News and announcements

Yade 2018.02a

Written for Yade by Anton Gladky on 2018-02-07

==================================================
yade-2018.02a
Wed, Feb 7 20:06:30 2018 +0100

Anton Gladky (15):
      Remove RELEASE file.
      Initialize gui in IPython 5.
      Add dependency on python-pyqt5.qtsvg.
      Fix PDF-compilation with sphinx>=1.4.9
      Remove comented lines in CMakeLists
      Test commit number two.
      Do not enable LINSOLV if CGAL not found
      Fix missing AND operator in prevoius commit
      Extend polyhedra breakage model by Mohr-Coulomb-Weibull failure criterion.
      Add examples for the PolyhedraBreak model
      Add one more Yade-Paper
      Update .gitignore
      Make newly added labels consistent with other labels.
      One more thesis, where Yade is mentioned
      Add RELEASE file

Bruno Chareyre (15):
      Fix https://bugs.launchpad.net/yade/+bug/1666339 (thx Robert)
      +5 journal papers
      +2 journal papers
      + Christian Jakob's PhD in references
      Put brackets in the right place (thx Robert).
      +4 journal papers
      1+ journal paper by V. Lapcevic
      Add editor to Yade workshop proceedings (me!)
      missing comma (sorry)
      turn ERROR into WARNING when ISCollider does not find spheres to determine verletDist
      +2 journal papers
      +2 journal papers
      +11 conference papers
      add missing year in a bibtex entry
      Fix kineticEnergy() for clumps

Chao Yuan (6):
      add porosity in cell info.
      fix compile error.
      add functions to get pore throat radius (by cells or spheres).
      -split computeEffectiveRadius() for obtaining reff by pos and radius; -clean redundant functions.
      -fix setPoreThroatRadius
      -add setPoreBodyRadius.

Francois Kneib (1):
      Fix typo in installation.rst doc.

Jan Stránský (7):
      fixed a typo in micro-stress example
      replaced L3Geom by ScGeom in tutorials
      Added subengines of CombinedKinematicEngine to labeled engines
      fixed a bug in ScGeom::getIncidentVel with avoidGranularRatcheting=False and O.periodic=True
      Updated Body::intrs doc, fixed typo in comment
      fixed a bug in ymport.UNVReader
      fixed one Polyhedra python method name

Jerome Duriez (9):
      Articles .bib entries: fixes https://bugs.launchpad.net/yade/+bug/1671045, plus update of entries data
      capillaryLaplaceYoung scripts: update of reference labels
      +1 master thesis
      A new post-processing engine to measure capillary stresses using alternate expressions than getCapillaryStress()
      Implementation improvement of new MeasureCapStress engine
      JCFpm model: code comment precised (https://answers.launchpad.net/yade/+question/644244)
      -1 check test (regarding NormalInelastic contact law which is about to be erased)
      -1 contact law (Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity and other NormalInelasticPM classes)
      Typos corrected in installation.rst

Martin Haustein (1):
      Add constant volume deformation engine.

Robert Caulk (4):
      Editorial change
      fix typo
      Fix typos
      Roll breakOccurred comments back 1 commit

T Sweijen (12):
      Dynamic version of two-phase flow,interpolation of saturation field when meshing, merging of tetrahedra to find pore units
      OMerge branch 'master' of https://github.com/yade/trunk
      provide access to per pore partial solid surface
      update of Dynamic Two-Phase Flow engine, removing old definitions, update comments, and added several averaging procedures for water pressure
      Function to track deforming pore units and to couple this to dynamic two-phase flow + cleaning of functions
      Minor fix for updating volume change
      fix for savePoreNetwork function - to avoid odd locations of cells along boundary
      fix of comments and cleaning up of redundant lines. Also, inclusion of initial and boundary conditions for dynamic imbibition
      Fix for mergeCells() function, to allow for using it more than once
      Update of initial conditions to allow for primary and secondary drainage/imbibition. Addition of compatibility check of boundary conditions. Removing some redundant functions.
      Fix in TPF Engine for simulations with Deformation + optimalization for TPF + deformation simulations, without swelling
      update of soluteFlowEngine, including a fundamental fix in equations and a function to export average concentration

