Print Page - an extremely weird problem( between the code and VNL)

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. ???

Code

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")

drag it to vnl,and observe its X,Y coordinates.
Can somebody explain it ?Thanks

vnl's version is 2008.....
besides,does the wrong coordinate with right picture have an effect on the self-consistent calculation?

It's really not as weird as it might seem once you understand how two-probe systems are constructed. I suggest you carefully study slides 8-11 in the basic ATK 2008.10 tutorial (http://quantumwise.com/documents/tutorials/ATK_TutorialSession_Part1_SCF.pdf). And then it's probably a good idea to read all the other slides too, plus the one on analysis (http://quantumwise.com/documents/tutorials/ATK_TutorialSession_Part2_Analysis.pdf)! :)

Also note that in ATK 2010.xx, two-probe systems are set up a bit differently.

thank you Anders Blom for your tutorial,i will read it as soon. :)

QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: youngjfly on May 8, 2010, 16:04