SCOPE: A Chemically-Aware Workflow-Automation Software for Molecules and Molecular Crystals

This repository contains the tutorials associated with SCOPE, a Python package designed to orchestrate computational chemistry workflows. SCOPE prepares, submits, and analyses quantum chemistry computations of individual molecules or molecule-based crystals, and organizes the results to simplify analysis.

SCOPE has four core pillars.

1. Chemical Species: Dedicated to encode the chemistry of the systems of interest. It can be expanded through add-ons
2. Computational Workflow: Dedicated to define dynamic computational workflows.
3. States: Dedicated to the analysis of results
4. Environment: Dedicated to file management and job execution in HPC clusters.

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Documentation

• The associated manuscript is under preparation. Preprint available here
• Source code is available here

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Installation

Python 3.12 is a strict requirement for these tutorials and the associated SCOPE packages.

This repository requires the installation of SCOPE and its add-ons. Once installed, then clone this repository to access the tutorial notebooks and data.

1-Environment setup

# create and activate a Python 3.12 environment
conda create --name scope python=3.12
conda activate scope
conda install pip

2-Install all SCOPE packages

Follow the installation instructions of SCOPE, and install all add-ons:

• scope-qc

3-Install notebook tools

pip install jupyter ipykernel nbformat matplotlib plotly

4-Download the tutorials

git clone https://github.com/QTC-IQAC/Scope_Tutorials.git
cd Scope_Tutorials

Then open any notebook from the tutorials/ directory and explore the accompanying files in Data/.

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Content

• Data folder with material discussed along the tutorials
• Tutorials, as python Notebooks

These are the topics covered in each tutorial:

1. The System class and its sources: the Specie, Cell and Atom classes
2. The Computational workflow: Branch, Workflow, Job, and Computation classes
3. The State class
4. The Data, Collection and VNM classes
5. The Input_data class, and scope input files
6. Running SCOPE - Part 1: File Structure
7. Running SCOPE - Part 2: Execution
8. Running SCOPE - Part 3: Detailed Actions
9. The Azo add-on: Subclasses, Analysis and Creation of Azo Systems

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License

This project is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International license (CC BY-NC-ND 4.0). See the LICENSE file for the full text.

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Acknowledgements

• The Spanish Ministerio de Ciencia, Innovación y Universidades for funding (Project PID2022-138265NA-I00)
• The EuroHPC Development Access Call (Project: EHPC-DEV-2024D11-031)
• The Centre de Supercomputació de Catalunya (CSUC) for Computational Resources