Add Activity03 (WIP)

Activity03/adsorbate.py

@@ -0,0 +1,45 @@
+from ase.build import bulk, add_adsorbate, fcc100
+from msspec.calculator import MSSPEC
+from msspec.utils import cut_cylinder
+import numpy as np
+
+cluster = fcc100('Ni', size=(2, 2, 2))
+add_adsorbate(cluster, 'Se', 1.55, 'hollow')
+#add_adsorbate(cluster, 'Se', 2.34, 'ontop')
+cluster = cluster.repeat((10,10,1))
+
+
+def get_index_close_to_origin():
+    iSe = [atom.index for atom in cluster if atom.symbol == 'Se']
+    R = np.linalg.norm(cluster.positions[iSe], axis=1)
+    i = iSe[np.argmin(R)]
+    return i
+
+cluster.center(about=(0,0,0))
+i = get_index_close_to_origin()
+cluster.positions -= cluster[i].position
+
+cluster = cut_cylinder(cluster, radius=10)
+emitter = get_index_close_to_origin()
+cluster.emitter = emitter
+
+if False:
+    cluster.edit()
+    exit()
+
+calc = MSSPEC(spectroscopy='PED', algorithm='expansion')
+calc.set_atoms(cluster)
+
+calc.source_parameters.theta = -60
+calc.calculation_parameters.scattering_order = 3
+calc.calculation_parameters.path_filtering = 'forward_scattering'
+[a.set('forward_angle', 30) for a in cluster] 
+calc.muffintin_parameters.interstitial_potential = 13.2
+
+data = calc.get_energy_scan(level='3d', kinetic_energy=[50,110,20], theta=0, phi=0)
+data = calc.get_energy_scan(level='3d', kinetic_energy=[50,110,20], theta=0, phi=45, data=data)
+
+data.view()
+
+
+#cluster.edit()