1. 13 Nov, 2020 1 commit
  2. 10 Nov, 2020 2 commits
    • Nicolas CHEVAUGEON's avatar
      [xFEM] xBoundary.h/cc are moved to xFEM/src/attic · 5c4579b3
      Nicolas CHEVAUGEON authored
      class xBoundary was only used as a parameter to some
      Mechanics::TreatmentOfNatEnv that was never actually used and which was
      passed around via a member of xData. It is nothing more than an early
      implementation of xSubMesh that was passed around via cut and past for a
      long time ... Therefore, xBoundary is now made obsolete and the files
      xBoundary.h/cc are moved to xFEM/src/attic.
      
      all its' use will be removed from xTest.
      
      Note : My first clang-format related bug.
      The file xDistanceNearestPointGenerator.h need to be included before
      xDistanceNearestPoint.h, otherwise some test case can't compile !!! indeed,
      it add some overload to cgal AABBPrimitive that needs to be visible for
      template instanciation that can take place via  xDistanceNearestPoint.h.
      But clang-format messed around and I had to force the inclusion of xDistanceNearestPointGenerator.h before xDistanceNearestPoint.h, by including it at the
      beginning of xDistanceNearestPoint.h, and preventing clang-format to reorder
      the include by inserting some comment.
      5c4579b3
    • Nicolas CHEVAUGEON's avatar
      m] library xGeomTools added · bc14d18b
      Nicolas CHEVAUGEON authored
      Main changes :
      - A new library xGeomTools is added in xGeom.
        *This library is meant to collect "simple" geometrical classes/functions.
         By "simple" we mean that they dependent only on xtensor, and xtool.
        *All the classes and functions of xGeomTools are in namespace xgeom.
        *For this commit it contains :
         xBoundingBox.h/cc, xOctreeGrid.h, xRegularGrid.h/cc, xSimpleGeometry.h,
         moved from xTensor or xFEM.
        *Previous library xGeom is split in two libraries : xDistanceNearest and
         xScanElement in respectivevly xGeom/xDistanceNearest
         and xGeom/xScanElement,
        *The old xGeom library do not exist any more.
        *Note that the 3 libraries contained in directory xGeom populate
         the namespace xGeom.
        *Global build option BUILD_XGEOM is removed.
        *Global build option BUILD_XGEOMTOOLS, BUILD_XDISTANCENEAREST,
          BUILD_XSCANELEMENT are added.
        *xGeom/CMakeLists.txt is removed
        *xUTil/cmakeUtil :
         FindxGeomTools.cmake, FindxDistanceNearest.cmake, FindxScanElement.cmake
         added, FindxGeom.cmake is removed.
        *xAnalyticalSolution, xCrack, xDoubleCut, xLegacySimpleCut, xDomainDecomp,
         xExport, xExt, xFEM, xInterfaceAOMD, xMeshInterface, xOctree, xMapping,
         xTLS, now depend on  xGeomTools.
        *xOctree and xTLS now depends on xDistanceNearest
      - xBoundingBox :
        *added member functions  inclose(), now used in xMesh, xSubMesh
        and xLagrangeMapping.
        *added default constructor and constructor for 2 xPoint.
        *default constructor now build an  empty "bb"  by havinh min(i) > max (i)
      - xRegularGrid : dependencies to xMesh are removed.
      - xMesh.h :  part of previous xOctreeGrid that was dependent of xMesh are
        no directly implemented in xMesh. (see xMesh::createGrid() and
        xMesh::locateElement)
      
