Update sources for new user version

1197b55 Merge branch 'dev' into 'master'
d954d3b Merge branch 'planx_inertia_fix' into 'dev'
cf7ccd7 fix inertia computaiton of planx in pre_lmgc
7c7b117 fix inertia matrix computation of PLANx
8a3cfa5 Merge branch 'PutBodyVector' into 'dev'
5ea882f Merge branch 'fix_SPSP' into 'dev'
fcf23a1 correction bug calcul Vbegin
886cdc6 modif des xxxxMAILx_put_vector
2827d26 Merge branch 'siconos' into 'dev'
99ab331 attempt to fix bug when quadrature of CSxxx not 0
a810416 set C_FLAGS of SiconosNumerics compilation through LMGC90
4422cb7 fix compilation error
988adae Merge branch 'logmes' into 'dev'
66f087a WARNING log messages always displayed
23af95c adding internal timer for nlgs_3d ExSolver function
d2ed071 switch some print to logmes and possibility to force message even if disabled
34ba5fd Merge branch 'nlgs_log' into 'dev'
bb08e85 Ajout d'un log dans ExSolver
46c9a09 Merge branch 'get_coor_POLYR_fix' into 'dev'
19aae6d fix get_coor_POLYR function call
01b04b3 Merge branch 'loi_preGAP_SGR_CLB' into 'dev'
9a2459e pta: reactivation loi preGAP_SGR_CLB
a086ba9 pta: correction pour merge
d9558f0 pta: reactivation de la loi preGAP_SGR_CLB dans le Core et le pre
94b51e4 Merge branch 'ExternalFEM' into 'dev'
1b053d6 Merge branch 'fix_gfortran44' into 'dev'
70bcd67 Merge branch 'mpi_without_mumps' into 'dev'
dae179c Merge branch 'ddm_fix' into 'dev'
5e1d76b Ajout de la fonction externalFEM_get_V dans Std_ExternalFEM.f90
4a4ef62 Modification de la syntaxe ExternalFEM_ComputeV. La boucle n'est plus faite dans LMGC90. Ceci corrige un bug pour les calculs periodiques
89b7955 Ajout d'un patch pour compilation avec GCC 4.4
dfe2a2b Autorise une compilation AVEC mpi mais SANS mumps
5556f20 Correction : ne marchait pas lorsque la fonction est lancée dans un thread mpirun
2b36d5e Merge branch 'perales_fix' into 'dev'
8422774 Ugly fix of seg fault when calling clean_memory and skipping He build
79a1cc9 add F. Perales fix according to change of library name in Xper
9f8363c Merge branch 'fix' into 'dev'
6043aca update warning/error messages when trying to import/use optional modules
4159a85 fix seg fault when using mecaMAILx_GpvVTKDrawAll when no mecaMAILx present
8c8bf84 Add wrap of reverse contact order for nlgs_3D
9043d15 fix README
53ae1fb Merge branch 'reload' into 'dev'
e1030dc When restarting a computation, get starting file increment
5327a89 possibility to read VlocRloc file of OUTBOX directory
e29245e possibility to read GPV file of OUTBOX directory
d273f69 possibility to read DOF file of OUTBOX for all body type
37a497a add a parameter to RBDY2_ReadIniDof routine to read output file
ca4ddcb Merge branch 'fix_RTA_laws' into 'dev'
321e8c1 correction bug 2
853b79c correction bug
39508df  prise en compte _nosldt
140fba9 one more modif
c7d3ecd one more modif
7168730 des modifs pour la loi gap_sgr_clb_g0 et les lois _nosldt et _noslds
0213711 Merge branch 'fix_bars' into 'dev'
3f42c22 correction in extrusion of group function and management of Q4 element
25ae2ad update coordinates of nodes in Track class of gmshutils
1d54535 no critical bug when using GpvVTKDrawAll with bar elements
51fa425 activate only linear prisme in SHB
c3826c4 use a list of points in Track class of gmshutils
9850972 fix in mesh tracking
229bea4 add point tracking in a mesh using gmshpy
6f1e8fd update comments in compute_center function of a_EF module
