2D and 3D Flow Analysis in Microfluidic Channels Including Mulitple Species Transport

2D AND 3D FLOW ANALYSIS IN MICROFLUIDIC
CHANNELS INCLUDING MULITPLE SPECIES

TRANSPORT.
Written and Tested by: Scott Stelick

sjs16@cornell.edu
Alliance for NanoMedical Technologies

Cornell University
Last revision 10/2/02
Problem Specification
Applicable ANSYS Products: ANSYS/Multiphysics, ANSYS/FLOTRAN, ANSYS/ED
Level of Difficulty: advanced
Interactive Time Required: 1-1/2 to 2 hours
Discipline: Computational Fluid Dynamics (CFD)
Analysis Type: steady-state
Element Types Used: FLUID141 and FLUID 142
ANSYS Features Demonstrated: Solid modeling, mapped meshing, defining an
abbreviation on the Toolbar, restart of FLOTRAN solution, multiple solutions, vector
displays, line graphs, path operations, trace particle animation, multiple species, fluid
mixing in microfluidic channels, fluid flow around obstacles in fluid channel.
Problem Description
This problem models laminar fluid flow in a small microfluidic channel. Two input arms
combine in the design creating laminar flow out of the single output channel. You will
first run a 2D analysis of the design and after this is completed, a 3D analysis will be
done. The final analysis will be fluid flow around an obstruction in the channel. Added
information is given on how to model complex 3D structures.
Constants and dimensions
All parameters and constants are either given in the tutorial or in the table at the end of
this tutorial.
Approach and Assumptions
You will perform two and three-dimensional analyses using the FLOTRAN element
FLUID141 and FLUID142, respectively. This problem is divided into three parts:
A laminar analysis of the 2D fluid flow and multiple species analysis of two different
fluids.
Extruding of the 2D model into a 3 dimensional design and multiple species analysis of
the two different fluids.
Velocity profiles of the fluids flowing in a microfluidic channel with obstructions are
modeled.
For all solutions, you will apply a uniform velocity profile at the inlet. This includes
specification of a zero velocity condition at the inlet in the direction normal to the inlet
flow. You will apply no-slip (zero velocity) conditions all
along the walls (including where the walls intersect the inlets and outlets). The fluid is
considered incompressible and you can assume that the properties will be constant. In
such cases, only the relative value of pressure is important, and a zero relative pressure is
applied at the outlet.
For the initial analysis, the flow is in the laminar regime (Reynold's number < 1000).
(Note that in a two-dimensional geometry, the hydraulic diameter is twice the inlet
height.)
For internal flows, the transition to turbulence occurs within the Reynolds number range
of 2000-3000.
Summary of Steps
Use the information in the problem description and the steps below as a guideline in
solving the problem on your own. Or, use the detailed interactive step-by-step solution
below.
Before you begin, delete any results files (.rfl) from previous CFD analyses that still
reside in your working directory. If you begin an ANSYS session to start a new CFD
analysis, and use the same jobname from a file stored from a previous CFD analysis, the
program will not start from scratch, but will restart and append to files with the same
name (Jobname.rfl and Jobname.pfl). To avoid this situation, delete these results files
when starting a new
CFD analysis. Another way of avoiding this situation is to change the jobname to one that
was not used in a previous CFD analysis. You can change the jobname in the product
launcher before starting ANSYS, or during an ANSYS session by choosing Utility Menu
> File > Change Jobname
Preprocessing (Laminar Analysis)
1. Set preferences.
2. Define element type.
3. Units.
4. Create Keypoints.
5. Create Areas from Keypoints.
6. Making areas with curved lines example.
7. Create the finite element mesh.

8. 2D meshing.
9. 3D meshing.
10. Extruding 2D models into 3D structures.
11. Unselecting 2D elements.
12. Establish Fluid properties.
13. Set execution controls.
14. Change reference conditions.
15. Multiple species setup.
16. Enter fluid properties.
17. Boundary conditions.
18. Execute FLOTRAN solution.
19. Post processing.
20. Plot velocity vectors.
21. Plot density variations.
22. Plot total pressure contours.
23. Animate velocity of trace particles instructions.
24. Path plot of velocity.
25. Construct single microfluidic channel with obstacles.
26. Mesh regions.
27. Apply boundary conditions.
28. Execute FLOTRAN solution.
29. Complex 3D modeling.
Launching ANSYS:
It is probably best to save your work on a Zip Disk in the computer IOMEGA Zip Drive.
Then, simply click on the ANSYS icon on the Windows Desktop. The ANSYS Launcher
menu should appear. It is shown at the top of the next page. The only input you will
likely need on this menu is specification of the Zip Drive as your Working Directory.
If you dont have a Zip Disk, or if you prefer to work on the computer hard drive instead,
then specify any directory (or, Folder) as your working directory. To browse and find
the desired working directory, click on the button with the three dots to the far right on
the Launcher Menu on the line that says Working Directory. Once the working
directory is specified, click on Run at the bottom of the Launcher Menu.
The ANSYS menus

should open up. You
will see a Main Menu,
illustrated
on
the
following page, and a
large black graphics
window. You are now
ready to begin creating
the
model
and
performing the analysis.
Enter an initial jobname
here, no spaces are
allowed.
ANSYS Launcher
Menu:
ANSYS Main Menu:

5
Note: Most of the required tasks are performed using menu picks from the ANSYS
Graphical User Interface, as specified in italics in the step-by-step instructions below. It
is sometimes more convenient, however, to enter certain commands directly at the
command line. The command line is seen on the screen as:
The method of direct command line entry is used in some cases in this exercise,
whenever this method is more convenient than using menu picks.
****IMPORTANT***: AS YOU WORK THROUGH THIS EXERCISE, WITHIN
ANSYS, ON THE ANSYS TOOLBAR (UPPER RIGHT), CLICK ON SAVE_DB
OFTEN!!!
THIS
TOOLBAR
APPEARS
AS:
At any point, if you want to resume from the previous time the model was saved, simply
click on RESUM_DB on this same Toolbar. Any information entered since the last
save will be lost, but this is a nice feature in the event that you make an input mistake,
and are unsure of how to correct it.
There are a number of ways to model a system and perform an analysis in ANSYS. The
steps below present only one method.
Set preferences.
6
You will now set preferences in order to filter quantities that pertain to this discipline
only.
1. Main
Menu
>
Preferences
2. Turn on FLOTRAN
CFD filtering
3. OK.
Define element type.

1.
2.
3.
4.
5.
6.
Main Menu > Preprocessor > Element Type > Add/Edit/Delete

Add an element type.
Choose 2D FLOTRAN element (FLUID141).
OK.
Close.
Units.
1. Main Menu > Preprocessor > Material prop
> material library > select units
2. Choose the cgs system
Note: All units shown in this tutorial are in cgs
units.
Main Menu > Preprocessor > Materials >
temperature unit
3. Choose the Celsius scale
Create Keypoints:
In fluid modeling, it is best to have a single area defined. Original tests were done where
rectangles were made and merged together. This method did not work well and it was
decided to enter the coordinates of all the vertices of the design and connect all the points
to create a 2D area. This 2D area can then extruded to make the 3D design.
To add keypoints to a coordinate system:
Preprocessor -> -Modeling- Create -> Keypoints -> In Active CS
Fill in the fields as shown below, then click APPLY. When you click on Apply, the
command is issued to create keypoint number 1 at (x,y)=(0.0501, -0.2645). Note that
when the Z field is left blank, in this case, the blank space defaults to zero, which is
desired. Since you clicked on Apply, instead of OK, then the keypoint creation box
remains open.
Create keypoint number 2 at (x,y)=(0.0678,-0.2822), using the input shown below. After
entering the input, again, click on APPLY:
Enter all of your keypoints in this manner. Units are in cm and for this design the
channel is 8.5 mm long and 250 microns wide.
Keypoint #
3
4
5
6
7
X Coordinate
0.34916
0.85
0.85
0
0
8
Y Coordinate
0
0
0.025
0.025
0
0.3146
When the final keypoint is entered, click on OK instead of APPLY. OK issues the
command and also closes the keypoint creation box.
Before moving on, it is probably a good idea to check the keypoint locations. Along the
top toolbar:
Choose: List -> Keypoints -> Coordinates Only. A box should open up with the keypoint
location information. If any keypoint is not in the correct location, at this point, you can
just re-issue the keypoint creation command for that particular keypoint. To do this,
choose: Preprocessor -> -Modeling- Create -> Keypoints -> In Active CS
Fill in the correct information for that particular keypoint in the box, and click OK.
The keypoint will be moved to the correct location. If you have some keypoint
incorrectly numbered above number 12, this will not cause a problem. Just be sure you
have keypoint numbers 1 thru 12 located correctly.
You can close the box listing the keypoint locations, by clicking, in that listing box, on
File-> Close.
Create areas.
In this design, all lines connecting the keypoints are straight lines so the following
command is used. If in your design, curved lines are used, the next section gives an
example of the process.
Main Menu > Preprocessor > -Modeling- Create > -Areas- Arbitrary > By Lines
Connect the points in numerical order and when done click OK on the picking menu.
The following area is created.
Curved lines will not be used in this tutorial but I will include information for reference.
If you have a curved line in your design the following example will show you how to
connect a tangent line between keypoints. This will make the analysis a little more
9
difficult because the areas are broken up but should still work fine. The example is from
another gas flow tutorial that is available in the ANSYS help menu.
Making areas with curved lines
1. Main Menu > Preprocessor > -Modeling- Create > -Lines- Lines > Tan to 2 Lines
2.Pick first line (upper line of left rectangle).
3.OK (in picking menu).

4.Pick the tangency end of the first line (upper right corner).

6.Pick the second line (upper line of the larger rectangle.

8.Pick the tangency end of the second line.
9.OK to create the line

The result is a smooth line between the two areas.
10
Now create the third area as an arbitrary area through keypoints.

10.Main Menu > Preprocessor > -Modeling- Create > -Areas- Arbitrary > Through
KPs
11.Pick 4 corners in counterclockwise order.
12.OK.
13.Toolbar: SAVE_DB
Meshing
Of all the steps in this process, meshing is by far the most important step to
get an accurate modeling of your system. Meshing breaks up the areas of
your design into user defined shapes. The smaller the shape the more
accurate the analysis will be but the downside being the finer the mesh, the
longer the processing time. A good balance is needed between processing
time and resolution of the solution.
For most fluid modeling applications, only a 2D model is required so from
now on I will separate the 2D and 3D commands.
2D Meshing (Do not use if modeling in 3D)

1. Utility Menu > Plot > Lines
11
2. Main Menu > Preprocessor > Mesh Tool

3. Choose Lines Set.
4. Pick all lines (in the picking menu).
Note (You can separate different regions of your design and mesh them differently if
you want, you will have to play with that stuff by yourself).
5. Apply (in the picking menu).
6. Enter 100 as the No. of
element divisions.
7. Enter 1 as the Spacing
ratio (-2 produces smaller
elements near both ends of
the line).
7. Apply.
8. On the meshtool
menu, pick the option
for free mesh and
also quad shape.
9. Click Mesh
10. Pick all lines (in the picking menu)
11. Close the meshtool menu
This will mesh the entire design and for 2D designs and should look like the following
image.
12
If only modeling in 2D, you can skip the next section and start again at adding boundary
conditions.
3D Meshing
The next step is to specify mesh controls in order to obtain a particular
mesh density.
2. Set global size controls.
3. Enter 0.005 for element edge length.
4. OK.
5. Mesh.
6. Pick All (in picking menu).
7. Close.
8. Close Mesh Tool.
9. SAVE_DB
Some error messages might

pop up because of irregular
size elements but ignore these for now.
13
Extrude the meshed area into a 3D meshed volume.

In this step, first changing the element type to Fluid 142, which is defined as element type
2, and then extruding the area into a volume generates the 3-D volume.
1. Main Menu > Preprocessor > -Modeling- Operate > Extrude > Elem Ext Opts
2. Choose 2 (FLOTRAN 142) for Element type number.
3. Enter 30 for the No. of
element divisions.
4. OK.
5. Main Menu > Preprocessor >
-Modeling- Operate > Extrude >
-Areas- By XYZ Offset
7. Enter 0,0,0.002 (Where 0.002
if the height of your channel in cm,
20 microns high) for offsets for
extrusion in the Z direction.
8. OK.
9. Close.
To examine the extruded design, use the commands in steps 10-11 below.
10. Utility Menu > PlotCtrls > Pan,
Zoom, Rotate
11. Choose ISO, then box zoom.
12. Close.
13. Toolbar: SAVE_DB.
Unselect 2-D elements.

14
Before applying boundary values to the microfluidic channels, unselect all FLOTRAN
141 elements used in the 2-D area mesh since they will not be used for
the analysis.
1. Utility Menu > Select > Entities
2. Choose Elements.
3. Choose By Attributes.
4. Choose Elem type num.
5. Enter 1 for the element type number.
6. Choose Unselect.
7. Apply.
The 3D modeling design should now be constructed. The FLOTRAN parameters must
now be setup and added to the model.
Multiple species Laminar Analysis (both 2D and 3D)
Establish fluid properties.
Fluid properties will be established for water in
the cgs system.
1. Main Menu > Solution > FLOTRAN Set
Up > Fluid Properties
2.
Choose CMIX for density.

Leave
viscosity and conductivity and specific
heat as constant.
3.
Click yes for allow density variations.
4.
OK.
5.
Enter 0.01 for viscosity and 0.04 for

conductivity. Leave specific heat at 1.
6.
OK. (for next screen that pops up)
15
Set execution controls.

Choose the execution control from the FLOTRAN
Set Up Menu.
1. Main Menu > Solution > FLOTRAN Set Up >
Execution Ctrl
2. Enter 40 Global iterations (Note: 40 global
iterations is arbitrary with no guarantee of
convergence.)
3. OK to apply and close.
Change reference conditions.

At the end of this tutorial there is a table of constants and reference conditions for water.
The reference conditions will have be changed to suit your design and units used.
1. Main Menu > Solution > FLOTRAN

Set Up > Flow Environment > Ref
Conditions
2. Change the reference pressure to
101350 (cgi units, equivalent to 1
atmosphere).
3. Change the nominal, stagnation, and
reference temperatures to 20oC.
4. Change bulk modulus to 0.21x1011
5. Change the temperature offset from
absolute 0 to 273.
7.
OK.
Species Setup
16
There are a lot of steps that will have to be completed for this process. It is the same for
2D and 3D designs.
FLOTRAN Set Up > solution options
2. Highlight the multiple species
transport box.
3. OK
This turns on the multiple species
transport. Now you have to define all
the parameters for each liquid that is
added to the system.
First define the number of different liquids that are added to the system. In this case, two
different liquids are being modeled.
1. Main Menu > Solution > FLOTRAN

Set Up > Multiple species
In this case 2 species were used.
2. Enter 2 for Number of
species
3. Make sure the Algebraic
species number is set at 2.
4. OK
After clicking ok, the following
screen appears. For each species all
the parameters have to input.
17
These windows are all connected so when OK is pressed it just brings you back to this
screen.
Main Menu > Solution > FLOTRAN

Set Up > Multiple species > Species
#1 > general the following window
appears:
1. Change the species name to
something
you
can
remember.
2. Change the molecular weight
of the fluid to the one you are
using (18 in this case).
3. Leave mass fraction to 0.5 if
there is 2 species. If you
have 3 then change it to 0.3, 0.3, and 0.4 for the different species. This number
has to add up to 1, regardless of how many species there are.
4.
OK
1. Main Menu > Solution >

FLOTRAN Set Up >
Multiple species > Species
#1 > solver
2. Set to Precond conj re
18
3. OK
(preconditioned conjugate residual method) for both species.
options have not really been tried.
The other solver
4. Change No of search
vectors used from 2
to 3.
5. OK
Species relaxation
FLOTRAN Set Up > Multiple
species > Species #1 >
relaxation
2. Change concentration relaxation
to 1.
3. OK
Enter fluid properties.

Main Menu > Solution > FLOTRAN Set Up > Multiple species > Species #1 >
properties menu.
19
Enter
all
density,
viscosity, conductivity,
mass fraction constants
and change the solution
options.
Enter
all
the
information you can on
all the constants.
All the data here is very important.

flow/mixing region.
To solve for density variations in the fluid
1. Select density.
2. OK.
3. For Density type enter
liquid.
4. For nominal value
enter the density (for
water it is 1 g/cm3)
5. Also enter first and
second coefficients if
you have them.
6. Click vary density yes.
7. OK
Do the same thing for the rest of the variables that you want solved and the parameters.
For constant inputs, enter CONSTANT for the type and enter the nominal value.
HINT!! If you want to plot density differences in the graphs later on, let the nominal
value for density of species 1 be 1.0 and the density of species 2 to be 1.001. Ansys will
apply colors to the two densities (red and blue) and with this little difference, mixing can
be plotted. You can also do the same for viscosity if that is to be plotted also.
20
1. Main Menu > Solution > FLOTRAN Set Up > Multiple species > Species #1 >
fluid properties > mass diffusion.
2. Enter 0.000013 for
the nominal value.
3. OK
4. SAVE_DB
The mass diffusion constant
is the most important
constant
for
mixing
modeling. Make sure the
constant for this is as
accurate as possible. (See
sheet at end of tutorial).
Click EXIT Properties Panels when done. Enter properties for both species.
One last thing to change:
1. Main Menu > Solution > FLOTRAN Set Up > Multiple species > Capping
2. Click yes for cap mass fraction.
3. OK
Click cancel to exit the main multiple Species panel.
Boundary Values
Now comes the fun part, adding velocities and pressures to the lines and areas.
It is slightly different for adding boundary values to 2D and 3D designs but for the most
part, it is similar so I will cover both at the same time.
A velocity of 0.1 cm/s is applied in the X direction (VX) at the inlet, and a zero velocity
is applied in the transverse direction at the inlet (VY in the Y direction). Zero velocities in
both directions are applied all along the walls, and a zero pressure is applied at the outlet.
Apply the inlet boundary condition.
21
1. Main Menu > Preprocessor > Loads > -Loads- Apply > -Fluid/CFD- Velocity >
On Lines (2D) [On Areas (3D)].
2. Pick the inlet line (the vertical
line at the far left).
3. OK
4. Enter 0.1 for VX. (2D and 3D).
5. Enter 0.0 for VY. (2D and 3D).
6. Enter 0.0 for VZ (3D only)
7. OK
Select the second

microfluidic design.
arm
of
the
On Lines (2D) [On Areas (3D)].
2. Pick the inlet line (angled line on the lower left).
3. OK
4. Enter 0.0707 for VX. (2D and 3D).
5. Enter 0.0707 for VY. (2D and 3D).
6. Enter 0.0 for VZ (3D only).
7. OK
22
The following picture should appear.
Next, apply the wall boundary conditions. Choose the lines that make up the walls and
then apply zero velocities in the X and Y directions.
On Lines (2D) [On Areas (3D)]
2. Pick the five lines
(or 8 areas) on the
top and bottom.
3. OK
4. Enter 0.0 for VX
and VY. [Enter
0.0 for VZ (3D)].
5. OK
One of the following pictures should appear for 2D or 3D.
2D
23
3D
Apply the outlet condition.

1. Main Menu > Preprocessor > Loads > -Loads- Apply > -Fluid/CFD- Pressure
DOF > On Lines. [On Areas (3D)].
2. Pick the outlet line (vertical line on the far right) or (output areas for 3D).
3. OK
4. Enter 0 for the
pressure value.
5. Set endpoints
to yes.
6. OK
7. Toolbar:
SAVE_DB.
After the flow rates and pressures are added to the model, the species will now be added.
In multiple species transport, there are 2 or more inputs and a single output so mixing can
be studied. For each input arm, both species have to be added.
Apply Species.
Main Menu > Preprocessor > Loads >
-Loads- Apply > -Fluid/CFD-Species >
On Lines (2D) [on Areas (3D)]
24
1. Click on the left vertical line.

2. APPLY
3. Pick species #1.
4. OK
5. Enter percentage of that species
for that input location. (1 is
100%). 1 in this case.
6. OK
7. Highlight yes for another
species.
8. OK
9. Click species #2
10. OK
11. Enter other loading factor

(0 for this case).
12. OK
13. Highlight No
25
14. OK
15. Repeat for the angled input. But reverse the species, 0 is now species 1 and 1.0 is
species 2.
16. SAVE_DB
Both species are now added to the two inputs and the image should look like the
following.
Everything should be setup up now and the solution can now be run.
Execute FLOTRAN solution.
1. Main Menu > Solution > Run FLOTRAN
2. Close the information window when the solution is done.
While running the FLOTRAN solution, ANSYS will plot the "Normalized Rate of
Change" as a function of the "Cumulative Iteration Number." This is the Graphical
Solution Tracker, which allows visual monitoring of the solution for convergence.
This step might take some time so be patient, especially the 3D modeling.
26
Post processing (Laminar Analysis)

Read in the results for post processing.
Enter the general postprocessor and read in the latest set of solution results, and then
create a vector plot.
1. Main Menu > General Postproc > -Read Results- Last set
Plot velocity vectors.
1. Main Menu > General Postproc > Plot Results > -Vector Plot- Predefined
2. Choose DOF solution.
3. Choose Velocity V.
4. OK.
2. Choose Nodal solution.
27
3. Choose Velocity Vx or Vy.

4. OK.
2D Vx
2D Vy
This gives the velocity

profiles for the x and y
direction
in
the
channels. Red is the
highest pressure.
28
3D Vx
These images show a generalized velocity profile in the microfluidic system. If using 3D
you can rotate the design to get a better angle.
Plot total density variations.
1. Main Menu > General Postproc > Plot Results > -Contour Plot- Nodal Solu
2. Choose other quantities.
3. Choose Density, DENS.
4. OK.
29
2D Density variations
3D Density
variations
These results show the mixing of the two species. If viscosity is varied, you can plot that
also. The degree of mixing depends on the mass diffusion constant. For this model that
constant was 0.00001, which is not accurate. I used this number to show off the mixing
modeling and this is not a real world model. Do some research for the fluids you are
using and make sure this constant is accurate.
Plot total pressure contours.
1. Main Menu > General Postproc > Plot Results > -Contour Plot- Nodal Solu
2. Choose Other quantities.
3. Choose Total Pressure, PTOT.
30
4. OK.
The resulting contour plot shows the total static and dynamic pressures that occur in the
system.
Animate velocity of trace particles.

Animation cannot be used with this design because of the small size. But in a larger
microfluidic channel a movie can be made of the motion. The following procedure can
be used to do that.
1. Main Menu > General Postproc > Plot Results > -Flow Trace- Defi Trace Pt
2. Pick two or three points around the inlet region and one or two points in the
recalculation region (along the upper wall of the transition region).
3. OK (in picking menu).
4. Utility Menu > PlotCtrls > Animate > Particle Flow
5. Choose DOF Solution.
6. Choose Velocity VX.
7. OK.
Ignore any warning messages about maximum number of loops (Choose Close).
The resulting trace plot shows the path of flow particles.
31
8. Make choices in the Animation Controller (not shown), if necessary, then choose
Close.
Make a path plot of velocity through the outlet.
1. Main Menu > General Postproc > Path Operations > Define Path > By Nodes
2. Pick the lowest
and then the highest
point just on the other
side where the two
fluids come together.
3. OK (in picking
menu).
4. Enter Mixers for
the Path Name.
5. OK.
6. File > Close (Windows)
Now specify the velocity in the X direction (VX) to map onto the path.
7. Main Menu > General Postproc > Path Operations > Map onto Path
8. Enter DENSITY as label.
9. Choose other quantities.
10. Choose DENS.
11. OK.
12. Main Menu > General Postproc > Path Operations > -Plot Path Item- On Graph
13. Choose the label DENSITY that you previously defined.
14. OK.
15. Close any warning messages.
32
This is the density profile immediately after the intersection of the two flows.
33
Fluid flow modeling with obstructions in the channel.

This tutorial is a simple model to show the important features for modeling fluid flow
with pillars and shapes in the fluid flow. The beginning is similar to the 2D model shown
above with few important differences. The design is a 250 m wide by 5 mm long
channel which has two 50 m square pillars evenly spaced in the channel.
Start the ANSYS program with a new jobname.
Set preferences.
only.
1.
Main Menu >

Preferences
2.
Turn
on
FLOTRAN
CFD
filtering
3. OK.
Define element type. (2D)

4.
5.
6.
7.
8.

OK.
Close.
Units
9.
Main Menu > Preprocessor > Material

prop > material library > select units
34
11. Main Menu > Preprocessor > Materials > temperature unit
Create Keypoints:
In fluid modeling, it is best to have a single area defined. Original tests were done where
rectangles were made and merged together. This method did not work well and it was
decided to enter the coordinates of all the vertices of the design and connect all the points
to create a 2D area. This 2D area can then extruded to make the 3D design.
command is issued to create keypoint number 1 at (x,y)=(0, 0). Note that when the Z
field is left blank, in this case, the blank space defaults to zero, which is desired. Since
you clicked on Apply, instead of OK, then the keypoint creation box remains open.
Enter all of your keypoints in this manner. Units are in cm and for this design the
channel is 8.5 mm long and 250 microns wide.
Keypoint #
2
3
4
5
6
7
8
9
10
11
12
X Coordinate
0.025
0.025
0
0.005
0.010
0.015
0.020
0.005
0.010
0.015
0.020
35
Y Coordinate
0
0.5
0.5
0.5
0.5
0.5
0.5
0.45
0.45
0.45
0.45
top toolbar:
choose:
Fill in the correct information for that particular keypoint in the box, and
click OK. The keypoint will be moved to the correct location. If you
have some keypoint incorrectly numbered above number 12, this will
not cause a problem. Just be sure you have keypoint numbers 1 thru 12
located correctly.
You can close the box listing the keypoint locations, by clicking, in that
listing box, on File-> Close.
Create areas
In this design, all lines connecting the keypoints are straight lines so the
following command is used.
Main Menu > Preprocessor > -Modeling- Create > -Areas- Arbitrary >
By Lines
Connect the four outside points to form the outside area then connect the
other keypoints so it forms two squares as shown in the picture at the
right. The following area is created.
36
Area subtraction.
To form the model system, the two small squares have to be subtracted from the larger
channel.
1. Main Menu > Preprocessor > -Modeling- Operate > Subtract
2. It ask you first for the area to subtract from so pick the larger area.
3. OK
4. Pick both of the small squares.
5. OK
You can always unpick an object by changing the setting on the picking
menu. This might have to be down in Step 1. Usually one square is also
highlighted so just it from pick to unpick in
the menu, un-highlight the square and click OK.
When done properly the following image should
be seen.
Meshing
Of all the steps in this process, meshing is by far the most important step to get an
accurate modeling of your system. Meshing breaks up the areas of your design into user
defined shapes. The smaller the shape the more accurate the analysis will be. With the
downside being the finer the mesh, the longer the processing time. A good balance is
needed between processing time and resolution of the solution.
37
Meshing for this is design slightly different than the channels in the first tutorial. The
regions around the square have to be meshed differently than the rest of the channel for
the modeling to be accurate.
1. Utility Menu > Plot > Lines
3. Choose Lines Set.
4. Pick the four lines that surround the full channel.
5. Apply (in the picking
menu).
6. Enter 100 as the No. of
element divisions.
7. Enter 1 as the Spacing ratio
(-2 produces smaller elements
near both ends of the line).
8. Apply.
9. No pick the 8 lines that
form the squares.
10. OK
11. Enter 15 for the No. of element divisions.
12. Enter 2 as the spacing ratio. (The reason for the two-mesh
spacing is to make the mesh element for the larger rectangle
and the space between the squares comparable. If this is not
done and all the lines are meshed the same, there will be no
flow between the squares and that is incorrect.)
13. On the meshtool menu, pick the option for free mesh and
also quad shape.
14. Click Mesh
15. Pick all lines (in the picking menu)
16. Close the meshtool menu
38
This will mesh the entire design and for should look like the following image.

Fluid properties will be established for
water in the cgs system.
NOTE: The images that follow in the
instructions below so not have the
correct values entered. The images
are from the tutorial above, change
the numbers accordingly.
FLOTRAN Set Up > Fluid Properties
8.
Choose Liquid for density,

viscosity and conductivity. Leave
specific heat as constant.
9.
There should be no variations in

the modeling so they should be all
no
10. OK
11. Enter 1.0 for density, 0.01 for viscosity and 0.04 for conductivity. Leave specific
heat at 1.
5. OK
Set Up Menu.
Execution Ctrl
39
2. Enter 40 Global iterations (Note: 40 global iterations is arbitrary with no guarantee

of convergence.)

At the end of this tutorial there is a table of constants and reference conditions for water.
The reference conditions will have be changed to suit your design and units used.

FLOTRAN Set Up > Flow Environment >
Ref Conditions
2. Change the reference pressure to
101350 (cgi units, equivalent to 1
atmosphere).
3. Change the nominal, stagnation,
and reference temperatures to 20oC.
absolute 0 to 273.
17. OK.
Boundary Values
Now comes the fun part, adding velocities and pressures to the lines.
A velocity of 0.1 cm/s is applied in the Y direction (VY) at the inlet, and a zero velocity is
applied in the transverse direction at the inlet (VX in the X direction). Zero velocities in
both directions are applied all along the walls and squares, and a zero pressure is applied
at the outlet.
40
1.
Main Menu > Preprocessor > Loads > -Loads- Apply > -Fluid/CFD- Velocity >
On Lines
2.
Pick the inlet line (the horizontal line at the bottom).
3. OK
4. Enter 0.0 for Vx.
5. Enter 0.1 for Vy.
6. Leave Vz blank
7. OK
Wall boundary conditions

Choose the lines that make up the vertical walls and also the lines that form the squares
and apply zero velocities in the X and Y directions.
1.
Main Menu > Preprocessor > Loads > -Loads- Apply > -Fluid/CFD- Velocity >
On Lines
2.
Pick All.
3. OK
4. Enter 0.0 for Vx and Vy.
5. OK
Apply the outlet condition
41
6.
Main Menu > Preprocessor > Loads > -Loads- Apply > -Fluid/CFD- Pressure
DOF > On Lines.
7. Pick the outlet line (horizontal line on the top).

8. OK
9. Enter 0 for the pressure value.
10. Set endpoints to Yes
11. OK
When all the boundary conditions are inputted, the design should look
like the following.

2. Close the information window when the solution is done.
While running the FLOTRAN solution, ANSYS will plot the "Normalized Rate of
Change" as a function of the "Cumulative Iteration Number." This is the Graphical
Solution Tracker, which allows visual monitoring of the solution for convergence.
Post processing
42
1. Main Menu > General Postproc > Plot
Results > -Vector Plot- Predefined
3. Choose Velocity V.
4. OK.
4. OK.
Vx
43
Vy
These images show the velocity profile for the microfluidic system above.
Make a path plot of velocity through the outlet.

2. Pick the nodes near the outlet of the squares.
4. Enter Velocity for the Path Name.
5. OK.
Now specify the velocity in the Y direction (Vy) to map
onto the path.
7. Main Menu > General Postproc > Path Operations >
Map onto Path
8. Enter Velocity as label.
44

10. Choose Velocity Vy.
11. OK.
12. Main Menu > General Postproc >
Path Operations > -Plot Path Item- On
Graph
13. Choose the label Velocity that you
previously defined.
14. OK.
Make a path plot of velocity through the outlet (second location).
2. Pick the nodes near the outlet of the squares.
4. Enter Velocity for the Path Name.
5. OK.
Now specify the velocity in the Y direction (Vy) to
map onto the path.
7. Main Menu > General Postproc > Path Operations
> Map onto Path
8. Enter Velocity as label.
10. Choose Velocity Vy.
11. OK.
45
12. Main Menu > General Postproc > Path Operations > -Plot Path Item- On Graph
13. Choose the label Velocity that
you previously defined.
14. OK.
These graphs show the velocity
profiles for two slices in the
modeling. Any area can be analyzed
in this way.
46
Complex 3D structure modeling

In this set of instructions, the steps for modeling fluid flow in complex 3D structures are
described. Many of the steps are similar to one shown above with several important
differences. I will model a simple microfluidic channel that has large interconnect
reservoirs on the ends of the channels. This will demonstrate what happens to the fluid
when needles and reservoirs are used in conjunction with small microfluidic channels.
Start a new ANSYS filename as shown above.
Set preferences.
only.
1.
Main
Menu
>
Preferences
2. Turn on FLOTRAN
CFD filtering
3. OK.
Define element type.

4.
5.
6.
7.
8.
9.

OK.
Close.
Units.
10. Main Menu > Preprocessor > Material
prop > material library > select units
47
Note: All units shown in this tutorial are in cgs units.

Main Menu > Preprocessor > Materials >
temperature unit
Create Keypoints:
Keypoints for the design will be entered here. What will be entered are the coordinate for
the channel, reservoirs and needle inputs. 2D areas will first be made then extruded into
the 3D design.
IMPORTANT!! When doing 3D modeling, the areas have to overlap slightly. Areas
that butt up against each other WILL NOT work with this simulation. Be aware of this
when inputting your points.
command is issued to create keypoint number 1 at (x,y)=(-0.06, 0.00625). Note that
when the Z field is left blank, in this case, the blank space defaults to zero, which is
desired. Since you clicked on Apply, instead of OK, then the keypoint creation box
remains open.
Enter all of your keypoints in this manner.
48
Keypoint #
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
X Coordinate
0
-0.15
-0.15
0
-0.06
0.3
0.29375
0.225
0.225
0.375
0.375
0.30625
0.3125
0.8
0.8
Y Coordinate
0.075
0.075
-0.075
-0.075
-0.00625
-0.00625
-0.36
-0.3
-0.45
-0.45
-0.3
-0.36
-0.00625
-0.00625
-0.075
Keypoint #
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
X Coordinate
0.95
0.95
0.8
0.86
-0.075
-0.075
-0.095
-0.095
0.29
0.29
0.31
0.31
0.895
0.875
0.875
0.895
Y Coordinate
-0.075
0.075
0.075
0.00625
-0.01
0.01
0.01
-0.01
-0.375
-0.395
-0.375
-0.395
-0.01
-0.01
0.01
0.01
top toolbar:
choose: Preprocessor -> -Modeling- Create -> Keypoints -> In Active CS
Fill in the correct information for that particular keypoint in the box, and click OK.
The keypoint will be moved to the correct location. If you have some keypoint
incorrectly numbered above number 12, this will not cause a problem. Just be sure you
have keypoint numbers 1 thru 12 located correctly.
You can close the box listing the keypoint locations, by clicking, in that listing box, on
File-> Close.
The keypoints should look like the image below.
49
Create areas.
In this design, all lines connecting the keypoints are straight lines so the following
command is used.
Main Menu > Preprocessor > -Modeling- Create > -Areas- Arbitrary > By Lines
There are seven separate regions that have to be made into areas. There are 3 small
squares that represent the needle inputs, 3 larger squares that are the reservoirs and the
microfluidic channel. So make three small square using the above command, three larger
squares and the microfluidic channel so it looks like the image below.
50
Save your work Toolbar: SAVE_DB

Extrude the meshed area into a 3D meshed volume.
In this step, first changing the element type to Fluid 142, which is defined as element type
2, and then extruding the area into a volume generates the 3-D volume.
Elem Ext Opts
2. Choose 2 (FLOTRAN 142) for
Element type number.
3. Enter 20 for the No. of element
divisions.
4. OK.
-Areas- By XYZ Offset
6. Choose the small squares that
represent the needles and extrude then 0.21 cm in the Z direction.
7. Apply
8. Choose the 3 larger
squares that represent the
reservoirs and extrude
then 0.20 cm in the Z
direction.
9. Apply
Inlet
10. Choose the microfluidic

channel and extrude it
0.01 cm in the Z
direction.
Inlet
11. OK
12. Close
The resulting 3D model should
look like the following:
51
Outlet
Unselect 2-D elements.

Before applying boundary values to the microfluidic channels, unselect all FLOTRAN
141 elements used in the 2-D area mesh since they will not be used for the analysis.
1. Utility Menu > Select > Entities
2. Choose Elements.
3. Choose By Attributes.
4. Choose Elem type num.
5. Enter 1 for the element type number.
6. Choose Unselect.
7. Apply.
Overlap 3D volumes.
This step you overlap the seven different volumes. I tried adding together the volumes
but that does not seem to work.
1. Main Menu > Preprocessor > -Modeling- Operate > Overlap
2. Pick all seven volumes.
3. OK.
The 3D modeling design should now be constructed.
Meshing
Of all the steps in this process, meshing is by far the most important step to
get an accurate modeling of your system. Meshing breaks up the areas of
your design into user defined shapes. The smaller the shape the more
accurate the analysis will be but the downside being the finer the mesh, the
longer the processing time. A good balance is needed between processing
time and resolution of the solution.
The next step is to specify mesh controls in order to obtain a particular mesh
density.
52
2. Set global size controls.

3. Enter 0.005 for element
edge length.
4. OK.
5. Mesh.
7. Close.
8. Close Mesh Tool.
9. SAVE_DB
Boundary Values
Now comes the fun part, adding velocities and pressures to the areas.
IMPORTANT!! Do not add velocities to the areas inside the volumes. Only the areas
that are exposed to the outside get boundary values.
A velocity of -0.1 cm/s is applied in the Z direction (VZ) at the inlet, and a zero velocity
is applied in the transverse direction at the inlet (VX, VY). Zero velocities in all three
dimensions are applied on all exterior areas, and a zero pressure is applied at the outlet.
On Areas.
2.
Pick the two needle inlets areas.
3. OK.
4. Enter 0.0 for VX.
5. Enter 0.0 for VY.
6. Enter -0.1 for VZ.
53
7. OK
Now, doing a couple of areas at a time, select all other outside areas (except for the
needle outlet) and apply a 0.0 to VX, VY and VZ.
8. OK
Apply the outlet condition.
1.
Main Menu > Preprocessor > Loads > -Loads- Apply > -Fluid/CFD- Pressure
DOF > On Areas.
2.
Pick the outlet needle area.
3. OK.
4. Enter 0 for
pressure value.
the
5. Set endpoints
yes.
to
6. OK.
After all the pressures and
velocities have been added
to the model, the following
picture will appear. This is
the most difficult step so be
careful and take your time.
If you miss an area, the simulation will not work.
Fluid properties will be established for water in the cgs system.
1. Main Menu > Solution > FLOTRAN Set Up > Fluid Properties
2. Choose liquid for density and viscosity. Leave conductivity and specific heat as
constant.
3. OK.
54
4. Enter 1.0 for density, 0.01 for viscosity and 0.04 for conductivity. Leave specific
heat at 1.
5. OK.
Set Up Menu.
Execution Ctrl
2. Enter 40 Global iterations (Note: 40 global
iterations is arbitrary with no guarantee of
convergence.)

At the end of this tutorial there is a table of
constants and reference conditions for water.
The reference conditions will have to be
changed to suit your design and units used.
1. Main Menu > Solution > FLOTRAN Set

Up > Flow Environment > Ref Conditions
2. Change the reference pressure to 101350
(cgs units, equivalent to 1 atmosphere).
3. Change the nominal, stagnation, and
reference temperatures to 20oC.
absolute 0 to 273.
55
6. OK.
The modeling should be ready to be run.
2. Close the information
window when the solution
is done.
While
running
the
FLOTRAN
solution,
ANSYS will plot the
"Normalized
Rate
of
Change" as a function of
the "Cumulative Iteration
Number." This is the
Graphical Solution Tracker,
which
allows
visual
monitoring of the solution
for convergence.
This step might take some
time so be patient, the output should look similar to the following.
Post processing (Laminar Analysis)
56
3. Choose velocity v.
4. OK.
4. OK.
Vx
57
Vy
This gives the velocity profiles for the x and y direction in the channels. Red is the
highest pressure. These images show that the output is turbulent.
These images show a generalized velocity profile in the microfluidic system. If using 3D
you can rotate the design to get a better angle.
58
Constant tables:
59
Density
N2 gas
1.1381
Coeff
1
300
H2 gas
H2O
O2 gas
0.0819
1.0
1.2998
300
300
300
Coeff 2 Molecular Viscosity

wt
Micro Pa
101325 28.018
.00001786
101325 2.016
101325 18
101325 31.99
.00000894
10
.00001206
7
For other constants check out the CRC handbook online at:
http://www.hbcpnetbase.com/hbcp/default.jsp
60
Mass
Diffusion
.0000160
1
.0000496
0.00001
.0000214
9
Conductivity
0.02598
0.1815
0.04
0.02674

2D and 3D Flow Analysis in Microfluidic Channels Including Mulitple Species Transport

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2D and 3D Flow Analysis in Microfluidic Channels Including Mulitple Species Transport

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2D AND 3D FLOW ANALYSIS IN MICROFLUIDIC

CHANNELS INCLUDING MULITPLE SPECIES

Written and Tested by: Scott Stelick

Alliance for NanoMedical Technologies

Last revision 10/2/02

7. Create the finite element mesh.

The ANSYS menus

ANSYS Main Menu:

Define element type.

Main Menu > Preprocessor > Element Type > Add/Edit/Delete

3.OK (in picking menu).

5.OK (in picking menu).

7.OK (in picking menu).

9.OK to create the line

Now create the third area as an arbitrary area through keypoints.

2D Meshing (Do not use if modeling in 3D)

2. Main Menu > Preprocessor > Mesh Tool

Some error messages might

Extrude the meshed area into a 3D meshed volume.

Unselect 2-D elements.

Choose CMIX for density.

Click yes for allow density variations.

Enter 0.01 for viscosity and 0.04 for

OK. (for next screen that pops up)

Set execution controls.

Change reference conditions.

1. Main Menu > Solution > FLOTRAN

1. Main Menu > Solution > FLOTRAN

Main Menu > Solution > FLOTRAN

1. Main Menu > Solution >

The other solver

Enter fluid properties.

All the data here is very important.

To solve for density variations in the fluid

Select the second

The following picture should appear.

Apply the outlet condition.

1. Click on the left vertical line.

11. Enter other loading factor

Post processing (Laminar Analysis)

3. Choose Velocity Vx or Vy.

This gives the velocity

Animate velocity of trace particles.

Fluid flow modeling with obstructions in the channel.

Main Menu >

Define element type. (2D)

Main Menu > Preprocessor > Element Type > Add/Edit/Delete

Main Menu > Preprocessor > Material

Establish fluid properties.

Choose Liquid for density,

There should be no variations in

2. Enter 40 Global iterations (Note: 40 global iterations is arbitrary with no guarantee

Change reference conditions.

1. Main Menu > Solution >

Pick the inlet line (the horizontal line at the bottom).

Wall boundary conditions

7. Pick the outlet line (horizontal line on the top).

Execute FLOTRAN solution.

Make a path plot of velocity through the outlet.

9. Choose DOF solution.

Complex 3D structure modeling

Define element type.

Main Menu > Preprocessor > Element Type > Add/Edit/Delete