Computer Exercise 2 - Fysik

#!/usr/bin/env python
from ase import *
from ase.io import read
from ase.optimize import BFGS
from ase.io import PickleTrajectory
import numpy as np
from gpaw import GPAW
atoms = read('C2H6.traj')
calc=GPAW(mode='lcao', basis='dzp', h=0.2, xc='PBE', nbands=8, txt='out_task6.txt')
atoms.set_calculator(calc)
traj= PickleTrajectory('EthaneRotation.traj', 'w') # makes a trajectory file
f = open('eigenvalues.txt','w') # Open a file for writing
f.write('# angle eigenvalue1 eigenvalue 2 ...\n')
maxstep=60
for nsteps in range(maxstep):
newatoms=atoms
atoms2rot=atoms[2:5] #These are the H atoms that are supposed to be rotated
angle=2*np.pi/(maxstep)
rotvector = atoms[0]. position - atoms[1]. position
atoms2rot.rotate(rotvector ,angle ,center='COM') #This rotates with angle around
#the z-axis and the center of mass
pos=atoms2rot.get_positions()
for n in range(len(atoms2rot)):
newatoms[n+2]. set_position(pos[n])
newatoms.set_calculator(calc)
traj.write(newatoms)
eigenvalues = calc.get_eigenvalues()
eigenvalues_s = ' '.join([str(i) for i in eigenvalues])
angle_s = str(angle*(nsteps+1)*180/np.pi)
# Write angle and eigenvalues to file
f.write(angle_s + ' ' + eigenvalues_s + '\n')
f.close() # close file
Task 3
Use the ag to look at the trajectory file. How much energy is required to rotate the ethane molecule? The
experimental value of the barrier is 0.13 eV.
To understand where the change in the conformational energy comes from we can plot the eigenvalues
of the KS-system during the rotation. Here we use a script that plots the stored eigenvalues as a function of
rotation. This you should not send to the queue, but instead run on the login node.
#!/usr/bin/env python
import numpy as np
import pylab as plt
data = np.loadtxt('eigenvalues.txt')
angles = data[:,0]
eigenvalues = data[:,1:]
plt.plot(angles , eigenvalues , 'o-')
plt.xlabel('Angle/[degrees]')
plt.ylabel('K-S eigenvalues/[eV]')
plt.show()
How large is the change in eigenvalues (especially the HOMO level)? Given how the total energy is
evaluated in normal DFT codes (see lecture notes) the conformational energy comes from the change in
eigenvalues.
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