b9d279f fix from bad merge
1fb16c8 Update SHB module
fb9008b remove ugly spaces
40890c0 adding gmshutils module in pylmgc90 package allowing to read inp file, write geo file and generate msh file from geo one
982c678 in mesh class, possibility to extruded a physical entity
870a065 add BARxx to possible 2D elements
65eefb2 visu axial stress/strain
4bc2f6e modif bar element ; add BARxx to pre ; modify name of function for ByElement fields
3f2381f passage mecaEF_iso en private, reactivation mecaEF_bar
db1ad43 Merge branch 'new_IQS_Stick' into 'dev'
16ce851 modifs pour loi xxx_STICK
6abf4d3 Merge branch 'inter_accessor' into 'dev'
11ac90a adding access to antagonist and candidat contactor index of an interaction
bafed69 fix swig file dependency to .h files
a2817cf Merge branch 'api' into 'dev'
5636726 add function to get number and color of contactors of a RBDY2
b2588a4 add dependency of overall to externalMBS module
75961da Merge branch 'fix_mbs_name' into 'dev'
b695ead fix lowercase name of wrap_mbs.h file in chipy.i.in
3509f90 Merge branch 'fix' into 'dev'
76b5433 buildMeshedAvatar function of pre_lmgc now to deepcopy of bulks and nodes objects
2abdc5b fix map use in therMAILx and poroMAILx too
3d389b2 fix bug when number of mecaMAILx and therMAILx are different
448f384 Merge branch 'mbs' into 'dev'
ce7a262 modify some comments
2951df1 fix strange bug when printing result of a function
8d904e8 link with FiberModel external MBS library
34d3679 fix case dependent name for compile and improve display function of mbs
ed4ab9c adding Nicolas Docquier's fix to use external mbs library
8ade4bf correction in call of get_inertia_frame_POLYR and cluster of PLANx in PRPL detection
e992417 adding third index to all tact2bdyty map to store on what type of body a contactor is tied to
bf790b5 draft of cmake link with robotran external mbs library
947a306 cmake file to look for external mbs library (empty)
0cf6615 prepare compiling with external mbs library
fe3177c diverses modfis pour prendre en compte le mbs
983e63c qq modif de fd liees au mbs
50286ce correct loading of interaction with mbs in nlgs_3D... no resolution yet
ddbae90 attempt to create MBS with POLYR contactors
f2d87ae genesis of a Multi Body System handler module
f7088e6 Merge branch 'these_riviere' into 'dev'
905488e ajout modif these jriviere
7f399cc Merge branch 'bug_fix' into 'dev'
b5aabfc fix therMAILx get_all function when used with mecaMAILx
211e38a fix bug when reading DOF.INI with more therMAILx than mecaMAILx
16bdd00 Merge branch 'rev_2015.3' into 'dev'
75dbab3 ugly trick to check metis version when compiling MUMPS-5.0.0
b61ff53 simple attempt to automatically set min and max time step when setting time step
e6a2d35 put numpy include dir flag befor Python's one
728c061 check cython version before compiling rTree python binding
273a8d2 Possibility to desactivate use of Python Framework use in CMake
5fa6f98 minor bug fix
6877226 fix error in orthotropic frame computation
3fab071 Maj to vtk field
2663812 remove obsolete buildMeshedAvatar method from mesh class
9ed5f0b fix typo in material of Pre sphinx doc
afc3e1b fix external fields (scalar/vector) in Pre sphinx doc
c5369e8 Merge branch 'fix_display' into 'dev'
b625851 un peu plus de commentaires
165e0bd fix de la visu des champs grad/flux en meca avec les modele builin
ae6c187 Merge branch 'dev' into 'master'

