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Installation & Setup🔗

This page covers:

  • installing neb-dynamics with either uv or pip
  • validating the CLI install
  • configuring electronic-structure backends
  • setting up the optional retropaths repository for network-growth features

Prerequisites🔗

  • Python 3.10+
  • Git
  • A shell environment where python, pip, and/or uv are available

1. Clone the repository🔗

git clone https://github.com/mtzgroup/neb-dynamics.git
cd neb-dynamics

2. Create/sync the environment🔗

uv sync

3. Verify install🔗

uv run mepd --help
uv run python -c "import neb_dynamics; print('neb_dynamics import OK')"

4. (Optional) Editable install workflow🔗

If you want your active environment to track local source edits directly:

uv pip install -e .

Install With pip🔗

Option A: Install from GitHub directly🔗

pip install "git+https://github.com/mtzgroup/neb-dynamics.git"

Option B: Install from a local clone🔗

git clone https://github.com/mtzgroup/neb-dynamics.git
cd neb-dynamics
pip install .

Editable local install:

pip install -e .

Verify:

mepd --help
python -c "import neb_dynamics; print('neb_dynamics import OK')"

Backend Setup (required to run calculations)🔗

NEB Dynamics needs a configured backend through your RunInputs (for example ChemCloud/QCOP/other supported engines).

ChemCloud setup🔗

  1. Sign up: https://chemcloud.mtzlab.com/signup
  2. Configure auth using either:
# Writes credentials to ~/.chemcloud/credentials
python -c "from chemcloud import setup_profile; setup_profile()"

or environment variables:

export CHEMCLOUD_USERNAME=your_email@chemcloud.com
export CHEMCLOUD_PASSWORD=your_password

Optional custom server:

export CHEMCLOUD_DOMAIN="https://your-server-url.com"

retropaths Setup (optional but required for network growth/template actions)🔗

retropaths is required for:

  • mepd netgen-smiles
  • MEPD Drive reaction-template growth actions (+ in the UI)

1. Clone retropaths🔗

git clone https://github.com/mtzgroup/retropaths.git ~/retropaths

2. Point NEB Dynamics to the repo🔗

NEB Dynamics checks RETROPATHS_REPO first, then ~/retropaths.

export RETROPATHS_REPO=~/retropaths

3. Locate your reactions library🔗

You typically pass a reactions.p file path in CLI/UI inputs:

ls "$RETROPATHS_REPO"/data/reactions.p

Use this file path with:

  • mepd netgen-smiles --reactions-fp ...
  • MEPD Drive Reactions File field

Quick Sanity Checks🔗

CLI check🔗

mepd --help

Drive check (local)🔗

uv run mepd drive --inputs examples/example_inputs.toml --no-open

If this starts and prints a URL, your installation path is healthy.