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Quick start

Make sure you first install and set up Martignac as described in the installation guide.

Hello, Martignac

Safeguards for first-time users

The installation guide provides a detailed explanation of the safeguards that are in place to prevent accidental data upload to NOMAD. Please make sure to read it before running Martignac for the first time.

You are now ready to run the workflows. For instance, to generate solutes in bilayers, go to the input absolute path (e.g., scripts/solute_in_bilayer). There should be two files

init.py

initializes the computational signac-workflow; defines the solutes chemistries to screen (here one single C4 bead, one P6-C3 molecule, and one P6-C3-N1 molecule). This solely tells signac which computational jobs are to be defined. The actual computation is defined in the project.py script.

import signac

from martignac.workflows.solute_generation import SoluteGenFlow

project = signac.init_project(path=SoluteGenFlow.workspace_path)

for solute_name in ["C4", "P6 C3, 0-1", "P6 C3 N1, 0_1 1_2 0-2"]:
    sp = {"type": "solute", "solute_name": solute_name}
    job = project.open_job(sp).init()
project.py

defines the workflow to run by importing the class and setting the desired workspace path. All computations will occur from this script, and the results will be stored in the workspace/ directory.

from martignac.workflows.solute_generation import SoluteGenFlow

if __name__ == "__main__":
    SoluteGenFlow(path=SoluteGenFlow.workspace_path).main()

You can simply run the two scripts by the following commands: 

python init.py
python project.py run

The results can be found in your output workspace/ directory. If you've decided to push the data to NOMAD, you can check the content of your uploads on the NOMAD webserver, by logging in and navigating to your Datasets. For instance, the url for the test database would be https://nomad-lab.eu/prod/v1/test/gui/user/datasets.