git-subtree-dir: src
git-subtree-split: 1197b55e6c0d6420fd7dd639f44604d44919f2c6

Getting last examples

a3e112b small fix in Taylor3D mesh example to use mumps
2dec6a7 use new interface or ReadIniDof to write command_post scripts
65dd94d various modif ; add One BARxx example

git-subtree-dir: examples
git-subtree-split: a3e112bc33e04fa2a939134b4925b82a9133c335

0459b53 fix display files writing in thermal3D example
967187c fix API in electrical example

git-subtree-dir: examples
git-subtree-split: 0459b53073c824920b993f347d96a4e2db868d3e

keep on preparing examples for version 2015.3

61c003c Merge branch 'ifort_fix' into 'dev'
02adcd3 get git revision number even if git version is < 1.8.5
f389139 ifort compilation bug fix

git-subtree-dir: src
git-subtree-split: 61c003caf1c247cd7d79fd22f287f045f198dc58

keep on preparing src for revision 2015.3

git-subtree-dir: examples
git-subtree-split: 791c9d3e7fc6911753deb056894cc1238c7a9a4c

Preparing 2015.2 version

git-subtree-dir: src
git-subtree-split: 918d12869cdac5aa6ad0eb252a7c0d155fb744a7

Preparing 2015.2 version

Get lmgc90_user_examples tag 2015.2

8073530 Merge branch 'rc2015.2' into 'master'
eaaae59 add new performance workshop
ba08e81 remove old performance workshop
4c62b85 adding membrane_3D example for workshop
e73e248 fix .pvd file location in RIGID_3D/thermal_3D example
f7f3b86 fix cylinder length in prepro_grains/cylinder3D example
de5bf3c renaming generation script to gen_sample.py for overall naming consistency
a661792 correction in .pvd file writing in electrical and thermal examples
c69b867 update readme file
0b9e2ed update wall3D example for 2015 release
7b9eb2e update wall2D example for 2015 release
8b50572 adding shell script to run an example
d691814 update prepro_mesh2D examples for 2015 release
ae02efe removing duplicate mur example
7f85315 update examples of Pre/prepro_grains for 2015 release
a574526 maj modele therm 3D
0b020d1 maj modele elec
80fabdd ajout mots cles manquant
aaafc8c update display commands in rigid multi physics example for workshop
c15ecf6 first update of Ateliers examples
c9227fd mise a jour des fct Ptr
9e98aa4 mise a jour des fct Ptr
1cde098 first update of poro and therMAILx example
ad9fc23 update mecaMAILx_RIGID_3D examples for 2015 release and add missing update of mecaMAILx_RIGID_2D
aafd04d update mecaMAILx_RIGID_2D examples for 2015 release
f0658ca remove duplicate example script
e8ad960 rename cubes_H8_explicit example in cubes_H8
d7a3d97 update mecaMAILx examples for 2015 release and remove cubes_H8 duplicate example
0b15238 update mecaMAILx_2D examples for 2015 release
8ef9c9b update RIGID_3D examples for rev 2015 ddm and thermal not working yet
8034525 update RIGID_2D example for new version
5aa3321 update SetField function names
REVERT: e5f8682 removing duplicate mur example
REVERT: 801823d Merge branch 'rc2015' of git-xen.lmgc.univ-montp2.fr:lmgc90/lmgc90_user_examples into rc2015
REVERT: 75681d7 update examples of Pre/prepro_grains for 2015 release
REVERT: 783cdf7 maj modele therm 3D
REVERT: 6c4b9fe maj modele elec
REVERT: 0de267e ajout mots cles manquant
REVERT: d80b3dd Merge branch 'rc2015' of git-xen.lmgc.univ-montp2.fr:lmgc90/lmgc90_user_examples into rc2015
REVERT: e5b8227 update display commands in rigid multi physics example for workshop
REVERT: b9110d0 first update of Ateliers examples
REVERT: acf58dc mise a jour des fct Ptr
REVERT: b4b1e8f mise a jour des fct Ptr
REVERT: 580a96b first update of poro and therMAILx example
REVERT: 03ceb24 update mecaMAILx_RIGID_3D examples for 2015 release and add missing update of mecaMAILx_RIGID_2D
REVERT: 13255ca update mecaMAILx_RIGID_2D examples for 2015 release
REVERT: d2b231c remove duplicate example script
REVERT: b1c2a99 rename cubes_H8_explicit example in cubes_H8
REVERT: 50fb915 update mecaMAILx examples for 2015 release and remove cubes_H8 duplicate example
REVERT: 2ee408d update mecaMAILx_2D examples for 2015 release
REVERT: 2994047 update RIGID_3D examples for rev 2015 ddm and thermal not working yet
REVERT: ea93075 update RIGID_2D example for new version

git-subtree-dir: examples
git-subtree-split: 104cc2e34f89d107f167f4f94b65e37856d5c911

