How to define the "Equivalent atoms" by hand ?

[fangyongxinxi]

Dear Sir,
I use ATK 2008, and want to get the equivalent atoms by hand, not by the default value.
My 2 questions are:
1. For the id_number_scattering_region, we can see it from the scattering region,
but  how can I get the id_number_left_electrode and the id_number_right_electrode.
2. It's neseccary to make the four atoms in a line ?
Thank you.

[youngjfly]

question2:it is not necessary to make them in a line .only ensure their difference of z coordinates
id_numbers_Left_electrode means what?

[zh]

Dear Sir,
I use ATK 2008, and want to get the equivalent atoms by hand, not by the default value.
My 2 questions are:
1. For the id_number_scattering_region, we can see it from the scattering region,
but  how can I get the id_number_left_electrode and the id_number_right_electrode.
2. It's neseccary to make the four atoms in a line ?
Thank you.

Print out the coordinates of atoms in the left and right electrodes. One can easily get the id number of each atom. When one chooses the equivalent atoms to align the electrodes and scatter region, the most important thing is to make the electrode and scattering region be connected perfectly, i.e., the periodicity of electrodes can be kept in the surface layers  of scattering region.

It is no necessary to make these four atoms in a line.

[fangyongxinxi]

Dear Sir,
I use ATK 2008, and want to get the equivalent atoms by hand, not by the default value.
My 2 questions are:
1. For the id_number_scattering_region, we can see it from the scattering region,
but  how can I get the id_number_left_electrode and the id_number_right_electrode.
2. It's neseccary to make the four atoms in a line ?
Thank you.

Print out the coordinates of atoms in the left and right electrodes. One can easily get the id number of each atom. When one chooses the equivalent atoms to align the electrodes and scatter region, the most important thing is to make the electrode and scattering region be connected perfectly, i.e., the periodicity of electrodes can be kept in the surface layers  of scattering region.

It is no necessary to make these four atoms in a line.

Dear Zh,
I still not clear about how to get the ID number of atoms in the electrodes.
Till now, I can get the ID number of the atoms in the scattering region, but for the atom ID number in the electrode, I don't know how to get them, because in this software, I don't find anywhere could display the positions of the electrode atoms, so I don't know how to get the exact ID number.
Looking for your reply. Thank you.

[fangyongxinxi]

move on.
In the ATK 2008 manual, page 411, take the picture Figure_66 for example.
we can see the id numbers (0-6) of the scattering region in the "Atomic Manipulator",
where could I find the id numbers of the electrodes atoms left_( 0-5), right_(0-2) ?

[zh]

Firstly, call "nlPrint(your configuration)" to print out the atomic coordinates of your configuration; and then collect it and make a file with XYZ format. Finally, visualize this xyz file with "JMOL" software (free), in this software, the id numbers of atoms (one thing should be pointed out, the id numbers in JMOL start from 1 rather than 0. In ATK, the id number starts from 0.) can be easily obtained by selecting "Display--->Label--->Name".

[zh]

move on.
In the ATK 2008 manual, page 411, take the picture Figure_66 for example.
we can see the id numbers (0-6) of the scattering region in the "Atomic Manipulator",
where could I find the id numbers of the electrodes atoms left_( 0-5), right_(0-2) ?

The id numbers of atoms can not be directly indicated using ATK. This figure is just a schematic one. 

[Anders Blom]

Fortunately, no equivalent atoms are needed to set up two-probe system in ATK 10.8! See the discussion in the upgrade guide.