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. 01 Sep, 2020 1 commit
    • Nicolas CHEVAUGEON's avatar
      [Xfiles] removing using xxx in global namespace in headers. · af6f2b76
      Nicolas CHEVAUGEON authored
          - lot of using std or using xfem or using std::string etc ..  were still present in global namespace in some header. Following a discussion with A. Salzman, I removed most of them.
      
          - In the transition from mPoint to xPoint, Some using point = xtensor::xPoint were defined inside some class (xMapping, xElementfor example... ). They were identifyed as confusing by A. Salzman and are now removed.
      
          Most of the changes in this commit reflect the previous change. The guideline is to avoid hiding namespace at least at global scope in header-file. This can avoid some confusion and some surprising and hard to track effects where some stuff compil or not depending on the order of inclusion of header files.
      af6f2b76
  5. 22 Jul, 2020 1 commit
  6. 02 Jul, 2020 1 commit
  7. 15 Jun, 2020 1 commit
  8. 12 May, 2020 1 commit
    • Nicolas CHEVAUGEON's avatar
      clang-formated · de534315
      Nicolas CHEVAUGEON authored
          removed comment and added file xFEM/src/xDomain.h
      
      [xfem] xDomain, zone_tag.
      
      Previously, we had a raw aomd tag, zone-tag, created throught xDomainStringManager with the name "zone". It was use to set that a mesh entity was belonging to a "zone" with a id related to a zone_name throught xZone. It was set for example using xClassifyOn and It was used in particular by the xEntityFilter xAccept, xAcceptNot, xAcceptOnZoneId, xAcceptUpperAdjancencies And xGeomElem getZone() member function.
      
          * I replaced the usage of a raw aomd tag by a new class xDomain defined in xDomain.h, implemented using an xDataManagerAOMD.
          * xClassifyOn, xAccept, xAcceptNot, xAcceptUpperAdjancencies and  xGeomElem::getZone() are reimplemented using this xDomain.
          *xAcceptOnZoneId was not reimplemented since it was almost the same as  xAccept. Previous usage of xAcceptOnZoneId(int) can be safely replaced by xAccept(int)
      
          *xDomainStringManager.h and xDomainStringManager.cc that where previously only use to set up the aomd tag zone_tag are removed.
          *xDomainAttachableData.h that used to define an mAttachableData suittable to attach domain information is now useless and removed
      
          *Since it was previously stored as an attachData, it was automatically destroyed each time an mEntity was destroyed. To have the same effect, the xMesh::del(mEntity *e) have been updated to clear the xDomain from mention of e.
      
          *The header inclusion #include "xDomainAttachableData.h", "xDomainStringManager.h" are removed where needed in the library :
           - xCut/xLegacySimpleCut/src/xMeshCut.cc, xFEM/src/xEntityFilter.cc, xFEM/src/xEntityToEntity.cc, xFEM/src/xGeomElem.cc, xFEM/src/xIntegrationRule.cc, xFEM/src/xMesh.cc, xPhysics/src/xpThermic.cc
      
          all the following files are clang-formated :
             xCut/xLegacySimpleCut/src/xMeshCut.cc
             xFEM/src/xEntityFilter.cc
             xFEM/src/xEntityFilter.h
             xFEM/src/xEntityToEntity.cc
             xFEM/src/xEntityToEntity.h
             xFEM/src/xGeomElem.cc
             xFEM/src/xIntegrationRule.cc
             xFEM/src/xMesh.cc
             xPhysics/src/xpThermic.cc
       Changes to be committed:
      	modified:   xCut/xLegacySimpleCut/src/xMeshCut.cc
      	new file:   xFEM/src/xDomain.h
      	deleted:    xFEM/src/xDomainAttachableData.h
      	deleted:    xFEM/src/xDomainStringManager.cc
      	deleted:    xFEM/src/xDomainStringManager.h
      	modified:   xFEM/src/xEntityFilter.cc
      	modified:   xFEM/src/xEntityFilter.h
      	modified:   xFEM/src/xEntityToEntity.cc
      	modified:   xFEM/src/xEntityToEntity.h
      	modified:   xFEM/src/xGeomElem.cc
      	modified:   xFEM/src/xIntegrationRule.cc
      	modified:   xFEM/src/xMesh.cc
      	modified:   xPhysics/src/xpThermic.cc
      de534315
  9. 10 May, 2020 1 commit
    • Nicolas CHEVAUGEON's avatar
      [xcut] xPhysSurf Updated to use cut function of xcut/xLegacySimpleCut/xMesh.h/cc · eae565dc
      Nicolas CHEVAUGEON authored
      xPhysSurf now store references to datamanager passed at construction to update them and pass them to the cut function. the datamanager have for now default value to the corresponding data Manager in xMesh. It uses the cut function defined in xcut/xLegacySimpleCut/xMesh.cc/.h
      