20e1c66 Merge branch 'fd_jul' into 'dev'
1f0fd27 modifs fd
6758129 Merge branch 'rc2015-2' into 'dev'
572b211 minor update of tutorial script of pre_lmgc sphinx doc
c6814ed correction erreur docstring
9d46c5f update readme
1735298 update readme
b2e81a3 put back extrudeRigids routine accidentally removed from pre_lmgc
a1b716e modif du wrap pour mp rigid
81dcf7f Merge branch 'compil_fix' into 'dev'
5da431e python rTree binding compilation only if numpy version greater than 1.6
8b94fd3 fix ifort compilation
74f6883 Merge branch 'add_wrap' into 'dev'
908c19e add wrap for 3D coupling with gmsh + fix typo somewhere
ebe6fbd Merge branch 'ddm_fix' into 'dev'
9a29d31 adding function to Std_ExternalFEM for standard DDM compilation
fce739c Merge branch 'bugs_fix_080315' into 'dev'
0d754a3 bug fix dans models et modif pour que ca compil avec ifort sur macos
9efd32c Merge branch 'models_vector_field' into 'dev'
e3542fd adding setter by elem or node on scalar and vector fields for ther, poro and multi
11048bc Merge branch 'Print_3D' into 'dev'
ec76bfc Merge branch 'DDM_V2.0' into 'dev'
c987102 Modif pour la DDM : - Ajout d'une variable DDM_SCHWARTZ, - Ajout d'un vecteur Vddm
1dce054 Correction d'un bug bloquant s'il MPI n'est pas utilisé
8e08a02 DDM pour Xper, V2
079a059 Merge branch 'fd_fixes_28012015' into 'dev'
c2f44c7 broutilles
0330e20 modifs
2ecf3e1 modifs intersection_wp
0226d6c modifs intersection polytopes
2239ec6 ajout nouvelle fonction intersection polytope
590b1e5 correction d'un message
3a56ee1 Merge branch 'wood_orthotropic_frame' into 'dev'
daaed5f use external vector field MARROW_POINT and MARROW_ORIENT in user orthotropic frame computation
e9faba5 fix call to set_ortho_frame_by_user
573375e Merge branch 'models_and_external_fields' into 'dev'
c2140ec split mecaMAILx_SetField automatic switch between SetFieldByNode and SetFieldByElem in distinct wrapped functions
3aa5227 change ext_f model keyword to extsf and ext_v to extvf
adfee3e Merge branch 'set_field_by_ele' into 'dev'
9906851 set vector field by element
5ee79f9 set field on elements in mecaMAILx
9a29907 Merge branch 'vector_field' into 'dev'
14437d0 adding external vector field at Gauss point
48b45d8 Remplacement d'un write en logmes dans mod_CSASp
fe976c9 Modification de la fonction display_tacinfo : Changement des write(*) en logmes
58c3f15 Merge remote-tracking branch 'origin/dev' into Print_3D
13d4967 Merge branch 'cmake_correction' into 'dev'
85d044f correct dependencies in contribs compilation and improve test of rtree
c3270d9 Merge branch 'Allegement_VTK' into 'dev'
839be09 Merge branch 'Optimisation_prep_nlgs_2D_3D' into 'dev'
9cbac27 Merge branch 'Timers_3D' into 'dev'
ef5b13a Allègement des fichiers VTK par codage des entiers et des doubles sur 32 bits au lieu de 64.
966b38e Optimisation de prep_nlgs en 2D et en 3D par sauvegarde des "reverse adjacents"
0671efd Remplacement de print par des logmes pour les CZM 3D, afin d'être homogène avec le 2D.
282354c Ajout de timers pour les CZM 3D, afin d'être homogène avec le 2D.
3bf6563 Merge branch 'fd0115_fixes' into 'dev'
46a7225 modif pour Morhr Coulomb intrinseque
302e655 Merge branch 'rtree_python_binding' into 'dev'
c40c5f5 adding test of python binding of rtree library
ec21e0e renaming rTree python module
18395a4 better binding with cython of rtree library
3b313e0 python API on rTree library using cython
REVERT: 5f57e5a correct openmp compilation error in nlgs_3D
REVERT: 3705bdb minor update of tutorial script of pre_lmgc sphinx doc
REVERT: 91dfd2d correction erreur docstring
REVERT: 0cb3eab update readme
REVERT: b6fc67b update readme
REVERT: c31a22e Merge branch 'rc2015' of git-xen.lmgc.univ-montp2.fr:lmgc90/lmgc90_dev into rc2015
REVERT: c74be7a put back extrudeRigids routine accidentally removed from pre_lmgc
REVERT: c92a255 modif du wrap pour mp rigid

