Fluidix

Getting Started with Fluidix© 2008 Adam MacDonald, Dr. David Pink, StFX University, OneZero Software

Introduction

This guide covers the basics of using Fluidix to build, simulate, and visualize a simple system

Many advanced and important features are not mentioned in this tutorial

Refer to the Fluidix User Manual for a thorough explanation of the purpose and function of all aspects of the user interface

At First Glance

The Fluidix control interface consists of four sections

Particles: for creating particles and specifying the interactions Springs: for specifying permanent bonds between particles Simulation: for setting properties and exporting a simulation Analyzer: for visualizing results and data analysis

The 3D display window is shown on the right

Dragging using the left mouse button will rotate the display Dragging using the right mouse button will zoom the display

The “World”

The first and only item in the “Structures” list is the “World”

All particles specified within the “World” structure are placed randomly throughout the entire simulation volume

The name of a structure can be edited by changing the text in the entry field

Particle Types

Each structure (including “World”) contains a set of particle types: a collection of particles with identical radius and mass

Add a particle type to “World” by clicking “Add”

Particles can be added or removed to/from a particle type by changing “Count”

Building a New Structure

A new structure can be created by selecting “World” and clicking the “Edit” tab

This will switch into “Edit” mode A local simulation of this structure’s particles is shown in the

display window Particles can be interactively positioned within the box Changes to the particle properties will be immediately evident in

the display window

Structural Springs

While in “Edit” mode, the “Springs” section has effect only on the structure currently being designed

Select the first and last particles in the structure, and click “Poly” to easily create a polymer

Positioning Structures

Click the “Move One” tab to leave “Edit” mode

Our polymer is visible in the small box at the origin

The six values in the “Move One” section can be used to set the position and rotation of this structure

Structure Instances

Multiple copies of a structure can be independently placed

The “Place All” section has a number of tools for placing many structure instances easily

Here, I place 100 instances of our polymer randomly throughout the world

Relations

Now, our simulation has two particle types: “Water” (100 particles in the “World” structure, placed randomly) “New Type” (2030 particles)

30 particles in the “World” structure, placed randomly 20 particles in each of 100 polymers (2000 total)

Three relations exist in the “Relations” list to account for each possible interaction between particles of these two types

Conservative Interaction

The energy-conserving repulsive interaction between pairs of particles A lower value means the particles are soft; they may penetrate

each other A higher value means the particles are hard; they repel very

quickly once they penetrate even a small amount

Since interactions are specified per pair of particle types, particles may be hard when interacting with one type of particle, but soft to another For example, “Water” particles may repel each other very

strongly, while “New Type” particles are allowed to pass through “Water” without effect

Dissipative Interaction

The non-energy-conserving interaction between pairs of particles Fast moving particles are slowed by a dissipative force A random force is applied according to the temperature The dissipative and random forces are scaled by this value

This interaction is the key of the DPD technique, allowing it to use a single soft particle to represent a cluster of molecules

Any value between 2 and 5 is acceptable for most cases

Particle Properties

Properties of individual particles can be specified in the “Particle Properties” section

Charge: the electrostatic charge of a particle

Mark: an integer tag which may be accessed by a custom plug-in

Hold: freeze a particle in place (use this feature temporarily to move particles individually while in “Edit” mode)

Track: print the position of this particle during the simulation

Changes to a particle will take effect on all instances of the structure containing that particle

Springs

While not in “Edit” mode, any two particles in the system can be specified to be connected by a permanent spring

The “Weld” function will attach all pairs of particles of two structure instances by a spring, if they are within the specified distance

This feature can be used to build a large object from many smaller structures For example, flat squares of 5x5 particles can be placed side by

side and welded into a large sheet

Boundary Conditions The size of the simulation volume can be specified using

the “World” values

In “Edit” mode, these values represent the size of the structure

Boundary conditions (what happens at the edges of the world) can be specified for each dimension

Periodic: particles wrap to the other side of the world, simulating an infinite system

Soft Walls: particles are repelled using a adaptive soft force which behaves like a physical surface (including dissipative and random components) and prevents layering

Hard Walls: particles are instantly reflected (velocity component reversed) upon reaching the edge of the simulation

Time

The time-step of the simulation is the amount of time that elapses during one iteration of Newton’s equations of motion (one simulation step) The default value of 0.02 is acceptable for most cases A lower value will increase interaction stability and accuracy A higher value will allow the simulation to progress through time

at a faster pace

The number of steps in the simulation and the frequency at which particle data is output to disk are set by the following “Frames” and “Output Every” values

Physical Parameters

Background water adds a static uniform fluid to the entire simulation This mean-field approach is used as a high-performance

alternative to filling the system with a high density of water particles

The temperature is used to control the random force of particle interactions (and background water)

Gravity enables a constant downward force on all particles

Custom Plug-ins

A custom plug-in specific to each system can be included to add infinite possibilities to your simulation

Plug-in code must be written in C and will be compiled into the simulation server when it is created

A number of tools are provided which easily add specific functionality to the plug-ins (water pump, 3D mesh, etc.)

Saving Your Project

To re-open your system for editing at a later time, you must save the project to disk

The “Save” button will allow you to create a “.prj” file storing all of your simulation parameters and settings

The “Open” button will prompt you to select a “.prj” file which will load your system into Fluidix

Executing the Simulation

When your system is ready, clicking the “Export Simulation” button will create an executable program

Running this program will start the simulation server

Many clients can connect to this server and help simulate your system in parallel

Use the “Run Now” checkbox to automatically run the server and connect one client on the local computer

Visualization

The “Analyzer” section operates independently of the rest of the program

Output from any simulation can be opened for viewing while any project is open or any server/client is running

Opening Output Data

1) Choose a “.sim” file containing simulation information

This step is optional; without this file advanced information about your simulation will not be available

After “Export Simulation,” this file is opened automatically

2) Select a “Frame Sequence”

This is a folder containing your output files from each step After “Export Simulation,” the folder is selected; just click “Open”

Appearance Select a particle type from the “Particles” list to change

the way those particles are displayed

Using “Show,” particles can be represented as spheres, points, or not at all

Set “Radius” to change the displayed size of spheres or points Use “Display Every” to show only a some of a high density of

particles

Use the “Springs” tab to choose which sets of springs should be displayed

Sometimes it is convenient to show only the springs of a polymer while completely hiding the particles

Dynamics

Using the control buttons, the sequence of output frames can be viewed intuitively

While a simulation is running, using “Play” without the “Loop” option will cause each output frame to be displayed as soon as it is created

Use the “Output .gif” option to write an animation to disk

Viewing a Specific Area

Using the “Selected Volume” values, a certain area of the simulation can be isolated for easy viewing For example: a cross section of a dense fluid

This tool also selects which particles are included in the data analysis

Basic Analysis

Viewing a number of useful plots is as easy as clicking the appropriate checkbox

Only a subset of the particles in the system are used Particle types which are displayed with “Spheres” or “Points” Particles that are within the “Selected Volume”

Use “Play” to see how the plot changes dynamically

Advanced Analysis

A custom analysis function can be written in C and executed on the simulation data Particles in the “Selected Volume” can be identified as well

Output data can be opened and viewed as a plot on the display window If time is the x-axis, the current simulation time will be identified

on the graph