*--* ex_intersect_surface_make_hole
*--* Header Begin
*--* LAGriT Example Input file
* Carl Gable
* gable -at- lanl -dot- gov
*
*
*--* Intersect a triangulated surface mesh with another triangulation
*--* Compute the intersection points
*--* Add the intersection points to the surface mesh
*--* Re-triangulate the surface mesh
*--* Assign material ID's to triangles have distinct material boundary information.
*--* Smooth and refine the mesh
*--*
*--* Calls:
*--* lagrit.input_build_shell
*--* lagrit.input_smash_shell
*--* lagrit.input_build_quads
*--* lagrit.input_refine_smooth
*--*
*--* Geometry definition in:
*--* lagrit.input_geom
*--*----------------------------------------------------
*--* Header End
*--* ex_intersect_surface_make_hole
*--*
*
* Create a spherical shell of triangles
*
* Build a tet sphere mesh and extract the exterior as a triangle mesh
*
infile lagrit.input_build_shell
dump / gmv / sphere_tri.gmv / cmo_tri
*
* Change the shape of the sphere
*
infile lagrit.input_smash_shell
dump / gmv / sphere_tri_invert.gmv / cmo_tri
*
* Build the quad surface for computing intersection with sphere
*
infile lagrit.input_build_quads
*
intersect / cmo_line / cmo_surf / cmo_tri
*
dump / gmv / intersect_line.gmv / cmo_line
*
define/NX/ 26 
define/NY/ 26 
*
* Create the quad surfaces
*
cmo/create/cmo_2///tri
cmo/setatt/cmo_2/ndimensions_geom/1 0 0/2
*
surface / s_cres / reflect /  sheet / cmo_tri
region / rin / le s_cres
region / rout / gt s_cres
mregion / mrin / le s_cres
mregion / mrout / gt s_cres
*
cmo / create / cmo_quad_pts / / / quad
quadxy NX NY/MIN MIN 0./MAX MIN 0./MAX MAX 0./MIN MAX 0.
*
cmo / create / cmo_quad_pts2 / / / quad
*
* Add in some points so the smooth/recon has more nodes
* to work with.
*
quadxy 10 10 /-1.95 -0.1 0.0 / -1.89 -0.1 0.0 &
             /-1.89  0.1 0.0 / -1.95  0.1 0.0
*
* Copy the points into a single MO
*
copypts / cmo_2 / cmo_line
copypts / cmo_2 / cmo_quad_pts
copypts / cmo_2 / cmo_quad_pts2
*
cmo / delete / cmo_line
cmo / delete / cmo_quad_pts
cmo / delete / cmo_quad_pts2
*
cmo / select / cmo_2
*
cmo/setatt/cmo_2/imt/1 0 0/1
cmo/setatt/cmo_2/itp/1 0 0/0
cmo/setatt/cmo_2/icr/1 0 0/0
*
* Triangulate the points
*
setpts
setsize
connect/delaunay
*
* Set the material ID of the triangles
settets / geometry
*
* Output the triangulation
*
dump / gmv / surf_with_pts.gmv / cmo_2
*
* Smooth the mesh
*
cmo / select / cmo_2
cmo / copy / cmo_2_save / cmo_2
cmo / select / cmo_2
*
* Run 10 iterations of smoothing
*
loop / do / NL 1 10 1 / loop_end &
      infile lagrit.input_refine_smooth
*
dump / gmv / smooth.gmv / cmo_2

finish