PHDtools

PHDtools is a Python library that contains a collection of generic tools that I developed to aid my computational work during my PhD.

Disclaimer : the package is generic and experimental, and contains tools that were useful to me during my PhD.
Handle with care!

Installation

Use the package manager pip to install PHDtools.

pip install .

Package oranization:

├── README.md               <- README file of the project.    
|
├── example
|   ├── data                <- data used in the tutorial examples.  
|   └── notebook            <- tutorial python notebooks.  
|
├── phdtools
|   |
|   ├── ASEtools            <- implementation of python tools 
|   |                          based on the ase.atoms library
|   |
|   ├── computes            <- generic tools for scientific data analysis
|   |                          and MD simulations. 
|   |
|   ├── descriptors         <- implementation of python tools 
|   |   |                      based on the quip descriptor library.
|   |   └── quip
|   |
|   └── plots               <- generic tools for aided python image plotting.
|
└── setup.py                <- package manager installer file.

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Roadmap

• Add MD simulation tools
  • trajectory unwrapper (v1.0.0)
• Add ase.atoms support (v1.0.0)
• Add quip SOAP/turbo-SOAP descriptors support (v1.0.0)
• Add FES computes and plot support (v1.0.0)
• Add project manager for ASEtools
• Add MD simulation tools
  • RDF
  • MDAnalysis tools
• Add structural motifs pipeline
• Add kinetic models / MSM model support
• Add ML tools

Support

Any kind of feedback is welcome, just be patient.

Authors and acknowledgment

All the materials have been developed by me (this is probably the reason why is not perfect), nonetheless I grateful for all the usefull discussion I had suring my PhD, which inspired me to create this repository.
In particular I would like to acknowledge:

• Dr. Riccardo Capelli
• Dr. Giovanni Doni
• Dr. Ioan-Bogdan Magdau