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ChangeLog
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==================================================
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/[email protected]/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/[email protected]/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
==================================================
yade-1.20.0
Fri, Oct 9 21:20:00 2015 +0200
Anton Gladky (57):
Remove RELEASE file.
Simplify definition of build flags
Fix some warnings during compilation.
For clang use -fstack-protector instead of -fstack-protector-strong
Ignore project files of idea IDE
Refactoring of Math.hpp
Make minieigen external package mandatory.
Add -fstack-protector-strong only for gcc >=4.9
Some warning fixes.
Add ENABLE_PROFILING option
Set some metric-measures in ViscElCap.
Revert adding frounding-math flag
Replace INSTALL_PREFIX by CMAKE_INSTALL_PREFIX
Remove deprecated in Yade BOOST_PYTHON_FUNCTION_OVERLOADS macros.
Fix some more compilation warnings.
Fix some more compilation warnings.
Minor fix in CMakeLists.txt
Fix hexagonal packing, should not be undesired overlap any more.
Make Serializable.hpp more readable.
Remove deprecated parameters.
Move STLReader into STLImporter
+1 master thesis at TU Freiberg.
Fix crash by export-VTK of interactions after body removal.
Split description of ViscoelasticPM to make it more readable.
Let exist interactions between clumpMembers of the same clump.
Skip force calculation in SPH-clump
Add warning about CGAL in Ubuntu 14.04 Trusty
Add ISC_TIMING pre preprocessor directive.
Drop support of Ubuntu 12.04 Precise
Merge pull request #46 from timpovall/master
Non invasive refactoring of InsertionSortCollider
Revert previous commit.
Add a second option to fix the compilation with CGAL on 14.04
Remove deprecated code with very old boost.
Implement viscous damping for capillary phase.
Fix SPH force calculation between clump members.
Fix compilation with QGLViewer>=2.6.3
Prepare Qt5-build.
Fix compilation against gqlviewer-qt4.
Fix check-script
+1 conference
First steps in Qt5.
Prepare Qt5 build.
Update python files due to Qt5.
Some more updates toward Qt5.
Qt5-migration is alsmot finished.
Fix Qt5 compilation.
Fix crash in Qt5.
Fix QThread issue.
Add information about compilation against Qt5.
Add missing function in TesselationWrapper
Remove some unused headers and defs.
Fix compilation if openmp is disabled
Fix compilation introduced in last commit.
Add talk, hold in Particles 2015
Add hourglass example
Add RELEASE file.
Bruno Chareyre (15):
Save relative rotations in ScGeom6D (unmark "nosave") since it is required for reloading correctly.
CohesiveFrictionalInteractions: removed "nosave" flags for contact moments
+1 journal paper
+1 journal paper
add a virtual function returning rotational stiffness of the interactions - returning zero if not overloaded
account for the rotational stiffness of interactions in GlobalStiffnessTimeStepper
apply the spin of the velocity gradient on particles in periodic BCs
small typo
Added book chapter
Installation: http://www.yade-dem.org/packages is required for an external library (eigen or cgal? not sure now)
more accurate defintion of fluctuational velocity/spin for kinetic energy in periodic BCs
correct value of volume for id<6 in TesselationWrapper when O.bodies does not have bounding objects
fix segfault when InteractionContainer::found() access out of bounds
add function has() to O.interactions to check if (id1,id2) exists + fix doc of O.interactions
remove useless int parameter of O.interactions.all(), instead filter non-real interactions optionaly based on bool
Chao Yuan (3):
-add getPotentialPendularSpheresPair() function.
-set pore throat radius between two fictious cells negative in invadeBoundary=true mode.
add a new version of capillary law. (pushed by Caroline)
Francois Kneib (2):
New viewer feature : display tori instead of spheres for 2D simulations. So if the viewer looks toward the right axis, on can see circles instead of disks. Modifications in pkg/common/Gl1_Primitives.*pp 3 new parameters in Gl1_Sphere : circleView, circleRelThickness, circleAllowedRotationAxis. A new condition to enable circleView. The code is based on initGlutGlList() method for spheres.
Add an example script for the tori DISPLAY feature.
Jan Stránský (4):
fixed compilation warning
added Polyhedra.setVertices function, which also updates internal variables (shape.v=... does not)
Added Facet.setVertices function to prevent memory leaks (see bug 1041084, #8)
corrected bug in utils.UnstructuredGrid.updateElements (question #267761)
Janek Kozicki (2):
Fix bug in InteractionContainer::eraseNonReal
Fix: CGAL ERROR: assertion violation!
