∞tools 🧰

👷‍♂️ Work in progress python package that provide various ∞RETIS tools for tasks like setting up simulations and analyzing data. 📈

🤝 Contributions of tools and modifications are welcome – feel free to submit your enhancements! 🚀

Installation

1. Clone the repository
2. (Optional) Create a virtual environment
3. Install with:

   python -m pip install -e .

Usage

inft -h

inft center_periodic

The command inft center_periodic can be run to re-center an .xyz trajectory to a certain atom index. For example, to center the first atom C at index 0 in the co2.xyz frame in examples/co2.xyz with cubic box length of 12.4138, the following command can be ran:

inft center_periodic -i co2.xyz -o co2_c.xyz -c 12.4138 -idx 0

Development practice

Current CLI capabilities is powered by the Typer python library.

Python files

Any function function_name in a python file *.py with the following structure

from typing import Annotated

def function_name(
    args1: Annotated[str, typer.Option("-args1", help="var1")],
    args2: Annotated[int, typer.Option("-args2", help="var2")],
    ):
    """
    Function description
    """

added to the folders inftools/exercises, inftools/tistools and inftools/xyz will automatically be callable via the terminal as

inft function_name -args1 var1 -args2 var2

Individual functions

Individual functions can also be added to the CLI library by including them in inftools/bin.py, as done for the wham function in the inftools/analysis folder:

from inftools.analysis.wham import wham

MAPPER["wham"] = wham

Testing

The CLI functions are tested by utilizing the pytest python library.

The tests included in the inftools/test folder can be ran by running the following command in the terminal:

pytest

We currently do not have a testing policy but please do include tests for the included CLI functions for higher coverage.