      Miscanelous changes along the way (removing useless dependencies)
      - xValue.cc : removed "useless" inclusions of "xApproxFunction.h",
        "xField.h", "xLevelSet.h", "xSpacePolynomial.h", "xTensors.h",
        "xTensorsPtr.h" "xVector.h" as well as useless using AOMD::mEdge
        and using AOMD::mEntity.
      - xValue.h : removed useless inclusions of  <set>,
        <boost/graph/adjacency_list.hpp>, <boost/graph/connected_components.hpp>,
        "xTensorsPtr.h", "xDebug.h", "xNearestNeighborInterface.h"
      - xValue_imp.h : removed useless includes "mEdge.h" and "xGeomeElem.h"
      - xValueManager.h - removed dependencies to xMesh.
      - some of AOMD include cascading in other files because of the previous
        removed inclusion were putting std::string in global namespace.
        std::string is now added in the following files :
        std::string xExport.h, xExportEnsight, xExportGmsh.h
        xExportTranslate.cc/h, xField.h, xFEM/src/xSpacePolynomial.h.
      - xData.cc inside void xData::ReadInfo(const char *filename),
        unused variable xBoundary crvboundary; is removed.
      - all modified and added files are clang-formatted.
      bc14d18b
  3. 09 Sep, 2020 1 commit
  4. 22 Jul, 2020 1 commit
  5. 25 Jun, 2020 1 commit
    • Nicolas CHEVAUGEON's avatar
      [xmapping] made fully independent from Trellis · 23c79dc2
      Nicolas CHEVAUGEON authored
      xmapping now have it's own enum type xReferenceElementType defined in
      xReferenceElement. It is there to replace Trellis mType inside xMapping.
      The xMappingBuilder are moved to xfem. Rational : The builder work on
      mEntity that are not supposed to be known by mapping.
      This being done the only dependencie left in xMapping is the dependecies to
      xtensor.
      
      a function is added in xAOMDEntityUtil.h to get the xReferenceElement from
      the mEntity, as well as conversion fonction from xReferenceElement to
      mType. In the current version of the library, this function is only used
      in xfiles to create  a Trellis_Util::GausIntegrator out of a xMapping.
      Therefore these conversion function might become useless when we make
      our own Trellis free Integrator.
      
      Most of the other change in this commit are consequencies of the above.
      Small other minor change are listed below :
      
      -xfiles_dependence.dot has been updated with xmapping dependencies.
      -delete mapping added in xElement::xyz2uvw ...
       this was missing and was causing a memory leak.
        (Note : It might be better for the builder to return smart pointer to
        mapping instead of newed pointer ... )
      - xTensor2 semi-colon were removed where it was useless and issued a warning.
      - xVector : copy assignement added. Rational : since we have a no default copy
        constructor, a default copy assignement is deprecated in the standard
        according to gcc
      23c79dc2
  6. 16 Jun, 2020 1 commit
    • Nicolas CHEVAUGEON's avatar
      [xmapping] xMapping now a full class, independant of Trellis_Util::Mapping. · 0c02f81b
      Nicolas CHEVAUGEON authored
          This is a continuation of the work of previous commit. The goal behing
          to reduce the dependancies to AOMD. This intermediate commit do that
          with minimal interface change and minimal other change to Xfiles
          libraries.
          new files  in xMapping/src :
          xLagrangeMapping.cc, xLagrangeMapping.h, xLagrangeMappingBuilder.cc,
          xLagrangeMappingBuilder.h, xMapping.cc, xMappingBuilderHolder.cc, xMappingBuilderHolder.h
      
          class xMapping, xLagrangeMapping, xConstantLagrangeMapping ...
          are now fully implemented in xmapping instead of behing typedef of some Trellis_Util::Mapping.
          This come with some minor interface change to minimize remaining deps to Trellis in xmapping :
          xMapping do not store any more the associated AOMD::mEntity, instead it just store the entityType (mType defined in AOMD_Internals.h) This type will probably
          change in a next commit, it's still needed for now in the present form, so that the the type returned by member getType() remain compatible with Trellis_Util::Integrator.
          interface change in xMapping :
          - member getEntity is removed.
          - member getType is added.
          - member interiorCheck was taking a useless AOMD::mEntity *loc as input, it is removed.
          - members PushBack are replaced by pushBack to conform to general xfile convention.
          - unused member simplexation is removed
          - There are now 3 normalVector members and they are not pure virtual any more :
      
            virtual void normalVector(double u, double v, double w, vector3d &n) const :
            compute the "natural" normal to a face mapping. it also work with line, making the assumption that the normal is orthogonal
            to the third axis. direction of the normal of course depends on the order of the nodes in the face up to a sign.
      
            virtual vector3d normalVector(const unsigned short *face_vertices, double s, double t) const:
            compute the normal to the face (resp line) given by face_vertices in term of the nodes number of the
            reference solid (resp face) upon with the mapping is constructed. s,t are the local parameter in the reference space of face
            (resp s in the reference space of the line). It proceed by finding out if the face is really a valid face of the solid,
            if so which one and how it is rotated compared to the corresponding reference face on the solid.
            Then it compute the coordinate u,v,w in the solid reference face corresponding to point s,t on the face,
            taking into account face number and rotations. It then select the normal in reference space according to the face number,
            and push it back to geometric space.
            For this to work,  data are defined in xMapping.cc for each type of mapping supported.
      
            vector3d normalVector(const unsigned short iface, double u, double v, double w) const:
            compute the exterior normal to the  numbered iface face relative to the underlying solid at point u,v,w  of the solid.
            iface is the relative face number to the solid we want to take the normal of.
            From this value, the normal in ref space is retrived.  it is then push to geometric space using the jacobian at u,v,w.
            This is the simplest candidate to use to replace previous usage of normalVector in the library.
      
