MoS2 and MoSe2 structures in Database, incorrect coordinates

[Anders Blom]

It has come to our attention, via the article Phys. Chem. Chem. Phys. 4, 4078 (2002) that the structures we have used in the Database in VNL for MoS₂ and MoSe₂ are not correct. This is, in fact, an error that has propagated into many standard references, such as Wyckoff's famous book which is what we used when generating the database. To fix the problem manually, the correct structures should be

Code: python

# Set up lattice
lattice = Hexagonal(3.1604*Angstrom, 12.295*Angstrom)

# Define elements
elements = [Molybdenum, Molybdenum, Sulfur, Sulfur, Sulfur, Sulfur]

# Define coordinates
fractional_coordinates = [[ 0.33333333,  0.66666667,  0.25      ],
                          [ 0.66666667,  0.33333333,  0.75      ],
                          [ 0.33333333,  0.66666667,  0.621     ],
                          [ 0.66666667,  0.33333333,  0.121     ],
                          [ 0.33333333,  0.66666667,  0.879     ],
                          [ 0.66666667,  0.33333333,  0.379     ]]

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

and

Code: python

# Set up lattice
lattice = Hexagonal(3.288*Angstrom, 12.9*Angstrom)

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

# Define coordinates
fractional_coordinates = [[ 0.33333333,  0.66666667,  0.25      ],
                          [ 0.66666667,  0.33333333,  0.75      ],
                          [ 0.33333333,  0.66666667,  0.621     ],
                          [ 0.66666667,  0.33333333,  0.121     ],
                          [ 0.33333333,  0.66666667,  0.879     ],
                          [ 0.66666667,  0.33333333,  0.379     ]]

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

The error will be fixed for ATK 13.8, and it should also be noted that if you run a geometry optimization (as you always should!) the mistake corrects itself. However, if you fail to do this, strange things will happen, and for instance the band gap of a MoS2 monolayer will be very wrong.

[Anders Blom]

Just as a note, this IS indeed fixed in ATK 13.8.