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Nanopore Geometry Experiment

Automated virtual experiment that calculates geometric properties of nanoporous materials using the Zeo++ software package.

Quick links

Launching the virtual experiment

On a local machine

Instructions

If you have a container runtime such as docker, podman, rancher desktop, etc available on your system you can execute the experiment by:

  1. creating a python virtual environment, activating it, and installing the python module st4sd-runtime-core[develop]
  2. cloning this repository
  3. launching the experiment

For example:

#!/usr/bin/env sh

: # Download virtual experiment
git clone https://github.com/st4sd/nanopore-geometry-experiment.git

: # Setup ST4SD runtime-core
python3 -m venv --copies venv
. venv/bin/activate
python3 -m pip install "st4sd-runtime-core[develop]"

: # Run experiment
elaunch.py -i docker-example/cif_files.dat \
      --applicationDependencySource="nanopore-database=cif:copy" \
      nanopore-geometry-experiment.package

Note: Make sure you run the git clone command in a directory that your container runtime (e.g.docker, podman, etc) can mount later when you execute the experiment.

Note: Using a container runtime is intended for small scale experiments and/or debugging your experiments. Use the kubernetes example below to launch larger experiments.

On Kubernetes

Follow our end to end example notebook to launch our nanopore-geometry-experiment experiment on your ST4SD Cloud instance.

Using custom database of CIF files

You may download the CIF files of your choosing to a PVC inside your OpenShift cluster (below we use the name nanopore-database-pvc), mount it as a volume and ask the virtual experiment instance to use the contents of the PVC as the contents of the nanopore-database application-dependency.

file_names = [""]
payload = {
  "volumes": [{
        "type": {"persistentVolumeClaim": "nanopore-database-pvc"},
        "applicationDependency": "nanopore-database"
    }],
  # other fields
}
rest_uid = api.api_experiment_start("nanopore-geometry-experiment", payload)

Note: The example notebook shows a full example.

Help and Support

Please feel free to create an issue and alert the maintainers listed in the MAINTAINERS.md page.

Contributing

We always welcome external contributions. Please see our guidance for details on how to do so.

License

This project is licensed under the Apache 2.0 license. Please see details here.