Messages

31

General Questions and Answers / AFM images

« on: June 3, 2025, 07:23 »

Dear All,

I need to obtain AFM images
1. I have seen AFM Cantilever Tip in the Builders. Can I use this?
2. Is there a tutorial or example I can refer?

Thanks
GN

32

Scripts, Tutorials and Applications / Re: Fixing atoms during the optimization

« on: June 3, 2025, 00:05 »

Thank you very much for the reply. 

No I just want to check whether I have done this correctly. So started with a simple example.

33

Scripts, Tutorials and Applications / Fixing atoms during the optimization

« on: May 30, 2025, 08:16 »

Dear All,

I have generated below file to do the geometry optimization with fix W atom. If I want to just fix the W atom without moving is this the correct way of doing this. Pls advice.  Thnaks


# Set up lattice
vector_a = [3.29, 0.0, 0.0]*Angstrom
vector_b = [-1.645, 2.849223578450803, 0.0]*Angstrom
vector_c = [0.0, 0.0, 22.97]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
elements = [Selenium, Tungsten, Selenium]

# Define coordinates
fractional_coordinates = [[ 0.            ,  0.            ,  0.418969960818],
                          [ 0.333333333333,  0.666666666667,  0.49180975185 ],
                          [ 0.            ,  0.            ,  0.564649542882]]

# Set up configuration
wse2_0001 = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )

# Add tags
wse2_0001.addTags('W', [1])

wse2_0001_name = "wse2_0001"


# %% Set LCAOCalculator

# %% LCAOCalculator

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

correction_extension = GrimmeDFTD3(exchange_correlation=exchange_correlation)

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

numerical_accuracy_parameters = NumericalAccuracyParameters(
    density_mesh_cutoff=500.0 * eV,
    k_point_sampling=k_point_sampling,
    occupation_method=GaussianSmearing(broadening=600.0 * Kelvin),
) 
calculator = LCAOCalculator(
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=numerical_accuracy_parameters,
    checkpoint_handler=NoCheckpointHandler,
    correction_extension=correction_extension,
)


# %% Set Calculator

wse2_0001.setCalculator(calculator)

nlsave('WSe2_0001_results.hdf5', wse2_0001)


# %% OptimizeGeometry

fix_atom_indices_0 = wse2_0001.indicesFromTags(['W'])

constraints = [FixAtomConstraints(fix_atom_indices_0)]

restart_strategy = RestartFromTrajectory(
    trajectory_filename='WSe2_0001_resultsopt.hdf5', object_id='optimize_trajectory'
)

optimized_configuration = OptimizeGeometry(
    configuration=wse2_0001,
    constraints=constraints,
    trajectory_filename='WSe2_0001_resultsopt.hdf5',
    trajectory_object_id='optimize_trajectory',
    restart_strategy=restart_strategy,
)

nlsave('WSe2_0001_resultsopt.hdf5', optimized_configuration, object_id='optgeom') 
                                                                                     

34

Scripts, Tutorials and Applications / Optimization issue of gold-perovskite system

« on: May 23, 2025, 07:34 »

Dear All,

I'm trying to run optimization of a gold-perovskite system. I have attached the inputs and log files. Can you please comment on how to resolve this. Thanks

[Wed May  7 16:17:22 2025]: Connection to server lost - reconnection attempt 4/5.
====================[Wed May  7 16:19:22 2025]: Connection to server terminated after failing 5 heartbeats
==============================

                            |--------------------------------------------------|
Calculating Density Matrix : ==================================================


===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 0 PID 252154 RUNNING AT in-005.stdct.loc
=   KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                        Resource Usage on 2025-05-07 16:29:11.463864:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        JobId: 80364.stdct-mgmt-02
        Project: personal-gayaninp
        Exit Status: 0
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        NCPUs: Requested(24), Used(24)
        CPU Time Used: 261:59:27
        Memory: Requested(46080mb), Used(5241176kb)
        Vmem Used: 8168140kb
        Walltime: Requested(168:00:00), Used(25:59:16)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        Execution Nodes Used: (IN-005[0]:ncpus=24:mem=47185920kb)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        No GPU-related information available for this job.

35

Scripts, Tutorials and Applications / K Path for the Band structure

« on: April 28, 2025, 10:22 »

Hi,

I am currently setting up a test run for the Te band structure calculation. I started with α-Te and generated an orthorhombic cell. I would like to calculate the band structure along the path Γ–X–S–Y–Γ. However, when I try to specify this path in the Brillouin Zone route, I encounter an error.

Could you please advise me on how to correctly define the k-point path for this orthorhombic structure in QuantumATK? Any suggestions would be greatly appreciated.

36

General Questions and Answers / Twister

« on: April 10, 2025, 06:56 »

Dear All,

Dear All,

This is my first time using QuantumATK, and I am currently working through some tutorials to get familiar with the software.


I noticed that there is an option called "Twister" (Exploring Graphene tutorial). However, I am unable to locate this feature in the version I’m using (W-2024.09-SP1).

Could you kindly guide me on where to find this option or let me know if it has been relocated or renamed in this version?

Thank you very much for your assistance.

Best regards,
GN