Yade 0.90

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Anton Gladky
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Release notes 

The main new feature is a moving build-system from scons to cmake.
It will hopefully bring better portability of the program on different platforms
and operating systems/distributions.


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Anton Gladky (142):
      Remove RELEASE file.
      Fix cmake-file to compile.
      Fix paths in core-files.
      Update CMakeLists.txt.
      Fix pygts module.
      Fix standalone compilation of InteractionLoop.hpp.
      Enable pymodules on cmake-build.
      Add version definition to cmake-build.
      Fix suffix and runtimeprefix in cmake-build.
      Fix compilation error with gcc-4.7
      Fix facetBox generation with height=0.
      Fix permissions on main.py.in file.
      Fix installation of binaries in cmake-build.
      Remove log4cxx from scons-file.
      Fix binary installation at cmake-build.
      Remove an explicit defining and importing of listdcxx.
      Install some py-files for cmake-build.
      Install glviewer in cmake-build.
      Fix path install in cmake-build.
      Update CmakeLists.
      Return explicite defining of libstdcxx. Causes error.
      Use rpath for lib-installation.
      Fix linking of core-libraries.
      Fix some more linkings in cmake-build.
      Reinitilize interactions after adding a body. Closes LP:1001194
      Move gui-cmake to gui-folder
      Move cmake for python modules to py-folder.
      Separate python modules in cmake-build
      Fix some liking in cmake-build
      Some fixes in cmake-build.
      Add autotest to check bug LP:1001194
      Give the newly created body an id, which is the size of bodyContainer. Remove lowestFree. Nicer fix for LP:1001194
      Add scene->doSort variable. One more fix for LP:1001194. Thanks to Bruno.
      Fix linking of opengl in cmake-build
      Fix vtk-linking in cmake-build
      Install pack.py for cmake-build
      Add notice about python-demgengeo
      Add URLs on python-demgengeo package. Fix links.
      Fix some more linking problems in cmake-build
      Fix plugin search path in cmake-build
      Cosmetic changes in cmake-build
      Fix performance tests.
      Fix overlinking in cmale-build
      Make vtk mandatory.
      Fix -batch binary in cmake-build
      Partly fix QT in cmake-build. Still not functional yet.
      Return vtk-feature, but not use it
      Fix gui in cmake-build.
      Minor fix in cmake-build
      Add 2 dependencies to install-section for cmake-build.
      Enable "options" for cmake-build.
      Remove technical output during cmake-build.
      Fix compilation error during non-gui cmake-build
      Revert vtk-feature. Not mandatory again.
      Add debug-build to cmake.
      Use Predicate functions, only when gts is enabled.
      Place -lrt flag into the right place.
      Fix rpath issue
      Remove combine_sources function.
      Fix header definitions in openmp-accu
      Fix check-test during no_gts build
      Fix import libstdcxx on old systems
      Display information about disabled features
      Add NOSUFFIX option for packaging.
      Add lrt to linking on cmake-build
      Fix linking problem of cgal libraries in cmake-build
      Fix "typo" in VTKRecorder. Thanks to Vaclav.
      Remove path to python in some scripts.
      Move all main libs to usr/lib/yade folder
      Move minieigen to py-folder
      Add doSort-option to InsertionSortCollider for forced resorting of interactions.
      Minor fix in cmake-build
      Link miniEigen with boost-python libs. Thanks to Klaus Thoeni.
      Fix version definition for git and bzr.
      Enable use of custom Boost-libraries. Thanks to Klaus Thoeni.
      Try to fix cgal compilation.
      Add possibility to set the lib-path.
      Fix libpath, if it is non-standard.
      Fix CGAL-feature for cmake-build.
      Fix libpath with scons.
      Fix version definition and generation of pdf.
      Change Version option to YADE_VERSION.
      Add option description into CMakeList file.
      Start to update installation documentation.
      Start to update documentation on installation.
      Describe compilation and installation processes with cmake.
      Minor fix in instalaltion section.
      Remove scons from documentation.
      Remove compilation instruction for Gentoo.
      Check, whether newly added bodies to a clump are already members of the existing clump. Closes LP:1017367
      Fix handling ipython 0.13 version.
      Return CHUNKSIZE option.
      Update documentation on installation.
      Better fix for ipython-versions. Hopefully the ipython-interface will not be broken in a future.
      Remove some bzr-notes from documentation.
      Remove scons.
      Minor fix in documentation.
      Add chainId parameter to body.
      Implement stopAtTime parameter.
      Add iterBorn and timeBorn parameters to interactions.
      Rename chainId to chain. Add python-wrapper to utils.facet
      Remove timeBorn option in interactions.
      Remove debug and rebuild options from docs and starting scripts (not functional with cmake)
      Fix execution error.
      Use vtkQuad for exporting boxes in vtk-format. (Closes: LP:1026474)
      Let to use relative paths in INSTALL_PREFIX variable.
      Remove clumps, if no bodies are present there. Fixes LP:1031644. Remove clump members from clumps during body erase. Move Clump.* files to core/
      Add "make doc" command for easier documentation build.
      Fix some warnings.
      Add bodiesHandling.facetsDimensions function to get parameters of group of facets.
      Replace the variables "max" and "min" on "minVal" and "maxVal" in spheresPackDimensions to escape coincidence withi function names
      Add README.rst file for github
      Add getBodyIdsContacts to get the list of bodies, contacting with the checked one.
      Keep pointers of interactions for all bodies, not only where otherId>Id. Add ENABLE_FIXBUGINTRS option.
      Fix an error in interaction container.
      Add checkIntrs flag into body to escape useless checks of interaction.
      Fix segfault with FIXBUGINTRS enbled.
      Add regression test to check the erasing of bodies, which are in contact.
      One more step to fix bug of facet-sphere mass interaction.
      Add function to disable some interactions, if the sphere contacts with several facaets of the same chain.
      Prevent errors in facetCylinder, if height=0.0
      Move fixbugintrs stuff from Newtonintegrator to shop.cpp and constitutive law.
      Move fixbugintrs stuff into viscoelasticpm, for a quicker compilation.
      Integrate some ideas into RockPM
      Some minor fixes in eigen-macroses.
      Remove testcode for fixing LP:850864
      Fix serialize-template for matrix6r.
      Fix version read from RELEASE file.
      Fix version number output at Yade start.
      Fix some compilation warnings.
      Fix warning due to mix class/struct definition.
      Honor the flags, which are set in environment.
      Fix compilation warning »_POSIX_C_SOURCE« redefiniert."
      Disable CGAL, if compilator is clang.
      Add information, how to compile Yade with Clang-compiler.
      Fix batch-mode on platforms, where cpuinfo is not available.
      Remove rebuild-option from batch-mode.
      Remove old testing macros in VTKRecorder.
      Remove accidentally added file in examples.
      Add normalVel parameter for SpheresFactory to set explicitely direction of velocity for newly generated particles. Backward compatibility is saved.
      Add RELEASE file for 0.90.0 version.

