108 lines
2.8 KiB
Python
108 lines
2.8 KiB
Python
|
# -*- encoding: utf-8 -*-
|
||
|
|
# vim: set fdm=indent ts=4 sw=4 sts=4 et ai tw=80 cc=+0 mouse=a nu : #
|
||
|
|
|
||
|
|
from msspec.calculators import PED, XRaySource
|
||
|
|
from msspec.utils import *
|
||
|
|
|
||
|
|
from ase.build import bulk
|
||
|
|
from ase.build import fcc111, add_adsorbate
|
||
|
|
from ase.visualize import view
|
||
|
|
from ase.data import reference_states, atomic_numbers
|
||
|
|
|
||
|
|
from matplotlib import pyplot as plt
|
||
|
|
import numpy as np
|
||
|
|
import sys
|
||
|
|
|
||
|
|
|
||
|
|
n = 1
|
||
|
|
symbol = 'Ge'
|
||
|
|
cluster = bulk(symbol, cubic = True)
|
||
|
|
cluster = cluster.repeat((10, 10, 10))
|
||
|
|
center_cluster(cluster)
|
||
|
|
a0 = reference_states[atomic_numbers[symbol]]['a']
|
||
|
|
cluster = cut_sphere(cluster, radius = a0 * (n+ .01))
|
||
|
|
cluster = cut_plane(cluster, z = 0.1)
|
||
|
|
view(cluster)
|
||
|
|
#sys.exit(0)
|
||
|
|
#cluster.absorber = 12
|
||
|
|
#cluster.absorber = get_atom_index(cluster, 0,0,-1*n*a0)
|
||
|
|
|
||
|
|
|
||
|
|
calc = PED(folder = './Ge')
|
||
|
|
calc.set_atoms(cluster)
|
||
|
|
|
||
|
|
calc.set_calculation_parameters(scattering_order = 3,RA_cut_off = 1,
|
||
|
|
mean_square_vibration = 0.0)
|
||
|
|
#calc.set_source_parameters(theta = -55., phi = 0.)
|
||
|
|
|
||
|
|
calc.set_source_parameters(energy = 100.)
|
||
|
|
calc.set_muffintin_parameters(interstitial_potential = 0)
|
||
|
|
|
||
|
|
|
||
|
|
if False:
|
||
|
|
level = '3d'
|
||
|
|
all_be = np.linspace(27., 32., 5)
|
||
|
|
all_theta = 76.
|
||
|
|
data = []
|
||
|
|
|
||
|
|
for be in all_be:
|
||
|
|
theta, Xsec, dirsig = calc.get_theta_scan(theta = 76., level = level,
|
||
|
|
binding_energy = be)
|
||
|
|
print '<'*80
|
||
|
|
print Xsec
|
||
|
|
data.append(Xsec - dirsig)
|
||
|
|
|
||
|
|
data = np.array(data).flatten()
|
||
|
|
print data
|
||
|
|
ax = plt.subplot(111)
|
||
|
|
ax.plot(all_be, data)
|
||
|
|
plt.show()
|
||
|
|
|
||
|
|
if True:
|
||
|
|
ax = plt.subplot(111)
|
||
|
|
for V in [0., 15.]:
|
||
|
|
level = '3d'
|
||
|
|
all_theta = np.arange(0., 80., 1.)
|
||
|
|
phi = 0.
|
||
|
|
|
||
|
|
calc.set_muffintin_parameters(interstitial_potential = V)
|
||
|
|
|
||
|
|
cluster.absorber = 18
|
||
|
|
surface_data = calc.get_theta_scan(theta = all_theta, level = level,
|
||
|
|
phi = phi)#, plane = -1)
|
||
|
|
|
||
|
|
cluster.absorber = 12
|
||
|
|
bulk_data = calc.get_theta_scan(theta = all_theta, level = level,
|
||
|
|
phi = phi)#, plane = -1)
|
||
|
|
|
||
|
|
theta0, Xsec0, dirsig0 = surface_data
|
||
|
|
theta1, Xsec1, dirsig1 = bulk_data
|
||
|
|
#plt.plot(theta0, Xsec0, label = 'surface')
|
||
|
|
#plt.plot(theta1, Xsec1, label = 'bulk')
|
||
|
|
plt.plot(theta1, Xsec0/Xsec1, label = 'Vint = {:.2f} eV'.format(V))
|
||
|
|
|
||
|
|
plt.ylim(None, 8)
|
||
|
|
plt.legend()
|
||
|
|
plt.show()
|
||
|
|
|
||
|
|
|
||
|
|
if False:
|
||
|
|
# compute
|
||
|
|
level = '2s'
|
||
|
|
ke = 156.5
|
||
|
|
|
||
|
|
all_theta = np.arange(0.,91.)
|
||
|
|
theta, phi, Xsec, dirsig = calc.get_stereo_scan(theta = all_theta, level = level,
|
||
|
|
kinetic_energy = ke)
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
# plot
|
||
|
|
X, Y = np.meshgrid(np.radians(phi), theta)
|
||
|
|
ax = plt.subplot(111, projection = 'polar')
|
||
|
|
ax.pcolormesh(X, Y, Xsec, cmap='gray')
|
||
|
|
#plt.title(r'z_0 = %.3f $\AA$' % z0)
|
||
|
|
|
||
|
|
plt.show()
|
||
|
|
|