Guidance on Boundary layer meshing and Misc.

[David Parker]

Hi Nishanth,

Great that the simulation is working!

1) After converting results, I see the results such as pressures and flows are given for different segment names. But how do I identify which segment corresponds to which segment_name?

The outletface_groupid.dat file contains information about which group ID belongs to which face.

Code: Select all

$ cat outletface_groupid.dat
right_int_iliac GroupId 5
left_ext_iliac GroupId 12
left_int_iliac GroupId 16
right_ext_iliac GroupId 19
right_renal GroupId 22
IMA GroupId 23
SMA1 GroupId 24
SMA2 GroupId 26
hepatic GroupId 29
splenic GroupId 30
left_renal GroupId 31
L2_lumbar GroupId 34
L4_left_lumbar GroupId 35
L4_right_lumbar GroupId 36
L3_right_lumbar GroupId 37
L3_left_lumbar GroupId 39

2) To specify the start and stop time when converting results, what do you mean by time here? By time, does it refer to the time given by time=(no. of timesteps)* (time step size). So if I am running my simulation for 5 seconds= (5000 timesteps)*(0.001 step size), if I specify start as 4 and stop as 5, SV1d says 'time out of range'.

This appears to be a bug. I will open an Issue on it.

3) How many iterations do you recommend me to run for 1D simulations?

That depends on what you are trying to simulate I think. People typically run a simulation of a couple of cardiac cycles.

4) Why is it rigid wall 1D simulation option not available?

The 1D solver is based on a formulation for deformable walls. The idea was to reproduce wave propagation phenomenon in vascular networks. Increasing Eh/r will allow you to simulate rigid walls but increasing it too high will cause the 1D solver to fail.

5) What is the order of Eh/r value, generally? Will material model affect the results significantly?

Examples from the documentation for Eh/r values

MATERIAL MAT1 LINEAR 1.06 0.04 120000.0 1.0 7.1e4
MATERIAL MAT1 OLUFSEN 1.06 0.04 120000.0 1.0 2.0e7 -22.5267 8.65e5

Don't forget that units are in cgs.

The material model will indeed affect the results. Do a few simulations with different values and see what happens.

Cheers,
Dave

[Nishanth Surianarayanan]

Hi Dave,

Thanks a lot for your time and help! Please let me know when you figure out the start and stop time issue in the convert results tab.

Best,
Nishanth

[David Parker]

Hi Nishanth,

I've fixed the problem with converting results and merged the fix into the current SV source. The fix will be in the next SV release which will be in July. Until then just convert all results.

Cheers,
Dave

[Nishanth Surianarayanan]

Hi Dave,

Okay, thanks for letting me know!

Best,
Nishanth

[Nishanth Surianarayanan]

Hi Dave,

Is it possible to use a IC File created using Last Step to restart.x.0 from a old simulation for running a new simulation using a different mesh?

Thanks,
Nishanth

[David Parker]

Hi Nishanth,

SV does not support this. You would need to project the last step restart results onto the new mesh and create a restart file from that. This would be quite involved I think!

Cheers,
Dave

[Nishanth Surianarayanan]

Hi Dave,

I am trying to see if boundary layer meshing is possible without adding spherical regional refinement on SimVascular for the various small branches of the aneurysm geometry. Instead of the spherical refinement and radius-based meshing, which does not work for my aneurysm model. I am planning to locally refine the branches through branch splitting using VMTK which you had suggested to me in one of your previous posts. After splitting into branches with a common ID assigned for each branch using VMTK, how do I assign different mesh sizes for each branch on SimVascular during meshing?

Hope this can overcome the boundary layer problem which I am encountering while using regional refinement on SimVascular.

Thanks,
Nishanth

[David Parker]

Hi Nishanth,

The .vtp file output from VMTK should have ModelFaceID and GroupIds arrays.

The ModelFaceID array is used by SV to define model faces. You can set a meshing edge size per face using the Meshing tool Local Size panel. It is easiest to use ModelFaceID but some of the face IDs will include multiple branches that may not provide you with the meshing control you want.

The GroupIds array identifies each branch with a group ID. You could use this data to create the ModelFaceID array. The group ID will include the vessel cap so you will need to make sure that caps are correctly assigned a separate face ID. Or you could just assign them the same face ID, remove the caps and let SV create them.

Cheers,
Dave

[yan qing]

Hi Dave:
I have ran a Romsimulation job, and I get the converting results.However I can't find the outletface_groupid.dat file in my job,I only the the files in the below picture:

1667475885(1).png (98.36 KiB) Viewed 1079 times

what should I do to find the caps with the Corresponding branch_seg?

1) After converting results, I see the results such as pressures and flows are given for different segment names. But how do I identify which segment corresponds to which segment_name?

The outletface_groupid.dat file contains information about which group ID belongs to which face.

Code: Select all

$ cat outletface_groupid.dat
right_int_iliac GroupId 5
left_ext_iliac GroupId 12
left_int_iliac GroupId 16
right_ext_iliac GroupId 19
right_renal GroupId 22
IMA GroupId 23
SMA1 GroupId 24
SMA2 GroupId 26
hepatic GroupId 29
splenic GroupId 30
left_renal GroupId 31
L2_lumbar GroupId 34
L4_left_lumbar GroupId 35
L4_right_lumbar GroupId 36
L3_right_lumbar GroupId 37
L3_left_lumbar GroupId 39

[David Parker]

Hi Yan,

The ROM simulation implementation has changed a bit the last couple of years. There does not appear to be any information that can be used to explicitly identify which caps correspond to which branch segments.

You can visualize the centerlines.vtp file using the BranchId field. That will show the branches with the ID used in the ROM simulation.

Cheers,
Dave