1. 28 Jan, 2021 1 commit
  2. 27 Jan, 2021 3 commits
    • Benoît LÉ's avatar
      [xExport] Added some functionnalities to xPostProcessingManager · 89c57a55
      Benoît LÉ authored
      - Added a getFileName() function, which calls the getFileName() of xExportManager
      (which has been made const)
      
      - Added an exportDebug function, to export values managers. In the future it could
      eventually be overloaded to export other debug files. A good example could be
      xCSRVector or matrixes, but it would introduced a dependency of xExport on xLinalg
      
      - Added a debug flag with a setDebugFlag function to add some debug output
      
      - Now the exportOnSpace functions automatically set the number of splits of the
      xExport to 1 (similarly to the old MyExport function of DamageGrowthBase in TLSImplicit)
      89c57a55
    • Benoît LÉ's avatar
      [xExport] Modified xPostProcessingManager API · 5230450c
      Benoît LÉ authored
      In the previous version, the values of some labels coming from the xParseData
      where imposed (so basically xPostProcessingManager could not work if some
      particular labels were not defined in the xParseData). The API has been modified
      to be usable with any custome labels.
      5230450c
    • Benoît LÉ's avatar
      [xTLS] Corrected xEvalTLSAdimLSFromLevelSetAndLCFront · 9d23f1fd
      Benoît LÉ authored
      An error was introduced in commit 4727e73e... "tagger" should be a member
      of xEvalTLSAdimLSFromLevelSetAndLCFront, created and modified in this class,
      and not an object coming from outside.
      9d23f1fd
  3. 26 Jan, 2021 1 commit
    • Benoît LÉ's avatar
      [xExport] Added xPostProcessingManager class · 5569e972
      Benoît LÉ authored
      Added new class xPostProcessingManager, which was previously in the XTLS/TLSElementbased
      appli (under the name PostProcessing).
      
      The main goal of this class is to encapsulate three xexport concepts:
      - The xexport::Export function
      - The xexport::xExportManager class
      - The xexport::xExportSensors class
      
      through the use of two main functions:
      
      - exportOnSpace : export a field/mesh/a level set with the Export function,
      using the frequency defined by the xExportManager. Note that if the field is a
      vector or tensor field, a given component can be exported by adding an extension to the
      name of the field in the parsed file. For instance, if a vector field named "displacement"
      is exported in the code, it can be exported by adding the name "displacement" in the
      export_manager field of the parsed file, but the first (second/third) component can also be exported
      b adding "displacement_1" ("displacement_2", "displacement_3"). Same for tensor fields (_11, _13, _23, etc)
      
      - exportOnTime : write a scalar quantity in a text file, using the xExportSensors class
      
      The saveMesh, saveField and saveDomain function from the former class PostProcessing were kept, and could
      be used in the future to implement restart.
      5569e972
  4. 19 Jan, 2021 2 commits
    • Alexis SALZMAN's avatar
      [xLinAlg] add reducing mechanism to mumps distributed interface · 9ca299e0
      Alexis SALZMAN authored
      When dealing with large number of cores with mumps distributed interface,
      if the size of the problem is small, poor performance are obtained with
      mumps library. The fact that matrix is presented in distributed format
      alleviate some internal optimization (available with centralize matrix
      format) and mumps among other has difficulty then to estimate its memory
      needs. This lead to underestimate memory evaluation during analyse phase
      which stop computation during factorization with a -9 error. Even if
      this memory issue is bypassed CPU time increase with number of cores
      when more then needed are used.
      
      In this commit a extra parameter ratio_reduce_comm_ is added to
      connectMatrix method of xLinearSystemSolverMumpsDistributed class.
      It correspond some how to an "ideal" ratio between the number of core to
      use for a given problem size "n". mx=ratio_reduce_comm * n is giving a
      roughs estimate of the maximum number of cores needed by mumps
      computation for a "n" size linear system. If the communicator given to
      mumps interface is larger then this mx estimate, only mx cores will be
      used with mumps. In this case interface will allocate its own memory to
      store matrix terms and user will have to use reduceMatrices() if he
      updates value in matrix storage connected to the interface. Because in
      this case interface groups matrix terms in the reduced set of core
      participating to mumps computation. Thus some communication need to be
      done every times terms changes in connected matrix. This alleviate some
      how the nice unique memory space shared between the connect matrix and
      mumps.
      
