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Small changes in the SPRKKR STO.py example.

This commit is contained in:
Sylvain Tricot 2020-07-09 10:56:59 +02:00
parent 8e49d87a5a
commit 54fc166eb4
1 changed files with 43 additions and 30 deletions
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41
tests/sprkkr/STO/STO.py
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@ -11,6 +11,7 @@ import numpy as np
import logging import logging
import sys import sys
import os import os
import shutil
import glob import glob
@ -78,8 +79,8 @@ if 'msspec' in sys.argv:
# Build the SrTiO3 cluster # # Build the SrTiO3 cluster #
########################################################################### ###########################################################################
# We start by loading the potential since it updates info in the STO cell # We start by loading the potential since it updates info in the STO cell
pot = SPRKKRPotential(STO, "SrTiO3/SrTiO3.pot_new", pot = SPRKKRPotential(STO, f"{prefix}/{prefix}.pot_new",
*glob.glob("SrTiO3/*PHAGEN.pot")) *glob.glob(f"{prefix}/*PHAGEN.pot"))
# tag each atom in the STO object to easily set the emitter in the # tag each atom in the STO object to easily set the emitter in the
# hemispherical_cluster function # hemispherical_cluster function
@ -94,7 +95,7 @@ if 'msspec' in sys.argv:
emitter_plane=1, emitter_tag=1) emitter_plane=1, emitter_tag=1)
# The created cluster is centered on the emitter atom, so defining # The created cluster is centered on the emitter atom, so defining
# the absorber attribute is straight forward: # the absorber attribute is straightforward:
cluster.absorber = get_atom_index(cluster, 0, 0, 0) cluster.absorber = get_atom_index(cluster, 0, 0, 0)
########################################################################### ###########################################################################
@ -105,38 +106,50 @@ if 'msspec' in sys.argv:
# minimalistic set of parameter for XPD scan # minimalistic set of parameter for XPD scan
calc.set_atoms(cluster) calc.set_atoms(cluster)
calc.source_parameters.energy = 700
calc.calculation_parameters.scattering_order = 2 calc.calculation_parameters.scattering_order = 2
# We need to impose a maximum number of tl to use because there is still
# a memory bug that I need to investigate. Anyway, usually 25 is not that
# bad for the kind of atoms and the photon energy of lab sources...
calc.tmatrix_parameters.lmax_mode = 'imposed'
calc.tmatrix_parameters.lmaxt = 25
data = None
for source_energy in np.arange(500., 1501., 100.):
calc.source_parameters.energy = source_energy
# Run a polar scan with the default MuffinTin potential for Ti(2p3/2) # Run a polar scan with the default MuffinTin potential for Ti(2p3/2)
data = calc.get_theta_scan(level='2p3/2') calc.tmatrix_parameters.potential = 'muffin_tin'
data = calc.get_theta_scan(level='2p3/2', data=data)
# Now we use the previously generated SPRKKR potential # Now we use the previously generated SPRKKR potential and run the same
# and run the same calculation with appending the data to the previous one # calculation
calc.tmatrix_parameters.potential = pot calc.tmatrix_parameters.potential = pot
data = calc.get_theta_scan(level='2p3/2', data=data) data = calc.get_theta_scan(level='2p3/2', data=data)
# To better see the differences, plot the normalized signal on the # To better see the differences, plot the normalized signal on the
# same graph # same graph
# pick up previous data # add a new dataset for storing normalized values
theta, muffintin_cs, sprkkr_cs = (data[0].theta.copy(), dset = data.add_dset(f"comparison at {source_energy} eV")
data[0].cross_section.copy(), # make a copy of previous scans values
data[1].cross_section.copy()) theta, muffintin_cs, sprkkr_cs = (data[-3].theta.copy(),
data[-3].cross_section.copy(),
data[-2].cross_section.copy())
# divide by the max # divide by the max
sprkkr_cs /= sprkkr_cs.max() sprkkr_cs /= sprkkr_cs.max()
muffintin_cs /= muffintin_cs.max() muffintin_cs /= muffintin_cs.max()
# add a new dataset with those values # add a new dataset with those values
dset = data.add_dset('comparison')
dset.add_columns(theta=theta, sprkkr=sprkkr_cs, muffintin=muffintin_cs) dset.add_columns(theta=theta, sprkkr=sprkkr_cs, muffintin=muffintin_cs)
# add a view for this dataset # add a view for this dataset
view = dset.add_view('Comparison', view = dset.add_view('Comparison',
title=r'Comparison of XPD polar scans for Ti(2p3/2)', title=(f'Comparison of XPD polar scans for '
r'Ti(2p3/2) at $h\nu$ = {:.0f} eV'.format(
source_energy)),
xlabel=r'$\Theta (\degree$)', xlabel=r'$\Theta (\degree$)',
ylabel='Normalized Signal (a.u.)') ylabel='Normalized Signal (a.u.)')
view.select('theta', 'sprkkr', legend='With SPRKKR potential') view.select('theta', 'sprkkr', legend='With SPRKKR potential')
view.select('theta', 'muffintin', legend='With internal MuffinTin potential') view.select('theta', 'muffintin', legend='With internal MT potential')
view.set_plot_options(autoscale=True) view.set_plot_options(autoscale=True)
# Pop up the final result # Pop up the final result
data.view() data.view()