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m-julian committed May 10, 2024
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[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
[![docs](https://img.shields.io/website-up-down-green-red/http/shields.io.svg)](https://studious-adventure-rr4kzlv.pages.github.io/)

`ichor` is a Python package used to simplify computational chemistry programs and aid with machine learning force field development. If you would like to request missing features or run into a bug, don't hesitate to create an [issue](https://github.com/popelier-group/ICHOR/issues).
`ichor` is a Python package used to simplify data management from computational chemistry programs and aid with machine learning force field development. If you would like to request missing features or run into a bug, don't hesitate to create an [issue](https://github.com/popelier-group/ICHOR/issues).

Here is a list of things that the package is intended to do:

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4. provide interfaces to workload managers on compute clusters to automate job submission
5. collate tools for machine learning dataset and model analysis, as well as molecular dynamics simulation benchmarking

Realistically, the file management part of `ichor` is very general, so it can be used to manage any type of data that might not be computational chemistry related. However, the focus of the source code itself is on computational chemistry data.
Realistically, the file management portion of `ichor` (as well as the workload manager integration) is very general, so it can be used for any type of data that might not even be computational chemistry related. However, the focus of the source code itself is on computational chemistry and machine learning force field development.

## Getting Started
---
The namespace package `ichor` is divided into three parts, `ichor-core`, `ichor-hpc`, and `ichor-cli`. The `ichor-core` sub package contains classes and functions which make it easy to read relevant file and analyze outputs of jobs. The `ichor-hpc` package is used to submit jobs on compute clusters (only SGE/SLURM supported at the moment). The `ichor-cli` is a command line interface, providing easy access to the most common tools from ichor.
The namespace package `ichor` is divided into three parts, `ichor.core`, `ichor.hpc`, and `ichor.cli`. The `ichor.core` package contains classes and functions which make it easy to handle a very large number of files, perform many calculations with the outputs contained in the file, as well as aid with machine learning force field development. The `ichor.hpc` package is used to submit jobs on compute clusters (SGE/SLURM). The `ichor.cli` package provides a simple to use command line interface (CLI), providing an easy access to access the most commonly used tools from ichor.

**You will need to create a `ichor_config.yaml` in your home directory for configuration settings, see the documentation for examples.**
**You will need to create a `ichor_config.yaml` in your home directory for configuration settings relating to compute clusters, see the documentation for examples.**

## Documentation

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