Initial commit for milan permuation stuff.
Just copied poisson_3d files over. Going to modify it to use tetgen
files now.
After making the tetgen cube semi working. Now I am going to make it
fully working within a driver code.
Initial commit of documentation for tetgen with oomphlib
Done the tetgen documentation and generated the mesh.
About to determine which mesh I want to use to do the experiments.
The meshes are tar'd up. I have to remember to untar the correct one.

Changes to be committed:
modified:   doc/tetgen_config.tex
new file:   tetgen_files_unit_cube/cube.poly
new file:   tetgen_files_unit_cube/cube_1_16.tar.gz
new file:   tetgen_files_unit_cube/gen_mesh.sh
Done more work on the poly file.
About to see why the cube_poly_bk file does not work.
the cube_poly file now works.
Added some stuff for permutation code. Testing it out on
optimized version to see if it's any faster
Small edit to format results files:

modified:   lagrange_square/test_f_calibration/format_results.sh
modified:   lagrange_square/test_f_calibration/format_results_Euclud.sh
Got the first part working in parallel, only need
to do milan's permutation

Changes to be committed:
modified:   .gitignore
modified:   poisson_3d_no_bpf.cc
modified:   run_trial.sh
modified:   tetgen_files_unit_cube/cube.poly
modified:   tetgen_files_unit_cube/gen_mesh.sh

Detailed info:

modified:   .gitignore
Added tetgen extensions, we now ignore the following
(because they are huge!):
*.edge
*.ele
*.face
*.node
But care must be taken, since different versions of Tetgen
generates different files... hmmm!!!!

Also added these for the latex output files:
doc/testshell.tex
doc/tetgen_config.aux
doc/tetgen_config.bbl
doc/tetgen_config.bcf
doc/tetgen_config.blg
doc/tetgen_config.dvi
doc/tetgen_config.fdb_latexmk
doc/tetgen_config.fls
doc/tetgen_config.log
doc/tetgen_config.nlo
doc/tetgen_config.out
doc/tetgen_config.pdf
doc/tetgen_config.ps
doc/tetgen_config.run.xml
doc/tetgen_config.synctex.gz(busy)

=====================================================================

modified:   poisson_3d_no_bpf.cc
1) When assigning the homogenous bcs, added code to output
the positions of each node, this is for testing purposes.
The code has been commented out. Will delete later!

2) Change the solver and tolerance!
2.1) GMRES to CG
2.2) 1e-8 to 1e-6 for both Newton tolerance and Solver tolerance.
Code is here (in diff format):

< trilinos_solver_pt->solver_type() = TrilinosAztecOOSolver::GMRES;
---
> trilinos_solver_pt->solver_type() = TrilinosAztecOOSolver::CG;

< Solver_pt->tolerance() = 1e-8;
---
> Solver_pt->tolerance() = 1e-6;

< this->newton_solver_tolerance() = 1e-8;
---
> this->newton_solver_tolerance() = 1e-6;

=====================================================================

3) modified:   run_trial.sh
Changed:
3.1) Cycle: 1V(2,2) to 1V(1,1)
3.2) Smoother: GS to Jacobi with damping 0.8
3.3) Strength: 0.7 to 0.25
3.4) Coarsening: Ruge Stuben to Falgout

Note: I think 3.3 is the main change which lowered
iteration counts so it is not dependent of the mesh size h.

Code is here (in diff format):

= AMG_ITER="--amg_iter 1"
< AMG_SMITER="--amg_smiter 2"
< AMG_SIM_SMOO="--amg_sim_smoo 1"
< AMG_STRN="--amg_strn 0.7"
< AMG_COARSE="--amg_coarse 1"
< AMG_PARAM="$AMG_ITER $AMG_SMITER $AMG_SIM_SMOO $AMG_STRN $AMG_COARSE"
---
= AMG_ITER="--amg_iter 1"
> AMG_SMITER="--amg_smiter 1"
> AMG_SIM_SMOO="--amg_sim_smoo 0" # 0 - jacobi, 1 - GS
+ AMG_DAMP="--amg_damp 0.8"
> AMG_STRN="--amg_strn 0.25"
> AMG_COARSE="--amg_coarse 6" # 1 - RS. 6 - Falgout
> AMG_PARAM="$AMG_ITER $AMG_SMITER $AMG_SIM_SMOO $AMG_STRN $AMG_COARSE
> $AMG_DAMP"

=====================================================================

4) modified:   tetgen_files_unit_cube/cube.poly
Changed boundary marker for nodes to 0. Setting it to 1 seems
to produce a .node file where the nodes at the corners are wrong.
I need to investigate why!

Code is here (in diff format):

< 1 0 0 0 1
< 2 1 0 0 1
< 3 1 0 1 1
< 4 0 0 1 1
< 5 0 1 1 1
< 6 0 1 0 1
< 7 1 1 0 1
< 8 1 1 1 1
---
> 1 0 0 0 0
> 2 1 0 0 0
> 3 1 0 1 0
> 4 0 0 1 0
> 5 0 1 1 0
> 6 0 1 0 0
> 7 1 1 0 0
> 8 1 1 1 0

=====================================================================

5) modified:   tetgen_files_unit_cube/gen_mesh.sh

Using the old Tetgen (Version 1.4.2 (April 16, 2007) on the wulfling)
the -r flag cannot be used with -p (when refinining the grid).
So I just removed them.

Code is here (in diff format):

= tetgen -pqa0.005 cube.poly
< tetgen -rpqa0.0025 cube.1
< tetgen -rpqa0.00125 cube.2
< tetgen -rpqa0.000625 cube.3
< tetgen -rpqa0.0003125 cube.4
< tetgen -rpqa0.00015625 cube.5
< tetgen -rpqa0.000078125 cube.6
< tetgen -rpqa0.0000390625 cube.7
< tetgen -rpqa0.00001953125 cube.8
< tetgen -rpqa0.000009765625 cube.9
< tetgen -rpqa0.0000048828125 cube.10
< tetgen -rpqa0.00000244140625 cube.11
< tetgen -rpqa0.000001220703125 cube.12
< tetgen -rpqa0.0000006103515625 cube.13
< tetgen -rpqa0.00000030517578125 cube.14
< tetgen -rpqa0.000000152587890625 cube.15
< #tetgen -rpqa0.0000000762939453125 cube.16
---
= tetgen -pqa0.005 cube.poly
> tetgen -rqa0.0025 cube.1
> tetgen -rqa0.00125 cube.2
> tetgen -rqa0.000625 cube.3
> tetgen -rqa0.0003125 cube.4
> tetgen -rqa0.00015625 cube.5
> tetgen -rqa0.000078125 cube.6
> tetgen -rqa0.0000390625 cube.7
> tetgen -rqa0.00001953125 cube.8
> tetgen -rqa0.000009765625 cube.9
> tetgen -rqa0.0000048828125 cube.10
> tetgen -rqa0.00000244140625 cube.11
> tetgen -rqa0.000001220703125 cube.12
> tetgen -rqa0.0000006103515625 cube.13
> tetgen -rqa0.00000030517578125 cube.14
> tetgen -rqa0.000000152587890625 cube.15
> tetgen -rqa0.0000000762939453125 cube.16
Deleted cube_hole.poly
Removing milan_permutation/tetgen_files from git history
edited .gitignore, removed the lines to do with tetgen, I am
going to remove the whole folder