Messages

16

General Questions and Answers / Re: spin

« on: May 31, 2010, 10:59 »

hey,budey
sodium doesn't belong to magnetic metal.it doesn't matter whether changing its spin or not.

it doesn't have much influence on transmission.

17

General Questions and Answers / Re: IndexError: index out of bounds

« on: May 28, 2010, 16:11 »

it may help if you construct the bulk in crystal cupboard.

18

General Questions and Answers / Re: How to construct a molecule on graphene?

« on: May 28, 2010, 16:09 »

i am new too.i think it is more convinent to construct the configuration with ATK.
i suggest you read the tutorial of ATK.it is extremly useful most of the time.
You can add any atom and coordinate by using the code.

19

General Questions and Answers / Re: Required for two probe system

« on: May 28, 2010, 16:03 »

but i think that the totorial is not enough,when i want to know the equations being used .
what should i do?

20

Scripts, Tutorials and Applications / Re: Function for calculating Projected Density of States

« on: May 27, 2010, 06:13 »

wonderful jobs.
By the way ,Anders B,you are skillful with Python.

21

General Questions and Answers / Re: Required

« on: May 26, 2010, 03:21 »

just change the parameters to what you want  in the code ,or it will keep default.

22

General Questions and Answers / Re: help explaining the physical meaning of these words

« on: May 24, 2010, 15:30 »

thank you for your good-to-excellent help.

23

General Questions and Answers / help explaining the physical meaning of these words

« on: May 22, 2010, 16:00 »

SingleZeta

SingleZetaPolarized; SingleZeta plus one basis orbital for the first unoccupied shell

DoubleZeta; two basis orbitals for each valence orbital

DoubleZetaPolarized; DoubleZeta plus one basis orbital for the first unoccupied shell

DoubleZetaDoublePolarized



Can someone explain these words to me ?And tell me their difference.
Thank you.

24

General Questions and Answers / Re: how to set the length of center scattering region?

« on: May 19, 2010, 14:04 »

add more surface atoms(same as electrode atoms)may help.

25

General Questions and Answers / Re: what's the meaning of this error?

« on: May 19, 2010, 14:01 »

thank you N

26

General Questions and Answers / what's the meaning of this error?

« on: May 15, 2010, 02:57 »

Traceback (most recent call last):
  File "opt_CoFe.py", line 99, in ?
    runtime_parameters = runtime_params
NLInternalError: Quasi Newton minimization unable to reach minimum with given force tolerance.


after optimizing the geometry,here comes the error.i don't know what to do .
somebody help me ,thanks very much

27

General Questions and Answers / Re: Very werid problem!

« on: May 11, 2010, 14:18 »

true

28

General Questions and Answers / Re: an extremely weird problem( between the code and VNL)

« on: May 9, 2010, 03:28 »

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

29

General Questions and Answers / Re: an extremely weird problem( between the code and VNL)

« on: May 8, 2010, 16:07 »

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

30

General Questions and Answers / an extremely weird problem( between the code and VNL)

« on: May 8, 2010, 16:04 »

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