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snappyHexMesh won't work - zeros everywhere!

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Old   March 23, 2011, 16:16
Default snappyHexMesh won't work - zeros everywhere!
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As you can probably tell I'm rather new to OpenFoam.
I'm having some trouble with snappyHexMesh.
I think I have set the case up correctly but when I run it, it does not refine the mesh and produces lots of zeros.

The print out of the terminal is shown here:

Code:
psypherdelic@Japtop:~/Documents/Computational/Small$ snappyHexMesh -overwrite
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  1.7.x                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 1.7.x-131caa989cd3
Exec   : snappyHexMesh -overwrite
Date   : Mar 23 2011
Time   : 19:14:00
Host   : Japtop
PID    : 2560
Case   : /home/psypherdelic/Documents/Computational/Small
nProcs : 1
SigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 3

Read mesh in = 0.07 s

Overall mesh bounding box  : (-5 -4 -3) (20 4 5)
Relative tolerance         : 1e-06
Absolute matching distance : 2.74408e-05

Reading refinement surfaces.
Read refinement surfaces in = 22.38 s

Reading refinement shells.
Read refinement shells in = 0 s

Setting refinement level of surface to be consistent with shells.
Checked shell refinement in = 0 s


Determining initial surface intersections
-----------------------------------------

Edge intersection testing:
    Number of edges             : 4224
    Number of edges to retest   : 4224
    Number of intersected edges : 0
Calculated surface intersections in = 44.92 s

Initial mesh : cells:1280  faces:4224  points:1701
Cells per refinement level:
    0	1280

Adding patches for surface regions
----------------------------------

Patch	Region
-----	------
small:

6	small_small

Added patches in = 0 s

Selecting decompositionMethod simple

Refinement phase
----------------

Found point (2.48781 1.00986 0.473258) in cell 404 on processor 0
Reading external feature lines.
Read feature lines in = 0.01 s


Surface refinement iteration 0
------------------------------

Marked for refinement due to surface intersection : 0 cells.
Marked for refinement due to curvature/regions    : 0 cells.
Determined cells to refine in = 0 s
Selected for refinement : 0 cells (out of 1280)
Stopping refining since too few cells selected.


Removing mesh beyond surface intersections
------------------------------------------

Found point (2.48781 1.00986 0.473258) in cell 404 in global region 0 out of 1 regions.
Keeping all cells in region 0 containing point (2.48781 1.00986 0.473258)
Selected for keeping : 1280 cells.
Edge intersection testing:
    Number of edges             : 4224
    Number of edges to retest   : 0
    Number of intersected edges : 0

Shell refinement iteration 0
----------------------------

Marked for refinement due to refinement shells    : 0 cells.
Determined cells to refine in = 0.05 s
Selected for internal refinement : 0 cells (out of 1280)
Stopping refining since too few cells selected.


Splitting mesh at surface intersections
---------------------------------------

Introducing baffles for 0 faces that are intersected by the surface.

Edge intersection testing:
    Number of edges             : 4224
    Number of edges to retest   : 0
    Number of intersected edges : 0
Created baffles in = 0.04 s


After introducing baffles : cells:1280  faces:4224  points:1701
Cells per refinement level:
    0	1280

Introducing baffles to block off problem cells
----------------------------------------------

markFacesOnProblemCells : marked 0 additional internal faces to be converted into baffles.
Analyzed problem cells in = 0.02 s


Introducing baffles to delete problem cells.

Edge intersection testing:
    Number of edges             : 4224
    Number of edges to retest   : 0
    Number of intersected edges : 0
Created baffles in = 0.03 s


After introducing baffles : cells:1280  faces:4224  points:1701
Cells per refinement level:
    0	1280

Remove unreachable sections of mesh
-----------------------------------

Keeping all cells in region 0 containing point (2.48781 1.00986 0.473258)
Selected for keeping : 1280 cells.
Edge intersection testing:
    Number of edges             : 4224
    Number of edges to retest   : 0
    Number of intersected edges : 0
Split mesh in = 0.03 s


After subsetting : cells:1280  faces:4224  points:1701
Cells per refinement level:
    0	1280

Handling cells with snap problems
---------------------------------

Introducing baffles for 0 faces that are intersected by the surface.

