[Gmsh] gmsh or gmshToFoam problem?

[Mark Starnes]

Hi Madeleine,

I've had similar issues and I'm afraid to say I
gave up trying to fix them with gmsh alone.  I now
use gmsh to generate surface meshes, engrid to
create boundary layers, volume meshes and the
openFoam export.  Finally, I use openFoam to 
refine the boundary layer.  The meshes
created often pass openFoam's mesh testing.  

However, other people may be able to help you
more.  I hope so:  it will help me too!  I felt it
a personal failure not to be able to manage the
meshing with gmsh alone.....

Good luck.

Best regards,

Mark.

On Tue, Jun 19, 2012 at 02:46:30PM +0200, Madeleine Vincent wrote:
> 
> gmsh friends -
> 
> I have a question regarding gmsh and the gmshToFoam utility within OpenFOAM,
> one of which seems to be not acting as I had presumed.
> 
> I have a simple mesh problem which I've distilled down to the it's basic form. 
> I am running a gmsh script (.geo) to create a 3D rectangular flow field with a
> circular cylinder in the middle.
> When I run gmsh, it meshes succesfully.  However, when I run gmshToFoam
> (conversion to the OpenFOAM polyMesh format), I end up with a mesh that is not
> usable. 
> 
> First of all, I get a warning saying:
> 
> 
> [warning]
> --> FOAM Warning :
>     From function polyMesh::polyMesh(... construct from shapes...)
>     in file meshes/polyMesh/polyMeshFromShapeMesh.C at line 619
>     Found 9022 undefined faces in mesh; adding to default patch.
> [/warning]
> 
> 
> 
> Invoking the "checkMesh" utility results in the following errors:
> 
> 
> [error]
> Checking geometry...
>     Overall domain bounding box (0 0 -0.75) (9 6 0.75)
>     Mesh (non-empty, non-wedge) directions (1 1 1)
>     Mesh (non-empty) directions (1 1 1)
>     Boundary openness (1.15651e-17 5.07766e-19 9.032e-18) OK.
>  ***High aspect ratio cells found, Max aspect ratio: 7.58943e+198, number of
> cells 3
>   <<Writing 3 cells with high aspect ratio to set highAspectRatioCells
>     Minumum face area = 6.81219e-06. Maximum face area = 0.177405.  Face area
> magnitudes OK.
>     Min volume = 1.33333e-300. Max volume = 0.0208743.  Total volume =
> 80.8949.  Cell volumes OK.
>     Mesh non-orthogonality Max: 89.2144 average: 30.4407
>    *Number of severely non-orthogonal faces: 1046.
>     Non-orthogonality check OK.
>   <<Writing 1046 non-orthogonal faces to set nonOrthoFaces
>  ***Error in face pyramids: 8 faces are incorrectly oriented.
>   <<Writing 8 faces with incorrect orientation to set wrongOrientedFaces
>     Max skewness = 2.23263 OK.
>     Coupled point location match (average 0) OK.
> 
> Failed 2 mesh checks.
> [/error]
> 
> 
> 
> The gmsh script (.geo file) is as follows:
> 
> 
> [script]
> // Everything is parameterized on the cylinder radius
> rad = 0.15;
> 
> //Characteristic length - used for mesh sizing
> lc = 4*rad;
> 
> //Plane dimesions
> planeLength = 60*rad;
> planeWidth = 40*rad;
> 
> //Cyclinder constants
> cir_x = 15*rad;          //The absolute X distance of the center
> cir_y = planeWidth / 2;  //The absolute Y distance of the center
> 
> //The bottom plane number
> bottomPlaneNum = 16;
> 
> //The extrusion thickness
> extThickness = rad*10;
> zBottom = -(extThickness/2.0);
> zTop    =  (extThickness/2.0);
> z = zBottom;   //The z-height of this plane.
