Source code for ase2sprkkr.examples.A7_SrTiO3_MSSPEC.STO

"""
SCF calculations for  SrTiO3 in combination with msspec code to generate
photoelectron diffraction.

Call with ``msspec`` and/or ``sprkkr`` commandline argument.
"""

from ase.lattice.tetragonal import SimpleTetragonalFactory
from ase.visualize import view
from ase2sprkkr import SPRKKR
import numpy as np
import sys
import glob


[docs] def main(args): # Define a Perovskite Factory class class PerovskiteFactory(SimpleTetragonalFactory): bravais_basis = [[0, 0, 0.0], [0.5, 0.5, 0.5],[0., 0.5, 0.5], [0.5, 0.5, 0], [0.5, 0.0, 0.5]] element_basis = (0, 1, 2, 2, 2) Perovskite = PerovskiteFactory() # Generate the base STO cell a0 = 3.905 STO = Perovskite(('Sr', 'Ti', 'O'), latticeconstant={'a': a0, 'c/a': 1.}, size=(1,1,1)) if 'view' in args: view(STO) # ########## SPRKKR part if 'sprkkr' in args: calc = SPRKKR(atoms=STO,mpi=['mpirun','-np','16']) calc.input_parameters.set(NL=3) calc.input_parameters.SCF.MIX=0.01 calc.input_parameters.SCF.NITER=1000 calc.input_parameters.CONTROL.add('NOSYM', True) out_scf=calc.calculate() calc.input_parameters='PHAGEN' calc.calculate(potential=out_scf.potential_filename) # ######### MsSpec part if 'msspec' in args: from msspec.calculator import MSSPEC from msspec.utils import SPRKKRPotential, hemispherical_cluster, \ get_atom_index ########################################################################### # Build the SrTiO3 cluster # ########################################################################### # We start by loading the potential since it updates info in the STO cell pot = SPRKKRPotential(STO, "SrTiO3_scf.pot_new", *glob.glob("*PHAGEN.pot")) # tag each atom in the STO object to easily set the emitter in the # hemispherical_cluster function [atom.set('tag', ('Sr', 'Ti', 'O').index(atom.symbol)) for atom in STO] # Create a hemispherical cluster centered on a Ti emitter from the # STO primitive cell used in the SPRKKR step. # For this example we use 4 planes and the Ti emitter (tag #1) is # located in the 2nd plane (numbering starts at 0) cluster = hemispherical_cluster(STO, planes=4, emitter_plane=1, emitter_tag=1) # The created cluster is centered on the emitter atom, so defining # the absorber attribute is straightforward: cluster.absorber = get_atom_index(cluster, 0, 0, 0) ########################################################################### # Set up the PhotoElectron Diffraction calculator # ########################################################################### # Create the calculator calc = MSSPEC(spectroscopy='PED', algorithm='expansion', folder='PED') # minimalistic set of parameter for XPD scan calc.set_atoms(cluster) 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) calc.tmatrix_parameters.potential = 'muffin_tin' data = calc.get_theta_scan(level='2p3/2', data=data) # Now we use the previously generated SPRKKR potential and run the same # calculation calc.tmatrix_parameters.potential = pot data = calc.get_theta_scan(level='2p3/2', data=data) # To better see the differences, plot the normalized signal on the # same graph # add a new dataset for storing normalized values dset = data.add_dset(f"comparison at {source_energy} eV") # make a copy of previous scans values theta, muffintin_cs, sprkkr_cs = (data[-3].theta.copy(), data[-3].cross_section.copy(), data[-2].cross_section.copy()) # divide by the max sprkkr_cs /= sprkkr_cs.max() muffintin_cs /= muffintin_cs.max() # add a new dataset with those values dset.add_columns(theta=theta, sprkkr=sprkkr_cs, muffintin=muffintin_cs) # add a view for this dataset dview = dset.add_view('Comparison', title=('Comparison of XPD polar scans for ' r'Ti(2p3/2) at $h\nu$ = {:.0f} eV'.format( source_energy)), xlabel=r'$\Theta (\degree$)', ylabel='Normalized Signal (a.u.)') dview.select('theta', 'sprkkr', legend='With SPRKKR potential') dview.select('theta', 'muffintin', legend='With internal MT potential') dview.set_plot_options(autoscale=True) # Pop up the final result data.view() if len(args) <= 1: print("Please specify either 'sprkkr', 'msspec' keywords or both " "of them on the command line")
# Just run the script only when directly called from command line if __name__ == "__main__": main(sys.argv)