      When the communicator given to mumps interface is smaller then this mx
      estimate the interface behaves has before. Same if ratio_reduce_comm_ is
      null.
      
      This solution represent an intermediate between centralized and full
      distributed matrix format for mumps. If ratio lead to mx=1 a even more
      clearer implementation would be to switch to centralized  matrix format
      for mumps. TODO.
      
      For now memory consumption is not optimized as regrouped terms on process
      that hold matrix may be duplicate (i.e. a term i,j may appearers many
      time due to its presence in many process). Its not a problem for mumps
      as it will sum them but it cost memory. Reducing this consumption is not
      so easy to do. Communication buffer have to transfers all those
      terms so their size may be important anyway. TODO.
      9ca299e0
    • Alexis SALZMAN's avatar
      [xLinAlg] change resize API and behavior of xDenseMatrix class · b65dc7d7
      Alexis SALZMAN authored
      After some discussion with other contributors the resize method of
      class xDenseMatrix have been changed so that it initialize its newly
      allocated memory with a defined value. By default this value is zero but
      it can be changed.
      
      Now use of resize guaranty a defined state for matrix term which avoid
      some issue like having nan in some location that cannot be cleaned out
      by use of *= operator with zero argument.
      b65dc7d7
  5. 15 Jan, 2021 1 commit
  6. 13 Jan, 2021 2 commits
    • Gilles MARCKMANN's avatar
      Remove xFEM dependency on mAttachableData dependency. Move class definitions: · 3fb4eab2
      Gilles MARCKMANN authored
          	- xAttachableString.cc 		-> xDoubleCut
          	- xAttachableChar			-> xInterface/AOMD 	(still used in TLSImplicit)
          	- xAttachableGP			-> xInterface/AOMD 	(still used in TLSElementBased)
          	- xAttachableEntitiesVector	-> xTLS 				(still used in TLSExplicit)
          	- xAttachableEntitiesSet		-> attic
      3fb4eab2
    • Alexis SALZMAN's avatar
      [XFEM] change API of LOCALVECTOR concept (xAssembler concept) · 1a4cd3f6
      Alexis SALZMAN authored
      This commit pass from () to [] operator for LOCALVECTOR concept of
      xAssembler concept. This is opening usage of assemble_vector method
      to a wider range of container types. LOCALVECTOR may now be a
      xCSRVector or a std::vector for example. xFemVector having both
      operator remains functional (maybe () operator should be removed now ?).
      
      Some comments are added to try to clarify LOCALVECTOR and LOCALMATRIX
      concept.
      1a4cd3f6
  7. 12 Jan, 2021 1 commit
    • Gilles MARCKMANN's avatar
      xFEM: · 4727e73e
      Gilles MARCKMANN authored
      - Mark xFEM/xAttachableXXX class as deprecated (they shall be moved or removed).
      
      xGeom:
      
      - change use of xAttachableChar : replace const unsigned int tag_nodes  by a const xAttachedDataManagerAOMD<char>& in constructor of xLevelSetToCGALAndTag.
      
      xTLS:
      
      - change use of xAttachableChar : replace const unsigned int tag_nodes by a xAttachedDataManagerAOMD<char> in:
      		- TLSGeomInterfaceSignedVectorLevelSet,
      		- reInitLevelSetFromFrontCGAL2,
      		- xEvalTLSAdimLSFromLevelSetAndLCFront
      		- xRefCutToIsoCGAL
      4727e73e
  8. 18 Dec, 2020 1 commit
    • Alexis SALZMAN's avatar
      [xFEM,xTLS]revamping the last commit regarding attached gauss point · 826905a8
      Alexis SALZMAN authored
      This is removing the statics and encapsulate things
      
      GP data manager is now encapsulated into a class
      xIntegrationRuleStoredDataManager from which all
      xIntegrationRuleStoredxxx class derive. This way xIntegrationRule
      is not anymore impacted and when xIntegrationRuleStoredxxx is deleted
      every thing is automatically cleaned. xIntegrationRuleStoredxxx is
      responsible of the management of attached gauss points to entity.
      
      xIntegrationRuleStoredDataManager encapsulate the DATAMANAGER thus in
      future switching to others things will be easy. It retake almost the
      same API as DATAMANAGER with other names.
      
