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autoPatch error, mesh quality related...?

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Old   October 6, 2011, 17:57
Default autoPatch error, mesh quality related...?
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Alex
Join Date: Apr 2010
Posts: 32
Rep Power: 16
Alexvader is on a distinguished road
Hi

I have made a mesh with gmsh,
gmshToFoam reports this :

Code:
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  1.5-dev                               |
|   \\  /    A nd           | Revision: 1861                                  |
|    \\/     M anipulation  | Web:      http://www.OpenFOAM.org               |
\*---------------------------------------------------------------------------*/
Exec   : gmshToFoam test.msh
Date   : Oct 06 2011
Time   : 22:53:35
Host   : iskandhar
PID    : 20516
Case   : /home/alex/OpenFOAM/alex-1.5-dev/run/icoLagrangianFoam/GSNewTest
nProcs : 1

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

Found $MeshFormat tag; assuming version 2 file format.
Starting to read points at line 5
Vertices to be read:82487
Vertices read:82487

Starting to read cells at line 82495
Cells to be read:470722

Unhandled element 15 at line 82497
Unhandled element 15 at line 82498
Unhandled element 15 at line 82499
Unhandled element 15 at line 82500
Unhandled element 15 at line 82501
Unhandled element 15 at line 82502
Unhandled element 15 at line 82503
Unhandled element 15 at line 82504
Unhandled element 15 at line 82505
Unhandled element 15 at line 82506
Unhandled element 15 at line 82507
Unhandled element 15 at line 82508
Unhandled element 15 at line 82509
Unhandled element 15 at line 82510
Unhandled element 15 at line 82511
Unhandled element 15 at line 82512
Unhandled element 15 at line 82513
Unhandled element 15 at line 82514
Unhandled element 15 at line 82515
Unhandled element 15 at line 82516
Unhandled element 15 at line 82517
Unhandled element 15 at line 82518

---------------------------------------------------
Unhandled element 1 at line 83347
Unhandled element 1 at line 83348
Unhandled element 1 at line 83349
Unhandled element 1 at line 83350
Unhandled element 1 at line 83351
Unhandled element 1 at line 83352
Mapping region 0 to Foam patch 0
Mapping region 0 to Foam cellZone 0
Cells:
    total:427626
    hex  :0
    prism:0
    pyr  :0
    tet  :427626

CellZones:
Zone    Size
    0   427626

Skipping tag  at line 553220
Patch 0 gets name patch0

--> FOAM Warning : 
    From function polyMesh::polyMesh(... construct from shapes...)
    in file meshes/polyMesh/polyMeshFromShapeMesh.C at line 582
    Found 42240 undefined faces in mesh; adding to default patch.
Finding faces of patch 0

FaceZones:
Zone    Size

Writing zone 0 to cellZone cellZone_0 and cellSet
End
the checkMesh report is as follows :

Code:
alex@iskandhar:~/OpenFOAM/alex-1.5-dev/run/icoLagrangianFoam/GSNewTest$ checkMesh
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  1.5-dev                               |
|   \\  /    A nd           | Revision: 1861                                  |
|    \\/     M anipulation  | Web:      http://www.OpenFOAM.org               |
\*---------------------------------------------------------------------------*/
Exec   : checkMesh
Date   : Oct 06 2011
Time   : 22:46:33
Host   : iskandhar
PID    : 19949
Case   : /home/alex/OpenFOAM/alex-1.5-dev/run/icoLagrangianFoam/GSNewTest
nProcs : 1

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

Create polyMesh for time = constant

Time = constant

Mesh stats
    points:           82487
    faces:            876372
    internal faces:   834132
    cells:            427626
    boundary patches: 2
    point zones:      0
    face zones:       0
    cell zones:       1

Number of cells of each type: 
    hexahedra:     0
    prisms:        0
    wedges:        0
    pyramids:      0
    tet wedges:    0
    tetrahedra:    427626
    polyhedra:     0

Checking topology...
    Boundary definition OK.
    Point usage OK.
    Upper triangular ordering OK.
    Face vertices OK.
    Number of regions: 1 (OK).