          Consequences elsewhere :
          -  xMapping/src/xLagrangeMappingBuilder.cc/.h
             xRegularCubeLagrangeMappingBuilder and  xCylindricalCoordinatesLagrangeMappingBuilder are moved to this file
            (previously they were in xMappingBuilderHolder.h/cc).
            xLagrangeMappingBuilder Familly now call new version of constructors for xLagrangeMapping.
      
          - Trellis/Util/Util/calculus/Integrator.h/cc
            GaussIntegrator do not store any more the entity, just the entityType. Constructor modifyed accordingly
      
          - xCrack/src/IntegratorSingularCrack2D.cc
            call to Trellis_Util::GaussIntegrator constructor modifyed accordingly
      
          - xCrack/src/SingularCrackMapping.h_cc xExt/src/InfiniteMapping.h_cc
            constructor of SingularCrackMapping and InfiniteMapping now call new version of xMapping and xLagrangeMapping Constructor and
            do not overload normalVector any more.
      
          - xExt/src/InfiniteOrLagrangeMappingBuilder.cc now call new version of xLagrangeMAppingConstructor.
      
          - xForm.h/.cc :
            bool integ_is_appro(xGeomElem* geo_integ, xGeomElem* geo_appro) is now implemented in the .cc file (otherwise xMapping need to be fully defined in xForm.h )
      
          - xGeomElem.h/.cc
           now xGeomElem store a AOMD::mEntity* ent as a direct member, since xMapping do not any more. Constructors and members are modifyed accordingly.
           xGeomElem member normalVector is implemented according to the new implementation of xMapping.
      
          - xRegularGrid.cc : implemented using the new version of interiorCheck.
      
          - xMapping/test/testxLagrangeMapping/main.cc has been modifyed to test the normal implementation and conform to the change in xMapping interface.
      
          - TLSVelocity.h :  Small changes to conform to the new xMapping interface.
      
          - Element.h now include "AOMD_Internals.h" because it needs AOMD::mEntity::mType
             which is not included throught xMapping.h any more.
      0c02f81b
  7. 04 Jun, 2020 1 commit
  8. 10 Apr, 2020 1 commit
    • Nicolas CHEVAUGEON's avatar
      [xfem] Reduces dependencies on xMesh.h. This has implications in other parts of the lib. · 9c703287
      Nicolas CHEVAUGEON authored
          Currently, xMesh.h, by cascading include, is visible by a too large part of
          the library. Change one Character of xMesh.h, and you need to recompile
          the world. The aim of this commit is to reduce these dependencies.
          It affect lots of files but only a little in each. As discuted in meeting,
          I won't clang format them all for this push, But I clang format the added files.
      
          ADDED FILES :
      
          1 xFEM/src/xMeshFwd.h
          2 xFEM/src/xIntegrationRuleFwd.h
          3 xInterface/AOMD/general/src/xAOMDEntityUtil.h
          4 xInterface/xOctree/src/OctreeUtilities.cc
      
          1 xMeshFwd.h : A forward header fo xMesh.h. Include this where you need to
           forward declare the type defined in xMesh, but not there full declaration.
           Typically include it in place of xMesh.h wherever you need the type previously
           defined in xMesh but not their full description (you only declare pointer or
           refs to xMesh, you just need xIter, xClassIter or xPartition or the type of
           partman used inside xMesh (parmanxMesh_t) )
      
          2 xIntegrationRuleFwd.h, same philosophie as above, a forward header for
           xIntegrationRule. it forward declare class xIntergrationRule and define the
           type def xGetPartion (the function used to parametrize how to get the sub
           elements in the xIntergrationRulePartition familly.
      
