55 lines
1.7 KiB
Python
55 lines
1.7 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.calculator import MSSPEC, XRaySource
|
||
|
|
from msspec.utils import *
|
||
|
|
|
||
|
|
from ase.build import fcc111, add_adsorbate
|
||
|
|
from ase.visualize import view
|
||
|
|
from msspec.iodata import cols2matrix
|
||
|
|
|
||
|
|
from matplotlib import pyplot as plt
|
||
|
|
import numpy as np
|
||
|
|
import sys
|
||
|
|
|
||
|
|
data = None
|
||
|
|
all_z = np.arange(1.10, 1.50, 0.02)
|
||
|
|
all_z=(1.1,)
|
||
|
|
for zi, z0 in enumerate(all_z):
|
||
|
|
# construct the cluster
|
||
|
|
cluster = fcc111('Rh', size = (2,2,1))
|
||
|
|
add_adsorbate(cluster, 'O', z0, position = 'fcc')
|
||
|
|
cluster.pop(3)
|
||
|
|
#cluster.rotate('z',np.pi/3.)
|
||
|
|
#view(cluster)
|
||
|
|
|
||
|
|
cluster.absorber = len(cluster) - 1
|
||
|
|
|
||
|
|
calc = MSSPEC(spectroscopy = 'PED', folder = './RhO_z')
|
||
|
|
calc.set_atoms(cluster)
|
||
|
|
calc.calculation_parameters.scattering_order = 3
|
||
|
|
calc.calculation_parameters.RA_cutoff = 1
|
||
|
|
calc.source_parameters.energy = XRaySource.AL_KALPHA
|
||
|
|
|
||
|
|
# compute
|
||
|
|
level = '1s'
|
||
|
|
ke = 723.
|
||
|
|
|
||
|
|
|
||
|
|
data = calc.get_theta_phi_scan(level=level, kinetic_energy=ke, data=data)
|
||
|
|
|
||
|
|
# OPTIONAL, this will create an image of the data that you can combine
|
||
|
|
# in an animated gif
|
||
|
|
dset = data[-1]
|
||
|
|
theta, phi, Xsec = cols2matrix(dset.theta, dset.phi, dset.cross_section)
|
||
|
|
X, Y = np.meshgrid(np.radians(phi), 2*np.tan(np.radians(theta/2.)))
|
||
|
|
fig = plt.figure()
|
||
|
|
ax = fig.add_subplot(111, projection='polar')
|
||
|
|
im = ax.pcolormesh(X, Y, Xsec)
|
||
|
|
theta_ticks = np.arange(0, 91, 15)
|
||
|
|
plt.yticks(2 * np.tan(np.radians(theta_ticks/2.)), theta_ticks)
|
||
|
|
plt.title(r"$z_0 = {:.2f} \AA$".format(z0))
|
||
|
|
plt.savefig('image{:03d}.png'.format(zi))
|
||
|
|
|
||
|
|
data.view()
|