Edge intersection testing:
    Number of edges             : 4224
    Number of edges to retest   : 0
    Number of intersected edges : 0
Created baffles in = 0.04 s


After introducing baffles : cells:1280  faces:4224  points:1701
Cells per refinement level:
    0	1280

Introducing baffles to block off problem cells
----------------------------------------------

markFacesOnProblemCells : marked 0 additional internal faces to be converted into baffles.
Analyzed problem cells in = 0.02 s


Introducing baffles to delete problem cells.

Edge intersection testing:
    Number of edges             : 4224
    Number of edges to retest   : 0
    Number of intersected edges : 0
Created baffles in = 0.04 s


After introducing baffles : cells:1280  faces:4224  points:1701
Cells per refinement level:
    0	1280

Remove unreachable sections of mesh
-----------------------------------

Keeping all cells in region 0 containing point (2.48781 1.00986 0.473258)
Selected for keeping : 1280 cells.
Edge intersection testing:
    Number of edges             : 4224
    Number of edges to retest   : 0
    Number of intersected edges : 0
Split mesh in = 0.04 s


After subsetting : cells:1280  faces:4224  points:1701
Cells per refinement level:
    0	1280
dupNonManifoldPoints : Found : 0 non-manifold points (out of 1701)
Edge intersection testing:
    Number of edges             : 4224
    Number of edges to retest   : 0
    Number of intersected edges : 0
getDuplicateFaces : found 0 pairs of duplicate faces.

Detected unsplittable baffles : 0

Merge refined boundary faces
----------------------------

mergePatchFaces : Merging 0 sets of faces.
Removing 0 straight edge points.
Refined mesh : cells:1280  faces:4224  points:1701
Cells per refinement level:
    0	1280
Writing mesh to time 3
Written mesh in = 0.21 s.
Mesh refined in = 0.53 s.

Morphing phase
--------------

Constructing mesh displacer ...
Using mesh parameters 
{
    maxNonOrtho     65;
    maxBoundarySkewness 20;
    maxInternalSkewness 4;
    maxConcave      80;
    minFlatness     0.5;
    minVol          1e-13;
    minArea         -1;
    minTwist        0.02;
    minDeterminant  0.001;
    minFaceWeight   0.02;
    minVolRatio     0.01;
    minTriangleTwist -1;
    nSmoothScale    4;
    errorReduction  0.75;
}


Checking initial mesh ...
Checking faces in error :
    non-orthogonality >  65 degrees                        : 0
    faces with face pyramid volume < 1e-13                 : 0
    faces with concavity >  80 degrees                     : 0
    faces with skewness >   4 (internal) or  20 (boundary) : 0
    faces with interpolation weights (0..1)  <  0.02       : 0
    faces with volume ratio of neighbour cells <  0.01     : 0
    faces with face twist <  0.02                          : 0
    faces on cells with determinant < 0.001                : 0
Detected 0 illegal faces (concave, zero area or negative cell pyramid volume)
Checked initial mesh in = 0.05 s


Smoothing patch points ...
Smoothing iteration 0
Found 0 non-mainfold point(s).

Scaling iteration 0
Moving mesh using diplacement scaling : min:1  max:1
Checking faces in error :
    non-orthogonality >  65 degrees                        : 0
    faces with face pyramid volume < 1e-13                 : 0
    faces with concavity >  80 degrees                     : 0
    faces with skewness >   4 (internal) or  20 (boundary) : 0
    faces with interpolation weights (0..1)  <  0.02       : 0
    faces with volume ratio of neighbour cells <  0.01     : 0
    faces with face twist <  0.02                          : 0
    faces on cells with determinant < 0.001                : 0
Successfully moved mesh

Smoothing iteration 1
Found 0 non-mainfold point(s).

Scaling iteration 0
Moving mesh using diplacement scaling : min:1  max:1
Checking faces in error :
    non-orthogonality >  65 degrees                        : 0
    faces with face pyramid volume < 1e-13                 : 0
    faces with concavity >  80 degrees                     : 0
    faces with skewness >   4 (internal) or  20 (boundary) : 0
    faces with interpolation weights (0..1)  <  0.02       : 0
    faces with volume ratio of neighbour cells <  0.01     : 0
    faces with face twist <  0.02                          : 0
    faces on cells with determinant < 0.001                : 0
Successfully moved mesh

Smoothing iteration 2
Found 0 non-mainfold point(s).