          3 xAOMDEntityUtil.h Some function previously defined in xMesh.h/cc,
           are in fact simple utility function applied on mEntity.
           There are place in the code where they are needed, but where you don't need
           xMesh. For now I moved the following one there, in namespace xiterface::aomd :
            - void getSubentities(AOMD::mEntity* e, const int d,
                                  std::vector < AOMD::mEntity * > &l);
            - void getSupportBoundary(AOMD::mEntity *in,
                                     std::set<AOMD::mEntity *> &supportBoundary )
           They are used in :
            xCut/xLegacySimpleCut/src/xRefCutToAOMD.cc,
            xGeom/src/xDistanceNearestPointGenerator_imp.h, xTLS/src/xRefCutToCGAL.cc
      
          4 OctreeUtilities.cc This is an implementation file for OctreeUtilities.h
            Following function are moved to the .cc :
            xLevelSetTo_ls_xyz_t_Adaptator::xLevelSetTo_ls_xyz_t_Adaptator(xLevelSet &ls_)
            double  xLevelSetTo_ls_xyz_t_Adaptator::operator()(x,y,z).
            using namespace xfem and using namespace xoctree; are removed from the global
            scope in OctreeUtilities.h
      
          INTERFACE CHANGES :
      
          - xIntegrationRulePartition familly : the getpartition function that
            parametrize how to go from the integ entity to it's sub entity must now be
            given explicitly as a first argument.
            Rational : when first introduced, this parametrization could be implicit
            thanks to a default argument set to the static xMesh::getPartition.
            This implied an unwanted dependencies of xIntegrationRule to xMesh, and make
            user code unclear on the real dependencies of there Integration rule to
            there cutting process. Concerned files :
            xCrack/src/IntegratorSingularCrack2D.cc,
            xCrack/src/IntegratorSingularCrack3D.cc, xFEM/src/xIntegrationRule.h,
            xFEM/src/xIntegrationRule.cc, xFEM/src/xIntegrationRuleStored.h,
            xFEM/src/xIntegrationRuleStored.cc, xPhysics/src/xpElastic.cc,
            xPhysics/src/xpFluidMechanics.cc, xPhysics/src/xpFluidMechanics.cc,
            xPhysics/src/xpThermic.cc, xTLS/src/TLSGeomInterface.cc,
            xTLS/src/TLSGeomInterfaceSignedVectorDistanceFunction.cc,
            xTLS/src/TLSGeomInterfaceSignedVectorLevelSet.cc,
            xTLS/src/TLSGeomInterfaceVectorLevelSet.cc
      
          - xCrack/src/xcFront.h : added begin and end to iterate on front_parts.
            used to simplify loops in
            in xCrack/src/xcFrontDomainManager.cc, xCrack/src/xcFrontManager.cc,
            xCrack/src/xcInteractionIntegralsOnCrack.cc
      
          - xCrack/src/xcInteractionIntegralsOnCrack.h
            xAcceptLocalPart is now template on the DATAMANAGER that store was_created_by
             affected files : xCrack/src/xcInteractionIntegralsOnCrack.cc
      
          - xFEM/src/xAlgorithm.h :
            DeclareInterpolationHanging : the datamanager needed need now to be
            explicitlty given (no default value). Rational:  again the default
            value hide to  the user the real dependencies of the algorithm.
      
          - xFEM/src/xValueCreators.h :
            * xMirrorCreator : used to interconnect xValue on "mirror" entity,
            typically used for periodic Boundary condition. Previously, it was
            using an xMesh pointer and internal call to AOMD's lookupForMirrorEntities,
            on this mesh. This is too dependend on both xMesh and AOMD. Looking closely,
            all that is needed for this algorithm to work is a way to get from one entity
            a list of entity it mirror. The new interface is based on that.
            At construction, full control is given to the user which just have to give
            an std::function that take a pointer to a mesh entity and return the list
            of mirror entity. the pointer to the mesh itself is not needed anymore.
            * xValueCreatorRegularAndHanging : no default value any more for the
            isHangingOn at construction (same rational as for the use of the other
            static datamanger of xMesh, if you use them, do it explicitly.)
            the pointer to the mesh is not needed any more at construction.
      
