Activity tutorial

[kmjens]

Description

Resolves issue #86

Add activity tutorial to hoomd-examples repo.
This includes:

• an introduction to active particles (defines ABPs, MIPS, Pe etc..)
• Active Brownian Particles (adding an active force to a 2D system)
• MIPS (demonstrating MIPs in 2D)
• Active Torque on Rigid Bodies (example of activity on rigid bodies. Explains that this shares mots of the same principles for adding linear active forces to rigid bodies)

Checklist:

• I have reviewed the Contributor Guidelines.
• I agree with the terms of the HOOMD-blue Contributor Agreement.
• My name is on the list of authors.

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[kmjens]

prek told me there was no files available to act on, yet fails the style check here.

[SchoeniPhlippsn]

Please keep the style of the previous tutorials. That means get rid of the introduction (especially as it is nearly identical to the one on the next page), and simply say something like: "This tutorial explains how to model active, self-propelled particles in MD simulations."

And then you say

"This tutorial assumes you are familiar with the concepts introduced in Introducing HOOMD-blue, Introducing Molecular Dynamics and Modelling Rigid Bodies."

Where are you confining particles?

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[kmjens]

changes made in newest commit about to be pushed. Wording on confinement corrected to reference Intro HOOMD tutorial where box compression (not confinement via walls) is introduced.

[SchoeniPhlippsn]

"Active particles are particles that can consume stored energy or energy from the environment and convert it into directed motion. There are many different types of active particles with different mechanisms for this realized self-propulsion. For example, a polystyrene bead coated with platinum on one side (i.e. an example of a simple Janus particle, a particle with 2 of more regions of distinct physical properties) will be propelled forward if submerged in a solution containing hydrogen peroxide. This occurs because the platinum catalyzes a chemical reaction that decomposes the hydrogen peroxide into oxygen gas and water. This localized reaction propels the particle forward. In this example, thermal and chemical energy is being consumed to generate the kinetic motion of the (now active) Janus particle."

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[SchoeniPhlippsn]

1. You have to mention that we model dry active matter.
2. Use the symbols for sigma $\sigma$ and gamma $\gamma$. Gamma is also not explained.
3. Instead of mentioning all the details about ABPs, MIPS and rigid bodies here, I would put them into the respective following pages

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[kmjens]

• dry active matter mention added.
• I believe there is already a brief one sentence explanation of gamma in the text that might have been missed (plz let me know if you still think this is insufficient):

In HOOMD-blue, the propulsion velocity is controlled by applying an active force to particles in the system. The relationship between these quantities is $v_{0} = F_{active} / \gamma$ where $\gamma$ is the translational drag coefficient (often = 1 in overdamped Brownian dynamics). 

• explanations moved to the appropriate sections

[SchoeniPhlippsn]

steady state diagram, not phase diagram! And where do you explain this?

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[kmjens]

yes, we omitted the steady state diagram in this iteration. Good catch.

[SchoeniPhlippsn]

You are not really highlighting the core mechanisms behind active phase separation.

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[kmjens]

removed

[SchoeniPhlippsn]

This is all the same thing again. I would either combine with Active Brownian Particle part or reduce significantly!

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[SchoeniPhlippsn]

Pe. let -> Péclet

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[SchoeniPhlippsn]

Using active torque here might be a poor choice, as you want to highlight here that you should not use the active force updater when you integrate over the rotational degrees of freedom

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[kmjens]

if use rigid bodies do not use dynamic updaters (very clear !) ; only for point particles. instead use active force to make clearer

[SchoeniPhlippsn]

Rotational self-propulsion means something different in active matter. It is the conversion of rotation into self-propulsion (think of the flagella of a bacterium or sperm). Use self-rotation instead.

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