Bruno Chareyre (61):
      - Direct solver used for periodic BCs and/or compressible fluid - saveVTK for periodic BCs - fix rare but possible junk permeability values (define max/min)
      -FlowEngine uses boost::thread to precompute triangulation and Cholesky factor while yade is running
      - interplate using barycenters of old trangulation, instead of voro-center of new triangulation, avoids inconsistencies - make sure voidVolume is positive (FIXME: hardcoded number a.t.m.)
      - normalize the definition of minimum void volume
      -add a simple getStress function (periodic or not)
      move an insert in a more logical place
      A new contact law adding creep (Standard Material Model) to CundallStrack
      -missing in previous commit
      restore the option to NOT homomDeform in periodic BCs (may be rarely used, e.g. when veru big bodies are part of the simulation)
      restore the option to NOT homoDeform (see previous commit too)
      - let PeriTriaxController accept very large bodies in the simulation. This change makes it possible to simulate bi-periodic BCs with 2 large planes bounding one coordinate. Example script comming soon.
      - remove junk output left after debugging work
      - compatibility of the 6D cohesive-moment law with periodic BCs. - add a simpler way to turn contacts cohesive one by one via an Ip::flag
      -fix force application in cohesive law (was breaking chained cylinder and sent buildbot error)
      replace Dem3Dof by ScGeom where CundallStrack is used
      -remove a series of contact laws as discussed in https://blueprints.launchpad.net/yade/+spec/cleancontactlaws
      remove contact laws (again), as discussed in https://blueprints.launchpad.net/yade/+spec/cleancontactlaws
      - Implement multithread solving for the periodic flow - Start implementing CHOLMOD solver using Eigen3 support - Fix flow engine compilation with cmake (some variable with multiple definitions breaking per-file compilation)
      - CHOLMOD handling in cmake
      - be quiet when cholmod is disabled
      remove some "cerr"
      -reset initCohesion flag for each contact after initializing (else it's rested at each step...)
      -add functions to export network constrictions and normal and track a point in the triangulation using secondary flow engine (Bruno+Wenrui)
      - better parameter (vector > 3 doubles)
      - use cell handles vector instead of CGAL's cell iterators for faster loops - make mirror permeabilities i->j vs. j->i exactly equal in the periodic cases to avoid non-positive definite matrices - fix a few mistakes in permeabillity min/max bounding (permeabilityFactor was not included, and the min was way too high, changing 50% of the values) - make multithread run possible also in the periodic case
      smallfix in documentation
      Fix compile warnings.
      - add export functions for writing system matrix to files
      reverts commit afa59f17d59a90d3049b9c51c41d28e29fc9081e, which messed up flow code.
      -fix conflict
      Document Tesselation wrapper a bit more. Add a complete example script.
      small optimizations in PeriodicFlow, start implementing matrix-based froce computation (commented blocks)
      documentation here and there
      documentaion fix
      - a unique function for fluid velocity in cells for both periodic and non-periodic - make fluid velocity computed correctly even on boundary cells with imposed pressure - the boundary are now included in computation average velocity in the simulation - A new function to get total flux through a boundary
      - Simplify the usage of GSTiemeStepper: no need to set dt at all as soon as GST is present, and setting dt manualy will not disable the timestepper. - Introduce density scaling
      example script for timestepper and density scaling
      Small change in the logic of cylinder-cylinder interactions
      sort exemple scripts
      documentation fix
      adapt the interface to the new timestepper logic
      doc hyperlink for density scaling
      fix compile error (sorry, it was working with chunksize>1)
      - remove a loop in Newton as suggested by Anton (Thanks) - update example script
      - adjustents of strain rate in ex. script
      Still smallfixes in density scaling
      Revert "Fix the computation of the shear lubrication force and add the torque of the viscous shear force applied on particles." This commit erased some of the previous changes. Please Donia double-check what you commit everytime.
      fix two compile warnings
      The \` are displayed correctly by sphinx. Get them back (at the price of many warnings?...)
      - remove some "invertSign" in stress functions - add a utils::function to change friction without the need to instantiate a TTCompression engine
      - make use of Shop::setContactFriction()
      make warning conditional or it will flood my terminal...
      example script for cohesive and/or rotational law
      some updates in this example script
      make autostop possible again (but still disabled by default)
      -enable 0-thickness bounding boxes
      example script for triax+clumps
      -A new function to grow particles and clumps
      cleaning script
      clean sources