      XPhysSurfOctree and xPhysSurf3 (from xPhysics) have also been updated.
       xPhysSurfOctree octree now use internal datamanager instead of some xMesh static tags to store it's internal data.
      
      Since xPhysSurfOctree have been changed a lot, the interface and the implementation of xScalarFunctionDerivDiscXFEMOctree (xfem/xApproxFunction.h.cc) have been updated.
      
      some loop are rewritten as range loop.
      
       modified and clang-formated :
      
        xAnalyticalSolution/CMakeLists.txt
        xCut/xLegacySimpleCut/src/xPhysSurf.cc
        xCut/xLegacySimpleCut/src/xPhysSurf.h
        xFEM/src/xApproxFunction.cc
        xFEM/src/xApproxFunction.h
        xPhysics/src/xPhysSurf3.h
        xPhysics/src/xPhysSurf3.cc
      eae565dc
  10. 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
  11. 10 Feb, 2020 1 commit
    • Alexis SALZMAN's avatar
      [XFiles] Introduce xvalues_t typdef and reset several names · 63a68f9f
      Alexis SALZMAN authored
      xvalues_t:
      =========
      This typedef represents a xValue<VT> type with VT the template parameter
      corresponding to the type of value stored in xValue.
      It is introduced to hopefully avoid misunderstanding with previously
      introduces value_t corresponding in most case to the type of value
      computed (for now we play mostly with arithmetic with those).
      
      Especially in xValueLinearCombinationXXX hierarchy we are dealing
      with xvalues_t, not value_t.
      
      It has been also introduced in xValueManagerDist to clearly separate the
      type of the values, value_t, from the type of the xValue<value_t> that
      store in the xValManager instance these information.
      
      This as been used as suggested by N.C. to set the type of the value_container_t
      and be more strict regarding the implementation
      
      value_manager_t:
      ===============
      In xField value_manager_t replace ValueManager to try to clarify
      situation.
      
      getValueManager:
      ================
      getValueManager and getDoubleManager are now rigorously the same. So this
      commit removes this last method that do have a name far to specific.
      
      This implies lost of changes everywhere ... but re-naming of instance have
      not been done accordingly to this new method name (to much work). Names
      such as double_manager or dm should be changed ... little by little
      
      Test will be updated soon.
      63a68f9f
  12. 04 Feb, 2020 1 commit
  13. 27 Jan, 2020 1 commit
    • Grégory LEGRAIN's avatar
      Let there be template fields ! · 3cc692f4
      Grégory LEGRAIN authored
      This is a first implementation of template fields in eXlibris.
      Thanks a lot to Alexis (@asalzman) and Nicolas (@nchevaugeon) for fruitful discussions !
      
      Fields can now handle other quantities than double (complex for instance).
      This has led to multiple changes:
      * xDoubleManager disappears
      * xValueDouble disappears
      * Assembly is now templatized
      
      However, the changes are small with respect to the interface in your applications (see the testcases).
      
      =========================
          Notable changes
      =========================
      
      xDoubleManager:
      ---------------
      Is replaced by  xValueManagerDist<T> ("Dist" stands for "distributed"). This template class handles other values  than double.
      