git-subtree-dir: src
git-subtree-split: 2ba7104259b0a9c3b01b4621dbb495c8827ceb7f

Get lmgc90_dev tag 2015.2

5f57e5a correct openmp compilation error in nlgs_3D
3705bdb minor update of tutorial script of pre_lmgc sphinx doc
91dfd2d correction erreur docstring
0cb3eab update readme
b6fc67b update readme

git-subtree-dir: src
git-subtree-split: 5f57e5a7c34b28971d3c93958a423cfcc14d8bdd

e5f8682 removing duplicate mur example
801823d Merge branch 'rc2015' of git-xen.lmgc.univ-montp2.fr:lmgc90/lmgc90_user_examples into rc2015
75681d7 update examples of Pre/prepro_grains for 2015 release
783cdf7 maj modele therm 3D
6c4b9fe maj modele elec
0de267e ajout mots cles manquant
d80b3dd Merge branch 'rc2015' of git-xen.lmgc.univ-montp2.fr:lmgc90/lmgc90_user_examples into rc2015
e5b8227 update display commands in rigid multi physics example for workshop
b9110d0 first update of Ateliers examples
acf58dc mise a jour des fct Ptr
b4b1e8f mise a jour des fct Ptr
580a96b first update of poro and therMAILx example
03ceb24 update mecaMAILx_RIGID_3D examples for 2015 release and add missing update of mecaMAILx_RIGID_2D
13255ca update mecaMAILx_RIGID_2D examples for 2015 release
d2b231c remove duplicate example script
b1c2a99 rename cubes_H8_explicit example in cubes_H8
50fb915 update mecaMAILx examples for 2015 release and remove cubes_H8 duplicate example
2ee408d update mecaMAILx_2D examples for 2015 release
2994047 update RIGID_3D examples for rev 2015 ddm and thermal not working yet
ea93075 update RIGID_2D example for new version

git-subtree-dir: examples
git-subtree-split: e5f8682eef4f74ebf9a107e233fb271cbdbf5035