          IMPLIED MODIFICATIONS:
      
          - replaced xMesh.h by xMeshFwd.h or include xMeshFwd.h or remove include xMesh.h
           in the following files :
            xCrack/src/CrackPostpro.h, xCrack/src/lCrack.h, xCrack/src/xcFront.h,
            xCrack/src/xcFrontDomain.h, xCrack/src/xcCrackBase.h,
            xCrack/src/xcFrontDomainManager.h, xCrack/src/xcFrontPart.h,
            xCrack/src/xcFrontSpaceManager.h, xCut/xDoubleCut/src/xElemCutDomainData.h,
            xCut/xDoubleCut/src/xPhysDomain.h,   xCut/xDoubleCut/src/xPolytopeOFF.cc,
            xCut/xDoubleCut/src/xPolytopeToAOMDElem.h,
            xCut/xLegacySimpleCut/src/xPhysSurf.h,
            xCut/xLegacySimpleCut/src/xPhysSurfVLS.h,
            xCut/xLegacySimpleCut/src/xRefCut.cc,
            xCut/xLegacySimpleCut/src/xRefCutToAOMD.h,  xExport/src/xPostPro.h
            xExt/src/DoubleCutting.h, xFEM/src/xApproxFunctionCorrectedShifted.cc,
            xFEM/src/xData.h, xFEM/src/xElement.cc,  xFEM/src/xGatherMesh.h,
            xFEM/src/xIntegrationRule.cc, xFEM/src/xIntegrationRule.h, xFEM/src/xRegion.h,
            xFEM/src/xRegularGrid.h, xFEM/src/xMeshFwd.h, xFEM/src/xSubMesh.h,
            xFEM/src/xSubMeshManager.cc, xFEM/src/xSubMeshManager.h, xFEM/src/xValue.cc,
            xFEM/src/xValue.h, xFEM/src/xValueManager.h, xFEM/src/xValue_imp.h
            xFEM/src/xVectorField.cc (include xRegion instead), xFEM/src/xVectorField.h,
            xFEM/src/xVectorLevelSet.h, xGeom/src/xDistanceNearestPointGenerator.h
            (use "xAOMDEntityUtil.h"), xInterface/xOctree/src/surf2LevelSet.h,
            xPhysics/src/xpThermic.cc,
            xTLS/src/TLSGeomInterfaceSignedVectorDistanceFunction.h,
            xTLS/src/TLSGeomInterfaceSignedVectorLevelSet.h, xTLS/src/TLSVelocity.h,
            xTLS/src/xRefCutToCGAL.cc
      
          - include xMesh.h in the following files :
            xCrack/src/ExportSensors.cc, xCrack/src/JintModalParks.cc,
            xCrack/src/lCrack.cc,  xCrack/src/xcFront.cc
            xCrack/src/xcFrontDomain.cc,  xCrack/src/xcFrontDomainManager.cc
            xCrack/src/xcInteractionIntegralsOnCrack.cc,
            xCut/xDoubleCut/src/xPolytopeToAOMDElem.cc
            xCut/xDoubleCut/src/xSignedVectorLevelSetEnrichment.h,
            xExport/src/xPostPro.cc,  xExt/src/SpaceLagrangeDualBoundary.cc,
            xExt/src/SpaceLagrangeDualMinBoundary.cc,
            xExt/src/SpaceLagrangeDualNewBoundary.cc, xExt/src/SpaceLagrangeDualSimple.cc,
            xFEM/src/xApproxFunctionCorrectedShifted.cc, xFEM/src/xCommandOnGeomElem.h,
            xFEM/src/xExtendShapeFcts.h, xFEM/src/xGatherMesh.cc,
            xFEM/src/xNonLocalInfoForKeysAndFcts.h, xFEM/src/xRegularGrid.cc,
            xFEM/src/xSubMesh.cc, xFEM/src/xValueCreators.cc,
            xInterface/xOctree/src/surf2LevelSet.cc, xPhysics/src/xPhysSurf3.cc,
            xPhysics/src/xpElastic.cc, xPhysics/src/xpFluidMechanics.cc,
            xTLS/src/TLSGeomInterfaceSignedVectorDistanceFunction.cc
      
           -removed useless forward declaration of xMesh in :
            xCrack/src/xcFrontSpaces.h, xCrack/src/xcInteractionIntegralsOnCrack.h,
            xCut/xLegacySimpleCut/src/xPhysSurfByTagging.h,
            xCut/xLegacySimpleCut/src/xPhysSurfParameter.h, xExport/src/xSensors.h,
            xExt/src/xPhysBand.h, xPhysics/src/xpFluidMechanics.cc,
            xTLS/src/TLSEnrichment.h, xTLS/src/TLSGeomInterfaceVectorLevelSet.h,
            xTLS/src/TLSValueCreatorRampHeaviside.h, xTLS/src/TLSVelocity.h,
            xTLS/src/xEvalWeightedDirectionalAverage.h
      
