kumaranu / ts-workflow-examples

This respository contains workflows to calculate transition state other relevant properties using QuAcc library.

Transition State Workflow Examples

This repository provides directly usable examples for Transition State (TS) workflows using NewtonNet and MACE. The examples include:

NewtonNet:

1. NEB + TS with Hessian
2. NEB + TS without Hessian
3. Geodesic + TS with Hessian
4. Geodesic + TS without Hessian

MACE:

1. NEB + TS with Hessian
2. NEB + TS without Hessian
3. Geodesic + TS with Hessian
4. Geodesic + TS without Hessian

Getting Started

Prerequisites

• Python 3.10
• Conda (for managing environments)

Installation

1. Create and Activate Conda Environment

   Create a new Conda environment with Python 3.10:

   conda create -n test_env python=3.10

   Activate the newly created environment:

   conda activate test_env

2. Clone the Repository and Install Dependencies

   Clone the repository from GitHub:

   git clone https://github.com/kumaranu/ts-workflow-examples.git

   Navigate to the cloned repository:

   cd ts-workflow-examples

   Install the package in editable mode:

   pip install -e .

   Install the additional requirements for testing:

   pip install -r tests/requirements.txt

Running Example Scripts

Navigate to one of the directories that contains example scripts inside the src/ts-workflow-examples directory. For example, to run a script from the geodesic_ts_with_hessian directory:

cd src/ts-workflow-examples/geodesic_ts_with_hessian

Run the desired script (for example, using_newtonnet.py):

python using_newtonnet.py

Note: Ensure that you are in the correct directory as the paths inside the input files are relative. This will allow the inputs and ML-model provided with the repository to run correctly.