[ase-users] Phonons example

[Jens Jørgen Mortensen]

Den 12-04-2018 kl. 17:21 skrev Horsley, Matthew A. via ase-users:
>
> Hi,
>
> I am new to ase, and I am using the Phonon example (I copied it 
> below). In the example, there is a parameter N, which controls the 
> size of the supercell. In the example, N=7, and the code runs fine. 
> However, if I change N to something larger or smaller (I tried 
> N=5,6,8), the code crashes with an error message (see below). Is there 
> a fix for this?
>

It looks like a calculation for one value of N is trying to use a pickle 
file from a calculation with a different value of N.  Use one folder for 
each N or give the files different names like this:

ph = Phonons(atoms, calc, supercell=(N, N, N), delta=0.05,
                  name='Al-{}'.format(N))

A better error message is on the todo list ...

Jens Jørgen

> Thanks!
> Matt
>
> Error msg:
>
> ---------------------------------------------------------------------------
>
> ValueErrorTraceback (most recent call last)
>
> <ipython-input-18-03ff49a02177>in <module>()
>
>      14
>
>      15# Read forces and assemble the dynamical matrix
>
> ---> 16ph.read(acoustic=True)
>
>      17
>
>      18 # High-symmetry points in the Brillouin zone
>
> ase\phonons.pyc in read(self, method, symmetrize, acoustic, cutoff, 
> born, **kwargs)
>
>     404
>
>     405# Slice out included atoms
>
> --> 406C_Nav =C_av.reshape((N,len(self.atoms),3))[:,self.indices]
>
>     407                 index =3*i +j
>
>     408                 C_xNav[index]=C_Nav
>
> ValueError: cannot reshape array of size 1029 into shape (125,1,3)
>
> Phonon example:
>
> from ase.build import bulk
>
> from ase.calculators.emt import EMT
>
> from ase.dft.kpoints import ibz_points, bandpath
>
> from ase.phonons import Phonons
>
> # Setup crystal and EMT calculator
>
> atoms = bulk('Al', 'fcc', a=4.05)
>
> calc = EMT()
>
> # Phonon calculator
>
> N = 7
>
> ph = Phonons(atoms, calc, supercell=(N, N, N), delta=0.05)
>
> ph.run()
>
> # Read forces and assemble the dynamical matrix
>
> ph.read(acoustic=True)
>
> # High-symmetry points in the Brillouin zone
>
> points = ibz_points['fcc']
>
> G = points['Gamma']
>
> X = points['X']
>
> W = points['W']
>
> K = points['K']
>
> L = points['L']
>
> U = points['U']
>
> point_names = ['$\Gamma$', 'X', 'U', 'L', '$\Gamma$', 'K']
>
> path = [G, X, U, L, G, K]
>
> # Band structure in meV
>
> path_kc, q, Q = bandpath(path, atoms.cell, 100)
>
> omega_kn = 1000 * ph.band_structure(path_kc)
>
> # Calculate phonon DOS
>
> omega_e, dos_e = ph.dos(kpts=(50, 50, 50), npts=5000, delta=5e-4)
>
> omega_e *= 1000
>
> # Plot the band structure and DOS
>
> import matplotlib.pyplot as plt
>
> plt.figure(1, (8, 6))
>
> plt.axes([.1, .07, .67, .85])
>
> for n in range(len(omega_kn[0])):
>
> omega_n = omega_kn[:, n]
>
> plt.plot(q, omega_n, 'k-', lw=2)
>
> plt.xticks(Q, point_names, fontsize=18)
>
> plt.yticks(fontsize=18)
>
> plt.xlim(q[0], q[-1])
>
> plt.ylabel("Frequency ($\mathrm{meV}$)", fontsize=22)
>
> plt.grid('on')
>
> plt.axes([.8, .07, .17, .85])
>
> plt.fill_between(dos_e, omega_e, y2=0, color='lightgrey', 
> edgecolor='k', lw=1)
>
> plt.ylim(0, 35)
>
> plt.xticks([], [])
>
> plt.yticks([], [])
>
> plt.xlabel("DOS", fontsize=18)
>
> plt.show()
>
>
>
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