Getting examples of 2015 release candidate

c31a22e Merge branch 'rc2015' of git-xen.lmgc.univ-montp2.fr:lmgc90/lmgc90_dev into rc2015
c74be7a put back extrudeRigids routine accidentally removed from pre_lmgc
c92a255 modif du wrap pour mp rigid
86b5389 Merge branch 'PU_solveur_jacobi_3D' into 'dev'
24d8422 Resolution de conflit pour le solveur jacobi
e9384cf Merge branch 'PU_mecamailx_get_pointer' into 'dev'
1da8e3a Merge branch 'PU_bug_correction' into 'dev'
ab71b19 Bug correction : L'appel de get_all_clalp ou de get_all_internal_clalp par le script python conduit à une segementation fault si il n'y a pas de clalp Le return doit etre tester sur nb_vclalp qui dimensionne le pointeur et non sur nb_clalp
0f027f8 Merge branch 'new_fix_czm' into 'dev'
58103ab correction bug ABP 2D + modif dans gestion du initial_friction des czm
c21c9a0 Merge branch 'modif_pre' into 'dev'
7df9bcf je vire le print de merde
a85c569 ajout d'un shrink dans rigidsFromMesh2D
e5aa2e2 Modification dans mecamailx de GetPtr en GetPtrBodyVector Ajout des éléments nécessaires dans parameters Suppression des éléments redontants dans overall
7dcbe2a Merge remote-tracking branch 'origin/dev' into PU_mecamailx_get_pointer
238185b Merge branch 'fix_Vth' into 'dev'
e14a4ca correction bug dans gestion dilatation thermique des DISKx & typo dans POLYG
0857e0e Merge branch 'tst_rtree' into 'dev'
eff817b Merge branch 'tst_rtree' of git-xen.lmgc.univ-montp2.fr:lmgc90/lmgc90_dev into tst_rtree
04b6116 modifs suite au remarques de Remy Mozul
04cca72 modif rtree
e428ad9 modif rtree
662f35d Merge branch 'fix' into 'dev'
c183fba Merge branch 'vtk_fix' into 'dev'
5ddcafc add accessor on xKSID for couette example coupled with gmsh
0ddba49 Merge branch 'ddm_fix' into 'dev'
d89aaf4 fix forgotten get_ptr_xxx call changes in ddm modules
d9ec4f2 fix introduced bug in previous commit
46c0cef correction in WriteDisplayFile API to add user field
46e9339 Merge branch 'extractContour_pre2D' into 'dev'
840beb6 Merge branch 'fix_PLPLx' into 'dev'
34b04be fix of a comment
6a7ac8f ajout fonction extraction contour en 2D
d12bc12 Merge branch 'fix_pre' into 'dev'
61d2cc5 correction de petites erreurs et typo du pre
5baaffb Merge branch 'PU_get_all_internal' into 'dev'
32cf755 Merge branch 'PU_vtk_display' into 'dev'
6084eff Merge branch 'openmp_fix' into 'dev'
0488cb0 compilation bug correction with openMP
dcf109f Merge branch 'yales' into 'dev'
0a7e0b1 Merge branch 'fix' into 'dev'
f44f804 Change name from get_xxx_ptr to get_ptr_xxx
48e060c using integer parameter instead of 10 characters string DIME
94dbb8b Changement du nom get_pointer_mecamailx en get_ptr_mecamailx Passage de l'identifiant du champ par entier plutot que par chaine de caractères Ajout des identifiants necessaires dans overall Ajout d'un wrapper
5b73113 Création d'un pointeur vers les différents champs de mod_mecamailx, afin de pouvoir y accéder et les modifier sans allocation.
243ab89 Ajout de fonctions permettant de recupérer les valeurs de "internal" pour les contacts de type CLALp et CSASp Ces fonctions sont utilisable dans les jeu de données pour pouvoir par exemple ajouter le champ "beta" aux sorties paraview lors des calculs avec zones cohésives.
3d125d3 Merge branch 'fix' into 'dev'
f9c9712 no longer taking into account invisible bodies when computing equilibrium state
107233c Merge branch 'dev_renouf' into 'dev'
9f90d00 mr:mauvaise initialisation dans les conditions limites
685e457 Ajout des sorties VTK pour Xper en 3D
1223295 Merge remote-tracking branch 'origin/dev' into PU_vtk_display
1cd6c7d possibility to compute only Fint in mecaMAILx_compute_bulk with MOREAU scheme
64ed47c  Déplacement des .pvd dans DISPLAY  Concaténation des .pvd en DDM
256b0b1 Merge branch 'ddm_concatenate_outbox' into 'dev'
8d1f66d Merge avec la branche dev
4c9fa02 Merge branch 'cmake' into 'dev'
6369c22 correction for correct git branch check
cede578 Merge branch 'cmake' into 'dev'
d8e39e8 check git branch differences when invoking make
59e6130 Modifications dans ddm_utils de concatenate_outbox() :
0150a02 correct typo in cmake warning
578b391 Merge branch 'cmake' into 'dev'
65fc483 Modification sur ddm_utils.py
7d697a7 remove warning on MACOS relating to RPATH
95804c6 add cmake variable to check compiled git branch
6c4f46b modele poiseuille dans elements erodes
ee6ff07 Modifications dans ddm_utils de concatenate_outbox() :    - Ajout des GPV    - Factorisation de la fonction de concatenation    - La concatenation n'est effectuée que si les fichiers sont présents

git-subtree-dir: src
git-subtree-split: c31a22e1cf64f32dee78465e36713200a795a0c2

Getting 2015 release candidate

git-subtree-dir: examples
git-subtree-split: da1441e0c9badaa3eea3340392829e28419adf2f

git-subtree-dir: src
git-subtree-split: 80af6d1044b89475ca6edf2e67b9cafdb5b709d7