      Example : xValueManagerDist<double> value_manager;
      
      In your end-user code (AND NOWHERE ELSE), you can define a convenient typedef :
      using  xDoubleManager = xValueManagerDist<double>;
      
      xValue:
      -------
      xValueDouble is replaced by xSingleValue<T> where T stands for the type which is stored.
      Move value creators in xValueCreators.h
      
      xStateOfValue:
      --------------
      is now template (should not influence end-user code)
      
      xStateDofCreator, xStateFixedCreator are also template.
      
      xField:
      -------
      now template against the approximated quantity: xField<double> for a double-valued field
      
      Major internal modifications: "everything" is handled by the specialization of getVal and getGrad. For example:
      template <class iterFct, class iterVal>
      static void getVal (iterFct it, iterFct ite, iterVal first, iterVal last, int size_Fct_Val,
                    const xGeomElem* geo_appro, const xGeomElem* geo_integ, std::complex<double>& v);
      
      xFormBilinear, xFormLinear:
      ---------------------------
      A new template is added (double by default):
      template <typename VT = double> class xFormBilinear;
      It corresponds to the type of quantity which is stored in the elementary stiffness matrices (note that xFemMatrix and other are now template). Usually, you can keep it as double, but this is not mandatory (see BUILD_COMPLEX_VALUED_OPERATORS in test case complex2d).
      
      xAssembler, xAssemblerTraitPolicy, xDispatcher are modified to take into account the other changes.
      
      ==============================
             EXAMPLES
      ==============================
      
      An example of complex-valued field is given in Xtest/xfem-para-test/complex2d (however, see issue #58)
      
      ========================================================
      KNOWN limitations/issues (that will be fixed later on):
      ========================================================
      
      * type dependent code in xField is still part of the class. We should try to move this code away from the core of the class (issue #60).
      * float and complex version of mumps are still not available, so you cannot fully run any float or complex testcases for the moment  (see issue #58)
      * the compiler on titan (gcc 4.8) has troubles during template deduction for some template functions (DeclareInterpolation, DeclareState), see issue #59. The syntax had to be modified in order to help the compiler, leading to verbose notations.
      3cc692f4
  14. 20 Dec, 2019 1 commit
    • Nicolas CHEVAUGEON's avatar
      removing dependencies of xfem on xcut. · f000b185
      Nicolas CHEVAUGEON authored
          Some constructor of enriched shape function that rely directly on an xPhysSurfxxxx are removed from xfem. They were only using the reference of the xLevelSet embeded inside xPhysSurf. directly call the constructors that take a level_set from no on.
      
          xValueCreatorRampedHeavyside from xValue.h/cc have been moved to xtls,
          since that's the only place were they are used. And that seems to be the
          last dep of xfem on xcut.
      
      Squashed commit of the following:
      
      commit 9fbec7ad8c294660691818027195f6e5dabac599
      Merge: f92e0ca 1714a22b
      Author: Nicolas CHEVAUGEON <nchevaug@titan.ec-nantes.fr>
      Date:   Fri Dec 20 17:32:58 2019 +0100
      
          Merge branch 'master' into removexfemtoxcutdependencies
      
      commit f92e0caceb0e245a27aaf2a26fe048a805600557
      Author: chevaugeon <nicolas.chevaugeon@ec-nantes.fr>
      Date:   Fri Dec 20 17:06:13 2019 +0100
      
          finishing clean up after removing dep on xLegacySingleCut in xFEM
      
      commit a727fa5d45ac07cf81f7d2f4c220995a6dbd55c7
      Author: chevaugeon <nicolas.chevaugeon@ec-nantes.fr>
      Date:   Fri Dec 20 15:34:41 2019 +0100
      f000b185
  15. 09 Dec, 2019 1 commit
    • Nicolas CHEVAUGEON's avatar
      remove the depencies of xFEM on xExport · 967e0a06
      Nicolas CHEVAUGEON authored
          Before the current commit, we had the problem that the xfem library depends on the export library and vice versa. This cyclic dependencies causes lot of problemes for the build.
          In particular, it was very difficult to make some of our test case build with cmake version 3.13.4
          To make xFEM independant of xExport, the main task was to move the Export algorithms out of the xFEM library. All these algorithm are now implemented in xExportAlgorithm.h/cc int the xExport library, under the xexport name space.
          That done, some dependencies remained in the xVectorLevelset.h/cc. This file previously contain our first version of vectorlevelset (that came before the signed vector distance function) and the first version of the 2d doublecut algorithm, embedded in the class xPhysSurfVLS. The class xPhysSurfVLS itself has been moved where I think it belong, to xCut/xLegacy and the xcut namespace in file xPhysSurfVLS.h/cc. This being done we are one step closer to also have removed the cyclic dependencies between xfem and xcut.
          Most of the other changes in the library reflect the fact that we now have to include xExportAlgorithm.h to have access to the Export algorithm which is now in name space xexport. The same work as been done in the xTest repository and will be commited next.
          A small "bug" in  xUtil/cmakeUtil/FindNoHeaderLibrary.cmake as also been corrected. (it was always printing lapack REQUIRED whatever the library that was missing)
      
       + small modif in FindTAUCS.cmake. It was freezing when TAUCS_INCLUDE_PATH was not set.
      
