ABINIT Discussion Forums

Dear abiniters,
Please ,how can I identify in output file that in xred thefirst or second line corresponds to atoms A or B or C, because I need to usethes coordinats in a new input file.
Moreover, if I want the irreductible coordiates,what should I do(I have 7 atoes which are replicates in the cell by symmetries to give 42 atomes).
So i amvery confused about this

Good Morning ziedhosni,
In the output file of your Abinit run you will notice three variables; typat, znucl and ntypat.

ntypat tells you how many types of atoms are in the system. For instance a ZnSb system would have: ntypat 2.

Using my ZnSb system as an example the znucl variable would then look like: znucl 20 51. For the atomic number of each atom.

Now my ZnSb system has 16 atoms (natom 16). 8 of which are Zn and 8 of which are Sb.

So in the output file of this system you will find a line that looks something like:
typat 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2
This means that the first 8 atoms are of type 1 and the last 8 atoms are of type 2.
Now from znucl we can see that type 1 is atomic number 20 or Zn and type 2 is atomic number 51 or Sb.

Now the xred (xangst xcart) coordinates in the output file will simply correspond to the ordering of typat. i.e. the first 8 are Zn and the last 8 are Sb.

Since you used symmetry to generate your coordinates it gets a bit more complicated because your typat will not be simply in order but a bit mixed up, but the same principle described above still applies.

The reduced coordinates are xred, the coordinates in Angstroms (not reduced) are xangst and I think xcart are the coordinates in atomic units (not reduced).

Hope this helps!