in the data preview but if we try to open it in the viewer/Builder the blank screen without configuration is viewing. What could be the possible reasons for this behavior? How can I resolve or debug this issue?

14

General Questions and Answers / Re: Documentation example is not working

« on: April 28, 2025, 07:04 »

Thank you for your response. I also tried it with *e but the error still persists : "NameError: name 'e' is not defined".
Here's the link to the file:https://docs.quantumatk.com/tutorials/combining_potentials/combining_potentials.html

15

General Questions and Answers / Documentation example is not working

« on: April 24, 2025, 10:02 »

https://docs.quantumatk.com/_downloads/230cae9ab632421ed113e69e59fb14aa/TiO2_Matsui.py
shows error
Traceback (most recent call last):
  File "/home/qtk/quantumatk/W-2024.09/bin/../atkpython/bin/atkpython", line 8, in <module>
    sys.exit(__run_atkpython())
             ^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 803, in __run_atkpython
  File "Tio2.py", line 32, in <module>
    potentialSet.addParticleType(ParticleType(symbol='O', mass=15.9994*atomic_mass_unit, charge=-1.098))
                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "build/atkpython/lib/python3.11/site-packages/tremolox/potentials/particletype.py", line 90, in __init__
  File "build/atkpython/lib/python3.11/site-packages/tremolox/potentials/potentialbase.py", line 335, in setParameter
  File "build/atkpython/lib/python3.11/site-packages/tremolox/potentials/potentialbase.py", line 155, in __setitem__
  File "build/atkpython/lib/python3.11/site-packages/tremolox/potentials/checks.py", line 139, in apply
TypeError: The parameter charge = -1.098 must have a unit that can be converted to e.