Examples

March 28, 2023 · View on GitHub

This is a collection of project examples, designed to demonstrate possible signac workflows and for the fast setup of new projects.

Usage

Simply clone or download this repository and copy the scripts related to a specific example into your project path. Example:

git clone https://github.com/glotzerlab/signac-examples.git
cp -r signac-examples/projects/flow.minimal/ my_project
cd my_project
signac init

Namespaces

Project names are divided into namespaces to avoid name clashes. These are namespaces used:

flow: These examples require signac-flow.
hoomd: These examples require HOOMD-blue.
qe: These examples require Quantum-Espresso.
gmx: The examples requires GROMACS.

If you intend to create your own library of example projects, consider placing them in a namespace clearly related to your organization.

Project Overview

idg-minimal

Minimal example for the calculation and storage of a phase diagram for an ideal gas with signac.

flow.2D-random-walk

A study on 2D Gaussian random walks using groups and aggregation.

flow.aggregation-mpi

This is an example of a signac-flow project using aggregation to split MPI communicators.

flow.aggregation-plotting

An example of plotting data using aggregation.

This project provides a demonstration of a complete GROMACS workflow using signac and signac-flow. The simulation flow follows Justin Lemkul's Lysozyme in Water Tutorial, illustrating how all key steps can be automated and simplified using signac and signac-flow. If you plan to use this to simulate a different system, note that the physics encoded by these parameter files may not be appropriate; you should modify the mdp files to model the appropriate physics correctly.

flow.gmx-mtools

Template for MoSDeF- and GROMACS-centric project managed with signac

flow.hello-world-optimization

This is a "hello world" example for an optimization flow project. It features the optimization of three mathematical functions, which are stand-ins for more expensive simulations.

flow.hello-world

This is a hello world example flow project. It features a hello operation, which prints Hello {job._id} to screen and writes the same string to a file.

flow.minimal

This is a minimal example for a signac-flow project.

flow.qe-minimal

This is a simple example on how to setup a signac-flow project for Density-functional theory (DFT) calculations with Quantum Espresso. Quantum Espresso can be installed with:

flow.hoomd.lj

An Introductory Walk-through Using signac with HOOMD-blue

flow.sklearn.init-ParameterGrid

This example projects shows how to use signac-flow in combination with scikit-learn. The scripts perform a grid search over model hyperparameters for a simple classifier, saving the results of each evaluated parameter set into a signac data space. Then, a confusion matrix is plotted for each set of model hyperparameters. The script dashboard.py can be used with signac-dashboard to visualize these plots.

Copyright Notice

UNLESS OTHERWISE STATED, ALL CODE PROVIDED AS PART OF THIS EXAMPLE COLLECTION (projects/*) IS RELEASED INTO THE PUBLIC DOMAIN!