      Now that static are removed xExtendShapeFcts had to be modified to store
      a reference of xIntegrationRuleStoredxxx so that adding GP to entity is
      possible through functor call like before but with a new parameter
      passing xIntegrationRuleStoredxxx viewd as a
      xIntegrationRuleStoredDataManager. The xIntegrationRuleStoredxxx
      instance and the xExtendShapeFcts generator are now more tied together.
      This induce that the xSpaceExtendedShape based on generator is tied to
      xIntegrationRuleStoredxxx and assemble is now a little more
      secure as the field (base on xSpaceExtendedShape) is now in coherence
      with xIntegrationRuleStoredxxx explicitly.
      
      Hope I did not break something somewhere. I mean test pass but there is
      not much of them on those things ....
      826905a8
  9. 17 Dec, 2020 1 commit
    • Gilles MARCKMANN's avatar
      Remove use of xAttachableGP in Xfiles. Now a datamanager is added to class to... · 64ed8890
      Gilles MARCKMANN authored
      Remove use of xAttachableGP in Xfiles. Now a datamanager is added to class to attach Gauss Points data.
          The type xGaussPoints is defined as std::vector<std::pair<xtensor::xPoint, double>> and the datamanager type is datamanager_gauss_points_t (defined in xIntegrationRule.h).
          A static function of xIntegrationRule allows to get the datamanger.
      
          Example 1:
              agp = new xfem::xGaussPoints;
              xfem::xIntegrationRule::get_gauss_points_datamanager().setData(*e) = *agp;
      
          Example 2:
              xfem::datamanager_gauss_points_t& _data_GP_= xfem::xIntegrationRule::get_gauss_points_datamanager();
              xfem::xGaussPoints* agp = _data_GP_.getData(*e);
      64ed8890
  10. 15 Dec, 2020 1 commit
  11. 11 Dec, 2020 2 commits
    • Alexis SALZMAN's avatar
      [xLinAlg] add forEach method to xGenericSparseMatrix class · 86b38d83
      Alexis SALZMAN authored
      This method pass in revue all the non null terms (topological sens) and
      run a functor on them. The functor is expected to have 3 arguments:
      - 2 integer i and j that contains row and column index of term.
      - one T val corresponding to term's value.
      The functor can do anything you want.
      
      This function offers to user a quick way to deal with all traits.
      It may be slightly less efficient then calling getMemoryAcces and by
      hand pass in in revue terms according to traits (to be checked). It
      depends on what you do.
      
      It will be used internally to replace many duplicated piece of code
      where looping on all terms is required. It is already in use with
      printMatrixMarket method. Has some test do check matrix market outputs
      we can already conclude that forEach is validate.
      86b38d83
    • Alexis SALZMAN's avatar
      108593b6
  12. 10 Dec, 2020 1 commit
    • Alexis SALZMAN's avatar
      [xFEM] Adding optimized version of DeclareState/DeclareInterpolation · db4eefd8
      Alexis SALZMAN authored
      A DeclareInterpolation2 and DeclareState2 is added to xAlgorithm.h in
      this commit. The idea is not to use them right away but instead to test
      them in your context by switching names (remove the 2 and add
      something to old version names). By context here I talk of compiler. For
      those who use something else then GNU g++, those new versions have to be
      validated because they use the following assertion not in the norm I
      think:
      The clear method of std::vector do not touch memory allocation.
      
      Thus the glob and loc vectors use memory management a small number of
      time (for the first set of key of each space for a priori one element
      per space at most). Otherwise the insert is relying on already allocated
      capacity.
      If this assertion is not verified with other compiler something will have
      to be added.
      
