Yade 2018.02a

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

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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

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