Creating and Setting up the vasp functional

Specifying vasp parameters

As shown in the quick primer above, it is relatively easy to setup a new Vasp. The parameters to the calculation are generally the VASP defaults. They can be changed directly in the constructor:

>>> from pylada.vasp import Vasp
>>> vasp = Vasp(ispin=2)
>>> print vasp.ispin
2

or later, after creation:

>>> vasp.ispin = 1
>>> print vasp.ispin
2

or even right at the moment when executing a calculation:

>>> vasp.encut = 1.2
>>> result = vasp(structure, ispin=2, encut=1)
>>> print vasp.encut
1.2

In the line above, vasp is called with ispin=2 and encut=1. However, specifying a vasp parameter directly at execution does not modify the vasp object itself, as indicated by the third line. The parameter is only modified for the duration of the run and not beyond.

At this point, it might have come as a surprise to see encut=1. What units are we talking about here? A number of parameters have enhanced behaviors with respect to the original VASP code, in order to make it easier to specify parameters valid for many calculations. encut one of those. It can be specified:

• as floating point smaller than 3, in which case it is a factor of the largest ENMAX of all the species in the calculation.

• as floating point larger than 3, in which case it will printed as is in the INCAR.

• as floating point signed by a quantity:

  >>> from pylada.physics import Ry
  >>> vasp.encut = 10*Ry
  

  In that case, the result will be converted to electron-Volts in the INCAR.

To see the full list of parameters defined by Pylada, do vasp.[TAB] on the ipython command line, or go Vasp.

Adding parameters Pylada does not know about

A large number of parameters control VASP. Pylada only knows about the most common. However, it is fairly easy to add parameters which are not there yet.

>>> vasp.add_keyword('encut', 300)

This will add a parameter to VASP. It will appear in the incar as “ENCUT = 300”, with the tag name in uppercase. The parameter can be later accessed and modified just as if it where a pre-existing parameter.

>>> print vasp.encut
300

The attribute vasp.encut is (in this case) an integer which can be manipulated as any other python integer. Any python object can be given. It will appear in the INCAR as it appears when transformed to a string (using python’s str function).

If you do not want a parameter printed to the INCAR, i.e. you want to use the VASP default for that parameter, then simply set that parameter to None:

>>> vasp.encut = None

Note

The examples above specifies a parameter which already exists, encut. In this case, when calling add_keyword(), the parameter is replaced with a simple integer (or float, or whatnot). Its special behavior described above is simply gone. If you do not like a special behavior, you can always do away with it.

Specifying kpoints

K-points can be specified in a variety of ways.

Simply as a KPOINTS file in string:

>>> vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"

As a 4xn matrix where the first three components of each row define a single kpoint in cartesian coordinates, and the last component its multiplicity. In that case, VASP does not reduce the kpoints by symmetry, as explained here.

>>> vasp.kpoints = [ [0, 0, 0, 1], [0.1, 0.1, 0.1, 3] ]

As a callable function which takes the vasp functional and the structure as input. It must return either a string defining a semantically correct KPOINTS file, or an array of kpoints as above.

>>> def some_function(functional, structure):
>>>   .... do something
>>>   return kpoints
>>>
>>> vasp.kpoints = some_function

This function is called before each execution. Hence the kpoint grid can be tailored to each call.

Specifying the pseudos and Hubbard U parameters

Pseudo-potentials must be specified explicitely:

>>> vasp.add_specie = 'Tc', '/path/to/pseudo/directory/Tc'

The first item is the name of the atomic specie. It corresponds to the type of the atom in the structure to compute. The second item is a path to a directory where the appropriate unzipped POTCAR resides. It will not affect calculations. For convenience, the path may be given with the usual unix short-cuts and/or with a shell environment variable.

>>> vasp.add_specie = 'Tc', '~/pseudos/$PAW/Tc'

To specify a Hubbard U parameter, do:

>>> from pylada.vasp.specie import U
>>> vasp.add_specie = 'Tc', '~/pseudos/$PAW/Tc', U('dudarev', l=2, U=1.5)

The species can be latter accessed through a dictionary in the vasp object:

>>> vasp.add_specie = 'Tc', '~/pseudos/$PAW/Tc'
>>> print vasp['Tc']
Specie('Tc', '~/pseudos/$PAW/Tc')
>>> vasp['Tc'].moment = 5

At which point, other elemental properties could be added for latter use in a script.

Note

It is possible to specify more species than exists in a given structure. Pylada will figure out at runtime.