      Besides this memory trick the main modification comes from valgrind
      study. It shows that xFiniteElement destructor and setKeys count
      respectively for 6.44% and 35.49% of 595 call to Declarinterpolation
      with a total of 304 640 elements treated (512 per call).
      KeysFor interfere in setKeys for 19.08%. As stated already by N.C.,
      clearly those computation are too costly compared to the generality or
      maintainability that they provides. The adopted solution was to remove
      xFiniteElement usage in those functions. That may hurt ... Maybe the
      loop on space, glob and loc ingredient may be encapsulate in something
      .. or xFiniteElement may be cleaned.
      
      For now those new versions are proof concept. Their performance shows up
      more then 20% gain in some application with many declareXXX.
      
      Note that new version pass test successfully.
      db4eefd8
  13. 09 Dec, 2020 3 commits
  14. 30 Nov, 2020 1 commit
    • Alexis SALZMAN's avatar
      [xExport] add to GmshMPIIO a file splitting mechanism · bc928091
      Alexis SALZMAN authored
      A new default parameter is added to xExportGmshMPIIO constructor. This
      parameter fix the numbers of files to be generated (see comments in
      sources for precise policy).
      
      This addition give a way to split huge results in smaller part more
      easily handled with GMSH. It might give also extra performance
      for large number of process by enlarging the number of file treated
      simultaneously by the file system.
      bc928091
  15. 13 Nov, 2020 2 commits
    • Alexis SALZMAN's avatar
      [xTool] add xDeltaMemory a basic memory profiler · 0628714a
      Alexis SALZMAN authored
      xDeltaMemory class is built in the same spirit as xDeltaTime.
      A "start" method capture a state and a "end" method do a comparison with
      previous captured state. This comparison give a measure of memory
      consumption between those two events.
      To be as precise as possible the usual string used to flag measure are
      now forcedly used by initAccu method and user must use startAccu,
      endAccu with the integer returned by initAccu.
      
      It give result like xDeltaTime as table with parallel statistic and Peak
      memory usage. This last information comes from getrusage (like
      xMemoryMonitor) and correspond to maximum resident set size. All other
      information are related to user request and do not represent the
      application true current memory consumption: malloc may have already
      reserve 2GB and user vector may use only 1.5GB. This is this last
      information that is given by xDeltaMemory.
      
      Only Heap is analyzed.
      
      Behind the curtain:
      ===================
      xDeltaMemory used deprecated GNU extension called hooks. malloc,realloc
      and free hooks give a way to set your own feature related to those
      function. In our case we want to count what user did ask for allocation.
      A ideal solution would be to use the size argument to count. But when
      freeing memory we just have a pointer in hand so its not easy to decrease
      our counter. Instead xDeltaMemory use malloc_usable_size which demangle the
      malloc information related to the accessible memory associated to
      pointer given by malloc.  xDeltaMemory over estimate then the real size
      asked by the user as  malloc_usable_size return the asked size plus the
      padding eventually added by malloc. But this is already a pretty
      accurate measure. Compare to xMemoryMonitor or the use of mallinfo here
      we place the measure in client application side. The others approaches
      can be qualified as system measuring snapshot. And thus they are harder
      to use for precise measure of user allocation.
      
      The deprecated aspect seem to last from a long time ... With gcc 8 on
      liger it is still available ....
      
      The GNU extension aspect is clearly a limitation. This is not portable !
      But all GNU specific aspect has been guarded by __GNUC__ macro so on
      other compiler xDeltaMemory will return 0 for all measure.
      
      To measure third party library calls, it will be possible only if
      the library is also compiled with a GNU compiler and malloc is in use.
      Somme test on liger with mumps show that xDeltaMemory provided almost
      the same information as MUMPS itself.
      
      Note that interleaving measure is possible. A specific counter track the
      start/end to deactivate hooks outside measuring sequence to avoid any
      extra computational cost.
      
      The implementation use static variable ! It is then not currently thread safe.
      
