From d00c537f30e49163b27c8fe9836ff13ec589af52 Mon Sep 17 00:00:00 2001
From: Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>
Date: Wed, 16 Jul 2025 16:54:37 +0200
Subject: [PATCH] Add Si vs scattering order

---
 msspecbook/Activity07/Si001_completed2.py | 70 +++++++++++++++++++++++
 1 file changed, 70 insertions(+)
 create mode 100644 msspecbook/Activity07/Si001_completed2.py

diff --git a/msspecbook/Activity07/Si001_completed2.py b/msspecbook/Activity07/Si001_completed2.py
new file mode 100644
index 0000000..684e4eb
--- /dev/null
+++ b/msspecbook/Activity07/Si001_completed2.py
@@ -0,0 +1,70 @@
+# coding: utf8
+
+import numpy as np
+from ase.build import bulk
+
+from msspec.calculator import MSSPEC, XRaySource
+from msspec.iodata import Data
+from msspec.utils import hemispherical_cluster, get_atom_index
+
+
+# Create the cluster
+a = 5.43
+Si = bulk('Si', a=a, cubic=True)
+cluster = hemispherical_cluster(Si,
+                                diameter=30, planes=4,
+                                emitter_plane=3,
+                                shape = 'cylindrical',
+                                )
+for atom in cluster:
+    atom.set('mean_square_vibration', 0.006)
+    atom.set('mt_radius', 1.1)
+cluster.emitter = get_atom_index(cluster, 0, 0, 0)
+
+# Create a calculator and set parameters
+calc = MSSPEC(spectroscopy='PED', algorithm='expansion')
+
+calc.source_parameters.energy = XRaySource.AL_KALPHA
+calc.source_parameters.theta  = -54.7
+calc.source_parameters.phi    = 90
+calc.spectroscopy_parameters.final_state = 1
+
+calc.tmatrix_parameters.tl_threshold = 1e-4
+calc.calculation_parameters.vibrational_damping = 'averaged_tl'
+calc.calculation_parameters.RA_cutoff = 2
+
+my_filters = ('forward_scattering', 'distance_cutoff')
+calc.calculation_parameters.path_filtering = my_filters
+calc.calculation_parameters.distance = 30
+calc.calculation_parameters.off_cone_events = 0
+[a.set('forward_angle', 40) for a in cluster]
+
+calc.set_atoms(cluster)
+
+# Compute and add previous data for comparison
+data = None
+for i in range(1,4):
+    calc.calculation_parameters.scattering_order = i
+    data = calc.get_theta_scan(level='2p',
+                                theta=np.arange(-30., 80., 0.5),
+                                phi=0,
+                                kinetic_energy=1382.28, data=data)
+
+# Put all orders on the same view
+dset = data[0]
+dset.add_columns(cs2=data[1].cross_section)
+dset.add_columns(cs3=data[2].cross_section)
+view1 = dset.views[0]
+view1.select('theta', 'cross_section', index=0, legend="Scattering order 1")
+view1.select('theta', 'cs2', legend="Scattering order 2")
+view1.select('theta', 'cs3', legend="Scattering order 3")
+
+
+no_filters = Data.load('path_filtering.hdf5')
+dset.add_columns(no_filters=no_filters[0].cross_section)
+view2 = dset.add_view('comparison', **view1._plotopts)
+view2._plotopts['legend'] = []
+view2.select('theta', 'cs3', legend="With path filtering")
+view2.select('theta', 'no_filters', legend="Without path filtering")
+
+data.view()