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# Activity 1: Getting started

MsSpec is a Fortran code with two components: Phagen (Written by R. Natoli) and Spec (written by D. Sébilleau). Phagen computes the phase shifts of the electronic wave propagating in the matter on a spherical harmonics basis. Spec uses those phase shifts to compute the multiple scattering process and simulate the intensity of different electronic spectroscopies.

In the most recent version of MsSpec, the program is interfaced with python (https://msspec.cnrs.fr/), allowing for much more flexibility and interplay with other simulation techniques.

## Building atomic systems

MsSpec works in the cluster approach. Building such a cluster for a calculation is a fundamental step. We use the python Atomic Simulation Environment (ASE) for this.

ASE is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations. Building atomic systems, structures… is pretty straightforward:

    # To build a molecule with ASE
    from ase.build import molecule
    # To view
    from ase.visualize import view

    # Create a water molecule
    water = molecule('H2O')
    # Display it
    view(water)

ASE atomic visualization
<scene> <group/> <group> <group> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> </group> <group> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> </group> </group> </scene>

## Barebone script for MsSpec

MsSpec can simulate different electronic spectroscopies like PED, AED, LEED, EXAFS, APECS and more will be included in the forthcoming version. However, it is really well-suited for PhotoElectron Diffraction simulation, and the python interface is only fully available for it at the moment. Since PED covers all the MsSpec features and concepts, we will focus on this technique.

There are typically 3 steps to follow to get a result with MsSpec:

1. Create a cluster

2. Create an ASE calculator

3. Run the simulation

### PED polar scan for Cu(001)

    1from ase.io import read
    2from msspec.calculator import MSSPEC
    3
    4
    5cluster = read('copper.cif')
    6# view the cluster
    7cluster.edit()
    8

ASE atomic visualization
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     9# The "emitter" atom is located in the middle of the 3rd plane
    10cluster.emitter = 10
    11
    12# Create a "calculator"
    13calc = MSSPEC(spectroscopy='PED', algorithm='inversion')
    14calc.set_atoms(cluster)
    15
    16data = calc.get_theta_scan(level='2p3/2')
    17
    18# Plot the result with the interactive GUI
    19data.view()
    20
    21# Or plot using matplotlib directly
    22from matplotlib import pyplot as plt
    23data[0].views[0].plot()
    24plt.show()

Fig. 1 Cu(2p) polar scan for the copper cluster above

## Shaping a cluster

Quiz

Based on the previous *.cif file, create a new cluster without the deepest plane and run the same calculation for the same emitter

Note

As the cluster will contain fewer atoms, the emitter index will be different

What do you conclude ?

Fig. 2 Comparison between 4 and 3 planes for an emitter in the 3rd plane.

Not all atoms contribute equally to the total signal. Some of them can be removed to save computation time and memory.

The number of atoms used for the calculation greatly impact the calculation time and memory. Most of the time, a cluster is shaped as an hemisphere to minimize the number of atoms to take into account

    from msspec.calculator import MSSPEC
    from msspec.utils import hemispherical_cluster, get_atom_index
    from ase.build import bulk
    from ase.visualize import view

    copper = bulk('Cu', cubic=True)
    cluster = hemispherical_cluster(copper, planes=3, emitter_plane=2)
    cluster.emitter = get_atom_index(cluster, 0,0,0)

    view(cluster)

ASE atomic visualization
<scene> <group/> <group> <group> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> </group> <group> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> <shape> <appearance> </appearance> </shape> </group> </group> </scene>

Fig. 3 Cu(2p) polar scan for the hemispherical cluster.