Show Posts
16
News and Announcements / MoS2 and MoSe2 structures in Database, incorrect coordinates
« on: June 14, 2013, 15:55 »
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
and
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.
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.
Besides, all operations have a point: we need to go from hexagonal to ortho, we need to repeat, and to extend the unit cell to fit the tube. The only non-obvious thing is perhaps the Swap Axes operations. These are there because the Tube Wrapper assumes a certain orientation of the system. The alternative would have been to allow selection of axes in the plugin, but that also comes with some logical complications.