Yade 2016.06a

Written for Yade by Anton Gladky on 2016-06-14

Dear Yade users and developers,

After almost 8 months of development I am glad to announce
the next Yade version 2016.06a. The complete changelog
you will find as always at the end of this message.

The versioning of releases is changed and now is in the
form YYYY.MMx. Where x is the letter, which can be
changed by minor updates in the stable releases.

Thanks all for contributions!


Tue, Jun 14 20:30:53 2016 +0200

Anton Gladky (88):
      Remove release.
      Clean some unused macroses (old wm3-stuff)
      Remove some global headers
      Raise minimal boost version to 1.47
      Add -DNDEBUG if compiling in release mode
      Tiny code refactoring
      Clean some warnings and old stuff.
      Return removed header back.
      Fix warning in newer matplotlib.
      Drop old commented stuff in python-scrips.
      Remove flags and preSteps from scene
      Remove deprecated findBoundDispatcherInEnginesIfNoFunctorsAndWarn
      Remove PISC_DEBUG.
      Fix typo in installation sections of doce. Thanks to Jan.
      Export normal and viscous part of the visco-elastic contact
      Remove confusing part in installation part of documentation regarding Qt5.
      Fix typo in CMakeLists
      Tiny updates of examples of LudingPM.
      Fix compilation warnings.
      Update formatting in SpherePack
      Fix an order of calculation of c in SpherePack
      Fix some compilation warnings.
      Fix cappitalization typo in Lapack (case-sensitive in this case).
      Respect VTK6 in PotentialParticles.
      Add .travis.yml for CI.
      Remove version restriction on sphinx.
      Use trusty as build-env.
      Add -y parameter to apt-get install.
      Fix numpy import on travis.
      Fix segfault during save/load of CapViscModels
      Add one more check-script (capillary models)
      Fix typo in check-script.
      Fix crash in Ig2_Facet_Polyhedra_PolyhedraGeom
      vtkExporter: increase number of leading zeros to 8
      Move implementation of methods of ForceContainer in cpp.
      Split implementation of ForceContainer in parallel and serial.
      Add zero-forces to the youngest body after simulation load. Closes LP:1560171
      Drop parallel execution in replaceByClumps. Closes LP:1559098
      Add import of polyhedras from the file.
      Add an opportunity to shift, scale and rotate imported polyhedrons
      Minor fixes in Polyhedra_splitter.
      Fix division by zero crash in Polyhedra
      Add CGAL_DISABLE_ROUNDING_MATH_CHECK, -frounding-math when CGAL is enabled.
      Fix some formatting issues.
      Non-invasive fixes in polyhedra_splitter.
      Get max-min coefs in polyhedra_splitter simpler.
      Use tuple as a parameter for SplitPolyhedraDouble
      Add check script for polyhedra crash.
      Use explicitly -DNDEBUG instead of CMAKE_CXX_FLAGS_RELEASE
      Check isnan in some coordinates before calling CGAL.
      Minor formatting fixes in Polyhedra.
      Add check-script for save/load of clumps.
      Disable checkPolyhedraCrush. It is unstable now.
      Fix checkPolyhedraCrush
      Remove polyhedra_utils import from "ymport"
      Add prefix std:: to isnan and isinf.
      Update checkPolyhedraCrush
      Update files for ppa-infrastructure.
      Undef NDEBUG in all polyhedra files.
      Add pause for checkSaveLoadClumps to escape race condition.
      Use variadic arguments in DynLibDispatcher.
      Fix crash in polyhedra, if maxFs=0.
      Fix checkPolyhedraCrush (remove qt)
      Remove unused functionality in Dispatcher.
      Set Qt5 by default.
      Add mathcmaker for normalCohesion and shearCohesion.
      Split QGLViewer.cmake on qt4 and qt5 versions.
      Add .gitattributes to ignore line endings.
      Migrate buildppa to python3.
      Replace some "#define"(s) by functions.
      Remove some machine-specific items in documentation.
      Add unit test for matchmaker.
      Replace vector by unordered_map data structure in Matchmaker.
      Minor fix in documentation.
      Replace some "defines" by functions.
      Remove numpy.hpp.
      Fix bug in polyhedra_splitter.
      Some cosmetic fixes in core-files.
      Enable C++14.
      Revert 2dc99 and ed8dcb.
      Use unordered_map instead of map for MapId2IntrT
      Use unordered_map only for Boost >= 1.56
      Back to C++11.
      Revert using unordered_map in Body.
      Scale mass and inertia in spheresModify.
      Reduce size of flags in Bounds of InsertionSortCollider
      Fix bug in MatchMaker.
      Add RELEASE file.

Bruno Chareyre (16):
      add labels to default engines for easier showcases
      fix ambiguous syntax, fixing https://bugs.launchpad.net/bugs/1514477
      introduce 2nd edition of the documentation and contact for consuting (in homepage)
      update the webpage about citation with 2nd edition, add 1st edition as an external reference, update pdf metadata
      fix one DOI of the 2nd ed. documentation
      Add missing toctree's for the citable book versions
      fix typo in installation page
      fixed DOI
      fix some hyperlinks pointing to the old geo.hmg.inpg.fr
      declare mask attribute for FlowEngine, fixes a compile error
      use FlowEngine's mask consistently
      implement standalone plastic-shear energy counter in CohesiveFrictional Law2
      define constrictions with consistent cell's ids (see https://answers.launchpad.net/yade/+question/288118)
      fix a compile error
      update boost version in prerequisites (installation page)
      Documentation: include unp in the equations of Law2_ScGeom6D_CohFrictPhys_CohesionMoment