Chiara Modenese (3):
      Check the body existence before creating an interaction. (Closes: LP:803774)
      Add a new entry to yade-conference.bib.
      Add some entries into yade-conferences.bib

Christian Jakob (9):
      improvements in Law2_ScGeom_CapillaryPhys_Capillarity
      Fix memory leak in capillary law and make isBroken flag compatible with fusionDetection
      include calm function
      fix mask bug in calm function
      export boxes with vtkrecorder (not tested, boxesCells missing)
      export boxes with vtkrecorder (visualization works, but is not ok)
      fix uniax.py and periodic.py example scripts
      fix and improvements of some example scripts
      delete unneeded file

Donia (2):
      Fix the computation of the shear torque.
      Fix the computation of the torque and rename some variables.

Donia Marzougui (12):
      Add spheres' rotation to the computation of the viscous shear force. Compute the viscous shear bulk stress.
      small fix in min Y
      Merge branch 'master' of github.com:yade/trunk
      Add the normal and tangential lubrication force Compute the viscous shear stress for each body
      Add rotation of spheres in the computation of velocity, Compute the viscous and normal stresses applied on each body, add the normal and shear lubrication forces
      Fix the names and tests of forces and stresses applied on particles
      Merge branch 'master' of github.com:yade/trunk
      Fix the computation of the shear lubrication force and add the torque of the viscous shear force applied on particles.
      Fix the computation of the shear lubrication force and add the torque of the shear viscous force applied on particles.
      Fix the computation of the shear lubrication force.
      Fix the computation of the normal lubrication force
      remove the computation of some characteristics lengths for two fictious spheres.

Francois Kneib (5):
      Add the contact between two different ChainedCylinders. -> add new contact geometry : "ChCylGeom6D" -> modified "Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D()" to instantiate the new contact geometry when it is necessary -> add new law : "Law2_ChCylGeom6D_CohFrictPhys_CohesionMoment()" -> add new CohFrictMat parameters : "CohFrictMat.cylCylNormalCoh" and "CohFrictMat.cylCylShearCoh". They are used to set the cohesion between two different ChainedCylinders ("CohFrictMat.normalCohesion" and "CohFrictMat.shearCohesion" was already used inside a ChainedCylinder). Fix bugs into "Ig2_Sphere_ChainedCylinder_CylScGeom6D" and "Ig2_Sphere_ChainedCylinder_CylScGeom"
      Fix an ScGeom6D bug : declare the cylCyl boolean variable as hidden in the YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY instead of in the ScGeom6D class core.
      Merge branch 'master' of github.com:yade/trunk
      -python function for handling grid objetcs
      Create new classes to add grid simulations. Grid are made of GridNodes and GridConnection (two new shapes inheriting from Sphere)

Jan Stránský (15):
      added periodic cell's deformation and strain measures
      improvement of Cell documentation
      Cell class improvement
      made stressTensorOfPeriodicCell deprecated
      Fixed bug in export.VTKExporter, corrected some docstrings
      little more fixes in export module docstrings
      Added Law2_ScGeom_CpmPhys_Cpm class other modifications of CpmMat related classes
      Added Ip2_FrictMat_CpmMat_FrictPhys functor
      corrected mistake from previous commit
      Fixed compilation issues in ConcretePM.cpp reported by Anton Added utils.setNewVerticesOfFacet function
      improved documentation (corrected some warnings and errors during building docs, added inherited-members directive)
      improvement of ymport.unv and export.VTKExporter
      add example file for previous commit
      fixed small bug in export.VTKExporter.exportFacetsAsMesh add geom.facetSphere
      another bug fix of export.VTKExporter.exportFacetsAsMesh

Klaus Thoeni (1):
      - add possibility to use local boost installation (e.g. -DLocalBoost=1.46.1)

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