Add STO example in the tests folder
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# coding: utf8
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# vim: set et sw=4 ts=4 fdm=indent nu cc=+1:
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from ase.lattice.tetragonal import SimpleTetragonalFactory
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from ase.visualize import view
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from ase.spacegroup import get_spacegroup
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from sprkkr.calculator import SPRKKR
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from msspec.calculator import MSSPEC, XRaySource
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from msspec.utils import *
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import numpy as np
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import logging
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import sys
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import os
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import glob
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logging.basicConfig(level=logging.DEBUG)
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logger = logging.getLogger(__name__)
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# Define a Perovskite Factory class
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class PerovskiteFactory(SimpleTetragonalFactory):
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bravais_basis = [[0, 0, 0.0], [0.5, 0.5, 0.5],[0.5, 0, 0], [0, 0.5, 0],
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[0.0, 0.0, 0.5]]
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element_basis = (0, 1, 2, 2, 2)
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ABO3 = Perovskite = PerovskiteFactory()
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# Generate the base STO cell
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a0 = 3.905
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STO = Perovskite(('Sr', 'Ti', 'O'),
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latticeconstant={'a': a0, 'c/a': 1.},
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size=(1,1,1))
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prefix = "SrTiO3"
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if 'view' in sys.argv:
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view(STO)
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# ########## SPRKKR part
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if 'sprkkr' in sys.argv:
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# create a SPRKKR calculator
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calc = SPRKKR(label=f"{prefix}/{prefix}")
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# attach the atoms to the calculator object
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calc.set_atoms(STO)
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# Here is how to modify input file
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# calc.input.control_section.set(DATASET="Fe", ADSI="SCF", POTFIL="Fe.pot")
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# calc.input.tau_section.set(nktab=250)
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# launch kkrscf
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calc.get_potential_energy()
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# calc2 = SPRKKR(label="Fe/Fe", task="phagen")
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# calc2.set_atoms(Fe)
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# calc2.input.control_section.set(POTFIL="Fe.pot_new")
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# calc2.phagen()
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#
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# EXPORT POTENTIAL FOR PHAGEN
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#
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#change task and command
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calc.set_command('PHAGEN')
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# Change output file
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calc.set_outfile(f"{prefix}_phagen.out")
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#to change task we need to replace input file tempate
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calc.set_inpfile(f"{prefix}_phagen.inp")
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calc.input.control_section.set(DATASET="PHAGEN", ADSI="PHAGEN")
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#set potetential file to converged potential
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conv_potfile=os.path.join(calc.potfile+'_new')
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calc.set_potfile(conv_potfile)
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#run given task
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calc.phagen()
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# ######### MsSpec part
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if 'msspec' in sys.argv:
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###########################################################################
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# Build the SrTiO3 cluster #
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###########################################################################
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# We start by loading the potential since it updates info in the STO cell
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pot = SPRKKRPotential(STO, "SrTiO3/SrTiO3.pot_new",
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*glob.glob("SrTiO3/*PHAGEN.pot"))
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# tag each atom in the STO object to easily set the emitter in the
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# hemispherical_cluster function
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[atom.set('tag', ('Sr', 'Ti', 'O').index(atom.symbol)) for atom in STO]
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# Create a hemispherical cluster centered on a Ti emitter from the
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# STO primitive cell used in the SPRKKR step.
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# For this example we use 4 planes and the Ti emitter (tag #1) is
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# located in the 2nd plane (numbering starts at 0)
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cluster = hemispherical_cluster(STO,
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planes=4,
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emitter_plane=1, emitter_tag=1)
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# The created cluster is centered on the emitter atom, so defining
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# the absorber attribute is straight forward:
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cluster.absorber = get_atom_index(cluster, 0, 0, 0)
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###########################################################################
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# Set up the PhotoElectron Diffraction calculator #
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###########################################################################
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# Create the calculator
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calc = MSSPEC(spectroscopy='PED', algorithm='expansion', folder='PED')
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# minimalistic set of parameter for XPD scan
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calc.set_atoms(cluster)
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calc.source_parameters.energy = 700
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calc.calculation_parameters.scattering_order = 2
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# Run a polar scan with the default MuffinTin potential for Ti(2p3/2)
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data = calc.get_theta_scan(level='2p3/2')
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# Now we use the previously generated SPRKKR potential
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# and run the same calculation with appending the data to the previous one
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calc.tmatrix_parameters.potential = pot
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data = calc.get_theta_scan(level='2p3/2', data=data)
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# To better see the differences, plot the normalized signal on the
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# same graph
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# pick up previous data
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theta, muffintin_cs, sprkkr_cs = (data[0].theta.copy(),
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data[0].cross_section.copy(),
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data[1].cross_section.copy())
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# divide by the max
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sprkkr_cs /= sprkkr_cs.max()
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muffintin_cs /= muffintin_cs.max()
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# add a new dataset with those values
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dset = data.add_dset('comparison')
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dset.add_columns(theta=theta, sprkkr=sprkkr_cs, muffintin=muffintin_cs)
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# add a view for this dataset
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view = dset.add_view('Comparison',
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title=r'Comparison of XPD polar scans for Ti(2p3/2)',
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xlabel=r'$\Theta (\degree$)',
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ylabel='Normalized Signal (a.u.)')
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view.select('theta', 'sprkkr', legend='With SPRKKR potential')
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view.select('theta', 'muffintin', legend='With internal MuffinTin potential')
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view.set_plot_options(autoscale=True)
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# Pop up the final result
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data.view()
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if len(sys.argv) <= 1:
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print("Please specify either 'sprkkr', 'msspec' keywords or both "
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"of them on the command line")
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