Error in creating data files in BL mesh

[Nishanth Surianarayanan]

Hi Dave,

I am unable to create data files properly for a boundary layer mesh. I am able to create data files for a mesh without a boundary layer. I am getting the error as shown below:

LINE 0000: mesh_and_adjncy_vtu mesh-complete/mesh-complete.mesh.vtu
LINE 0001: set_surface_id_vtp mesh-complete/mesh-complete.exterior.vtp
LINE 0002: set_surface_id_vtp mesh-complete/mesh-surfaces/IMA.vtp 2
LINE 0003: set_surface_id_vtp mesh-complete/mesh-surfaces/L2_lumbar.vtp
LINE 0004: set_surface_id_vtp mesh-complete/mesh-surfaces/L3_left_lumba
LINE 0005: set_surface_id_vtp mesh-complete/mesh-surfaces/L3_right_lumb
LINE 0006: set_surface_id_vtp mesh-complete/mesh-surfaces/L4_left_lumba
LINE 0007: set_surface_id_vtp mesh-complete/mesh-surfaces/L4_right_lumb
LINE 0008: set_surface_id_vtp mesh-complete/mesh-surfaces/SMA1.vtp 8
LINE 0009: set_surface_id_vtp mesh-complete/mesh-surfaces/SMA2.vtp 9
LINE 0010: set_surface_id_vtp mesh-complete/mesh-surfaces/hepatic.vtp 1
LINE 0011: set_surface_id_vtp mesh-complete/mesh-surfaces/inlet.vtp 11
LINE 0012: set_surface_id_vtp mesh-complete/mesh-surfaces/left_ext_ilia
LINE 0013: set_surface_id_vtp mesh-complete/mesh-surfaces/left_int_ilia
LINE 0014: set_surface_id_vtp mesh-complete/mesh-surfaces/left_renal.vt
LINE 0015: set_surface_id_vtp mesh-complete/mesh-surfaces/right_ext_ili
LINE 0016: set_surface_id_vtp mesh-complete/mesh-surfaces/right_int_ili
LINE 0017: set_surface_id_vtp mesh-complete/mesh-surfaces/right_renal.v
LINE 0018: set_surface_id_vtp mesh-complete/mesh-surfaces/splenic.vtp 1
LINE 0019: fluid_density 1.06
LINE 0020: fluid_viscosity 0.04
LINE 0021: initial_pressure 0
LINE 0022: initial_velocity 0.0001 0.0001 0.0001
LINE 0023: prescribed_velocities_vtp mesh-complete/mesh-surfaces/inlet.
LINE 0024: bct_analytical_shape womersley
LINE 0025: bct_period 1.0
LINE 0026: bct_point_number 2
LINE 0027: bct_fourier_mode_number 2
LINE 0028: bct_create mesh-complete/mesh-surfaces/inlet.vtp inlet.flow
LINE 0029: bct_write_dat bct.dat
LINE 0030: bct_write_vtp bct.vtp
LINE 0031: pressure_vtp mesh-complete/mesh-surfaces/IMA.vtp 0
LINE 0032: pressure_vtp mesh-complete/mesh-surfaces/L2_lumbar.vtp 0
LINE 0033: pressure_vtp mesh-complete/mesh-surfaces/L3_left_lumbar.vtp
LINE 0034: pressure_vtp mesh-complete/mesh-surfaces/L3_right_lumbar.vtp
LINE 0035: pressure_vtp mesh-complete/mesh-surfaces/L4_left_lumbar.vtp
LINE 0036: pressure_vtp mesh-complete/mesh-surfaces/L4_right_lumbar.vtp
LINE 0037: pressure_vtp mesh-complete/mesh-surfaces/SMA1.vtp 0
LINE 0038: pressure_vtp mesh-complete/mesh-surfaces/SMA2.vtp 0
LINE 0039: pressure_vtp mesh-complete/mesh-surfaces/hepatic.vtp 0
LINE 0040: pressure_vtp mesh-complete/mesh-surfaces/left_ext_iliac.vtp
LINE 0041: pressure_vtp mesh-complete/mesh-surfaces/left_int_iliac.vtp
LINE 0042: pressure_vtp mesh-complete/mesh-surfaces/left_renal.vtp 0
LINE 0043: pressure_vtp mesh-complete/mesh-surfaces/right_ext_iliac.vtp
LINE 0044: pressure_vtp mesh-complete/mesh-surfaces/right_int_iliac.vtp
LINE 0045: pressure_vtp mesh-complete/mesh-surfaces/right_renal.vtp 0
LINE 0046: pressure_vtp mesh-complete/mesh-surfaces/splenic.vtp 0
LINE 0047: noslip_vtp mesh-complete/walls_combined.vtp

ERROR: could not open file (mesh-complete/walls_combined.vtp).ERROR: command could not be processed.

How can I solve this issue?

Here is my project if you want to take a look: https://drive.google.com/drive/folders/ ... sp=sharing

Thanks for your help!

Best,
Nishanth

[Nishanth Surianarayanan]

Hi Dave,

Just wanted to update something which I found to be peculiar. Inside mesh-complete file, I observed that many walls_combined.vtp files were created instead of a single walls_combined.vtp file. Probably this is why I am getting the error. Please see the screenshot of my mesh-complete folder below:

inside_meshcomplete.PNG (67.27 KiB) Viewed 887 times

How can I correct this?

Thanks,
Nishanth

[Nishanth Surianarayanan]

Hi Dave,

The below is the screenshot of the data file folder when I created a simulation file for that mesh.

inside_best_fine_steady_data_folder.PNG (14.34 KiB) Viewed 851 times

I am using the latest windows version of SimVascular (2020.04.06). I am able to create mesh files for meshes without boundary layers, but with regional refinements. However, when I add boundary layers, I am facing this issue.

Looking forward to hearing from you.

Thanks,
Nishanth

[David Parker]

Hi Nishanth,

I've done some testing and have determined that the problem is caused by the separation of the mesh wall into disjoint regions

Mesh surface colored by face ID.

Screen Shot 2020-06-09 at 4.27.42 PM.png (491.56 KiB) Viewed 822 times

The disjoint regions are created by the Regional Refinement spheres

Screen Shot 2020-06-09 at 4.36.09 PM.png (146.71 KiB) Viewed 822 times

The meshing code checks for disjoint regions and then writes out separate files for them, not sure why. Like you mentioned, this only happens with boundary layer meshing. Let me dig into the code and see what is going on.

Cheers,
Dave

[Nishanth Surianarayanan]

Hi Dave,

Thank you so much for checking into the issue. Please update me if you find a solution.

Best,
Nishanth

[David Parker]

Hi Nishanth,

I've created a GitHub Issue for this https://github.com/SimVascular/SimVascular/issues/672.

Cheers,
Dave

[Nishanth Surianarayanan]

Hi Dave,

Thank you for creating it. Please let me know once this issue is resolved. It'd be really helpful.

Thanks,
Nishanth

[Nishanth Surianarayanan]

Hi Dave,

Is it possible to install svSolver on Ubuntu 14.04? Can you guide me if we can install it through a separate procedure?

Thanks,
Nishanth

[David Parker]

Hi Nishanth,

You should be able to build svSolver on Ubuntu 14. You will need to build using a locally installed version of VTK (see https://github.com/SimVascular/svSolver). The apt-get install command listed there might be a bit different for mpich, might need to use a version number (e.g. apt-get install mpich2 ).

Cheers,
Dave

[Nishanth Surianarayanan]

Hi Dave,

Thanks for letting me know.

Thanks,
Nishanth