Manual Update for RC

[ramirezfranciscof]

We need to update the manual for the upcoming release. I will be taking charge of this and go around asking for the corresponding authors of the corresponding sections.

Expect me.

[ramirezfranciscof]

New structure proposal:

1. Introduction
   1.1 What is LIO?
   1.2 Installation Guide
   1.3 MD-Engine Interface
   1.4 Tips and tricks - Optimizing your runs
   1.5 Quick Reference

2. Model Hamiltonian
   2.1 Density Functional Theory
   2.2 Tight Binding Interface
   2.3 External Electric Fields
   2.4 Single Atom Potentials
   2.5 Effective Core Potentials

3. Ground State Calculations
   3.1 Single-point and MD calculations
   3.2 Geometry optimizations
   3.3 Restraints

4. Electron Dynamics
   4.1 Real Time TD-DFT
   4.2 Electronic transport
   4.3 Ehrenfest Dynamics

5. Post-Processing Tools
   5.1 TD-Analize: Electronic Spectra
   5.2 CubeGen: Orbital and Density Visualization

[fedepedron]

Looks good, though the titles make me feel like I'm reading a chemistry textbook. I would keep the level of theory at a safe minimum (that's what publications are for) and emphasise the practical/user level aspects.
I would also need a miscellaneous section for specific functionalities, like ghost atoms or electronic properties, since I do not see those easily fitting in the aforementioned sections.

[ramirezfranciscof]

What about this?

5. Other Settings
   5.1 Ghost Atoms
   5.2 Properties Calculations

6. Post-Processing Tools
   6.1 TD-Analize: Electronic Spectra
   6.2 CubeGen: Orbital and Density Visualization

Regarding the titles, maybe we could add a bit of a description in the introduction on what is in each section, but I can't think of another way of phrasing/grouping them.

[Nick-Chaos]

quiza este modelo venga mejor para el manual q el q esta actualmente: https://www.overleaf.com/read/fjgjmbvwhmyg