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AiiDAlab ISPG applications

ATMOSPEC - ab initio workflow for UV/VIS spectroscopy of organic molecules.

Installation

This Jupyter-based app is intended to be run within the AiiDAlab environment.

If you already run AiiDAlab you can install the latest version from Github by running the following command from within the AiiDAlab Docker container.

aiidalab install aiidalab-ispg@git+https://github.com/danielhollas/aiidalab-ispg.git@main

See below for complete installation instructions on a local machine.

Usage

TODO: A few screenshots / animated gifs illustrating how to use the app.

License

MIT

Acknowledgements

This project has been funded by European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 803718, project SINDAM).

Local installation

NOTE: The details of some of the commands will depend on your OS and its version. The concrete examples are based on Ubuntu 20.04.

Install dependencies

  1. Install ORCA

NOTE: If you're downloading for Linux, choose the "shared-version", which has much smaller download size.

  1. Install Docker
sudo apt install docker.io

Then add yourself to the docker unix group and restart the shell session

sudo usermod -a -G docker $USER
  1. Install pipx
sudo apt install python-venv pipx
  1. Install aiidalab-launch to manage the AiiDAlab containers
pipx install aiidalab-launch

If pipx is giving you trouble, you should be able to install via pip as well.

Download the ATMOSPEC Docker image

docker pull ghcr.io/ispg-group/atmospec:latest

This image is built and published in a separate Github repository, which you can visit for more information.

Setup AiiDAlab launch

While you can launch the Docker container directly using the docker command, it is much more convenient to use the aiidalab-launch application.

Let's first modify the default profile to include to ATMOSPEC app from this repo

aiidalab-launch profile edit default

This should open your default text editor. Copy-paste the following profile configuration (substitute path to ORCA and the Docker image name if needed)

port = 8888
default_apps = [ "aiidalab-ispg@git+https://github.com/ispg-group/aiidalab-ispg.git@main",]
system_user = "jovyan"
image = "ghcr.io/ispg-group/atmospec:latest"
home_mount = "aiidalab_atmospec_home"
extra_mounts = ["/absolute/path/to/orca/:/opt/orca:ro",]

With this configuration, all the data will be stored in a separate Docker volume aiidalab_atmospec_home. Alternatively, you can specify the absolute path to a directory in your file system to store the data, for example

home_mount = "/home/username/aiidalab_atmospec_home/"

Launch and manage container

  • Launch the container
aiidalab-launch start

This command will print the URL that you can then access in the browser. With the configuration above it should be http://localhost:8888

  • Stop the container
aiidalab-launch stop
  • Print container status
aiidalab-launch status
  • Run a command inside a running container
aiidalab-launch exec -- <command>
  • Entering the container
docker exec -it -u jovyan aiidalab_atmospec /bin/bash

To display all available commands

aiidalab-launch --help

Development

Re-install packages for development in the container

aiidalab-launch exec -- pip install --user -e /home/aiida/apps/aiidalab-ispg/