# How to access the raw data and plot the results of this work

## AiiDA data and archive files

We provide AiiDA archive files that contain and allow to inspect the full provenance of all calculations that we performed in this study.
For further information on how to use this information, we refer to the README_AiiDA.txt file.

You can check the following section for scripts and data to reproduce the figures of the paper, that do require the use of AiiDA. For an easy and quick
installation of AiiDA (for the purpose of plotting the results) and to import the related archive, see the README_AiiDA.txt file.

## Raw data

The raw (input and output) data of the simulations are contained in the corresponding file raw_inputs_outputs_scripts.tar.gz. You can extract them using:

>>> mkdir raw_inputs_outputs_scripts && tar -xzvf raw_inputs_outputs_scripts.tar.gz -C raw_inputs_outputs_scripts

The data are obtained from the AiiDA workchains using the "verdi process dump <process pk>" functionality of AiiDA: 
subdirectories are automatically generated following the hierarchy of the calls performed by the workflow in order to perform a given simulation.

In the case of LaCoPO, the raw data for the muons search are contained under "raw_inputs_outputs_scripts/LaCoPO/raw_data/raw-data-FindMuonWorkChain". Different supercells are indexed starting 
from zero, e.g. "07-supercell_01-PwRelaxWorkChain" contains the data on the second muon candidate supercell (and 7th step of the workflow). The indexing convention is the same as shown in the plots.

Data concerning the estimation of the supercell size are under the subdirectory “raw_inputs_outputs_scripts/LaCoPO/raw_data/raw-data-FindMuonWorkChain/01-IsolatedImpurityWorkChain“.

The Quantum ESPRESSO inputs and outputs data are contained in the "PwCalculation" folders.

### The force_difference_data folder

Additional raw data, computed without AiiDA and used for validation of the IsolatedImpurityWorkChain workflow, are contained under the "force_difference_data" directory. This contains
Quantum ESPRESSO inputs/outputs for given supercells done with and without the muon, used then to compute the force differences for each atom of the cell. 

### The cif_files folder

In this folder there are all (and the unique) the simulated material+muon supercells, named as H<muon index>.cif (muon index starting from 1, at variance with the convention in the raw_data of the AiiDA workchains) 
and the list of the corresponding total energies. The "unique_mu_in_inputcell.cif" file contains all the muon in the starting unit cell, to analyse them at the same time.
These data are generated when running the plotting scripts (see last section of this file). The cif files can be visualized using the 
the VESTA visualization software (https://jp-minerals.org/vesta/en/). "Unique" list contains the supercells which are not symmetric replica of other ones in the set.

## Plotting the results* 

To plot the results, you can use the scripts which are collected under the "scripts" directory for each material. Scripts should be executed from the "scripts" directory to be 
able to parse correctly all the data (and not only the one contained in the AiiDA archive). 
NB: To import the AiiDA archive, please see the README_AiiDA.txt file.

There are different types of plotting scripts:

- plot_supercell_convergence.py (to display the forces and force differences for the supercell size estimation)
- plot_findmuon_fields.py (to plot the local magnetic fields at the muon site)
- plot_supercell_comparison.py (to compare the supercell size and some LiF and Fe observables like magnetic fields and total energies)
- plot_hubbard_dependency.py (to compare the CuO lowest muon sites for different Hubbard U values)
- plot_radial_distance.py (to plot the radial displacement of CaF2 atoms surrounding the charged or neutral muon)

The plots are saved in the main directory of a given material.

In the plots of the local magnetic fields, Bc is the contact field, Bdip is the dipolar and Bmu is the total field felt by the muon. 

*NB: some of the results are plotted partially using raw_data, so be sure to download all the needed files and run the scripts from the corresponding "scripts" directory.