Hakkim, SIESTA will automatically detect the molecule, chain, slab, or bulk type depending on how close the images of each atom are across the x, y, and z dimensions of your simulation cell. This is done in the shaper.f subroutine. If your unit cell is big enough in all 3 dimensions such that no orbitals interact (in a certain range) in your atom list's periodic image, you will have a molecule. If they interact in one dimension, you will have a chain (or nanowire), two, a slab, and all three dimensions, a bulk system.
If you are seeking to do a force minimization calculation on a bulk system and you are getting "System type = molecule" in the output, you need to check the dimensions of your unit cell to make sure it is small enough that image atoms in all three dimensions will interact with the atoms whose position you've explicitly declared in the unit cell. Maybe your dimensions are proportionally correct to the crystal you'd like to simulate but your lattice constant is too big. On Wed, Nov 14, 2012 at 9:36 AM, Hakkim Vovusha < [email protected]> wrote: > HI, > > I am doing force minimization calculation (periodic system) in siesta and > I have found in the output Siesta: System type = molecule but i need to > change the molecule into bulk i.e. Siesta: System type = bulk. Can any one > help how to change these molecule into bulk. > > with regards > hakkim > -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about
