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Fixing atoms during the optimization

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gayani2025:
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') 
                                                                                     

AsifShah:
Hi,

Looks right.

But out of curiosity, why would you keep W as fixed in WS2?

gayani2025:
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.

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