      New atomic test case:
      =====================
      A small test show how  to use xDeltaMemory and is for now the only
      documentation.
      
      TODO
      ====
      doc+xNoDeltaMemory class
      0628714a
    • Alexis SALZMAN's avatar
  16. 12 Nov, 2020 1 commit
    • Alexis SALZMAN's avatar
      [CMAKE] Add option to xTensor and xMapping creation · 8ce1bff4
      Alexis SALZMAN authored
      xTensor and xMapping library were not managed by any options. For sure
      both may/are (I don't know) needed by almost all other libraries. But it
      is not the question of "need" but the question of "when" that those new
      option answer to.
      
      In many free project the moto to get them in use is
      "configure/cmake, make, make install"
      
      Here if we consider that all ours repositories works like that, xFiles
      and xTest and ...(Applis) may be compiled separately with steps:
      "make install"
      Introducing those options gives a way to avoid xMapping and xTensor
      compilation all the time. They are compiled and installed when dealing
      with xFiles. Then there is no need to compile then for  XTest ....
      Actual vision is to use the same GEMUtil CMakelist.txt and switch option.
      That introduce this constraint but maybe in future we will split that
      file in some peaces : option block, Xfiles, xTest, APPLI.
      8ce1bff4
  17. 10 Nov, 2020 3 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
      [Xfiles_dependence.dot] dependencies graph updated · d4aca3b7
      Nicolas CHEVAUGEON authored
      Xfiles_dependence.dot that contains the "handmade" dependancies graph
      between the libraries in xfiles have been updated, based on the
      CMakeLists.txt.
      d4aca3b7
    • 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
  18. 06 Nov, 2020 1 commit
    • Nicolas CHEVAUGEON's avatar
      [xFEM, xMapping] xGeomElem code is simplifyed mostlty by using improved xMapping interface. · b71ddff8
      Nicolas CHEVAUGEON authored
      xGeomElem code is simplifyed (and improved ?) in the following way :
      
      - All the members now have version with the correct camelCase style. The old version are kept (for example GetDetJac is "cloned" to getDetJac), but are marked as "deprecated" in the their doxygen documentation. I tryed to use the [[deprecated]] attribute on them but unfortunatly, it's c++14 and we still can't use this version of the standard. I kept all the old version there since xGeomElem is used all over the places, but I would like to remove them in a near future ...
      
      - xBoundingBox xGeomElem::getBoundingBox() const take the place of void xGeomElem::GetBoundingBox(xtensor::xPoint& min, xtensor::xPoint& max) const.
      
      - The implementation take advantages of improved interface to xMapping.h
        for example :
        xtensor::xPoint xGeomElem ::getCDGxyz() const
        {
         double u, v, w, x, y, z;
         mapping->COG(u, v, w);
         mapping->eval(u, v, w, x, y, z);
         return xtensor::xPoint(x, y, z);
        }
        is replaced by
        xtensor::xPoint xGeomElem::getCDGxyz() const { return mapping->eval(mapping->COG()); }
        and
        void xGeomElem::setUVWForVertex(int inod) which was almost 200 lines
        is replaced by
        void xGeomElem ::setUVWForVertex(int inod) { uvw = mapping->getMappingVertex(inod); }
        where mapping->getMappingVertex(inod); just return data that where already in xMapping.
      
      - setting/clearing  the mapping or integrator members of the class was complicated because we have to keep track of differents life  time for  these pointers depending if they where defaulty allocated or pass by the user and eventulaly shared by differents
        xGeomElem. This is now simplifyed using a unique_ptr and classic ptr, allowing to use the implicitly declared destructor for
        xGEomElem.
        This pave the way for better mapping management in the  futur (I'm thinking of high order mapping that would be expensive
        to construct, that we might wan't to store in the builder ...)
      
      - we now have move constructor, move assignment and swap for xGeomElem, making them more usable in standard containers.
      
