.. _vaspintro:
VASP SrVO3 Relax Everything
=============================
Here we will do structural relaxation for all degrees of freedom for spin polarized
SrVO3. To perform a VASP run we will need four files: **INCAR, KPOINTS, POSCAR, POTCAR**.
All of the input/output files can be viewed here:

INPUT: :download:`INCAR` | :download:`KPOINTS` | :download:`POTCAR` | :download:`POSCAR`      

OUTPUT: :download:`CONTCAR` | :download:`OSZICAR`  | :download:`OUTCAR`  | :download:`vasp.out` 

Now let us go through things step-by-step. Below is the INCAR that we will use:

.. code-block:: bash

  ISPIN = 2             # Do a spin polarized calculation
  MAGMOM= 0  4  0 0 0   # Initialization for magnetic moment on each atom
  PREC = med            # Settings for grids, med usually OK.
  IBRION= 2             # Conjugate gradient relaxation
  NSW=50                # number of ionic steps in relaxation
  ISIF= 3               # relax all ions and lattice vectors
  ISMEAR = -5           # use tetrahedron method to do k summations
  ENCUT=375             # plane wave cuttoff (ie. 1.5*max(ENMAX) from POTCAR)

This is a KPOINTS file. We choose a mesh of 12x12x12 which should be reasonable.

.. code-block:: bash

  coord.13.02           # This is a string
   0                    # 0 means automatically generate grid
  Gamma point shift     # Shift the gamma point
   12 12 12             # Kpoint mesh along each reciprocal lattice vector
   0 0 0                # amount to shift the gamma point

This is the POSCAR, which defines the crystal structure. Let us pull the
V atom out of its equilibrium position so we can see if it relaxes back
to the ideal position.

.. code-block:: bash

  title                 # string
  1.                    # scale structure by this parameter
  3.825  0.000  0.000   # vector1 x y z
  0.000  3.825  0.000   # vector2 x y z
  0.000  0.000  3.825   # vector3 x y z
  1   1   3             # Number of each species in unit cell
  Direct                # use direct coordinates (aka. fractional, lattic)
  0.5   0.5  0.5  Sr    # 0.5*v1+0.5*v2+0.5*v3 is position of Sr
  0.01  0.0  0.0  V     # etc
  0.5   0.0  0.0  O
  0.0   0.5  0.0  O
  0.0   0.0  0.5  O

In order to build the POTCAR file, you need to concatenate the POTCAR for all 
the atomic species that are in your unit cell. This needs to be done in the same
order that the elements appear in your POSCAR. A POTCAR is constructed using a 
particular exchange-correlation functional. If we wanted to make a GGA (PW91) POTCAR
for this system we would simply cat them like so:

.. code-block:: bash

  $ cat /home/cam1/vasp/POTCAR_pawgga/{Sr_sv,V,O_s}/POTCAR > POTCAR

This assumes that the POTCAR is at the above location of /home/cam1/vasp/POTCAR_pawgga.
Please note that there are sometimes mutliple POTCAR for a given atom. In this case
we are using the soft oxygen (hence the _s). It is generate with a lower cutoff and hence
it is much more efficient. I have not seen any major problems with it, though do understand
that some of these softer PAWs will melt down once in a while. Let us grep the relevant 
information from it so you can be sure that you actually got what you wanted.


.. code-block:: bash

  # this is the PAW that was used...
  $ grep -e LEXCH -e TITEL POTCAR
     LEXCH  = 91
     TITEL  = PAW_GGA Sr_sv 10Feb1998
     LEXCH  = 91
     TITEL  = PAW_GGA V 07Aug2001
     LEXCH  = 91
     TITEL  = PAW_GGA O_s 04May1998

Now let us run vasp. I will use nohup (no hang up) to be sure that my job is not killed
if I close my shell and i will send it to the background with the ampere. 

.. code-block:: bash

  $ nohup vasp > vasp.out &

It should be noted that on most modern machines it is much faster to run the parallel version of vasp.
This is executed as follows for a quad core machine:

.. code-block:: bash

  $ nohup mpirun -n 4 /usr/local/bin/vasp5-intel-parallel > out &



VASP will generate a number of relevant files. For this relaxation run we will be concerned
with **CONTCAR, OSZICAR,  OUTCAR, and  vasp.out**.  Let us start with OSZICAR which has the
total energy as a function of electronic iteration in addition to the magnetic moment for the
final iteration. This is also contained in the standard output:

.. code-block:: bash

  $ grep E0 OSZICAR | tail -1
  3 F= -.39400602E+02 E0= -.39400602E+02  d E =-.564340E-02  mag=     0.0000

We see that no magnetism was found and that the cohesive energy is E0. 
Now let us look at the final structure:

.. code-block:: bash

  title                     
     1.00000000000000     
       3.8575446041168937    0.0000000000000000    0.0000000000000000
       0.0000000000000000    3.8563755551641532    0.0000000000000000
       0.0000000000000000    0.0000000000000000    3.8563755551641532
     1   1   3
  Direct
    0.5017796114257187  0.5000000000000000  0.5000000000000000
    0.0022042565045450  0.0000000000000000  0.0000000000000000
    0.5020495206645594  0.0000000000000000  0.0000000000000000
    0.0019833057025874  0.5000000000000000  0.0000000000000000
    0.0019833057025874  0.0000000000000000  0.5000000000000000

We are free to shift a column by whatever we want:
 
.. code-block:: bash

  $ periodica.py CONTCAR shift="-0.00220426 0 0"

  title     
  1.0
  3.85754460   0.00000000   0.00000000
  0.00000000   3.85637556   0.00000000
  0.00000000   0.00000000   3.85637556
  1 1 3
  d
  0.49957535   0.50000000   0.50000000  Sr
  -0.00000000   0.00000000   0.00000000  V
  0.49984526   0.00000000   0.00000000  O
  -0.00022095   0.50000000   0.00000000  O
  -0.00022095   0.00000000   0.50000000  O

We can see that the structure has come fairly close to relaxing back to the
perfect cubic structure.  We would probably need to turn up the convergence
parameters to do better.