           -replaced include xIntegrationRule.h by xIntegrationRuleFwd.h
            or remove xIntegrationRule.h :
            xCut/xDoubleCut/src/xPhysDomain.h, xFEM/src/xAlgorithm.h, xFEM/src/xField.h,
            xFEM/src/xIntegrationRule.h, xFEM/src/xSpace.h, xTLS/src/TLSGeomInterface.h
      
          - Trellis/Util/Util/include/mPoint.h
            Added stream operator <<  for mPoint.
          - lCrack.cc/h :
            int lCrack::dim() const,  void lCrack::setV1Ddebug(std::function ...),
            lCrack::~lCrack  are moved to lCrack.cc.
            using namespace xfem moved from global scope to inside namespace xcrack
          - xCut/xDoubleCut/src/xElemCutDomainData.cc :
            now include "mVertex.h"
          - xCut/xLegacySimpleCut/src/xPhysSurf.cc/h  :
            int   xPhysSurfBase::dim() const,   xPhysSurf::~xPhysSurf() and
            xPhysSurfOctree::xPhysSurfOctree  implementations moved to xPhysSurf.cc
          - xExt/src/SpaceLagrangeDualBoundary.cc/h :
            OutsideVertex::OutsideVertex(const xLevelSet* f) and
            AOMD::mEntity* OutsideVertex::operator()(AOMD::mEntity* e) are now
            implemented in the .cc file
          - xFEM/src/xData.cc : data member in xData::nb_evo now initialized to 0
          - xFEM/src/xElement.cc :
            xElement::xyz2uvw(const Trellis_Util::mPoint& xyz) this function that
            invert the mapping was constructing a temporary xMesh in case of QHAD and HEX,
            containing only one element..  This was way more to much than needed,
            since Trellis_Util::Mapping used in this function just need an mEntity.
            I replaced the construction of an xMesh by the construction of the correct
            mEntity only.
          - xFEM/src/xLevelSet.h :  added now needed include unordered_map
          - xFEM/src/xLevelSetOperators.cc :
            call xRegion::dim() instead of xRegion::getMesh()->dim() rational :
            remove deps on xMesh, clearer.
          - xFEM/src/xLevelSetOperators.h :
            removed using std::cout/endl at global scope, added include xEntityFilter
          - xFEM/src/xMesh.h :
            removed using std::map, std::vector, std::set, std::string at xfem scope,
            now   include  xMeshFwd.h, getSupportBoundary and getSubentities now moved to
            xInterface/AOMD/general/src/xAOMDEntityUtil.h
          - xFEM/src/xRegularGrid.h/cc :  xRegularGrid::xRegularGrid implementation
            moved to .cc
          - xFEM/src/xRegularGrid.h : #define TOL 1.e-06 at xfem scope,
            replaced by  constexpr static  double TOL  = 1.e-06; in xfem::xRegularGrid
          - xFEM/src/xSpace.cc now include "xIntegrationRule.h"
          - xFEM/src/xValueCreatorLinkOnFrontFiltered.cc, in ::buildTable
            a non-standard variable size array was used (vertices).
            Replaced by a std::vector.
          - xFEM/src/xVectorField.cc some loop where rewritted.
          - xInterface/xOctree/src/surf2LevelSet.cc implementation of  surface2LevelSet
            constructors,  computeWeightedPseudoNormals::proceed(),
            surface2LevelSetNarrowBand  are moved to the .cc
            rational : these functions call some xMesh member functions)
          - xPhysics/src/xpEval.h/cc ElementLengthMaterialVariablesVisitor_c moved to .cc
            rational : constructor use some member of xMesh.
          - xPhysics/src/xpPhysicalFormulation.cc  : used xRegion member dim, begin and end instead of asking the same on a region "all" meshes's. (rational : reduce deps on xMesh, clearer code)
      
