Getting started with pyscal

pyscal has three levels of objects. The fundamental one is Atom object which is used to store all properties that belong to an atom. The next object is System. System consists of multiple Atom objects and the simulation box. The final object is the Trajectory which stores a complete trajectory. In this example, we will look at Atom and System.

This example illustrates basic functionality of pyscal python library by setting up a system and the atoms.

In [1]:
import pyscal.core as pc
import numpy as np

The System class

System is the basic class of pyscal and is required to be setup in order to perform any calculations. It can be set up as-

In [2]:
sys = pc.System()

sys is a System object. But at this point, it is completely empty. We have to provide the system with the following information-

  • the simulation box dimensions
  • the positions of individual atoms.

Let us try to set up a small system, which is the bcc unitcell of lattice constant 1. The simulation box dimensions of such a unit cell would be [[0.0, 1.0], [0.0, 1.0], [0.0, 1.0]] where the first set correspond to the x axis, second to y axis and so on.
The unitcell has 2 atoms and their positions are [0,0,0] and [0.5, 0.5, 0.5].

In [3]: = [[0.0, 1.0], [0.0, 1.0], [0.0, 1.0]]

We can easily check if everything worked by getting the box dimensions

In [4]:
[[0.0, 1.0], [0.0, 1.0], [0.0, 1.0]]

The Atom class

The next part is assigning the atoms. This can be done using the Atom class. Here, we will only look at the basic properties of Atom class. Now let us create two atoms.

In [5]:
atom1 = pc.Atom()
atom2 = pc.Atom()

Now two empty atom objects are created. The basic poperties of an atom are its positions and id. There are various other properties which can be set here. A detailed description can be found here.

In [6]:
atom1.pos = [0., 0., 0.] = 0
atom2.pos = [0.5, 0.5, 0.5] = 1

Alternatively, atom objects can also be set up as

In [7]:
atom1 = pc.Atom(pos=[0., 0., 0.], id=0)
atom2 = pc.Atom(pos=[0.5, 0.5, 0.5], id=1)

We can check the details of the atom by querying it

In [8]:
[0.0, 0.0, 0.0]

Combining System and Atom

Now that we have created the atoms, we can assign them to the system. We can also assign the same box we created before.

In [9]:
sys = pc.System()
sys.atoms = [atom1, atom2] = [[0.0, 1.0], [0.0, 1.0], [0.0, 1.0]]

That sets up the system completely. It has both of it's constituents - atoms and the simulation box. We can check if everything works correctly.

In [10]:
[<pyscal.catom.Atom at 0x7ff8f0c770f0>, <pyscal.catom.Atom at 0x7ff8f0c77130>]

This returns all the atoms of the system. Alternatively a single atom can be accessed by,

In [11]:
atom = sys.get_atom(1)

The above call will fetch the atom at position 1 in the list of all atoms in the system. Due to Atom being a completely C++ class, it is necessary to use get_atom() and set_atom() to access individual atoms and set them back into the system object after modification. A list of all atoms however can be accessed directly by atoms.

Once you have all the atoms, you can modify any one and add it back to the list of all atoms in the system. The following statement will set the type of the first atom to 2.

In [12]:
atom = sys.atoms[0]
atom.type = 2

Lets verify if it was done properly

In [13]:

Now we can push the atom back to the system with the new type

In [14]:

Reading in an input file

We are all set! The System is ready for calculations. However, in most realistic simulation situations, we have many atoms and it can be difficult to set each of them
individually. In this situation we can read in input file directly. An example input file containing 500 atoms in a simulation box can be read in automatically. The file we use for this example is a file of the lammps-dump format. pyscal can also read in POSCAR files. In principle, pyscal only needs the atom positions and simulation box size, so you can write a python function to process the input file, extract the details and pass to pyscal.

In [15]:
sys = pc.System()

Once again, lets check if the box dimensions are read in correctly

In [16]:
[[-7.66608, 11.1901], [-7.66915, 11.1931], [-7.74357, 11.2676]]

Now we can get all atoms that belong to this system

In [17]:

We can see that all the atoms are read in correctly and there are 500 atoms in total. Once again, individual atom properties can be
accessed as before.

In [18]:
[-5.66782, -6.06781, -6.58151]

Thats it! Now we are ready for some calculations. You can find more in the examples section of the documentation.