Introduction The code has been implemented by Jonathan Campeggio. For doubts and suggestions, please write an e-mail to jonathan.campeggio@gmail.com.

The Python files present in the folder can behave both like stand-alone scripts and modules. They can be imported with the statement import modulename

in a user's Python file and the function called by the dot notazione modulename.methodname(parameters)

Required libraries Provo a fare un file wheel per rendere il codice autocoerente The code mainly relies on built-in Python libraries. The user has to install the following libraries to use the Python files:

1. numpy
2. seaborn
3. matplotlib

Documentation Preparator.py This program build a scan along the distance substrate-surface. In particular, it generates a series of folders each of them containing the CP2K input file and the coordinates. To use it, use the terminal command inside the folder where there is the script python3 Preparator.py positions.xyz NAtoms z0 input.inp output.out

Where:

1. positions.xyz is the file that contains the starting xyz coordinates. The coordinates are expressed in Å.
2. NAtoms is the number of atoms of the substrate.
3. z0 is the z coordinate of the nearest substrate atom to the surface.
4. input.inp is the input file (in the present article is the CP2K input)
5. output.out is the name of the output xyz coordinates to be stored in each folder.

The code's aim is to describe the neighborhood of z0. The interval in Å is [z0 - 1 , z0 + 6]. The grid has a tighter spacing of $0.1$ Å in the range [z-0.5, z+0.5] Å, then the spacing becomes broader. The variable relativeDisplacements can be edited to modify this grid.

TrajectoryAnalyzer.py This code is useful to handle a trajectory coordinates file. It can be used both as a standalone script and as a module. The user can use the following command to use the script: python3 TrajectoryAnalyzer.py trajectory.xyz atom1 atom2 atmo3 atom4 atom5 atom6 output.out

Where:

1. trajectory.xyz is the xyz trajectory file
2. atom1 and atom2 are the indices (1-based integers) that describe the bond distance
3. atom3 atom4 atom5 atom6 are the indices (1-based integers) that describe the dihedral angle
4. output.out the name of the output file.

A user can find more interesting the usage as a module. After the importing (import TrajectoryAnalyzer.py), the user can use the implemented function to analyze a general trajectory.

For example, the function timeCatcher(trajectory.xyz) reads the trajectory and it stores the time in a numpy array. The most flexible function in the module is savingOutput(filename, **kwargs). It concatenates the numpy arrays given in iput as keyword arguments and it saves in the filename file. Along with the $3$ catcher functions (distanceCatcher, angleCatcher, and dihedralCatcher), it allows the user to completely analyze the trajectory trends of bond distances, bond angles, and dihedral angles.

The code is extensively commented on, and it extensively uses type hints.

Launcher.py As in the publication, one can have to analyze a series of trajectories. Launcher.py performs the same operation of the previous code, but for all the folders in a given path. The command is: python3 Launcher.py path trajectory.xyz atom1 atom2 atmo3 atom4 atom5 atom6 output.out

where path is the path where all the folders containing the trajectory.xyz files are stored.