      Note on xGeomElem :
       - I think set/getOrientation are not very usefull, probably bug prone, and I think they should be removed.
       - I'm not sure we still need the integrator to be included in the xGeomElem, Integration behing performed in most cases using an
         xIntegrationRule  and xCommandOnGeomElem that could set directly the current point instead of setting it using both xGeomElem::setIntegrationPointNumberForDegree and xGeomElem::setUVW(int ipt)
      
      4 access functions have been added in class xMapping to access data that where already there, but not accessible outside xMapping.cc :
         -size_t getNbMappingVertices() const;
         -xtensor::xPoint getMappingVertex(size_t i) const;
         -static size_t getNbMappingVertices(xReferenceElementType type);
         -static xtensor::xPoint getMappingVertex(xReferenceElementType type, size_t i);
      b71ddff8
  19. 05 Nov, 2020 1 commit
    • Nicolas CHEVAUGEON's avatar
      [xFEM/test] added 2 atomic test for 3d search structure · a7cd5a68
      Nicolas CHEVAUGEON authored
      First, I added a test directory inside xFEM for xFEM Atomic test that was missing. (As usual Atomic test means that the test do not need other library that the current tested library dependencies)
      A new Build option is added, corresponding to the xFEM Atomic test  : BUILD_XFEM_TEST. It must be set to ON in your parent CMakeFiles.txt for this test to be builded, thanks to the Xfiles/CMakeLists.txt that will add the subdirectory xFEM/test to the build if BUILD_XFEM_TEST is set to ON
      
      In xFEM/test I added two tests cases :
      testxOctreeGrid and testxRegularGrid, along with there references.
      
      Some other tests from in Xtest/xfem-seq-test for example could also be moved here.
      a7cd5a68
  20. 04 Nov, 2020 2 commits
    • Alexis SALZMAN's avatar
      [xMapping] rm warning about potential non initialized variable usage · 6bb4eac4
      Alexis SALZMAN authored
      In both files some variable were potentially not initialized and
      nevertheless used for some computation.
      After checking with N.C. for xLagrangeMapping.cc the case were
      knots.size() is null is impossible => assert. Then a simple init with
      first point remove the warning and set without ambiguity x1,y1,z1.
      For xMapping.cc the switch was not defaulted and thus DetJac may remain
      unset. Setting it to 1 and put a default case in switch solve the prb.
      6bb4eac4
    • Nicolas CHEVAUGEON's avatar
      [XFEM, xExport, xInterface/xOctree] dependences to AOMD's octree is removed and related changes. · 22fa74d5
      Nicolas CHEVAUGEON authored
      xFEM/src/xOctreeGrid.h is a new file. It introduce a octree grid search
        structure to use in place of the AOMD::octree that was used in xMesh
        for the locateOctree members functions. It permits to construct an octree
        search structure on top of a collection of mesh entity.
      
      xFEM/src/xRegularGrid.h/cc has been modifyed so that :
       - it uses the xBoundingBox class.
       - The member function name have been changed to reflect the camel case
         convention, common to the rest of the xFEM library.
       - getElementsForPoint now return a vector of {element, localcoordinate} pair,
         so that the local coordinate of the target point in each element that
         contains it is now accessible.
       - The code have been clarifyed and simplifyed.
      
      xBoundingBox.h :
        - added 2 member function in xBoundingBox :
         /// return the center of the bounding box
         xPoint center() const { return (min + max) * 0.5; }
         /// return a vector from min to max
         xVector<double> diag() const { return xVector<double>{min, max}; }
        - Note that following a discussion with A. Salzmann, xBoundingBox could
          be moved in a near futur to namespace xgeom and the file might be part
          of a new library (xGeomTools maybe)
      
