
Creating a first input for TranSIESTA
=====================================

IMPORTANT: Read the entire thing, then go back and start.
You may think it is stupid, but having an overview of what the purpose
of the assignment is makes the steps easier! 

REMEMBER: TranSIESTA has it's transport direction in the z-direction.
          Hence this assignment needs your chain to increase in the 
          z-direction.

The goal is to get a feel for what is important for constructing
your first example. It is expected that many of you makes mistakes doing this
exercise, so please do not be afraid to ask. :)

1. Draw up your system on a piece of paper
   Your goal should be to construct a chain
   of atoms with some kind of defect in the middle
   of the chain. 
   The defect need not be severe.
   Here is an example of how the chain might look.
   
    1     2     3     4     5     6    7     8     9    10    11    12
   
    o --- o --- o --- o --- o --- o -- o --- o --- o --- o --- o --- o ---

   Where in the above example the defect is between atom 6 and 7.
   (If you want a more exciting defect PLEASE DO SO! :) )
   

2. Test and try and setup your electrode.
   This should ALWAYS be your first step in TranSIESTA.
   Defining your electrode correctly has a huge influence on the system.

   Make a chain and run transiesta on the electrode.
   Try with 2, 3, 4 atoms and check the supercell for the range of the orbitals 
   to ensure a connectivity only on 2 principal layers.

   Which one would suspect to be the best one?
   Hint: You can find the orbital range in the output of siesta and calculate
         it.

3. Create your full structure.

   Do the following steps:
     a) Input your first electrode
     b) Input some more atoms and then a defect (you can make it longer than
        the suggested 12 atoms, and if you have some "funny" looking defect, 
        please introduce it). 
        After the defect input some more atoms.
     c)	Input your last electrode

   Ensure that both electrodes are the same (the second electrode
   is just the first electrode with an offset).

4. Run the electrode calculation with "many" k-points in the transport
   direction.

5. Run your full structure.

   Also run tbtrans on it.


HINT: look at the first exercise we did today. You can if you want base your
      1D system on this. It is advised to think about the electrode design and
      how it was constructed to get a proper feel for TranSIESTA.
      See, if you did not read everything first you would not see this hint!?!?
   
      And you wouldn't see this happy face before proceeding:

                .---.
               | o o |
               |  >  |
               | '-' |
                '---'