      Squashed commit of the following:
      
      commit 1f50932ee6a6a4dde8cd35d5793112a6f4b934d4
      Merge: 9e3ba9e db82eb04
      Author: Nicolas CHEVAUGEON <nchevaug@titan.ec-nantes.fr>
      Date:   Mon Dec 9 10:36:16 2019 +0100
      
          Merge remote-tracking branch 'origin/master' into remove_xexport_dep
      
      commit 9e3ba9e57013dfa2de1e39163b29faa409a2cb21
      Author: Nicolas CHEVAUGEON <nchevaug@titan.ec-nantes.fr>
      Date:   Mon Dec 9 10:02:36 2019 +0100
      
          finishing the move of Export algo to xexport.
          + small modif in FindTAUCS.cmake. It was freezing when TAUCS_INCLUDE_PATH was not set.
      
      commit fa64d29ddc406acd5225774b7aae487072b0666c
      Merge: 8a6a9557 f94d6e0
      Author: Nicolas CHEVAUGEON <nchevaug@titan.ec-nantes.fr>
      Date:   Fri Dec 6 12:05:11 2019 +0100
      
          Merge branch 'tryingtobuild' of http://git.gem.ec-nantes.fr/nchevaugeon/Xfiles_Save into remove_xexport_dep
      
      commit f94d6e0b722c7066f526d7e45970a2c02ed27d9d
      Author: chevaugeon <nicolas.chevaugeon@ec-nantes.fr>
      Date:   Fri Dec 6 09:38:34 2019 +0100
      
      commit b3ac48f0d5d5d29ea8ab8f5798775e607598525b
      Author: chevaugeon <nicolas.chevaugeon@ec-nantes.fr>
      Date:   Wed Dec 4 16:30:33 2019 +0100
      
          remove the depencies of xFEM on xExport
      
          Before the current commit, we had the problem that the xfem library depends on the export library and vice versa. This cyclic dependencies causes lot of problemes for the build.
          In particular, it was very difficult to make some of our test case build with cmake version 3.13.4
          To make xFEM independant of xExport, the main task was to move the Export algorithms out of the xFEM library. All these algorithm are now implemented in xExportAlgorithm.h/cc int the xExport library, under the xexport name space.
          That done, some dependencies remained in the xVectorLevelset.h/cc. This file previously contain our first version of vectorlevelset (that came before the signed vector distance function) and the first version of the 2d doublecut algorithm, embedded in the class xPhysSurfVLS. The class xPhysSurfVLS itself has been moved where I think it belong, to xCut/xLegacy and the xcut namespace in file xPhysSurfVLS.h/cc. This being done we are one step closer to also have removed the cyclic dependencies between xfem and xcut.
          Most of the other changes in the library reflect the fact that we now have to include xExportAlgorithm.h to have access to the Export algorithm which is now in name space xexport. The same work as been done in the xTest repository and will be commited next.
          A small "bug" in  xUtil/cmakeUtil/FindNoHeaderLibrary.cmake as also been corrected. (it was always printing lapack REQUIRED whatever the library that was missing)
      967e0a06
  16. 27 Sep, 2019 1 commit
    • Grégory LEGRAIN's avatar
      [xTensor] Templatize xTensor · c8b56a21
      Grégory LEGRAIN authored
      xVector, xTensor2* and xTensor4 are now template classes
      xTensor4Isotropic, xTensor4AnisoPlaneStrain and xTensor4AnisoPlaneStress
      remain double-valued objects as they make sense only in this context.
      
      By default, value type is double, so that you may only have to replace
      xVector by xVector<> and so on in your code.
      
      Update Tensor operations such that xTranspose, xVonMisesNorm etc...
      Theya are also double-valued by default : xTranspose<> is equivalent to
      xTranspose<double>
      
      Update the rest of the repository accordingly
      c8b56a21
  17. 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