William Chèvremont (25):
      Adding Electrostatic interaction
      Adding Electrostatic interaction (forgot cpp file)
      Fix the electrostatic law
      Merge branch 'master' of https://github.com/yade/trunk
      Correction of ElectrostaticPhys
      Adding lubrication force w/o FlowEngine
      Merge branch 'master' of https://github.com/yade/trunk
      Merge branch 'master' of https://github.com/yade/trunk
      ElectrostaticMat derive from CohFrictMat instead of FrictMat
      Merge branch 'master' of https://github.com/yade/trunk
      Fix lubrication laws
      set more realistic default values for ElectrostaticMat
      Lubrication can process other physics
      Adding yade-oar and Lubrification resolution by implicit method
      Revert "Adding yade-oar and Lubrification resolution by implicit method"
      Revert "Revert "Adding yade-oar and Lubrification resolution by implicit method""
      Merge branch 'master' of https://github.com/yade/trunk
      fix lubrication
      fix plot Matrix3 suffix (yz instead of yx)
      Merge branch 'master' of https://github.com/yade/trunk
      Fix CMakeList
      Test
      Fix warnings
      Debug lubrification
      Insert other resolution method

bchareyre (59):
      fix the flipCell() function
      fix compile error
      flipping periodic cell -> small/doc fix
      move PBC example scripts
      cleaning examples
      documentation on changing the boundary conditions in FlowEngine and derivatives
      Robert Caulk's guide to cloud computing inserted in doc
      return a consistent set of constrictions in the periodic case (some constrictions were previsously skipped inconsistenty)
      re-apply the fix of rev 26efbec to getConstrictionFull()
      fix a compile warning
      fix an indentation problem in shinx document - hopefully fixing the buildbot
      fix unicode warning (documentation build)
      add a reference url
      fix compiler warning
      small fix in getConstriction() + a typo
      new logic for interating on facets in periodic triangulations (following ref. Rev.26efbec and followers)
      new data 'crackArea' added to DFNFlow cells and updated automatically - first step toward solving the artificial compressibility of fluids in cracks
      #define DFNFLOW commented out
      small updates in doc, fixing compile errors and some warnings
      add exemple script for two-phase flow with 2PFV technique, related to Yuan and Chareyre (2017)
      extended version of ForceEngine with its own fluid solver (by J. Chauchat)
      move HydroForceEngine to independent source files.
      Minor changes in authorship and inline comments
      Critical bugfix for collision detection in periodic boundary conditions. Bounds lists were left partially unordered, then some interactions were never detected (my toughest yade debugging until now).
      Minors & cosmetic.
      fix feature NewtonIntegrator::densityScaling
      Introduce a tolerance on overlap determination (in periodic BC only), avoiding false negative due to round-off errors. (usage in a separate commit).
      A simpler and faster version of spatialOverlapPeri. Only one call to floor(), ~20% speedup for ISCollider::action. Tolerance introduced to fix detection failures.
      Keep the values of sorted bounds in the [0,size] range in ISCollider.
      small scale optimization in ISCollider
      Fix collision detection again (amending commit c7c8e6f62d452c8). Don't move bounds below the starting point of the sort, else partial (only) ordering can occure.
      Don't start blinking the 0-body when opening inspector + make it possible to un-highlight before/after closing the inspector by selecting empty space.
      Fix miscommit in d2211bd747d74eaea569ac88e.
      remove a function that was declared but undefined (leading to runtime error)
      cite recent reference on timestep
      TwoPhaseFlowEngine::getNeighbors now returning less than 4 neighbor cells if some of them are infinite (normally only one)
      a function + python wrap for invading one single pore and updating the clusters
      fix cluster invasion/update (thx Son for spotting the bug)
      fix doctest's target following b5ca352
      fix doctest in addData (re-apply c011decc36)
      fix doctest indentation (after 36c016bd)
      TesselationWrapper wrapping CGAL's AlphaShapes for defining an alpha-contour
      remove function definitions from FlowEngine.hpp
      preliminary version of 'extended' alpha shape contour
      further extension and debugging of alphaShape code
      nearly working version of the extended alpha-contour
      small fix
      proper calculation of alphaCaps areas in TesselationWrapper
      If FlowEngine::meshUpdateInterval<0 do not update the mesh at fixed intervals
      fix a compile warning - probably leading to undefined behavior
      apply d71813b for the periodic flavor of FlowEngine
      re-insert the comment on Qt4->Qt5 since it may still help (partial revert of 1c06b6ad9d2)
      Remove the declaration of (redundant and undefined) FlowEngine::currentTess, while there is already Network::currentTess. Fix https://bugs.launchpad.net/yade/+bug/1732210.
      Use a relevant upperbound (i.e. 0.5*period) for the the maximum body size in periodic boundary conditions.
      Update the position of the clump members relative to the clump itself ("local" coordinates) when applying growParticles(). It is no longer necessary to perform additional operations (updateProperties()) after growing clumps.
      make checkClumpHopper.py less time demanding
      fix bug/1291977 and a typo
      fix some compile warnings in TwoPhaseFlowEngine
      enable TWOPHASEFLOW by default

