2. Tutorials

For beginer, we warlmy recommand to try the get started tutorial with the help of the overview page.

The space discretization tutorial and the liquid mixture one should help you understanding the structural analysis available and how to deal with complexe systems.

Then, the optical analysis overview present the main goal of : perform QM/MM calculation to obtained the first hyperpolarizability in the liquid phase. You can try the more advanced QM/MM tutorial which presents how to refine the PE environment description, see [1] or [2] Chapter IV, and how to compute the first hyperpolarizability up to the quadrupole order. See [2] Chapter VI.

A short tutorial about the second hyperpolarizability is proposed for advanced users, see [1].

Finally, we explain how to write by yourself a new MoleculeType, which is the backbone of , for any molecule not yet available. This tutorial may require some knowledge about the functionment explained throughout this wiki.

Every tutorial are in the directory Tutorials which you should find in the GitHub repository. Each sub-directory correspond to a tutorial. In every directory you will find input for , sometimes QM results, and also a jupyter notebook file (.ipynb) that can be used for the analysis. The trajectories needed for the tutorials are in Tutorials/Traj.

• 2.1. Overview
  • 2.1.1. Goal and Perquisite
  • 2.1.2. Frog purposes
  • 2.1.3. Key Objects
  • 2.1.4. Steps
  • 2.1.5. Frog Files and Directory Structure
• 2.2. Get started
  • 2.2.1. Goal and Perquisite:
  • 2.2.2. The Parameter file:
  • 2.2.3. Run Frog:
• 2.3. Space Discretization
  • 2.3.1. Goal and Perquisite:
  • 2.3.2. Parameter file:
  • 2.3.3. Analysis:
• 2.4. Mixture and structural analysis
  • 2.4.1. Goal and Perquisite:
  • 2.4.2. Parameter file:
  • 2.4.3. Run and analysis:
• 2.5. Optical Analysis
  • 2.5.1. Goal and Perquisite:
  • 2.5.2. Parameter file:
  • 2.5.3. Procedure:
  • 2.5.4. Analysing the results:
• 2.6. Quadrupole and Long range QM/MM
  • 2.6.1. Goal and Perquisite:
  • 2.6.2. Parameter file:
  • 2.6.3. Procedure:
• 2.7. Gamma calculation
  • 2.7.1. Goal and Perquisite:
  • 2.7.2. Overview:
  • 2.7.3. One Parameter file:
  • 2.7.4. Procedure:
• 2.8. How to read results
  • 2.8.1. Open the pickle results
  • 2.8.2. Plot the diagrams
  • 2.8.3. Advance: open any molecular value
• 2.9. Molecular Type Module
  • 2.9.1. Goal and Perquisite:
  • 2.9.2. Procedure:
  • 2.9.3. General informations
  • 2.9.4. Structural analysis:
  • 2.9.5. Optical properties:
  • 2.9.6. Final remarks

[1] (1,2)

Guillaume Le Breton, Oriane Bonhomme, Emmanuel Benichou, and Claire Loison. First hyperpolarizability of water in bulk liquid phase: long-range electrostatic effects included via the second hyperpolarizability. Physical Chemistry Chemical Physics, 24:19463–19472, 2022.

[2] (1,2)

Guillaume Le Breton. Génération de second harmonique non-résonnant de liquides : de la réponse moléculaire à la mesure expérimentale. PhD thesis, Université Lyon 1, 2022. Thèse de doctorat dirigée par Bénichou, Emmanuel Loison, Claire et Bonhomme, Oriane Physique & Chimie Lyon 1 2022. URL: http://www.theses.fr/2022LYO10015.