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Tutorials for ESPResSo

Overview

This folder contains tutorials that introduce the use of ESPResSo for different physical systems.

Launch with Binder Launch with Gitpod

Introductory tutorials

  • Simulate a simple Lennard-Jones liquid
    Modelling of a single-component and a two-component Lennard-Jones liquid.
    Guide
  • Error analysis
    Statistical analysis of simulation results
    Guide Part 1 | Part 2
  • Visualization
    Using the online visualizers of ESPResSo.
    Guide

Intermediate tutorials

  • Charged systems
    Modelling of ion condensation around a charged rod.
    Guide
  • Langevin dynamics
    Modelling of Brownian motion and measurement of diffusion coefficients.
    Guide
  • Ferrofluid
    Modelling of a monolayer ferrofluid system.
    Guide Part 1 | Part 2 | Part 3
  • Lattice-Boltzmann
    Simulations including hydrodynamic interactions using the Lattice-Boltzmann method.
    Guide Part 1 | Part 2 | Part 3
  • Polymers
    Modelling polymers with hydrodynamic interactions.
    Guide
  • Raspberry electrophoresis
    Extended objects in a Lattice-Boltzmann fluid, raspberry particles.
    Guide
  • Machine-learned interatomic potential
    Atomistic simulations using the MACE-MP-0 model.
    Guide

Advanced tutorials

  • Active matter
    Modelling of self-propelling particles.
    Guide
  • Electrokinetics
    Modelling electrokinetics together with hydrodynamic interactions.
    Guide
  • Electrodes
    Modelling electrodes and measuring differential capacitance with the ELC method.
    Part 1 | Part 2
  • Constant pH method
    Modelling an acid dissociation curve using the constant pH method.
    Guide
  • Widom particle insertion method
    Measuring the excess chemical potential of a salt solution using the Widom particle insertion method.
    Guide
  • Grand-Canonical Monte Carlo Simulating a polyelectrolyte solution coupled to a reservoir of salt.
    Guide

Using the tutorials

To run the tutorials, you need ESPResSo and a Jupyter environment. For installation instructions, please see the user guide sections Quick installation and Setting up a Jupyter environment.

Tutorials are available as Jupyter notebooks, i.e. they consist of a .ipynb file which contains both the source code and the corresponding explanations. They can be viewed, changed and run interactively. To generate the tutorials in the build folder, do:

make tutorials

All tutorials can be viewed with their solutions online.

Running the tutorials interactively

To view the tutorials in the build folder, run the following commands:

cd doc/tutorials
../../ipypresso lab

This will launch a web browser in which the notebooks for the tutorials can be viewed and run. For more details, please see the user guide section on running notebooks, which walks you through the Jupyter interface.

Video lectures