NOMAD's pedestrian dynamics extension

This is a collection of the NOMAD parsers for the following codes:

• Vadere

This plug-in parses simulation output from a Vadere simulation (*.scenario, postvis.traj) into a dictionary. In addition, it computes macroscopic quantities from the microscopic data:

This plug-in provides a NOMAD parser, a NOMAD schema and normalizing functionalities. If you are not familiar with these concepts, please read our overview of NOMAD concepts.

Re-using existing NOMAD plug-ins

NOMAD provides several plug-ins for "computational data" that are data produced by simulators. This plug-in is based on the plug-in nomad-schema-plugin-run. The source code of this plug-in is publicly available on github and under the Python package registry.

Developing and testing the plug-in locally (this does not require a running NOMAD Oasis)

This plug-in was tested with Python3.9.

To test the plug-in you need to install the Python package nomad-lab. The plug-in nomad-schema-plugin-run requires a nomad-lab version that is not published under the Python package index registry (see the issue

We recommend the following steps to avoid dependency conflicts:

1. Create a virtual Python3.9 environment and activate it:

python3.9 -m venv myvirtualenv
source myvirtualenv/bin/activate

2. Install nomad-lab using NOMAD's internal registry:

pip install https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/files/472e0cb3bc16d51251a84464686db9e1ce80791a945ffa5faa3e69ee869b6012/nomad-lab-1.3.6.dev41+g0347838e4.tar.gz

3. Install the plug-in

pip install nomad-schema-plugin-run

Note: the automatic dependency handling (step 3) would try to install nomad-lab over the Python package registry. Because the required nomad-lab version is not published under the Python package registry the dependency handling fails. We prevent from this by manually installing nomad-lab in step 2.

After your system setup simply run the *.py tests in tests directory. Please also see the documentation.

Running the plug-ins in a NOMAD oasis

Please follow the instructions from: https://nomad-lab.eu/prod/v1/docs/howto/oasis/plugins_install.html

Warning

The setup instructions seems to be constantly changing.

I used the option with the derived Docker image. Setup an oasis without plug-ins (detailed information can be found in the documentation-1):

Download the nomad-oasis.zip

unzip nomad-oasis.zip
cd nomad-oasis
sudo chown -R 1000 .volumes
docker compose pull

Create the derived Docker image. Copy the following content into an empty Dockerfile (textfile named "Dockerfile")

FROM gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:latest

# Switch to root user to install packages to the system with pip
USER root

# for installing a python repo from github
RUN apt-get update && apt-get -y install git

RUN pip install --upgrade pip

# installs nomad version 1.3.6 - which is required by the nomad-schema-plugin-run depencency. 
# Automatic dependency resolving is not working! 
# REPLACE the following line as soon as a stable nomad version is available
RUN pip install https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/files/472e0cb3bc16d51251a84464686db9e1ce80791a945ffa5faa3e69ee869b6012/nomad-lab-1.3.6.dev41+g0347838e4.tar.gz

# Install your plugin here, e.g.:
RUN pip install git+https://github.com/pedestrian-dynamics-HM/nomad-pedestrian-dynamics-extension.git@main

# Remember to switch back to the 'nomad' user
USER nomad

Replace the Docker image "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:latest" by the derived image in nomad-oasis/docker-compose.yaml:

  worker:
    restart: unless-stopped
    #image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:latest
    image: nomad-with-plugins

  north:
    restart: unless-stopped
    #image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:latest
    image: nomad-with-plugins

  app:
    restart: unless-stopped
    #image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:latest
    image: nomad-with-plugins

Start the oasis

docker compose up -d

Open http://localhost/nomad-oasis in your browser.

Uploading entries

One can upload a single simulation run or a collection of simulation runs. This repository contains *.zip-files for testing both functionalities:

• archive of a single simulation run
• archive with multiple simulation runs

The following snapshot was taken after uploading the two archives to an empty oasis: