Seeking examples of valveless pumping in a cylinderic tube

[Yiming Gan]

Hi All,

I've successfully set up IBAMR and run examples on it! The bio-problem that I try to simulate is peristaltic pumping/impedance pumping in a cylindric tube. I wonder if there are related examples and codes that I can learn from in IBAMR. 

In the publication webpage, I find the IB code used in the following paper already valuable to me!  

 Acharya S, Kou W, Halder S, Carlson DA, Kahrilas PJ, Pandolfino JE, Patankar NA. Pumping patterns and work done during peristalsis in finite-length elastic tubes. J Biomech Eng. 2021;143(7):071001

Best,

Yiming

University of Rochester

[Boyce Griffith]

You might take a look at the example in IBFE/explicit/ex7, which is a pressurized channel flow model with flexible and rigid sections. It isn’t the same setup, but it should give at least a rough idea of how to set this up.

[Yiming Gan]

I supposed I should look at the main2d file? However, it turns out to be a mess like this. Should I open the file with other softwares?

Best,

Yiming

[Boyce Griffith]

On Feb 21, 2022, at 2:10 PM, Yiming Gan <germa...@gmail.com> wrote:

I supposed I should look at the main2d file?

I would recommend looking at the source code and input files.

However, it turns out to be a mess like this. Should I open the file with other softwares?

Best,

Yiming

<Screenshot from 2022-02-21 14-08-58.png>

On Monday, February 7, 2022 at 10:34:05 AM UTC-5 Boyce wrote:

On Feb 4, 2022, at 10:58 PM, Yiming Gan <germa...@gmail.com> wrote:

Hi All,

I've successfully set up IBAMR and run examples on it! The bio-problem that I try to simulate is peristaltic pumping/impedance pumping in a cylindric tube. I wonder if there are related examples and codes that I can learn from in IBAMR. 

In the publication webpage, I find the IB code used in the following paper already valuable to me!  

 Acharya S, Kou W, Halder S, Carlson DA, Kahrilas PJ, Pandolfino JE, Patankar NA. Pumping patterns and work done during peristalsis in finite-length elastic tubes. J Biomech Eng. 2021;143(7):071001

You might take a look at the example in IBFE/explicit/ex7, which is a pressurized channel flow model with flexible and rigid sections. It isn’t the same setup, but it should give at least a rough idea of how to set this up.

Best,

Yiming

University of Rochester

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<Screenshot from 2022-02-21 14-08-58.png>

[Yiming Gan]

Thanks! The input file makes sense to me. However, I have trouble finding where the source codes are. Could you specify a path which contains all the solvers and source codes? Thanks for answering my naive questions!

Best,

Yiming

[Boyce Griffith]

On Feb 21, 2022, at 2:17 PM, Yiming Gan <germa...@gmail.com> wrote:

Thanks! The input file makes sense to me. However, I have trouble finding where the source codes are. Could you specify a path which contains all the solvers and source codes?

The source code is in the directory where you cloned the repository (if you used git to get a copy of the code), or where you unpacked the archive file (if you downloaded the software from GitHub).

[Yiming Gan]

I see! I should look at the folder 'IBAMR' instead of 'ibamr-objs-opt'.

Yiming

[Boyce Griffith]

On Feb 21, 2022, at 2:20 PM, Yiming Gan <germa...@gmail.com> wrote:

I see! I should look at the folder 'IBAMR' instead of 'ibamr-objs-opt'.

Yes --- all of the source code (and input files) are in there.

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[Yiming Gan]

Dear all,
For IBFE Ex7, I loaded the upperoutput.ex2 and loweroutput.ex2. I assume that there are the lagrangian nodes. I plot them as mesh and there velocity over time in the following figure. The velocity quiver makes sense to me. However, I don't see any movement of the lagrangain points by eyes through the video. I wonder if I plot the lagrangian points the right way? 

Yiming

[Boyce Griffith]

On Feb 22, 2022, at 10:28 AM, Yiming Gan <germa...@gmail.com> wrote:

Dear all,
For IBFE Ex7, I loaded the upperoutput.ex2 and loweroutput.ex2. I assume that there are the lagrangian nodes. I plot them as mesh and there velocity over time in the following figure. The velocity quiver makes sense to me. However, I don't see any movement of the lagrangain points by eyes through the video. I wonder if I plot the lagrangian points the right way? 

You may still need to apply the displace operator to the structures using "dX" as the displacement vector field.

Yiming<Screenshot from 2022-02-22 10-24-31.png>

To view this discussion on the web visit https://groups.google.com/d/msgid/ibamr-dev/258d663a-394f-442a-8b40-c7debc808233n%40googlegroups.com.
<Screenshot from 2022-02-22 10-24-31.png>

[Yiming Gan]

Dear Boyce,

Thanks. Yeah, the displace of dX make sense to me. It seems that the upper flexible part of the beam is pumping the fluid. Yet I wonder how to visualize the movement of the beam structure directly instead of a quiver? For example, how can I make the black line(mesh) deform as the quiver inplies? The displace operactor only works on a quiver.

Best,

Yiming

[Boyce Griffith]

On Feb 22, 2022, at 10:37 AM, Boyce Griffith <boy...@gmail.com> wrote:

On Feb 22, 2022, at 10:28 AM, Yiming Gan <germa...@gmail.com> wrote:

Dear all,
For IBFE Ex7, I loaded the upperoutput.ex2 and loweroutput.ex2. I assume that there are the lagrangian nodes. I plot them as mesh and there velocity over time in the following figure. The velocity quiver makes sense to me. However, I don't see any movement of the lagrangain points by eyes through the video. I wonder if I plot the lagrangian points the right way? 

You may still need to apply the displace operator to the structures using "dX" as the displacement vector field.

I am attaching an older email from the mailing list that shows how to do this.

[Boyce Griffith]

On Feb 22, 2022, at 11:42 AM, Yiming Gan <germa...@gmail.com> wrote:

Dear Boyce,

Thanks. Yeah, the displace of dX make sense to me. It seems that the upper flexible part of the beam is pumping the fluid. Yet I wonder how to visualize the movement of the beam structure directly instead of a quiver? For example, how can I make the black line(mesh) deform as the quiver inplies? The displace operactor only works on a quiver.

Are you applying the displace operator to the mesh?

Best,

Yiming

To view this discussion on the web visit https://groups.google.com/d/msgid/ibamr-dev/ccc8e1f2-d3c0-46a6-8de1-4e29b66337ecn%40googlegroups.com.
<Screenshot from 2022-02-22 11-39-05.png>

[Yiming Gan]

Thanks! This is awesome! I nailed it.

Best,

Yiming