yade-users team mailing list archive

[Anton Gladky <gladky.anton@xxxxxxxxx>]

Dear all,

Yade 0.95.0 is available for download [1].
The Ubuntu stable packages [2] and Debian packages for experimental
branch [3] are ready. The full changelog is attached.

Thanks all, who contributed in this version.

[1] https://launchpad.net/yade/trunk/0.90/+download/yade-0.95.0.tar.gz
[2] https://launchpad.net/~yade-pkg/+archive/stable
[3] https://buildd.debian.org/status/package.php?p=yade&suite=experimental

Anton

Anton Gladky (41):
      Remove RELEASE file.
      Fix compilation warning.
      Fix typo in git-command.
      Remove doxygen from installation section.
      Add notification message for yade-batch.
      Enable SnapshotEngine.
      Minor fix in documentation.
      Fix pack.py as suggested by Kneib François.
      Remove all Py_BEGIN_ALLOW_THREADS and Py_END_ALLOW_THREADS to prevent race conditions in python-bindings. (Closes LP:1056684)
      Return back some Py_BEGIN_ALLOW_THREADS, as the previous commit freezes autotests.
      Add url to Chen`s thesis.
      Add Tran`s publications.
      Remove duplicate.
      Minor fix in references.
      Search numpy during configuration step.
      Search loki-library and headers during compilation step.
      Resize interactionsOnBody, if it is necessary. (Closes: LP:1105177)
      Fix compilation.
      Add omp.h header into ParallelEngine
      AddNUMPY_INCLUDE_DIRS to cmake.
      Remove --debug option from yade-batch template.
      Remove debug-option from yade-batch.
      Fix import of Image-module in Ubuntu Raring.
      Fix segmentation fault in bodyNumInteractionsHistogram. (Closes: LP:1087680)
      Use default {CMAKE_CXX_FLAGS_DEBUG for Debug-build instead of hardcoded.
      Make the bug LP:1087680 visible again.
      Fix segmentation fault in bodyNumInteractionsHistogram.
      Return back the opportunity to keep all interaction pointers for each body
      Use interaction pointers in body class instead of iteration over all interactions in body::py_intrs.
      Add visualisation to Jakob`s scripts.
      Merge pull request #32 from jakob-ifgt/master
      Merge pull request #33 from jakob-ifgt/master
      Add python-argparse into installation section.
      Merge pull request #34 from jakob-ifgt/master
      Remove scripts/debian as it is maintained in Debian itself
      Remove extra/boost_python_len.hpp as it was for very old boost-versions.
      Remove extra/foreach.hpp_local. Not used anywhere.
      Remove site_scons. Forgotten during cmake-migration.
      Remove convexHull2d. Was blocked.
      Remove boost-python-indexing-suite-v2-noSymlinkHeaders.
      0.95.0