>                // NOTE - For 2D, the plane is centered at 0, so
>                // the z value used will be -(h/2)
> 
> //Rectangular plane (Counter-clockwise, starting in lower left corner)
> Point(1) = {0,           0,          z, lc};
> Point(2) = {planeLength, 0,          z, lc};
> Point(3) = {planeLength, planeWidth, z, lc};
> Point(4) = {0,           planeWidth, z, lc};
> 
> //Circle
> Point(5) = {cir_x,       cir_y,       z, lc};    // Center point
> Point(6) = {cir_x,       cir_y + rad, z, lc};    // 12 o'clock
> Point(7) = {cir_x + rad, cir_y,       z, lc};    // 3
> Point(8) = {cir_x,       cir_y - rad, z, lc};    // 6
> Point(9) = {cir_x - rad, cir_y,       z, lc};    // 9
> 
> //Lines
> Line(1) = {1, 2};
> Line(2) = {2, 3};
> Line(3) = {3, 4};
> Line(4) = {4, 1};
> Circle(5) = {6, 5, 7};
> Circle(6) = {7, 5, 8};
> Circle(7) = {8, 5, 9};
> Circle(8) = {9, 5, 6};
> Line Loop(9) = {1, 2, 3, 4};
> Line Loop(10) = {5, 6, 7, 8};
> 
> //Surface
> // Don't add any line loop(s) specific to meshing
> Plane Surface(bottomPlaneNum) = {9, 10};
> 
> //Extrude the bottom surface in the z direction a total of extThickness units.
> // This extrusion is centered on 0 (from -h/2 to +h/2)
> newSurfs[] = Extrude {0,0,extThickness} {
>   Surface{bottomPlaneNum};
> };
> 
> //Name the surfaces
> Physical Surface("topAndBottom") = {bottomPlaneNum, newSurfs[0]};
> Physical Surface("nearAndFar") = {newSurfs[2], newSurfs[4]};
> Physical Surface("outlet") = {newSurfs[3]};
> Physical Surface("inlet") = {newSurfs[5]};
> Physical Surface("cylinder") = {newSurfs[9], newSurfs[8], newSurfs[7], newSurfs
> [6]};
> 
> Physical Volume(1) = {newSurfs[1]};
> 
> //Meshing
> fineness = 15;
> 
> Field[4] = Cylinder;
> Field[4].Radius = 1.5*rad;
> Field[4].VIn = lc / fineness;
> Field[4].VOut = lc / 2;
> Field[4].XAxis = 0.0;
> Field[4].XCenter = cir_x;
> Field[4].YAxis = 0.0;
> Field[4].YCenter = cir_y;
> Field[4].ZAxis = 1.0;
> Field[4].ZCenter = 0.0;
> 
> Field[6] = Box;
> Field[6].VIn = lc / (fineness / 3);
> Field[6].VOut = lc;
> Field[6].XMin = cir_x - 3*rad;
> Field[6].XMax = cir_x + 10*rad;
> Field[6].YMin = cir_y - 3*rad;
> Field[6].YMax = cir_y + 3*rad;
> Field[6].ZMin = zBottom -0.000001;
> Field[6].ZMax = zTop    +0.000001;
> 
> // Use minimum of all the fields as the background field
> Field[100] = Min;
> Field[100].FieldsList = {4, 6};
> Background Field = 100;
> 
> [/script]
> 
> 
> 
> I have no problem with the 2D case -- I use Layers{1} and Recombine within the
> extrusion command. This works well.
> 
> I have also seen that using many layers within the 3D case will also produce a
> mesh that passes the checkMesh utility.  But this doesn't provide a good 3D
> mesh, as the domain is segregated throughout in these distinct layers, and it
> doesn't take into account the finer meshing (in the Z direction) around the
> cylinder.
> 
> So I'm wondering if this is an issue in the meshing of gmsh, or the gmshToFoam
> utility?  And what remedy might be available. 
> 
> Thank you very much for any help you are able to provide.
> 
> Madeleine P. Vincent
> 

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-- 
Dr. Mark Starnes
Principal Physicist
FT Technologies
Church Lane
Teddington
TW11 8PA

web:  www.fttech.co.uk
DDI:  0208 614 2730