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README.md

Examples

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 root directory. Example:

#!bash
$ git clone https://github.com/glotzerlab/signac-examples.git
$ mkdir my_project
$ cd my_project
$ signac init MyProject
$ cp -r ../signac-examples/projects/flow.minimal/* ./

Namespaces

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

  • std: Standard examples that only require the signac core package.
  • 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

std.idg-minimal

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

std.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.

std.flow.hello-world-optimization

This is a minimal example for how to implement an iterative optimization project with signac-flow. This project dynamically spawns new jobs as a result of previous results.

std.flow.minimal

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

std.hoomd.lj-minimal

Minimal example for the generation of a phase diagram for a Lennard-Jones fluid with signac and HOOMD-blue.

std.flow.hoomd.lj

The example project features the generation of a p-V phase diagram of a simulated Lennard-Jones (LJ) fluid and an ideal gas estimate. The LJ fluid is sampled via molecular dynamics using the HOOMD-blue particle simulation toolkit.

std.flow.qe-minimal

The example project shows how to setup and execute a DFT calaculation with Quantum-Espresso and signac.

std.flow.gmx-lysozyme-in-water

An example on how to integrate signac with GROMACS, following the tutorial by Justin A. Lmekul.

std.flow.gmx-mtools

An example on how to integrate signac with GROMACS and mtools. This example is licensed under the MIT-License!

Copyright Notice

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

The full copyright notice can be found in LICENSE.txt.

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