Scaling iteration 0
Moving mesh using diplacement scaling : min:1  max:1
Checking faces in error :
    non-orthogonality >  65 degrees                        : 0
    faces with face pyramid volume < 1e-13                 : 0
    faces with concavity >  80 degrees                     : 0
    faces with skewness >   4 (internal) or  20 (boundary) : 0
    faces with interpolation weights (0..1)  <  0.02       : 0
    faces with volume ratio of neighbour cells <  0.01     : 0
    faces with face twist <  0.02                          : 0
    faces on cells with determinant < 0.001                : 0
Successfully moved mesh

Patch points smoothed in = 0.23 s


Calculating patchDisplacement as distance to nearest surface point ...
Calculated surface displacement in = 0 s


Moving mesh ...

Iteration 0
Moving mesh using diplacement scaling : min:1  max:1
Checking faces in error :
    non-orthogonality >  65 degrees                        : 0
    faces with face pyramid volume < 1e-13                 : 0
    faces with concavity >  80 degrees                     : 0
    faces with skewness >   4 (internal) or  20 (boundary) : 0
    faces with interpolation weights (0..1)  <  0.02       : 0
    faces with volume ratio of neighbour cells <  0.01     : 0
    faces with face twist <  0.02                          : 0
    faces on cells with determinant < 0.001                : 0
Successfully moved mesh
Moved mesh in = 0.08 s


Repatching faces according to nearest surface ...
Repatched 0 faces in = 0 s


Edge intersection testing:
    Number of edges             : 4224
    Number of edges to retest   : 2532
    Number of intersected edges : 0
Snapped mesh : cells:1280  faces:4224  points:1701
Cells per refinement level:
    0	1280
Writing mesh to time 3
Written mesh in = 0.16 s.
Mesh snapped in = 0.52 s.

Shrinking and layer addition phase
----------------------------------

Using mesh parameters 
{
    maxNonOrtho     65;
    maxBoundarySkewness 20;
    maxInternalSkewness 4;
    maxConcave      80;
    minFlatness     0.5;
    minVol          1e-13;
    minArea         -1;
    minTwist        0.02;
    minDeterminant  0.001;
    minFaceWeight   0.02;
    minVolRatio     0.01;
    minTriangleTwist -1;
    nSmoothScale    4;
    errorReduction  0.75;
}



Merging all faces of a cell
---------------------------
    - which are on the same patch
    - which make an angle < 30 degrees
      (cos:0.866025)
    - as long as the resulting face doesn't become concave by more than 90 degrees
      (0=straight, 180=fully concave)

Merging 0 sets of faces.

No faces merged ...

Merging all points on surface that
- are used by only two boundary faces and
- make an angle with a cosine of more than 0.866025.

No straight edges simplified and no points removed ...

No layers to generate ...
Layer mesh : cells:1280  faces:4224  points:1701
Cells per refinement level:
    0	1280
Writing mesh to time 3
Written mesh in = 0.14 s.
Layers added in = 0.14 s.
Finished meshing in = 68.56 s.
End
Any help would be very much appreciated as I have a project due in tomorrow and have been trying to get this to work for the last few days.

Many thanks
Sean
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Old   March 23, 2011, 16:45
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I think the problem could be my .stl file.
After running surfacecheck on the file a number of illegal triangles have been highlighted.

The output says:

Code:
--> FOAM Warning : 
    From function validTri(const triSurface&, const label)
    in file surfaceCheck.C at line 95
    triangle 4003 vertices ((358781 358783 358785) 0) has the same vertices as triangle 1156530 vertices ((358785 358783 358781) 0) coords:3((485.578 56.0774 4250.1) (485.586 56.0746 4250.1) (485.592 56.0727 4250.1))
Surface has 1 illegal triangles.
Dumping conflicting face labels to "illegalFaces"
Paste this into the input for surfaceSubset
and

Code:
Surface is not closed since not all edges connected to two faces:
    connected to one face : 258
    connected to >2 faces : 1
Conflicting face labels:262
Dumping conflicting face labels to "problemFaces"
Paste this into the input for surfaceSubset
so...
I used the command:

Code:
surfaceSubset illegalFaces small.stl small2.stl
but this returned the error:
Code:
--> FOAM FATAL IO ERROR: 
keyword localPoints is undefined in dictionary "illegalFaces"

file: illegalFaces

    From function dictionary::lookupEntry(const word&, bool, bool) const
    in file db/dictionary/dictionary.C at line 395.

Help!! :/
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Old   March 27, 2011, 22:11
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I am still needing help, thank you.
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