Regional Refinement issue

Provides a system for patient-specific cardiovascular modeling and simulation.
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Maria Nicole Antonuccio
Posts: 19
Joined: Fri Nov 30, 2018 3:36 am

Regional Refinement issue

Post by Maria Nicole Antonuccio » Wed Apr 17, 2019 2:35 am

Dear SimVascular community,

I'd like to launch a simulation with both boundary layer meshing and regional refinement. My model is an aorta with a coarctation, and I'd like to refine the mesh in the coarctation region.

I was able to generate the mesh using TetGen successfully. When I attempted to launch the simulation, it finished immediately. The folder "n-procs_case" was correctly creating, but no restart file and svLS_NS.log were created. I performed the boundary layer meshing, setting up the following parameters:
  • Portion of edge size: 1
  • Numbers of layers: 3
  • Layer decreasing ratio: 0.5
I wanted to simulate six cardiac cycles. I tried using several computers and changing both the max edge global size and the local size of the sphere, but all the tests failed. Moreover, I computed dt using the CFL formula to be sure to input the correct time step.

Without the local refinement, it was possible to launch the simulations with different max edge global sizes and setting only boundary meshing refinement. As max edge global sizes, I entered: 0.15, 0.12 (estimated max edge global size), 0.105 and 0.08 and the simulations ran successfully with all of these parameters.

In the attachments, you can see some images of the mesh, obtained setting both boundary layer meshing (as previously indicated and by means the estimated max edge global size) and regional refinement (setting up 0.06 as local size).

Your help would be appreciated.

Thanks in advance,
Maria Nicole.
Attachments
MeshStatistics.png
MeshStatistics.png (15.43 KiB) Viewed 106 times
CoARefinement2.png
CoARefinement2.png (354.74 KiB) Viewed 106 times
CoARefinement.png
CoARefinement.png (271.11 KiB) Viewed 106 times
BoundaryLayerMeshing.png
BoundaryLayerMeshing.png (205.28 KiB) Viewed 106 times

User avatar
David Parker
Posts: 169
Joined: Tue Aug 23, 2005 2:43 pm

Re: Regional Refinement issue

Post by David Parker » Thu Apr 18, 2019 10:28 am

Hi Maria Nicole,

When the simulation failed a window should pop up. Click on the Show Details button will display information about what caused the failure. What information is shown there?

If you upload your project to a place I can download it (e.g. DropBox) then I'll have a look. You don't need to include the Images directory.

Cheers,
Dave

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Maria Nicole Antonuccio
Posts: 19
Joined: Fri Nov 30, 2018 3:36 am

Re: Regional Refinement issue

Post by Maria Nicole Antonuccio » Mon Apr 22, 2019 1:45 am

Dear David,

I thank you for valuable support. Here the message I could read when the simulation crashed:


The process ID for myrank (0) is (485).
The number of processes is 24.
Solver Input Files listed as below:
------------------------------------
The process ID for myrank (2) is (532).
The process ID for myrank (4) is (527).
The process ID for myrank (5) is (545).
The process ID for myrank (9) is (552).
The process ID for myrank (10) is (560).
The process ID for myrank (11) is (562).
The process ID for myrank (12) is (563).
The process ID for myrank (17) is (565).
The process ID for myrank (19) is (564).
The process ID for myrank (22) is (569).
The process ID for myrank (23) is (570).

Local Config: solver.inp

The process ID for myrank (1) is (481).
The process ID for myrank (3) is (497).
The process ID for myrank (6) is (546).
The process ID for myrank (7) is (539).
The process ID for myrank (8) is (529).
The process ID for myrank (13) is (559).
The process ID for myrank (14) is (554).
The process ID for myrank (15) is (556).
The process ID for myrank (16) is (557).
The process ID for myrank (18) is (567).
The process ID for myrank (21) is (566).

Default Input File: Not Setup.
The process ID for myrank (20) is (568).

Parameter Values setup as below:
----------------------------------------------

Time Varying Boundary Conditions From File: True
BCT File Type: DAT
Number of BCT Files: 1
BCT Matching Type: Global Node ID
BCT Time Scale Factor: 1.0
Equation of State: Incompressible
Time Step Size: 0.002
Number of Timesteps: 2139
Viscous Control: Viscous
Number of Timesteps between Restarts: 20
Print Average Solution: True
Print Error Indicators: False
Number of Force Surfaces: 1
Surface ID's for Force Calculation: 1
Force Calculation Method: Velocity Based
Apply Wall Deformation: False
Number of Surfaces which Output Pressure and Flow: 0
Density: 1.06
Viscosity: 0.04
Solver Type: svLS
svLS Type: NS
Number of Krylov Vectors per GMRES Sweep: 100
Number of Solves per Left-hand-side Formation: 1
Tolerance on Momentum Equations: 0.05
Tolerance on Continuity Equations: 0.4
Tolerance on svLS NS Solver: 0.4
Maximum Number of Iterations for svLS NS Solver: 10
Maximum Number of Iterations for svLS Momentum Loop: 10
Maximum Number of Iterations for svLS Continuity Loop: 400
Time Integration Rule: Second Order
Time Integration Rho Infinity: 0.5
Flow Advection Form: Convective
Quadrature Rule on Interior: 2
Quadrature Rule on Boundary: 3
Number of Elements Per Block: 255
Number of Coupled Surfaces: 4
Pressure Coupling: Implicit
Number of RCR Surfaces: 4
List of RCR Surfaces: 3 4 5 6
RCR Values From File: True
Backflow Stabilization Coefficient: 0.2
Deformable Wall: False
Residual Control: True
Residual Criteria: 0.001
Minimum Required Iterations: 4
Step Construction: 0 1 0 1 0 1 0 1
Solver Task: Full Simulation

24-procs_case/ does not exist or is unusable
creating a new one

ERROR opening file [geombc.dat.1].
/usr/local/sv/svsolver/2019-02-07/svsolver: line 58: 485 Segmentation fault (core dumped) $SV_HOME/bin/svsolver $*

I uploaded my project here:

https://drive.google.com/drive/folders/ ... TSpH5yk_er

Kind regards,
Maria Nicole

User avatar
David Parker
Posts: 169
Joined: Tue Aug 23, 2005 2:43 pm

Re: Regional Refinement issue

Post by David Parker » Wed May 15, 2019 11:33 am

Hi Maria Nicole,

I was busy with a lot of development issues and lost track of this. Were you able to resolve the problems you were having?

Cheers,
Dave

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