.. _siesta2:

----------------------------
Siesta 2: Molecular Dynamics
----------------------------

This exercise is intended to illustrate a Molecular Dynamics run with
the SIESTA calculator. The system is a Si(001) surface, in the 2x1
reconstruction with asymmetric dimers. The simulation cell contains
two dimers. An H2 molecule approaches the surface, above one of the
dimers, and dissociates, ending up with a H atom bonded to each of the
Si atoms in the dimer (and thus leading to a symmetric dimer). You can
get the ``xyz`` file with the initial geometry :svn:`doc/exercises/siesta2/geom.xyz`.

.. literalinclude:: siesta2.py

Note that both H atoms are given an initial velocity towards the
surface through the lines::

  p = atoms.get_momenta()
  p[0,2]= -1.5 
  p[1,2]= -1.5 
  atoms.set_momenta(p)

Run the program, and check the results. You can visualize the dynamics
using the trajectory file with the help of the ASE :mod:`gui`. For
example you can visualize the behaviour of the potential and total
energies during the dynamics by doing::

  $ ase-gui -b si001+h2.traj -g i,e,e+ekin

The :option:`-b` option turns on plotting of bonds between the atoms.
Check that the total energy is a conserved quantity in this
microcanonical simulation.

You can also use VMD to visualize the trajectory.  To do this, you
need a ``.xyz`` file that you can write using :command:`ase-gui`::

  $ ase-gui si001+h2.traj -o si.xyz -r 2,2,1

Then simply open the file using VMD::

  $ vmd si.xyz

and set Graphics/Representations from the main menu in order to get a
nice picture.

You can also try to repeat the simulation with a different
:mod:`dynamics <md>`. For instance you can model a canonical ensemble
with the Langevin dynamics, which couples the system to a heat bath::

  dyn = Langevin(atoms, 1 * fs, kB * 300, 0.002, trajectory=traj)






