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Given the following text description, write Python code to implement the functionality described below step by step
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Description:
 Making and manipulating structures with ASE
For preparing and manipulating crystal structures we will be using the ASE Python library. The documentation is rather accessible and even includes a refresher of Python basics. You can read it here, in preparation for the first lab
Step1:  Now we verify that our structure indeed has atoms in the right places
Step2:  We can make a supercell of this structure by rescaling the cell. Here we use NumPy's matrix capability.
Step3:  It is possible to change the position of the first atom directly like this
Step4:  Similarly, we can change the type of the first atom by reassigning the atomic number
Step5:  Or we can remove an atom altogether to form a vacancy. We simply use the pop() method of Python lists.
Step6:  Now let's write the structure to a file so was can visualize what we've done to it. Crystallographic Information File (CIF) format is the most common for periodic structures today, and is understood by most structure visualizers and converters.
Step7:  We cans use VESTA to look at the result, or the ASE built-in viewer like so
Step8:  To generate a surface slab supercell we can use ASE builder like so, and write it to a file
Step9:  You can look at the structure in VESTA and also get the atomic positions and cell information
Step10:  In the lab you will need to perform numerical sweeps of several parameters. You can use Numpy
Step11:  To plot the results, you can use Matplotlib
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Python Code:
from ase.spacegroup import crystal
a = 4.5
Na_unitcell = crystal('Na', [(0,0,0)], spacegroup=229, cellpar=[a, a, a, 90, 90, 90])
print('hello')
Explanation: Making and manipulating structures with ASE
For preparing and manipulating crystal structures we will be using the ASE Python library. The documentation is rather accessible and even includes a refresher of Python basics. You can read it here, in preparation for the first lab: https://wiki.fysik.dtu.dk/ase/python.html.
Here we will learn various functionalities of ASE, particularly how to make crystal structures, generate supercells, remove an atom to form a vacancy, and change an atom’s position.
ASE Atoms object holds all the information about our structure and has methods for manipulating it. Once we finish with the structurem, we will export it to a simple Python dictionary that is then used to generate the LAMMPS data and input files.
First we will create a crystal structure of Na metal. For this we will import the necessary spacegroup tools, so that we don't have to manually set up the cell and coordinates.
End of explanation
Na_unitcell.positions
Na_unitcell.get_chemical_symbols()
Explanation: Now we verify that our structure indeed has atoms in the right places
End of explanation
import numpy
multiplier = numpy.identity(3) * 2
print(multiplier)
from ase.build import make_supercell
Na_supercell = make_supercell(Na_unitcell, multiplier)
Na_supercell.positions
Explanation: We can make a supercell of this structure by rescaling the cell. Here we use NumPy's matrix capability.
End of explanation
Na_supercell.positions[0] = (0.5, 0.5, 0.5)
Explanation: It is possible to change the position of the first atom directly like this:
End of explanation
print(Na_supercell.numbers)
Na_supercell.numbers[0] = 3
Na_supercell.get_chemical_symbols()
Explanation: Similarly, we can change the type of the first atom by reassigning the atomic number
End of explanation
Na_supercell.pop(15)
Explanation: Or we can remove an atom altogether to form a vacancy. We simply use the pop() method of Python lists.
End of explanation
from ase.io import write
write('sc.struct', Na_supercell)
Explanation: Now let's write the structure to a file so was can visualize what we've done to it. Crystallographic Information File (CIF) format is the most common for periodic structures today, and is understood by most structure visualizers and converters.
End of explanation
Na_supercell.edit()
Explanation: We cans use VESTA to look at the result, or the ASE built-in viewer like so:
End of explanation
from ase.build import bcc100
slab = bcc100('Na', size=(2,4,3), vacuum = 10.0)
write('slab.struct', slab)
Explanation: To generate a surface slab supercell we can use ASE builder like so, and write it to a file
End of explanation
slab.positions
slab.cell
slab.edit()
Explanation: You can look at the structure in VESTA and also get the atomic positions and cell information
End of explanation
x = numpy.linspace(-5,5,10)
y = x*x
print(x)
Explanation: In the lab you will need to perform numerical sweeps of several parameters. You can use Numpy
End of explanation
import matplotlib.pyplot as plt
plt.plot(x,y)
plt.show()
Explanation: To plot the results, you can use Matplotlib
End of explanation
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