Compute TAWSS and OSI

[Surabhi Rathore]

Hi,

I would like to thank you for the SimVascular Team for developing a great tool for the blood flow simulation and for the forum discussion.
I am happy that I successfully did the blood flow simulation for the .stl file for the patient specific model.
However, I have some of the follow up questions regarding the post processing.

1.) I extracted the all_results for all time steps into a folder by utilizing the command
/usr/local/sv/svsolver/2019-02-07/svpost -all -indir simulation -outdir steady_converted_results/ -start 0 -stop 200 -incr 10 -vtp all_results -vtp all_results
and all the extracted results could be seen in the screenshot.
As, I only have all_results_xxxxxx.vtp, all_results_xxxxxx.vtu and average_results.vtp files only. I do not have all_results_pressure.txt, all_results_flows.txt and others files. I do not know why, please give me suggestion how to develop rest of the files?
I think this is the reason I am not able to compute the TAWSS, OSI other variables.

2.) When, I was running the about command there is some massage is coming at every steps. I want to know what is the meaning of this massage?? Please explain.

3.) And last question related to the time steps which I am seeing in the paraview is 0.11111, 0.2222, ..., 0.9999, 1.
But, I set the .flow values and I choose the Womersely profile
0.0 -150
1.0 -150
and in the solver I set the time step value (delta t)= 0.005
No. of Time steps (n) = 200 and did the simulation for 1 cycle.
When, I was trying to do the animation by using the paraview I am not able to see the change at every time step and it exit within mlsec, why so ??
I am curious to know how to make a movie for the computed variables?

Please explain me and also give me the suggestions how to solve the problems??

Best regards,
Surabhi

[David Parker]

Hi Surabhi,

1) The all_results_pressure.txt, all_results_flows.txt and others files of that type are currently only computed when converting results using the SV GUI Simulations tool. There is an open Issue to add this functionality to the svpost program. In the mean time you can use a program here https://github.com/ktbolt/cardiovascula ... flow-files to compute those files.

2) I assume you mean messages like Reducing (vin plane traction) results. These messages describe what svpost is doing when processing the restart files. Reducing (vin plane traction) results means that it is trying to read vin plane traction results from the restart file. If those results are not found then you will see Note: No (vin plane traction) results.

3) Simulation results are written for Number of Timesteps between Restarts: that is in the solver.in file. If Number of Timesteps between Restarts:20 and Time Step Size:0.005 then you will have results for 0.0, 20*0.005, 2*20*0.005, etc.

Cheers,
Dave

[Surabhi Rathore]

Hi Dave,

Thank you for your reply.
I generated the .txt files of the results through GUI.

When, I am seeing the all_results.vtp file which I converted using the Single file option. I followed the instruction given in the link
viewtopicPhpbb.php?f=188&t=8617&p=23689&start=0&view=

In paraview when I am opening the all_results.vtp file but unable to see TAWSS and OSI.

Please let me know if there is anything which I am missing.

Your suggestions will be a great help to me.


Thanks
surabhi

[David Parker]

Hi Surabhi,

If you don't write the results to a single file you will then see a file named average_result.vtp that contains vOSI and vTAWSS.

This data is also written to the .vtp file when writing to a single file but it is more difficult to visualize using ParaView.

Cheers,
Dave

[Surabhi Rathore]

Hi Dave,

Sorry, I am still not able to see the vOSI and vTAWSS in the average_results.vtp file also.
I am in need to see the those results for the presentation. Please help me.

I first thought it might be related to the steady flow but when I simulated the results for the PC-MRI flow rate data (means, pulsatile velocity profile).
I converted the results in the single file as well as without single file. I also have .txt file.
But, not able to see the only these parameters.

Please give me any your inputs or let me know where I am lacking to understand the point. As you mentioned that it is bit tricky. Is it possible that you could tell me the steps? I look forward for your response.

Thanks
Surabhi

[David Parker]

Hi Surabhi,

I'm seeing that when converting results setting the start time to 0 does not write out OSI. Set the start time to whatever your increment value is.

Cheers,
Dave

[Surabhi Rathore]

Hi Dave,

Thanks.
Now, I am able to see the results for vOSI and vTAWSS.

Here, I have some problems related to the FSI simulation in both ways.

I did the svFSI solver setting in the GUI like this /usr/local/sv/svFSI/2018-07-03/svfsi

1.) When, I am running the simulation for svFSI through GUI then I am not able to run the simulation because there is some error.

Screenshot from 2019-12-14 19-12-10.png (265.34 KiB) Viewed 1647 times

.

2.) When, I am trying to run the simulation using the command line then I am getting one message and further no progress in the simulation for a long time.

Screenshot from 2019-12-14 19-50-14 - 1.png (155.14 KiB) Viewed 1647 times

Please provide me solution for the successful simulation of svFSI.

Thanks,
Surabhi

[David Parker]

Hi Surabhi,

1) The mpi error is from a incompatibility between the Ubuntu version that the installed svFSI was built with and what version you are running on. You will need to run svSolver under Ubuntu 16 I think.

2) It seems that the format of the svFSI solver input .txt file has changed. I will update the SV svFSI tool to write the correct file format. We are planning on a new SV release the end of this week.

Cheers,
Dave

[Surabhi Rathore]

Hi Dave,

May I know the update of the FSI solver. As you assured that it will be out soon for the Ubuntu 18.04.

I am using Ubuntu 18.04 on the VM VirtualBox6.0.
I am want to simulate some results for the FSI.

Please let me know about it.

Best,
Surabhi

[David Parker]

Hi Surabhi,

I have placed an installed for svFSI for Ubuntu 18.04 on SimTK SimVascular. This for the last version of svFSI that supports the solver input file created by SV.

Be sure to let me know if you have any problems using it.

Cheers,
Dave