README.md

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.