Creating a geometry file:

There are two ways to create a geometry file.  One is to compute the
geometry from an existing vog file, and the other is to compute it
from a solidMesh surf file (along with exact surface normals).

To compute an approximate geometry from an existing vog file use the
computegeom command executed as follows:

For example, if you have a grid file called sphere.vog then you can get the
geometry created in a file called "sphere.geom" by executing:

computegeom -o sphere.geom sphere

The computegeom utilitity uses heuristics to detect creases in the geometry
where the surface normals are allowed to abruptly change.  The threshold used 
for the detection of creases can be set with the -theta_r (ridge theta) option.
The default is 15 degrees, but for a low quality coarse surface mesh, this may
need to be set to a much larger value (about 40-50).  For a good quality surface
mesh with subtle ridges, a lower value might be helpful.  It is helpful to 
remove the rebuild surfaces that have high aspect ratios (or other non-viscous
surfaces such as farfield).  These surfaces can be removed from the
reconstruction using the -ignore_bc option.  The -geom_output can be used to
output a doubly refined surface mesh that can be used to visualize the
reconstructed geometry using solidmesh.

alternatively you can get a the geometry from exact normals by using
the command getgeom.  For example if you have the files sphere.surf
(surface mesh) and sphere.surfn (surface normals) then you can get the
geometry file "sphere.geom" by executing the command:

getgeom sphere


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Tools for adapting to a curved geometry:

To adapt a viscous grid you will need to adjust your grid file so that
points near the viscous boundary are tagged consistently.  The tool
viscousFix performs this step.  In this operation you mark the all
points that are within a specified delta of the viscous boundary if
any are marked within this delta.  The tool is given the viscous
boundary condition(s), the specified delta, the input tag file, the
output tag file and the case name.  Note, this code will read the
topology file written to the output directory and so assumes that chem
was run in the same directory.  An example that corrects a tag file
"refine.dat" to with a surface delta of .05 meters from the viscous
boundary "orb" and outputs to the file "vrefine.dat" is given below:
                                                                     v(iter)
viscousFix -bc orb -delta 0.05 -tag refine.dat -o vrefine.dat sphere 0
                                                              ^casename

Once the grid is adapted, then we can deform to the curved boundary
with the command adjustpos.  For example if we are have a linear
refined mesh given by "sphere2l.vog", we can generate the curvature
adjusted mesh called "sphere2.vog" where the geometry was defined in
"sphere.geom" using the command:

adjustpos -i sphere2l.vog -o sphere2.vog -g sphere.geom 

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Note, all of the commands will give you a help screen if run with no
arguments.