Bruno Chareyre (68):
      Give the git clone adress that will work always (previous one is blocked at 3SR lab)
      enable setting FlowEngine by number of steps or by deformation aplitude
      a fix in bibtex
      -remove excess verbosity
      - add thread number attribute to change the number of thread of interactionLoop dynamicaly during simulations. Also usefull combined with parallel engine (for fine grain tuning of thread number in each subprocess)
      1. Add thread number to parallel engine, can be changed dynamicaly. Uncouples the number of threads in parallel engines and in slaves.     2. Enable nested parallel regions (disabled on many systems by default) else the parallel engine is doing no good
      1. Replace one loop on cells by an optimized vector<Cell> iterator     2. Clean an horrible block of code (not only ugly, it was also slow)
      - introduce a position buffer for faster updates of volumes
      Use retriangulation conditions more consistently. The solvers are not swapped before a given fraction of the permutation interval now, to reduce overheads.
      small change in the initialization logic, now defining the two position buffers if "first"
      make ompThread an attribute of Engine, as it likely to be used more and more in the future. It is then inherited by InteractionLoop and ParallelEngine
      Parallelize volume updates and the computation of fluid forces
      fix a typo introduced in previous commit, giving compile error in FlowEngine
      remove traces of the SpherePadder module, which is broken and unmaintained (with author's agreement)
      make grids periodic
      use EpsVolPercent_RTRG consistently in periodic flow: negative value is ignored, just like the non-periodic case
      Adapt setContactProperties to pass argument in radians to Shop::setContactFriction
      -fix conversion mistake (radian/degree)
      update variable names to denote the unit of friction angle (rad), and make this explicit in the documentation
      - include elasticity in the normal lubrication force     - fix ompThreads assignment in flow engine, resulting in numThreads=-1 by default, then "libgomp: Out of memory"
      Fix the F9-F12 keys binding for IPython>=0.12
      -add the correct prefactor in normal lubrication relation     -overlap the two triangulations during one iteration in order to have the "previous" forces     defined in the normal lubrication equation
      Update the documentation of the ompThreads attribute.
      - fix again the offset of ids in SpherePack.toSimulation (previous fix was assuming two bodies per clump)
      - fix https://bugs.launchpad.net/yade/+bug/923929 again, as shown by François it could still happen in some cases (see example in the bug report)
      - remove the check/throw when generating aperiodic 2D packings, since the algorithm actually support that.
      Define O.engine with a default list at startup, with example script and notes in the documentation.
      remove utils prefix
      - Updates and improvements in the triax-tutorial material     - smallfix in a note in introduction.rst
      fixed version of the triax script for clumps
      Remove first iteration form "--performance" option measurements
      -transfer the normal lubrication force correctly when retriangulating
      -doc fix
      -fix the sign of the normal lubrication force in the periodic case
      fix compile warning (actually fix the functions as well, as they were not returning results at all!)
      - doc fix
      -remove remaining debug lines
      periodic update of publications
      fix a typo in bibtex file, +1 ref
      - one fix in articles, yet more references in conferences
      fix/add Tran's reference
      - use "orientation" parameter in utils.box (fix bug/1111514)
      - improved version of TriaxialStressController, controling not onlt stress but also strain rate     - making the interface more similar (but still not exactly like) PeriTriaxController.     - TriaxialCompressionEngine and ThreeDTriaxialEngine become almost useless     - reflected in the example script which now uses only TriaxialStressController
      -micro-fix (no need to define an initial timestep)
      -code cleaning
      - fix the default value of orientation in utils.box. [1,0,0,0] is NOT a quaternion.
      -add a few python bindings to the periodic engine for manipulations of the internal tesselation
      -fix the detection of (not) already computed tesselation
      -make volume() functional also when PeriodicFlow is actually in use
      uncouple the compilation of flow code and linsolv, so that it is possible to effectively compile the flow engines without cholmod
      remove useless "sigma_iso" and "isAxisymetric" members from TTController
      - make an old engine deprecated, not compiled now, to be removed later
      more #ifdef guards, to allow flow engine without linsolv
      remove sigma_iso from the triax example script
      fix syntax error in a doc string (blocking the buildbot https://yade-dem.org/buildbot/builders/yade-full/builds/1741/steps/shell_3/logs/stdio)
      -deprecation warnings in ThreeD and TriaxialCompression engines
      -change the default value of FlowEngine::pressureForce, a flow engine is supposed to compute a flow by default...
      smallfix in example script
      - 3 new references
      - add "Open Source Discrete Element Method" explicitely in the home page, google has to find us
      nicer documentation of equations for stiffness definition
      remove useless #define
      - ship a copy of ipython_directive.py from ipython/HEAD for ipython 0.13
      ipython version was checked in two different places, forgot the second one. Still no confirmation of the fix.
      - some lines comited by mistake, sorry for that.
      - escape crash on non-iterable __doc__ (some qt class)     - define new attributes needed for ipython_directives.py >= 0.13     - fix existing *.rst to use strictly 3 blank spaces in multiline directives (i.e. "   ...:")
      - reference name Tran2012a appearing twice -> renaming Tran2012b
      - re-introduce the @supress of Christian (removed during experiments)

Christian Jakob (21):
      add addToClump() method in yadeWrapper
      improvements in clump logic - part 1
      Improvements in clump logic - part 2
      Added new example script, that show usage of addToClump() and releaseFromClump()
      Improvements in clump logic - part 3 + 4.
      shorten the code of replaceByClumps()
      add a check of python input for replaceByClumps() method
      further improvements in clump logic
      some fixes in documentation of wrapper and state
      fix documentation of clumpTemplate in utils.py
      Merge remote branch 'upstream/master'
      let replaceByClumps return a list of tuples with new clump ids and associated sphere ids
      Merge remote branch 'upstream/master'
      avgNumInteractions now takes care of clumps
      some improvements for previous commit
      doc fix in utils.py and exclude unused Clump.hpp in _utils.cpp
      updated documentation of clumps in user manual and small fixes in doc in yadeWrapper
      Merge branch 'master' of github.com:yade/trunk
      bug fix in replaceByClumps, that could lead to set negative masses on bodies and shorten the code
      yet another doc improvement in wrapper and user manual concerning replaceByClumps method
      replaced errors by warnings in addToClump and releaseFromClump in wrapper

Donia Marzougui (5):
      Fix the computation of viscous forces by using the     correct positions of bodies (updated in     buildTriangulation), and fix some variable names.
      Remove fictious spheres from the computation of edge surfaces (employed in the computation of viscous forces)
      Correct the computation of the viscous and normal stress per particle.
      Correct the sign of some parameters in the computation of the viscous forces.
      Correct the normal lubrication force.

