Takes into account commit 65fe407b in Xfiles

Corresponding to commit 362685b2ca in Xfiles.

Corresponding to commit 362685b2 in Xfiles

Takes into account commit 32fbe17bd67dd1fb33932f4bba9ced5db1ebe618 in Xfiles.

Corrected parenthesis bug in exportOnSpace function, in the version which is
used to export xTensor2.

Remark : It was quite surprising that the code could even
compile before ...

May be useful if exporting a certain quantity requires some computations, but
we want to do these computations only in the case where this quantity is
supposed to be exported.

Added typedef, class member, modified initAssembler, setAssemblerCoeff and added
getAssemblerTranspose accordingly.

README file is prefered to NOTICE.

TLSDuctile is under GNU GPL license.

Updates the CMakeLists.txt to take into account the new_cmake modifications and the REQUIRED option in the find_package()

Revert "Splitted updateMaterialVariables into two functions: updateMaterialVariablesFromLevelSet can be used to deal with any internal variable which depends on the level set (not only the damage variable), updateMaterialVariables must then be used to update the other material variables (like eps_ref for instance)"

This reverts commit 857b3d0c.

Splitted updateMaterialVariables into two functions: updateMaterialVariablesFromLevelSet can be used to deal with any internal variable which depends on the level set (not only the damage variable), updateMaterialVariables must then be used to update the other material variables (like eps_ref for instance)

dam_pull_out
============
Adapting to para version

FastMarchingInterface,TLSGeom,TLSSolver
=======================================
Modify groups (sm, sub mesh) to enter FM with known fixed and volatile
values. This is following new FM interface. It correct bug with previous
interface where progression of the front was stopped by re-initialisation
process (all new variation of phi removed by fast marching).
Now buildBndIntNonlocal (TLSGEOM) is creating 2 set (bnd_part_nonlocal
and bnd_nonlocal) in replacement of the original bnd_nonlocal. Those
sets split boundary of non local zone in :
* boundary with local mesh element (bnd_nonlocal)
* boundary with part boundary (bnd_part_nonlocal)
Has before it is do_bnd_in that control if we create bnd_part_nonlocal or
not by calling GetBoundary or GetInteriorBoundary.
In GetBoundary a dirty hack is used to identify part boundary and remove
Gama_c.
When do_bnd_in is 0 bnd_part_nonlocal exist but is empty.

For FM, bnd_part_nonlocal is used has known volatile value. Says those
part boundary value may or may not be re-initialized by FM. In the
latter case those values are used for velocity computation as new extra
modes with their values unmodified. This imply that on part
boundary the level set live its own life when phi gradient enter the
part.

Unfortunately as can be seen, for now, in new dam_gamain test, setting
bnd_part_nonlocal as volatile values may stop progression of the front
just like before when all modified values are reset by FM.

N. Chevaugeon suggested to create only volatile values for non modified
values (values not updated during current time step). This look like a
promising solution because removing these values from bnd_part_nonlocal
and put them in bnd_nonlocal force them to be still present in velocity
computation. It ensure that variation of phi is not destroyed. But it
does not insure anymore that phi gradient norm is 1 around those values.
This somehow must be the case when gradient direction start to be collinear
to part boundary. In that case epsilon_ratio was supposed to do the job
but for rather blunt variation of phi it is not clear if this will fits
ours needs. So filtering like that bnd_part_nonlocal seems interesting.
TODO

About epsilon_ratio it have been forced to zero because really strange
result where obtain with it (non same result in case where
bnd_part_nonlocal is empty, non deterministic computation !???).
To be analyzed.

dam_gamain
==========
This test case is to check if and how gamin feature works.
It is a simple plate with a shear loading that force creation of crack
with an angle of -45 degres (x axes). A default( removing of 2 elements)
is placed in the diagonal of the plate a little closer to left upper
corner. Mesh is regular and chosen to intentionally offers a line of
nodes from default to corner. lc is chosen rather big so that number of
element per lc is important.

Without gamin non-local zone progress toward corner. When reaching
part boundary modification of phi on it are clearly done by FM re-init only.
It arrive to a point where bluntly in on step all corner is extra damaged (phi>lc).
With gamain when reaching part boundary modification comes clearly from
phi update in far more slower way. Crack continue on the diagonal.
Unfortunately process is stopped by the case of delta-phi removed by FM.
(see above for perspectives)

In both case it is not clear how boundary condition have to be handle in
omega+ zone. Without treatment like here it impose force on almost
damaged material which induce maybe other estimate strain. To be check.

Conflicts:
	CMakeLists.txt

Add small changes related to outputs (damage_peak, peak_step) and implement primitve for exponential hardening function

Conflicts:
	src/TLSSolver.cc
        resolved : just two header set on the same line

* clean up unused feature.

it affects:
  - Export.cc
  - Import.cc

* improvement of transfer of displacement field after remeshing

it affects:
  - Formulation.cc

* correct a small bug that happens sometimes in restart, "mean" vectors
had wrong size after restart. It was always too long and filled with NaN.

it affects:
  - FormulationQS.cc

* had several "guards" that end computation and give an error message when
something goes wrong.

it affects:
  - TLSSolver.cc
  - FormulationQS.cc

* correct an error in the getGrad function of CohesiveLinearHardeningFunction

it affects:
  - MaterialFunction.cc

* swap orientation in comp mesh generation. It seems that it is test case dependent.
TO BE INVESTIGATED if your comp_mesh has two colours when plotting in GMSH.

it affects:
  - MeshGeneration.h

* correct a bug resulting from \Gamma_in recent commit. FastMarchingModeExtension
was updating phi based on \Gamma_in. The obtained phi was not anymore corresponding
to the iso-lc discretisation, it leads to damage equal to 1 inside the mechanical domain.
It leads to singular stiffness matrix.

it affects:
  - TLSSolver.cc

* add an epsilon_ratio (between 0 and 1) in order to control the fmeik internal epsilon involved when comparing
scalar values (a < b + epsilon is now a <b + epsilon_ratio*"edge length")

it affects:
  - FastMarchingInterface.h
  - TLSSolver.{h,cc}
  - FormulationQSRemeshAniso.{h,cc}

* modify anticipated end of program: now lambda doesn't have to belong to [0, 1].

it affects:
  - FormulationQS.cc

* change dissipated energy calculation. It is based on the primitive of function h(d).

it affects:
  - FormulationQS.cc
  - MaterialElasticDamage.cc
  - MaterialFunction.{h,cc}

* compute nonlocal part bounding box

it affects:
  - TLSGeom.{h,cc}
  - TLSSolver.cc

* minor simplification when transfering phi field, now only "int_duplicated" region is used.

it affects:
  - MeshGeneration.{h,cc}
  - TLSGeom.cc
  - Formulation.cc
  - TLSSolver.cc

* bug correction when transfer boundary and interior "in" after remeshing.

it affects:
  - TLSGeom.cc

* bug correction in correctLevelSetField: add a forgotten absolute value.

it affects:
  - TLSSolver.cc

* place guards with error message to help user detect bugs

it affects:
  - FormulationQS.cc
  - TLSSolver.cc

Modification, mainly buf_nodal_vec passed into a xDistVector and declare
state in parallel are removed. This version have minimal change to work
in // context with only one proc. Many comment are present to explain
what have to be changed to work in distributed context. The previous
commit have been tagged (WITHMODIF) to be able to get back to it when we
will try to pass in distributed context.
Many guard are present. They will be efficient to avoid mistake. Many
other guard with comment are missing but this work will be done only if
we pass in distributed context.