First Steps¶
This is short and direct introduction to some of the basic functionalities from pychemia. To keep things simple, we will be using only the mandatory libraries, and we will not call any external simulation packages.
You can use the official python terminal for executing this examples, however, you can gain some extra advantage by using the far more powerfull IPython terminal. On Linux machines with Debian, Ubuntu or Linux Mint, you can use the following command to install the IPython terminal:
sudo apt-get install python-ipython
or for python 3.x:
sudo apt-get install python3-python
On MacOS using macports,
sudo port install py27-ipython
or for python 3.x
sudo port install py35-ipython
FCC crystal of gold¶
Most of the case of use for pychemia start with a Structure. A PyChemia Structure stores atomic positions and cell parameters for periodic structures. Lets start with a very simple structure, the FCC structure of gold. One way of creating and structure is by directly specifying atomic positions and cell parameters, for example:
$ ipython3-3.5
Python 3.5.1 (default, Mar 2 2016, 03:38:02)
Type "copyright", "credits" or "license" for more information.
IPython 4.2.0 -- An enhanced Interactive Python.
? -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help -> Python's own help system.
object? -> Details about 'object', use 'object??' for extra details.
In [1]: import pychemia
In [2]: a=4.05
In [3]: b=a/2
In [4]: fcc = pychemia.Structure(symbols=['Au'], cell=[[0, b, b], [b, 0, b], [b, b, 0]], periodicity=True)
In [5]: fcc
Out[5]: Structure(symbols=['Au'], cell=[[0.0, 2.025, 2.025], [2.025, 0.0, 2.025], [2.025, 2.025, 0.0]],
reduced=[[0.0, 0.0, 0.0]], periodicity=True)
You have created your first structure on PyChemia. The structure contains one atom of Gold and the cell is the primitive cell of a FCC structure with one atom. You can ‘see’ the structure using the ‘print’ function:
In [6]: print(fcc)
1
Symb ( Positions ) [ Cell-reduced coordinates ]
Au ( 0.0000 0.0000 0.0000 ) [ 0.0000 0.0000 0.0000 ]
Periodicity: X Y Z
Lattice vectors:
0.0000 2.0250 2.0250
2.0250 0.0000 2.0250
2.0250 2.0250 0.0000
We can now be interested in see the spacegroup of the structure just created. A pychemia.crystal.CrystalSymmetry
object allow us to get access to symmetry calculations provided by the spglib library:
In [7]: cs=pychemia.crystal.CrystalSymmetry(fcc)
In [8]: cs.number()
Out[8]: 225
In [9]: cs.symbol()
Out[9]: 'Fm-3m'
Both the space group number and the International symbol are accessible from the CrystalSymmetry object. Now we can use the CrystalSymmetry object to recreate the convenctional FCC cell:
In [10]: fcc_conv=cs.refine_cell()
In [11]: fcc
fcc fcc_conv
In [12]: fcc_conv
Out[12]: Structure(symbols=['Au', 'Au', 'Au', 'Au'], cell=4.05, reduced=[[0.0, 0.0, 0.0], [0.0, 0.5, 0.5],
[0.5, 0.0, 0.5], [0.5, 0.5, 0.0]], periodicity=True)
In [11]: print(fcc_conv)
4
Symb ( Positions ) [ Cell-reduced coordinates ]
Au ( 0.0000 0.0000 0.0000 ) [ 0.0000 0.0000 0.0000 ]
Au ( 0.0000 2.0250 2.0250 ) [ 0.0000 0.5000 0.5000 ]
Au ( 2.0250 0.0000 2.0250 ) [ 0.5000 0.0000 0.5000 ]
Au ( 2.0250 2.0250 0.0000 ) [ 0.5000 0.5000 0.0000 ]
Periodicity: X Y Z
Lattice vectors:
4.0500 0.0000 0.0000
0.0000 4.0500 0.0000
0.0000 0.0000 4.0500
The lattice vectors are now making a cube, and the structure is made of 4 gold atoms. Now we can want to create a supercell, 2x2x1 using the supercell method:
In [13]: fcc221=fcc_conv.supercell(size=(2,2,1))
In [14]: print(fcc221)
16
Symb ( Positions ) [ Cell-reduced coordinates ]
Au ( 0.0000 0.0000 0.0000 ) [ 0.0000 0.0000 0.0000 ]
Au ( 0.0000 2.0250 2.0250 ) [ 0.0000 0.2500 0.5000 ]
Au ( 2.0250 0.0000 2.0250 ) [ 0.2500 0.0000 0.5000 ]
Au ( 2.0250 2.0250 0.0000 ) [ 0.2500 0.2500 0.0000 ]
Au ( 0.0000 4.0500 0.0000 ) [ 0.0000 0.5000 0.0000 ]
Au ( 0.0000 6.0750 2.0250 ) [ 0.0000 0.7500 0.5000 ]
Au ( 2.0250 4.0500 2.0250 ) [ 0.2500 0.5000 0.5000 ]
Au ( 2.0250 6.0750 0.0000 ) [ 0.2500 0.7500 0.0000 ]
Au ( 4.0500 0.0000 0.0000 ) [ 0.5000 0.0000 0.0000 ]
Au ( 4.0500 2.0250 2.0250 ) [ 0.5000 0.2500 0.5000 ]
Au ( 6.0750 0.0000 2.0250 ) [ 0.7500 0.0000 0.5000 ]
Au ( 6.0750 2.0250 0.0000 ) [ 0.7500 0.2500 0.0000 ]
Au ( 4.0500 4.0500 0.0000 ) [ 0.5000 0.5000 0.0000 ]
Au ( 4.0500 6.0750 2.0250 ) [ 0.5000 0.7500 0.5000 ]
Au ( 6.0750 4.0500 2.0250 ) [ 0.7500 0.5000 0.5000 ]
Au ( 6.0750 6.0750 0.0000 ) [ 0.7500 0.7500 0.0000 ]
Periodicity: X Y Z
Lattice vectors:
8.1000 0.0000 0.0000
0.0000 8.1000 0.0000
0.0000 0.0000 4.0500