Francois Kneib (24):
      Continue the implementation of grids :     - add GridConnexion Aabb     - add GridNode-GridNode Ig2 functor : Ig2_GridNode_GridNode_GridNodeGeom6D     - add GridNode-GridNode contact geometry : GridNodeGeom6D     - add an example script : examples/grids/Simple_Grid_Falling.py     - update utils.py (minor change)
      Add the possibility of avoiding the contact detection between a group of particle.     -> the vector "avoidSelfInteractionMasks" contains a list of masks : all particles having the same mask will not collide if this mask is inside this list.     -> the "mayCollide" method now check this too.     -> avoidSelfInteractionMasks can be set in python with a list of int.
      Add the Sphere-GridConnection frictionnal contact :     -> new contact geometry : ScGridCoGeom     -> new Ig2 : Ig2_Sphere_GridConnection_ScGridCoGeom     -> new Law2 : Law2_ScGridCoGeom_FrictPhys_CundallStrack     -> update utils.py to handle the new contact type (using avoidSelfInteractionMasks)
      Merge branch 'master' of github.com:yade/trunk
      Add the contact following and avoid multiple contact when a sphere is sliding on a grid.
      -Grids : Fix some minor bugs in Ig2_Sphere_GridConnection_ScGridCoGeom::go(...).     -Collider : Change the vector of masks "avoidSelfInteractionMasks" to a single mask "avoidSelfInteractionMask".
      Create and correct documentation.
      Grids :     - modify the rendering.     - Apply correct DEM laws in utils.py to set right kn, ks, kr, and ktw. Now the grid behavior no longer depends on the spacial discretization you make.
      Modified setContactFriction method.     Now it has to be used with an angle in radian unit, no longer in degrees.
      Try to fix documentation in this files, everywere "yref" appears in the online documentation.
      Fix Grid periodicity, and allow periodic sphere-grid contacts.
      Disable a boring warning into the grid construction.
      Fix a bug in SpherePack.toSimulation. There was a big problem when you tried to add clumped SpherePack (with makeClumpCloud() for example).
      Corrected toSimulation() (for the last time I hope :-) ).
      Fix a bug in growParticles(...) method.     Growing a clump is now really homothetic. Before that, growing clumps seemed to be homothetic but at the next timestep the original position of members was reseted.
      Add Inelastic ChainedCylinder behavior law (by Ignacio Olmedo).     Create inelastic material and related physics, Ip2 and Law2.     Example script and complete documentation will come soon.
      Add the ability to save to a file a SpherePack containing some Clumps.     Into SpherePack : now the toFile method writes a fifth column containing the clump number (-1 if the sphere isn't clumped). The fromFile method uses the new information to append clumped Spheres.     Into Shop : loadSpheresFromFile method is modified to read and return the fifth column. Old files with 4 columns are still compatible.     Into CapillaryTriaxialTest and CohesiveTriaxialTest : Shop::loadSpheresFromFile is sometimes used here, so remove the clumpId information to match the "BasicSphere" typedef.
      getStress(...) method : exclude gridNode-gridNode contacts for the stress computing.     growParticles(...) method : avoid growing gridNode and gridConnection.
      Fix some Grids bugs.
      A minor spelling correction.
      Add a little class summary and explanations into Grid.hpp.     Fix a bug into utils.py when creating a Grid in a non-periodic scene.
      In the sphinx documentation, add the https GitHub read-only method : git clone https://github.com/yade/trunk.git
      Avoid GridNode-GridNode contact stiffnesses (kn and ks) to be changed when the growParticles(...) method is used. (GridNodes are not concerned by this method).
      Add a missing space in the dependencies code lines.

François Kneib (1):
      Correct a remaining bug into the toSimulation() python function.

Jan Stransky (9):
      little modifications
      added example script for CombinedKinematicEngine
      little modifications of ConcretePM
      modification of ConcretePM, improved utils.intrsOfEachBody function
      improved yade executable: optparse->argparse, yade executable is now loadable as python module
      modified yade executable, fixing bug 1134422
      complete optparse->argparse, --generate-manpage should work
      improvement of ConcretePM, remover warnings in pack module (randomDensePack and randomPeriPack functions)
      modified ConcretePM, corrected Peri3dController related examples

Jan Stránský (1):
      minor changes

françois (1):
      makeClumpCloud(...) now takes a "seed" parameter to generate always the same pack.

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