Burak Er (1):
      Implement deformable elements

ChiaWeng Boon (1):
      Commit Potential Particles: non-spherical particles for DEM

Francois Kneib (8):
      TesselationWrapper : add a security that prevents user to access the strain tensor of a particle (aka deformation) outside its boundaries.
      Fix a tensor access in local displacement calculation.
      Fix a bug in Tesselationwrapper: one of the bounding planes was not rightly positionned.
      Fix in TesselationWrapper: allow the tesselation to compute right triangulation in the boundaries of a periodic boundaries conditions simulation.
      Add 5 setters for bodies pos,vel,ori,angVel,color to workaround the memory leak bug when assigning attributes from python (see https://bugs.launchpad.net/yade/+bug/1041084). They are not supposed to stay in the code for a long period (remove them when the bug is solved), but are useful in sims that massively change values of python/c++ binded attributes.
      Simplify one line in TesselationWrapper.
      Fix the debug build that failed to compile due to a mistake in pkg/dem/Polyhedra.cpp
      Fix the inspector GUI for Qt5, thanks to Mark S. Bentley.

Jan Stránský (30):
      Merge pull request #47 from booncw/master
      Potential particles modification
      Merge branch 'master' of github.com:yade/trunk
      Potential particles modifications
      added forgotten file from previous commit
      Modified python interface for O.forces.addF(...,permanent=True) and addT(...,permanent=True)
      fixed some warnings during docs build
      Added frictAngle MatchMaker for Ip2_FrictMat_CpmMat_FrictPhys
      set b.aspherical=True in utils.polyhedron and utils.tetraPoly
      Polyhedra modification
      Added a material model for mortar layer
      Polyhedra.setVertices improvement, preventing memory leaks (question #290947 and bug #1570679)
      Interaction::reset explicitly resets also its functorCache
      Fixed a strange bug in Law2_PolyhedraGeom_PolyhedraPhys_Volumetric and shearForce
      Added useRef parameters to VTKExporter.exportPolyhedra and VTKExporter.exportInteractions
      Modified MortarMat
      Merge branch 'master' of github.com:yade/trunk
      fixed computation of shearForce in Law2_PolyhedraGeom_PolyhedraPhys_Volumetric
      added and modified examples for MortarMat
      Merge branch 'master' of github.com:yade/trunk
      added MatchMaker for E in Ip2_CmpMat_CpmMat_CpmPhys
      Fixed a bug in pack.inSphere, related to question #292846
      Merge branch 'master' of github.com:yade/trunk
      VTKRecorder, added orientation for box export (question #293635)
      Modification of CPM
      Fixed ymport.textPolyhedra function (bug #1582775)
      added x_y_z_r_attrs format to ymport.textExt
      Added an example for generation of 'agglomerate' packing
      Fixed Law2_Cpm default parameter to keep backward compatibility (question #294657)
      Better default value from previous commit

Jerome Duriez (12):
      +1 journal paper
      Incorporating previous +1 paper in JCFpm doc
      + another journal paper
      makeCloud doc changes with the hope to make it clearer for all users
      Doc of TriaxStressController.porosity precised
      Doc improvements of previous commit improved
      Last doc improvement of previous commit
      normalForce and shearForce convention (sustained by #2) precised in docs
      fabricTensor() now ok for non-periodic simulations. revertSign attribute removed as well
      getSpheres*() functions: getting rid of dynamic test, see http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg11956.html
      fabricTensor(): unify the behavior regarding boundary interactions whether split=0 or 1: they are now disregarded in both cases
      fabricTensor(): re introducing all kind of interactions in the loop, with the new possibility defining a cutoff. See http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg11982.html

Klaus Thoeni (23):
      fix some typos and add some more details
      fix Anton's previous commit (make doc was not working)
      fix documentation for Note
      some polishing
      gts shift and scale apparently only take three float values, hence changed
      Merge branch 'master' of github.com:yade/trunk
      move grid specific functions in separate module and add some more doc
      add some more examples, show same functionality as with chained cylinders
      update doc
      add Grid and pFacet references
      Initial version of the PFacet implementation (contributed by Anna Effeindzourou)
      Examples for creating pfacets
      update tests according to new gridpfacet module
      remove postLoad function as not used, this fixes as well serialization problem in --test
      better handling of double contacts, get gid of function ScGem goOneWay
      improved documentation
      add definition for cylinder and cylinderConnection basen on gridConnection, add warning for chainedCylinder usage
      examples for cylinder and cylinderConnection
      example with many cylinders and 2 pFacets
      QT5 is default now
      correct some typos
      similar to example in chained-cylinder-roots.py
      add reference

Raphael Maurin (6):
      HydroForceEngine: modify the turbulent fluctuations formulation and add a new DRW model The turbulent fluctuations model takes now the form of a function of HydroForceEngine and is not anymore called from a flag. In addition, an alternative DRW model has been added.
      HydroForceEngine: adapt the averageProfile function for bi-disperse mixtures. Evaluate the streamwise, spanwise and wall-normal average particle velocity for the two defined types of particles.
      HydroForceEngine: modify turbulent fluctuation model. Add a fluctuation along the spanwise (y) direction. Reset the fluctuation to zero when the particle is out of the flow (fix a bug) Comment a bit more the turbulentFluctuation function
      HydroForceEngine, hpp file completing the last commit
      Add references
      add a link in the publications

bchareyre (1):
      compute external work correctly in TriaxialStressController

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