          ADDED std:: in front of standard symbol
           By cascading inclusion, using namespace std was visible in some files
           (comming from some AOMD include). After the change in the inclusion hierachy,
           namespace std is not visible any more in some header file. I choose to not add
           using namespace std at global scope of a header file, and add to std::
           in front of standard symbols. Concerned files :
           xCrack/src/JintParks.h, xCrack/src/xcFrontManager.cc,
           xCut/xDoubleCut/src/xSignedVectorLevelSet.h,
           xCut/xDoubleCut/src/xSignedVectorLevelSet_imp.h,
           xExport/src/xExportAlgorithm.cc, xExport/src/xPostProVTU.h,
           xExt/src/MaterialCommand.h, xExt/src/SpaceLagrangeDualNewBoundary.cc,
           xExt/src/SpaceLagrangeDualNewBoundary.h, xExt/src/ValueOldAndCurrent.h,
           xFEM/src/xAlgorithm.h, xFEM/src/xDistStateOfValue_imp.h, xFEM/src/xElement.cc,
           xFEM/src/xMaterialSensitivity.h, xFEM/src/xSpacePolynomialQH.h,
           xFEM/src/xSubMesh.h, xFEM/src/xValueLinearCombination_imp.h,
           xFEM/src/xVectorLevelSet_imp.h, xFastMarching/src/FMUpdater.h,
           xTLS/src/TLSGeomInterface.h, xTLS/src/TLSVelocityModeEshelby_imp.h,
           xTLS/src/xEvalLSAdvanceFromImposedConditions_imp.h
      
          ADDED using namespace std :
           Same reason as above, I added using namespace std in .cc files that needed it :
            - xCrack/src/xcFrontDomain.cc, xCrack/src/xcFrontSpaceManager.cc,
              xExport/src/xPostProMSH.cc, xExt/src/SpaceLagrangeDualNewBoundary.h,
              xExt/src/SpaceLagrangeDualSimple.cc
      
          removed using namespace xfem :
            xFEM/src/xGatherMesh.h
      
          replace some old style cast by static_cast :
            - xExt/src/SpaceLagrangeDualNewBoundary.cc
      9c703287
  9. 14 Jun, 2019 1 commit
    • Gilles MARCKMANN's avatar
      refactoring 2019: renames namespace, creates new directories, ... · e6039c6a
      Gilles MARCKMANN authored
          rename directory and namespaces. Modifications below:
      
          Original directory (Master)    ->             New directory (refactoring)                 Namespace (refactoring)
          ===========================                   ===========================                 =======================
      
          Xfiles:
          =======
      
          Util
             |_eXlibris_tools                           xTool                                     xtool::
             |
             |                                          xUtil
             |_cmakeUtile                                   |_cmakeUtile
             |
             |_FloUtil                                      attic
             |_Split                                        attic
             |_doxygen_tools                                attic
             |_tags_tools                                   attic
      
          Xcrack                                        xCrack
               |_ xCrack                                     |_ src                               xcrack::
               |
               |_ xCrackFMM                                  attic
      
          Xcut                                          xCut
             |_XdoubleCut                                  |_xDoubleCut                           xcut::
      
          Xdomaindecomp                                 xDomainDecomp
                      |_DomainManager                               |_DomainManager               xdomaindecomp::
                      |_Solvers                                     |_Solver                      xdomaindecomp::
      
          Xext
             |_AnalyicalSolutions                       xAnalyticalSolution
             |                  |_Elastic2D                               |_Elastic2D             xanalyticalsolution::
             |
             |_Xext                                     xExt
                  |_src                                    |_src                                  xext::
                  |
                  |_ImageProcessing                        attic
      
          Xfem
             |_Xfem ___________________________________ xFEM                                      xfem::
                                               \_______ xCut
                                                \          |_xLegacySimpleCut                     xcut::
                                                 \
                                                  \____ xExport                                   xexport::
                                                   \___ xTensor                                   xtensor::
                                                    \__ xMapping                                  xmapping
                                                     \_ xQuadrature                               xquadrature::
      
          FastMarching                                  xFastMarching
                     |_src                                          |_src                         xfastmarching::
                     |   |_FMSkeleton                               |   |_Skeleton                xfastmarching::skeleton
                     |                                              |
                     |_xDistFM                                      |_xDistFM                     xfastmarching::
                             |_xDistFM                                      |_src                 xfastmarching::
      
          Geom                                          xGeom                                     xgeom::
      