Checking patch topology for multiply connected surfaces ...
    Patch               Faces    Points   Surface topology                  
    patch0              42240    21122    ok (closed singly connected)      
    defaultFaces        0        0        ok (empty)                        

Checking geometry...
    This is a 3-D mesh
    Overall domain bounding box (-0.05 -0.05 -0.05) (0.33 0.08 0.05)
    Mesh (non-empty) directions (1 1 1)
    Mesh (non-empty, non-wedge) dimensions 3
 ***Boundary openness (-1.57384e-17 -8.99149e-06 -5.84373e-05) Threshold = 1e-06 possible hole in boundary description.
 ***Open cells found, max cell openness: 1, number of open cells 10 Threshold = 1e-06
  <<Writing 10 non closed cells to set nonClosedCells
  <<Writing 2 cells with high aspect ratio to set highAspectRatioCells
    Minumum face area = 6.1923e-08. Maximum face area = 2.40286e-05.  Face area magnitudes OK.
    Min volume = 6.78547e-25. Max volume = 2.93558e-08.  Total volume = 0.0024085.  Cell volumes OK.
    Mesh non-orthogonality Max: 154.128 average: 23.0245 Threshold = 70
   *Number of severely non-orthogonal faces: 4.
 ***Number of non-orthogonality errors: 10.
  <<Writing 14 non-orthogonal faces to set nonOrthoFaces
 ***Error in face pyramids: 16 faces are incorrectly oriented.
  <<Writing 14 faces with incorrect orientation to set wrongOrientedFaces
 ***Max skewness = 213.4, 4 highly skew faces detected which may impair the quality of the results Threshold = 4
  <<Writing 4 skew faces to set skewFaces

Failed 5 mesh checks.

End
the autoPatch reports this, failing :

Code:
alex@iskandhar:~/OpenFOAM/alex-1.5-dev/run/icoLagrangianFoam/GSNewTest$ autoPatch 14
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  1.5-dev                               |
|   \\  /    A nd           | Revision: 1861                                  |
|    \\/     M anipulation  | Web:      http://www.OpenFOAM.org               |
\*---------------------------------------------------------------------------*/
Exec   : autoPatch 14
Date   : Oct 06 2011
Time   : 22:51:21
Host   : iskandhar
PID    : 20359
Case   : /home/alex/OpenFOAM/alex-1.5-dev/run/icoLagrangianFoam/GSNewTest
nProcs : 1

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

Create polyMesh for time = 0

Mesh read in = 1.59 s


Feature:14
minCos :0.970296

Assigned 32400 faces to patch auto0

Assigned 28 faces to patch auto1

Assigned 287 faces to patch auto2

Assigned 112 faces to patch auto3

Assigned 1168 faces to patch auto4

Assigned 768 faces to patch auto5

Assigned 2632 faces to patch auto6

Assigned 287 faces to patch auto7

Assigned 28 faces to patch auto8

Assigned 288 faces to patch auto9

Assigned 287 faces to patch auto10

Assigned 2664 faces to patch auto11

Assigned 287 faces to patch auto12

Assigned 104 faces to patch auto13

Assigned 104 faces to patch auto14

Assigned 112 faces to patch auto15

Assigned 28 faces to patch auto16

Assigned 288 faces to patch auto17

Assigned 28 faces to patch auto18

Assigned 1 faces to patch auto19

Assigned 28 faces to patch auto20

Assigned 28 faces to patch auto21

Assigned 28 faces to patch auto22

Assigned 28 faces to patch auto23

Assigned 28 faces to patch auto24

Assigned 28 faces to patch auto25

Assigned 28 faces to patch auto26

Assigned 112 faces to patch auto27

Assigned 1 faces to patch auto28

Assigned 28 faces to patch auto29

Assigned 1 faces to patch auto30

Assigned 1 faces to patch auto31

--> FOAM Warning : 
    From function SolverInfo::SolverInfo(const dictionary& dict,const objectRegistry &obr)
    in file SolverInfo/SolverInfo.C at line 61
    Can't find phi-field with name phi
Assumin incompressible solver


Attempt to cast type polyMesh to type fvMesh

    From function refCast<To>(From&)
    in file /home/alex/OpenFOAM/OpenFOAM-1.5-dev/src/OpenFOAM/lnInclude/typeInfo.H at line 106.

FOAM aborting

Aborted
alex@iskandhar:~/OpenFOAM/alex-1.5-dev/run/icoLagrangianFoam/GSNewTest$

Are these errors related...?

Are there any tools in OF allowing me to heal this mesh...?

BTW what is the best OSS mesher to OF, is it gmsh or Netgen...?

My mesh was built out of a *step file created by a commercial cad package...

BRGDS

Alex
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