shifting unit cell along an axis after shifting an electrode along that axis

[namrata]

hello everyone ,
i have already shifted one electrode along the desired axis but there is problem in shifting the unit cell along with the electrode . plz help !!

[Anders Blom]

You'll have to be much more specific than that, I'm afraid, otherwise there's no way to assist.

[namrata]

hello
i shifted my two probe system's right electrode in x direction using X_shift in right electrode coordinates . so , the right electrode atoms moved out of the right electrode unitcell. to cover atoms by the unitcell i tried elongating my left and right unit cell along x axis but when i did this the electrode repetitions got separated and my electrodes got distorted .
i think u have got what i want ?
plz help!!

[zh]

Please rearrange the sentence for your question to make sure that other people can understand it, especially for the 2nd sentence.

the electrode atoms are now moving out of the right electrode unitcell so i tried elongating my left and right unit cell along x axis but when i do this the electrode repetitions get separated and my electrodes get distorted .

Due to the translational symmetry, the coordinations of all atoms in an unit cell can be shifted together, while this does not affect the self-consistent calculation.  If you shift only the atomic coordinations in the right electrode along the x direction, it is no necessary to elongate the cell vectors electrodes along the x direction. Actually, this elongation of cell vectors of electrodes means that you are extending the unit cell.

[namrata]

hello zh
thanks for ur reply
one more query plz

you mean that whether electrode atoms are there inside the unitcell or not that has no effect on the scf calculations ??

but i have seen the z shaped graphene nanoribbon script on the wesite in it the right electrode is shifted and both the unitcells left and right are elongated to encorporate all atoms of both the electrodes. so , i was trying that all atoms of my electrodes are there inside the unitcell.

please clarify i m a beginer .

[zh]

No, in principle, it does not affect the scf calculation.

The graphene nanoribbon  is quasi-one-dimensional system. In the simulation of graphene nanoribbon, the periodic condition is applied so that the vacuum is included in its unit cell. In details, if it is assumed that the ribbon is along the z direction, the vacuum is put along the x and y directions. In this case, the thickness of vacuum in the x and y direction should be sufficient in order to avoid the interaction between replicas of ribbon, in other words, the lengths of unit cell vectors along the x and y direction should large enough, at least, they must be 10% larger than the width of ribbon.