jduriez (15):
      Email address changes
      Capillary script solveLiqBridge.m: change in attributes order (with small consequences), plus other minor changes
      Capillary scripts: removing one useless test, and including commented time measurement commands
      Capillary scripts: Introducing .py versions for 2 (out of 3) .m files. Plus minor change in one .m file
      Doc: precising Collider.avoidSelfInteractionMask
      +2 book/proceedings chapters (and formatting changes)
      Doc of Shop::aabbExtrema precised
      Doc typos and small improvements in VTK post-processing descriptions
      Small doc changes in TriaxialStressController.particlesVolume and porosity
      Doc: minor change in package installation (distro name)
      Doc: typo in user manual
      Misleading comment removed in UnsaturatedEngine.cpp
      Doc: typo correction in TriaxialStressController.stressMask
      grids examples: moving qt.View() at the end of the scripts so that the window view is correctly scaled with respect to the model
      Doc of Ig2_Sphere_PFacet_ScGridCoGeom updated: replacing inexistant ScPFaceCoGeom with ScGridCoGeom, and Facet with PFacet, fixes 4. of https://bugs.launchpad.net/yade/+bug/1746037

luc scholtes (6):
      update of the JCFPM particle model with new or adapted functionalities to record number of cracks and associated released energy. An example script will be provided.
      add possibility to define residual friction angle (broken contacts) different from friction angle (bonded contacts)
      some cleaning and clarifying of crack aperture calculation
      update of file. mistakes in previous commit
      update due to mistake. Thank you Robert
      update due to mistake. Thank you Robert

raphm1 (10):
      HydroForceEngine: add an optional input parameter to account for convective acceleration The input convective acceleration term take the form of a depth dependent vector
      yade-article.bib: add a journal paper
      Add proceedings
      Add two functions getStressProfile_contact: to evaluate the stress profile considering only the contact contribution getDepthProfile_center: to evaluate solid depth profile (solid velocity and volume fraction) considering particles as points
      Fix error from commit e4f601d
      Add 2 references and 1 paper
      HydroForceEngine: update the 1D RANS fluid coupling Modify the formulation of the fluid resolution in order to merge it with the existing variables of HydroForceEngine. Fix errors in the fluid momentum balance resolution. Clarify the mesh definition. Evaluate all the components necessary to solve the equations inside the fluidModel function. Introduce the possibility to account for fluid lateral wall friction in the equations. Make it possible for the user to access only the fluid resolution without introducing any particles or launching a DEM simulation. Update the documentation.
      HydroForceEngine: new examples and validations Introduce a new sedimentTransport script, which make use of the fluid coupling (1D RANS) Complete the sedimentTransport example script and add a post-processing example. Add validations for the fluid resolution without particles, considering logarithmic law and poiseuille flow. Add a file commenting the different examples and validation scripts.
      HydroForceEngine: small modifications
      HydroForceEngine: fix errors in the fluid resolution

