hi everyone,i found a strange phenomenon minutes ago;
first, a two-probe-configuration in my script ,the coordinates of the atoms in central-region is wrong,but when i drag it to vnl,the picture is just what i want to get.then i move the mouse to one atom of them,i find that the coordinate of that atom is not coincide with the coordinate of the script.How odd!
the picture is right.
from ATK.TwoProbe import *
# Li chain lattice constant
a =2.05
# Construct the electrode unit cell
unit_cell = [
[3*a, 0.0, 0.0 ],
[0.0, 3*a, 0.0 ],
[0.0, 0.0, 4*a ]
] * Angstrom
# Define the electrode
electrode_Co = PeriodicAtomConfiguration(
super_cell_vectors = unit_cell,
elements = 4*[Cobalt],
fractional_coordinates = [
(0.5, 0.5, float(i)/4.0) for i in range(0,4)]
)
# Setup the two-probe scattering region
# The atoms in the central region
elements =[Cobalt, Cobalt, Cobalt, Carbon,
Carbon, Carbon, Carbon, Carbon,
Hydrogen, Hydrogen, Hydrogen, Hydrogen,
Hydrogen, Iron, Carbon, Carbon,
Carbon, Carbon, Carbon, Hydrogen,
Hydrogen, Hydrogen, Hydrogen, Hydrogen,
Cobalt, Cobalt]
d=5
z=6*a+d
positions = [
[4.35, 4.35, 4*a],
[4.35, 4.35, 5*a],
[4.35,4.35,6*a],
[ 4.73919 , 5.54389999, z-1.60856],
[ 4.73877003, 3.16335998, z-1.60963],
[ 5.60394 , 4.3535 , z-1.61524],
[ 3.34037005, 5.08904997, z-1.61793],
[ 3.34012007, 3.61865 , z-1.61376],
[ 5.09579002, 6.64246998, z-1.53029],
[ 5.09504001, 2.06411991, z-1.53191],
[ 2.40435003, 5.76681004, z-1.54651],
[ 2.40367006, 2.94073997, z-1.55516],
[ 6.75891005, 4.35323 , z-1.54403],
[ 4.35 , 4.35 , z],
[ 4.73919 , 5.54389999, z+1.72744],
[ 4.73877003, 3.16335998, z+1.72637],
[ 5.60394 , 4.3535 , z+1.72076],
[ 3.34037005, 5.08904997, z+1.71807],
[ 3.34012007, 3.61865 , z+1.72744],
[ 5.09579002, 6.64246998, z+1.80409],
[ 5.09504001, 2.06411991, z+1.78949],
[ 2.40435003, 5.76681004, z+1.78084],
[ 2.40367006, 2.94073997, z+1.79197],
[ 6.75891005, 4.35323 , z+1.80571],
[4.35,4.35,z+d],
[4.35,4.35,z+d+a]
] * Angstrom
# Combine electrode and scattering region
# into a two-probe system
two_probe_conf = TwoProbeConfiguration(
electrodes = (electrode_Co,electrode_Co),
scattering_region_elements = elements,
scattering_region_cartesian_coordinates = positions,
)
# Export the two-probe configuration to a VNL file
vnl_file = VNLFile("CoFeCo.vnl")
vnl_file.addToSample(two_probe_conf, "CoFeCo")
