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

2. 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

3. 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

4. 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

5. 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”

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 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

18. 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.)

19. 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

20. 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

21. 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

22. 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”

23. 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

24. 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

25. 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

26. 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

27. 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