remche (4):
      Fixing clang compilation
      Adding path for CGAL ans GMP include dir to cmake (for exotic installations)
      Merge branch 'master' of https://github.com/yade/trunk
      Adding the correct include dir for CGAL

robcaulk (15):
      added tmux command tip
      Fixed bug with multithread+compressible flow and addressed backgroundAction() FIXME for eigenSolve()
      fixed inheritence problem when LINSOLV=OFF
      Added option to let new bond breaks in JCFpmPhys control retriangulation in FlowEngine
      add fracture interpolation functionality
      GPU accelerated PFV solver
      GPU acceleration guide
      Avoid compiling suitesparse GPU solver if -DCHOLMOD_GPU=OFF
      improve GPU doc
      Merge branch 'master' of github.com:yade/trunk
      improve GPU acceleration guide
      add the ability to threshold trickpermeability to 2 or more facets, default behavior should remain same as before this commit
      fix variable naming inconsistencies
      Merge branch 'master' of github.com:yade/trunk
      fix multithreading issue with imposed fluxes

williamchevremont (1):
      Typo

Read more

2nd Yade workshop April 26-27, 2018

Written for Yade by Jérôme Duriez on 2018-01-19

The second Yet Another Discrete Element workshop: Discrete-based modeling of multi-scale coupled problems, will take place in Aix-en-Provence (south of France), on April 26-27, 2018

This international conference is free of charge, please see https://2ndyadeworkshop.sciencesconf.org/ for all details.

Updated on 2018-01-19.

Yade 2017.01a

Written for Yade by Anton Gladky on 2017-01-19

Dear Yade users and developers,

After almost 7 months of development I am glad to announce
the next Yade version 2017.01a. The complete changelog
you will find as always at the end of this message.

Thanks all for contributions!

Anton

==================================================
yade-2017.01a
Thu, Jan 19 22:07:25 2017 +0100
Anton Gladky (20):
      Remove RELEASE file.
      Add some notes about how to make releases.
      Make Yade compatible with VTK7.
      Use C++11 constructions for InteractionLoop.
      Optimize using of ndarray.
      Partly fix webpage help show. LP:1598174
      Final fix for LP:1598174
      Add missing dependency on python-pyqt5.qtwebkit.
      Fix load/save in GUI-QT5.
      Drop unused typedef.
      Disable LAW2_SCGEOM_CAPILLARYPHYS_Capillarity1 by default.
      Remove some deprecated scripts.
      Increase the size of force container.
      +1 paper.
      Provide a proper functioning with IPython5.
      Add -fext-numeric-literals to fix FTBFS against boost_1.62
      Fix yade with IPython5.
      Update distro names in documentation
      Add missing header include <csignal>
      Add RELEASE file.

Bruno Chareyre (12):
      +2 articles (thanks to Bettina Suhr)
      + 1 proceedings (thanks to Bettina Suhr)
      Update citing_yade.bib
      revert the revert ca0e29ac57
      list authors of the doc as in doi:10.5281/zenodo.34073
      a note on using distcc and ccache
      minor editing of installation page
      Master thesis Morales2012a
      Introduce Network::surfaceSolidThroatInPore() for partial solid surfaces per half-throat
      make the recursion conditional for invasion in multiphase flow
      push a file missing in commit e91ff135b7
      Yade bibtex: "and others" invalid for less than 9 authors

Chao Yuan (4):
      Add cell label for phase cluster. NW-res label 0, W-res label 1, disconnected w-clusters start from 2. label can be saved in savePhaseVtk.
      fix comment on label.
      clean UnsaturatedEngine, move all functions to TwoPhaseFlowEngine.
      Revert DryingEngine.