      xFEM/src/xMesh.h/cc has been modifyed so that :
        - It uses the xBoundingBox class were usefull, implying some interface
          change :
           * std::pair<xPoint, xPoint> compute_bounding_box(mEntity* e)
             is changed to :
             xBoundingBox compute_bounding_box(const mEntity& e);
           * void compute_bounding_box(xPoint& min,xPoint& max) const;
             is "deprecated", but is still there during the transition.
             it is replaced by :
             xtensor::xBoundingBox compute_bounding_box() const;
        - locateElementOctree and locateElement have changed interface,
          reflecting the changes in xRegularGrid and the use of xOctreeGrid instead of
          AOMD's octree.
        - Better control of the search structure in xMesh, since now the octree or
          the regular grid can both be cleared, updated or accessed by calling
          respectively xMesh Members   createOctree(), clearOctree(), getOctreeGrid(),
          createGrid(), clearGrid(), getRegularGrid.
        - The search structure pointers are now managed in a unique_ptr.
        - xMesh::copyMeshInternal now copy the search structures if needed instead
          of throwing.
        - AOMD_SharedInfo.h, autopack.h, OctreeCreate2.h (from AOMD) are not
          included anymore.
      
      xCrack/src/CrackPostpro.cc,  xCrack/src/ExportSensors.cc/h, modified so that it
        reflect the change in xMesh::locateElement
      
       xExport/src/xSensors.cc/h :
        -modified so that it reflect the change in xMesh::locateElement,
        -Trellis_Util::mPoint replaced by xtensor::xPoint
        -small changes to simplify the implementation
        -clang-format first the first time I think.
      
      xInterface/xOctree/src/surf2LevelSet.cc/h
        -modifyed to use xBoundingBox
        -surface2LevelSet::getBB(xPoint&, xPoint&) is replaced by
         const xBoundingBox &getBB() const { return BB; }
        -surface2LevelSet members xPoint BBmin, BBmax are replaced xBoundingBox BB;
        -a bug was found in the process :
         In surface2LevelSet::createMeshBBox that create an xMesh out of grid,
         the grid point coordinate were computed as :
          double xyz[3] = {BB.min(0) + i * elemSizeX, BB.min(1) +
                                       j * elemSizeY, BB.min(2) + k * elemSizeY};
         instead of :
           double xyz[3] = {BB.min(0) + i * elemSizeX, BB.min(1) +
                                        j * elemSizeY, BB.min(2) + k * elemSizeZ};
         The bug is corrected, but reference of test case
         xinterface-xoctree-test/surface2LevelSet had to be changed.
      
      All modifyed files have been clang-fomated.
      22fa74d5
  21. 03 Nov, 2020 3 commits
    • Nicolas CHEVAUGEON's avatar
      [xMapping] adding some virtual member to xMapping. · 661796b4
      Nicolas CHEVAUGEON authored
      xMapping now include xTensor/src/xBoundingBox.
      
      The following virtual member function of xMapping have been added.
      They all have default implementation in terms of the one existing before.
      They mostly simplify code when using them, and do not need to be implemented i
      in derived class (but could for optimization purpose)
      
       virtual xtensor::xPoint eval(const xtensor::xPoint &uvw) const;
       virtual tensor deval(const xtensor::xPoint &uvw) const;
       virtual bool invert(const xtensor::xPoint &xyz, xtensor::xPoint &uvw) const;
       virtual double jacInverse(const xtensor::xPoint &uvw, tensor &invjac) const;
       virtual double detJac(const xtensor::xPoint &uvw) const;
       virtual bool inReferenceElement(const xtensor::xPoint &uvw) const;
       virtual xtensor::xPoint COG() const;
       virtual double pushBack(const xtensor::xPoint &uvw, size_t vsize, vector3d *vec) const;
       virtual double pushBack(const xtensor::xPoint &uvw, std::vector<vector3d> &vec) const;
       virtual double pushBack(const xtensor::xPoint &uvw, size_t vsize, tensor *tens) const;
       virtual xtensor::xBoundingBox boundingBox() const;
      
      interface change in xMapping :
          virtual bool interiorCheck(const xtensor::xPoint &p, double u, double v, double w) const; changed to virtual bool interiorCheck(const xtensor::xPoint &p, xtensor::xPoint &uvw) const;
      
