Installation Guide

Prerequisites

ORCA 5.0.4 specifically requires OpenMPI version 4.1.1

Step-by-Step Installation

Clone the repository and navigate to the directory:

$ git clone https://github.com/mhyeok1/dand.git
$ cd dand

Set Up Conda Environment

Create and activate the environment:

# Create environment from configuration file
$ conda env create -f environment.yml

# Activate the environment
conda activate ts

# Install Dandelion
pip install -e .

Always ensure you are in the ‘ts’ environment when using Dandelion

Install pyGSM

Install the Growing String Method implementation:

$ git clone https://github.com/ZimmermanGroup/pyGSM
$ cd pyGSM
$ pip install -e .

Test the installation by running:

$ gsm

Install ORCA

  1. Download ORCA 5.0.4 from the ORCA portal.
  2. Extract the downloaded file:
$ tar -xf orca.tar.xz

Configure Environment Variables

Add these settings to your .bashrc file:

# Open .bashrc
vi ~/.bashrc

# Add these lines:
export PATH="/path/to/orca:$PATH"
export PYTHONPATH=/path/to/pyGSM:$PYTHONPATH
export OMP_NUM_THREADS=1
export OMP_STACKSIZE=16G
ulimit -s unlimited

Apply changes:

$ source ~/.bashrc

Verification

After installation, verify that all components are working:

  1. Ensure you’re in the ‘ts’ environment
  2. Check if commands dand, gsm, and orca work

Continue: How-to-use