Francois Kneib (1):
      Fix O.engines in examples/cylinders/cylinderconnection-roots.py

Jan Stránský (11):
      fixed a small bug in shear force computation in CPM model
      Added PolyhedraSplitter example
      Changed L3Geom to ScGeom in tutorial example scripts
      fixed a minor compilation issue in ConcretePM
      Fixed call of _utils.interactionAnglesHistogram with default arduments
      making all Law2::go virtual
      Matrix_computeUnitaryPositive, changed computeThinX to computeFullX flags
      User's manual, added how to visualize force chain in Paraview
      UnstructuredGrid: fiexd little bug in manual setting of facet position from vertices
      added pack.inHalfSpace and pack.inConvexPolygon + example script
      fixed another little bug in utils.UnstructuredGrid

Jerome Duriez (11):
      Doc clarification for TriaxialStressController.externalWork (http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg12083.html)
      Doc of utils.readParamsFromTable() hopefully improved
      Friendlier BibTex entries for 2015 doc. To avoid Smilauer and et al in manuscripts
      Doc Getting help section updated to reflect current practice
      Including interface orientation data in CapillaryPhys code
      Capillary scripts commit (http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg12103.html). Located in a new examples/capillaryLaplaceYoung folder intended to illustrates capillary Law2. With one new simulation script example and another old one, moved here
      Typo and minor corrections of previous capillary commit
      Capillary law2: erasing when necessary sphere-non sphere interactions (bug LP: #1628273) + minor changes
      Capillary law2: restricting test shape. Plus minor change in capillaryLaplaceYoung/README text file
      Doc: small updates in PartialEngine and KinematicEngines
      References .bib files: including new entries

Raphael Maurin (4):
      HydroForceEngine: add a condition to ignore particles fixed on the sideWalls.
      Add an example for the use of HydroForceEngine
      HydroForceEngine: new fluctuation model for the example script + small correction Add new simple discrete random walk fluctuation model, to be used with the new example script fluidizedBed.py Change the condition for applying the fluid force from p>0 to p>=0, which is more appropriate
      Add two example scripts for the use of HydroForceEngine One simple example to get familiar with the application of buoyancy (buoyantParticles.py). One example simulating a fluidized bed configuration to get familiar with both the application of a fluid velocity profile and of turbulent fluctuation with the DRW models (fluidizedBed.py)

bchareyre (19):
      fix invalid pointer, thanks Jerome (https://lists.launchpad.net/yade-dev/msg12791.html)
      (doc) clarify the meaning of TriaxialStressController::externalWork
      fix 1 compile warning
      reordering bib references
      remove latex/multicolumn from sphinx conf.py (compile error on some systems)
      Law2_ScGeom_CapillaryPhys_Capillarity: cache getClassIndex() for use in a loop
      fix wrong access to a Network::boundary by index
      FlowEngine: enable the definition of continuum scale permeability independent of particle sizes
      Introduce DryingEngine (two phase flow with convection in one phase)
      Implement Darcy scale permeability in FlowEngine, introduce alphaShapes (commented), some code cleaning and smallfixes
      (FlowEngine) optionaly include/skip bounding cells when calculating the average pore pressure
      fix negative volumes issue in triangulation cells, consistentlyy remove the includeBoundary option (a workaround) in averageVelocity
      TwoPhaseFlowEngine: better integration of fluid clusters
      merging PhaseCluster code with r3975
      fix compile warnings
      small optimization in Clump::updateProperties
      update phaseCluster attributes: volume, interfacial area, etc. + various smallfixes in the cluster labelling
      further improvement of the cluster labeling in multiphase model
      2PFLOW engine: remove useless int from getInterfaces()'s parameters

booncw (2):
      Pushing Potential Blocks based on CWBoonEtAl2012 Computers&Geotechnics/CWBoon 2013 PhD thesis, but using CLP as linear programming Solver. CLP can be downloaded from Synaptic Package Manager: coinor-clp, coinor-libclp-dev, coinor-libclp1, coinor-libosi1v5. To enable this, set ENABLE_POTENTIAL_BLOCKS to ON in CMakeLists.txt"
      revising Potential Blocks to the latest version to run slope analysis

raphm1 (1):
      ViscoelasticPM : fix resolution problem in find_cn_from_en function Change the value of the initial perturbation for the resolution of the equation to obtain the damping from the restitution coefficient. Allows for a much wider range of resolution in terms of mass, stiffness and restitution coefficient. Put a limiter to avoid division by zero and force the loop to print the warning message if "error" goes to nan (no warning in these cases previously)

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!

Anton

==================================================
yade-2016.06a
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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