This python script is written to convert OpenFOAM mesh to nek5000 element mesh.
For information about OpenFOAM, please visit http://www.openfoam.com/
For information about nek5000, please visit http://press3.mcs.anl.gov/nek5000/
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Notes:
Mesh in OpenFOAM is conventional CFD mesh. Operation is performed on each cell. 
However, in nek5000, each cell is actually an element. And in each element, nek5000 
will distribute chebyshev polynomials to solve N-S equations. As a result, the element 
in nek5000 is contains hundreds of cells in conventional CFD definition. 

Nek5000 only accept hex element. As a result, the cell in OpenFOAM must also be hex cell.
However, for each hex cell, OpenFOAM only has the information on 8 vertices. That is to say,
in OpenFOAM, hex cell in is the format of hex8. 
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Author: Haomin Yuan, 
Post doctoral at Argonne National Laboratory, Nuclear Engineering Division.
[email protected]

Start: 10/30/2015
End: 12/2/2015
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Files:

foamToNek.py			: main function, setting openfoam case and nek case path.
geoElement.py			: difinition of geometry element like points,faces,cells, etc.
arrayConstructor.py		: read openfoam mesh and construct arrays for geometry elements.
reaWriter.py			: write element information into .rea file. 

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OpenFOAM mesh structure:
All mesh information is stored in five files in OpenFOAM:
1. points, it contains all vertices location for each cell
2. faces, it contains the index number of vertices for each face
3. owners, faceID point to face owner cell id
4. neighbour, faceID point to face neighbour cell id
5. boundary, it tells the start face number and number of faces for each boundary patch.

For more information about mesh structure in OpenFOAM.
Please refer to OpenFOAM user guide, or <The OpenFOAM Technology Primer>
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Usage:
To properly use this cript, there are several steps:

1. After your OpenFOAM mesh is contructed, change the boundary condition settings in boundary file,
which you could find in YOUR_OPENFOAM_CASE/constant/polyMesh/boundary

here is a example of unchanged bounadry file 
 
 wall
    {
        type            wall;
        nFaces          2400;
        startFace       88300;
    }
    inlet
    {
        type            patch;
        nFaces          500;
        startFace       90700;
    }
    outlet
    {
        type            patch;
        nFaces          500;
        startFace       91200;
    }

Because foamToNek will read the boundary condition type in this file. Please change the boundary file to:

  wall
    {
        type            W;
        nFaces          2400;
        startFace       88300;
    }
    inlet
    {
        type            v;
        nFaces          500;
        startFace       90700;
    }
    outlet
    {
        type            O;
        nFaces          500;
        startFace       91200;
    }

the 'W','v','O' are the keywords that accept by nek5000 for boundary setting. 
For more options abour boundary conditions, please refer to nek5000 manual. 

2. in foamToNek.py there are several string variables should be changed.
change:
polymesh = 'YOUR_OPENFOAM_CASE/constant/polyMesh/'
nekCase = 'YOUR_NEK_CASE'
reaFile = nekCase + 'YOUR_ORG_REA'
newReaFile = nekCase + 'NEW_REA'

3. excute python script by
python foamToNek.py

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Test cases:
There are two cases have been tested using the mesh converted from openfoam.
3dbox and pipe.
folder foamBox and foamPipe contains the openfoam mesh for box and pipe. 

new* files in 3dbox and pipe folder are mesh converted from openFOAM.
genmap is ok.
And running nek case is ok. 

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Limitations:
1. Only hex8 element could be constructed. This means if geometry curvature is siginificant,
the conversion may not good. 
2. If the total cell number in OpenFOAM is too large, it will takes a long time for python to 
read through all files. For exampole, for 30,000 cells, the conversion takes 10 mins. 
3. No thermal boundary condition is considered now, but could be implemented by request.