          Xinterfaces                                   xInterface
                    |_XAOMDInterface                             |_AOMD                           xinterface::aomd::
                    |                                            |
                    |_GraphInterface                             |_Graph
                    |              |_ParMetis                    |     |_ParMetis                 xinterface::parmetis::
                    |                                            |
                    |_XoctreeInterface                           |_xOctree                        xinterface::xoctree::
                    |                                                    |
                    |_xSplitMeshInterface                                |_xTemplateRefineMesh    xinterface::xtempaterefinemesh::
                    |
                    |
                    |_SolverInterfaces                   xLinAlg
                                     |_SolverBase              |_SolverBase                       xlinalg::
                                     |_SuperLu                 |_xInterfaceSuperLu                xlinalg::
                                     |_Taucs                   |_xInterfaceTaucs                  xlinalg::
                                     |_Lapack                  |_xInterfaceTaucs                  xlinalg::
                                     |_Mumps                   |_xInterfaceMumps                  xlinalg::
                                     |_BasicIterSolver         |_xInterfaceBasicIterSolver        xlinalg::
                                     |_Pastix                  |_xInterfacePastix                 xlinalg::
                                     |
                                     |_NonLinearSolver         attic
                                     |_PetscParallel           attic
                                     |_PetscSeq                attic
                                     |_SparsKit                attic
                                     |_Itl                     attic
                                     |_Mtl                     attic
                                     |_KSPParallel             attic
      
          MeshMachine                                   xMeshTools
                    |_DistMesh                                   |_xDistMesh                      xmeshtool::
                    |_SplitMesh                                  |_xTemplateRefineMesh            xmeshtool::
                    |
                    |_FastMarching                               attic
                    |_LinearAlgebra                              attic
                    |_Stlmesh                                    attic
      
          Octree                                        xOctree                                   xoctree::
      
          Physics
                |_Physics                               xPhysics
                        |_Materials                            |_Materials                        xphysics::
                        |_src                                  |_src                              xphysics::
      
          xTLS
             |_trunck
             |_xTLS                                     xTLS                                      xtls::
      
          ============================================================================================
      
          Xfem splitting:
          ===============
      
          xCut
             |_src
                 |__ xDoubleCut
                 |             |__(unchanged)
                 |
                 |__ xLegacySimpleCut
                                    |__ xPhysSurfByTagging.cc
                                    |__ xPhysSurfByTagging.h
                                    |__ xPhysSurf.cc
                                    |__ xPhysSurf.h
                                    |__ xPhysSurfParameter.cc
                                    |__ xPhysSurfParameter.h
                                    |__ xRefCut.cc
                                    |__ xRefCut.h
                                    |__ xRefCutToAOMD.cc
                                    |__ xRefCutToAOMD.h
                                    |__ xRefCutToIsoZeroVector.cc
                                    |__ xRefCutToIsoZeroVector.h
                                    |__ xRefMesh.cc
                                    |__ xRefMesh.h
      
          xExport
                |_src
                    |__ xExport.cc
                    |__ xExportEnsight.cc
                    |__ xExportEnsight.h
                    |__ xExportGmsh.cc
                    |__ xExportGmsh.h
                    |__ xExportGmsh_imp.h
                    |__ xExport.h
                    |__ xExportManager.cc
                    |__ xExportManager.h
                    |__ xExportTranslate.cc
                    |__ xExportTranslate.h
                    |__ xPostPro.cc
                    |__ xPostPro.h
                    |__ xPostProMSH.cc
                    |__ xPostProMSH.h
                    |__ xPostProVTU.cc
                    |__ xPostProVTU.h
                    |__ xSensors.cc
                    |__ xSensors.h
      
          xTensor
                |_src
                    |__ xPoint.h
                    |__ xTensor2.cc
                    |__ xTensor2.h
                    |__ xTensor2Sym.cc
                    |__ xTensor2Sym.h
                    |__ xTensor3.h
                    |__ xTensor4.h
                    |__ xTensorOperations.h
                    |__ xVector.cc
                    |__ xVector.h
                    |__ xVectorScalarProd.h
      
      =============================================================================================
          cmake variables rules for module Xfiles/xFoe (no more Xfiles/Xfoe) :
      
                Xfiles/xFoe  => find_package(xFoe)  => xFoe_INCLUDE_DIR  / xFoe_LIBRARIES
      
          in C++ source files, namespace are in lower cases: xfoe
      
      =============================================================================================
      
          New xfastmarching namespace have been introduced but pack/unPack helping function
          must remain in :: namescpace (i.e. in no namescpace). This is to let FMupdaterGeneric
          call ::pack  ::unPack in a generic way (no assumption on VECT or TRANSPORTED
          namespace)
      
      =============================================================================================
      
          Macro Super for SuperLU 5 (experimental ) added in xinterface superlu
      
      =============================================================================================
      
          modifiyed xCSRVector.h and cc so that the .h does not include xBlasDef.h since it can produce conflict when including xVector.h in superLU interface
      
      =============================================================================================
      e6039c6a