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General Questions and Answers / VCA methods to set Cs2AgBi_xSb_1-xBr6

« on: October 21, 2022, 06:29 »

Dear Sir

I need to set for VCA methods with Cs2AgBi_xSb_1-xBr6, which is a basis set to try in the tutorial

VirtualCrystalBasis = VirtualCrystalBasisSet([BasisGGASG15.Bismuth_Medium,BasisGGASG15.Antimony_Medium], x=x)

basis_set = [
    VirtualCrystalBasis,
    BasisGGASG15.Cesium_Medium,Silver_Medium,Bromine_Medium,
    ]

I got an error see below
[0x7FF80B7EACF0] ANOMALY: meaningless REX prefix used
+------------------------------------------------------------------------------+
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+------------------------------------------------------------------------------+
x_range [0.  0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1. ]
x_range [0.  0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1. ]
x_range [0.  0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1. ]
x_range [0.  0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1. ]
x_range [0.  0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1. ]
x_range [0.  0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1. ]
[0x7FF80B7EACF0] ANOMALY: meaningless REX prefix used
Traceback (most recent call last):
  File "vca2.py", line 50, in <module>
    BasisGGASG15.Cesium_Medium,Silver_Medium,Bromine_Medium,
AttributeError: '_BasisGGASG15' object has no attribute 'Cesium_Medium'
[0x7FF80B7EACF0] ANOMALY: meaningless REX prefix used
Traceback (most recent call last):
  File "vca2.py", line 50, in <module>
    BasisGGASG15.Cesium_Medium,Silver_Medium,Bromine_Medium,
AttributeError: '_BasisGGASG15' object has no attribute 'Cesium_Medium'
[0x7FF80B7EACF0] ANOMALY: meaningless REX prefix used
Traceback (most recent call last):
  File "vca2.py", line 50, in <module>
    BasisGGASG15.Cesium_Medium,Silver_Medium,Bromine_Medium,
AttributeError: '_BasisGGASG15' object has no attribute 'Cesium_Medium'
[0x7FF80B7EACF0] ANOMALY: meaningless REX prefix used
Traceback (most recent call last):
  File "vca2.py", line 50, in <module>
    BasisGGASG15.Cesium_Medium,Silver_Medium,Bromine_Medium,
AttributeError: '_BasisGGASG15' object has no attribute 'Cesium_Medium'
[0x7FF80B7EACF0] ANOMALY: meaningless REX prefix used
Traceback (most recent call last):
  File "vca2.py", line 50, in <module>
    BasisGGASG15.Cesium_Medium,Silver_Medium,Bromine_Medium,
AttributeError: '_BasisGGASG15' object has no attribute 'Cesium_Medium'
[0x7FF80B7EACF0] ANOMALY: meaningless REX prefix used
Traceback (most recent call last):
  File "vca2.py", line 50, in <module>
    BasisGGASG15.Cesium_Medium,Silver_Medium,Bromine_Medium,
AttributeError: '_BasisGGASG15' object has no attribute 'Cesium_Medium'
Traceback (most recent call last):
  File "vca2.py", line 50, in <module>
    BasisGGASG15.Cesium_Medium,Silver_Medium,Bromine_Medium,
AttributeError: '_BasisGGASG15' object has no attribute 'Cesium_Medium'
[0x7FF80B7EACF0] ANOMALY: meaningless REX prefix used
Traceback (most recent call last):
  File "vca2.py", line 50, in <module>
    BasisGGASG15.Cesium_Medium,Silver_Medium,Bromine_Medium,
AttributeError: '_BasisGGASG15' object has no attribute 'Cesium_Medium'

How can Solve it?
Thank you
Abdulmutta

VCA.py
# -*- coding: utf-8 -*-

x_range = numpy.linspace(0, 1.0, 11)
print('x_range', x_range)
for x in x_range:
    filename = 'cabb-x%i.hdf5' % (x*100)

# -------------------------------------------------------------
# Bulk Configuration
# -------------------------------------------------------------

# Set up lattice
lattice = Triclinic(8.12345201*Angstrom, 8.12345201*Angstrom, 8.12345201*Angstrom, 60.0*Degrees, 60.0*Degrees, 60.0*Degrees)

# Define elements
elements = [Caesium, Caesium, Silver, Bismuth, Bromine, Bromine, Bromine,
            Bromine, Bromine, Bromine]

# Define coordinates
fractional_coordinates = [[ 0.75    ,  0.75    ,  0.75    ],
                          [ 0.25    ,  0.25    ,  0.25    ],
                          [ 0.5     ,  0.5     ,  0.5     ],
                          [ 0.      ,  0.      ,  0.      ],
                          [ 0.749194,  0.250806,  0.250806],
                          [ 0.250806,  0.250806,  0.749194],
                          [ 0.250806,  0.749194,  0.749194],
                          [ 0.250806,  0.749194,  0.250806],
                          [ 0.749194,  0.250806,  0.749194],
                          [ 0.749194,  0.749194,  0.250806]]

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

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Basis Set
#----------------------------------------


VirtualCrystalBasis = VirtualCrystalBasisSet([BasisGGASG15.Bismuth_Medium,BasisGGASG15.Antimony_Medium], x=x)

basis_set = [
    VirtualCrystalBasis,
    BasisGGASG15.Cesium_Medium,Silver_Medium,Bromine_Medium,
    ]

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

k_point_sampling = MonkhorstPackGrid(
    na=4,
    nb=4,
    nc=4,
    )
numerical_accuracy_parameters = NumericalAccuracyParameters(
    density_mesh_cutoff=80.0*Hartree,
    k_point_sampling=k_point_sampling,
    )

calculator = LCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=numerical_accuracy_parameters,
    )

bulk_configuration.setCalculator(calculator)
nlprint(bulk_configuration)
bulk_configuration.update()
nlsave(filename, bulk_configuration)

# -------------------------------------------------------------
# Optimize Geometry
# -------------------------------------------------------------

constraints = [BravaisLatticeConstraint()]

bulk_configuration = OptimizeGeometry(
    bulk_configuration,
    max_forces=0.05*eV/Ang,
    max_stress=0.1*GPa,
    max_steps=200,
    max_step_length=0.2*Ang,
    constraints=constraints,
    trajectory_filename='None',
    optimizer_method=LBFGS(),
    constrain_bravais_lattice=True,
)
nlsave(filename, bulk_configuration)
nlprint(bulk_configuration)

# -------------------------------------------------------------
# Bandstructure
# -------------------------------------------------------------
bandstructure = Bandstructure(
    configuration=bulk_configuration,
    route=['Y', 'G', 'X', 'V', 'U', 'R', 'Z', 'T'],
    points_per_segment=20,
    bands_above_fermi_level=All,
    method=Full,
    )
nlsave(filename, bandstructure)