       Modified files :
         xMapping/src/xMapping.cc
         xMapping/src/xMapping.h
      
       and
         xFEM/src/xRegularGrid.cc
         modified to reflect xMapping::interiorCheck interface change
      661796b4
    • Nicolas CHEVAUGEON's avatar
      [xtensor] added file xboundingBox.h · 6371e2c6
      Nicolas CHEVAUGEON authored
       in file xTensor/src/xBoundingBox.h
       added class xBoundingBox in xTensor.
       it helps to manipulate bounding box thanks to the member functions,
       and will permit to remove some code duplication regarding bounding box
       intersection or checking if a point is inside a bounding box,
       compared to a model were we just pass around two xPoint.
      6371e2c6
    • Nicolas CHEVAUGEON's avatar
      [xtensor] added member function in class xPoint · e6740a5b
      Nicolas CHEVAUGEON authored
       added member function in class xtensor::xPoint :
        double & operator [] (int i);
        double operator [] (int i) const;
        xPoint operator / (double other) const;
        xPoint& operator /= (double other)
        xPoint& operator -= (const xPoint &other)
        bool operator == (const xPoint & other) const
      
       xTensor/src/xPoint.h   clang-formated
      e6740a5b
  22. 05 Oct, 2020 5 commits
    • Alexis SALZMAN's avatar
      [xFEM] a priori performance enhancement of xfieldStorageFull · d26022a1
      Alexis SALZMAN authored
      This commit remove usage of AOMD EntityHashKey and EntityEqualKey for unordered_map
      container. Using default hash and equalkey based on address (the key is a
      pointer) is a priori more efficient.
      d26022a1
    • Alexis SALZMAN's avatar
      [xMeshTool] add a new Parmetis partition function with weight · bc7d89a7
      Alexis SALZMAN authored
      This commit is adding template function setParmetisPartitionWithWeight that
      use a set of weights per element to optimize ParMetis partitioning based on
      multi criteria (the weights).  The template parameter (an int) is fixing the
      number of weights per element. The interface is kept simple. Only an extra
      xAttachedDataManagerAOMD is used to passe weights set per element.
      
      No test case for now but it have been heavily tested in some apps.
      
      This function is using almost the same algo as the one used for
      setParmetisPartition in the cc file. It is rather dirty (code
      duplication) but efficient.
      
      It add also a new dependency in terms of cmake. xInterfaceParMetis must
      now be added in cmake to use xLoadBalanceTools. But anyway from my point
      of view it should already be the case. Normally xInterfaceParMetis should
      embedded ParMetis and in cmake finding metis/parmetis lib should not be
      done.... Modern cmake would do even more by setting all this dependency
      setting for you .....
      bc7d89a7
    • Alexis SALZMAN's avatar
      [xInterface][AOMD] add func to xMeshToolAOMD and xAOMDEntityUtil+misc · 3af9ff86
      Alexis SALZMAN authored
       * Add a getPoint function to simplify xPoint creation from mVertex (no
         need of vector like getPoints which is more general).
      
       * make alive commented (in xMesh) printMesh and printEntity functions.
         They will certainly move to AOMD interface one day. But for now
         please let them stay active has I use then for debugging in my
         application. No time to do a test case on the subject.
      
       * To avoid warning on unused variable clean creation of object returned
         by many function that are not used afterward.
      3af9ff86
    • Alexis SALZMAN's avatar
      [xFEM] hopefully simplifying xMesh source · 62dcf4fb
      Alexis SALZMAN authored
      Has we are in the middle of a big change the modify state stuff were
      appearing in xMesh despite their AOMD nature. To simplify, comments are
      removed and  xinterface::aomd::modifyAllState function is use in replacement
      of the ugly set of  12 calls to modifyState method. This will certainly
      disappear in the future
      
      Remove comment regarding printMesh/printEntity. A future commit will
      bring them back alive.
      62dcf4fb
    • Alexis SALZMAN's avatar
      Xfiles] miscellaneous change related to warnings · 953b8f8d
      Alexis SALZMAN authored
      Changes are:
        * unused variable
        * wrong order for explicit member creation
        * wrong sign comparison
        * change int to size_t
        * virtual destructor addition to avoid in future a possible memory leek
      953b8f8d
  23. 28 Sep, 2020 1 commit