Jerome Duriez (5):
Add missing space in error message
Doc of sphSph attribute of plotDirections precized
Introduction of surface tension as an attribute, and comments about code objects related to capillary files
Addition in doc of Omega.engines to state it is = to O.engines in python
Removal of python O.engines reference
Raphael Maurin (9):
getStressProfile: output format modification + add calculation of granular temperature and kinetic stress tensor
Law2_ScGeom_ViscElPhys_Basic: add a new formulation + check Add a new formulation of the law when imposing in the material young, poisson, and normal restitution coefficient. The effective spring constants ks and kn are evaluated "classically" with the young modulus and the poisson's ratio. The specificity of the formulation stands in the fact that it is the restitution coefficient of the contact (en = 2*en1*en2/(en1+en2)) that is imposed, and not the damping constant. To achieve this, the damping constant of the contact is evaluated resolving numerically the analytical expression 21 of [Schwager2007] (with a minus sign, there is a mistake in the article) with a Newton-Raphson algorithm (This was made by Francois Kneib). This does not seem to affect the calculation time. With this formulation, there is no tangential viscous damping, and it is usually not possible to access value of normal restitution coefficient lower than 0.1 (in that case the numerical resolution does not converged in the maximum 15 iteration allowed in the code) Together with the new formulation, add a short check script to verify that the imposed restitution coefficient is the one obtained.
Law2_ScGeom_ViscElPhys_Basic: complete the documentation Add a more precise documentation of the law integrating the last commit. I didn't complete the formulation associated with Pournin2001 (precising en,es,tc) as I am not using it and I do not know it much.
Fix compilation error in the documentation of Law2_ScGeom_ViscElPhys_Basic Error inserted in commit d47b8574e8fcc2dc09b926404f08081f2194cfde
Add a function in shop to evaluate average depth profiles of particle velocity (x,y,z components), and solid volume fraction.
HydroForceEngine: switch averageProfile function into a method + modify documentation
Tutorial examples: remove all deprecated 'utils.' and GravityEngine in the example scripts
Modify getDepthProfile to possibly average on spheres of selected radius only
HydroForceEngine: modify averageProfile function to handle bi-disperse sample Add evaluation of the average solid volume fraction and drag force depth profiles considering the two particle size (taken as input) as independent.
Timothy Povall (1):
Removed line calling FindVTK.cmake, as this file no longer exists
thomassweijen (1):
Updates towards merging of both capillarity codes
==================================================
yade-1.14.0
Tue, 21 Apr 2015 22:36:55 +0200
Anton Gladky (36):
Remove RELEASE file.
Fix typo in SPH.
Move SPH-body parameters into body->state.
Add one more kernel function in SPH.
Change sign in calculation of viscosity in SPH
Simplify Lucy kernel function
Remove Cs parameter from VTK-export (sph only).
Implement second variant of BSpline kernel function.
Fix typo in Bspline kernel functio (sph).
Fix date typo in Changelog
Move Vf and Vmin from Body`s parameter to Body->state.
Replace struct intReal by standard std::pair
Prevent returning of a real value from void-function.
Fix probably a wrong using of if-condition.
Minor fix of using of std::abs function.
Drop some if-conditions, which have always constant value.
Drop default inclusion of DFNFLOW.
Add some missing #ifdef YADE_CGAL.
Fix check-script for LIQMIGRATION.
Drop -frounding-math compiler flag from FindCGAL.
Drop embedded floating_point_utilities_v3.
Reintroduce floating_point_utilities_v3.
Add missing files from last commit.
Add LiqMigrEnabled parameter.
Fix compilation with GCC-5. (Closes: #778190)
+2 Project works
Add an opportunity to list works, other than master thesis.
Fix body unselecting. (Closes: LP:1423130)
Fix MatplotlibDeprecationWarning: The use of 0
Remove DirSearchYade, MicroMacroAnalysis and someFile.pdf
Clean current directory after --check
Check file existance before its moving and removing.
Add information, how to be notidied after each commit.
Add an opportunity to set frictAngl through MatchMaker in ViscEl
Add an option coordNumber to be exported in VTK.
Add one more master thesis.
Bruno Chareyre (28):
FlowEngine: set cell's id in periodic triangulations + couple smallfix
fix bad bugs in DFNFlowEngine following uninitialized 'isClump'
use the dedicated solver in DFNFlowEngine
some code documentation
FlowEngine: discard blocked cells completely when assembling the permeability matrix
#undef DFNFLOW
FlowEngine: enhanced setter macro, detect changes in imposed pressure and update the linear system accordingly
explicit error message when trying to interpolate capillary forces out-of-range of the data files
fix save/load QGL camera state via text files
Documentation. Define sign convention globaly in TriaxialStressController docstring, not repeated in attributes documentation
bib reference of 1st workshop
fix mistakes in conferences.bib
+13 journal papers using yade
+14 conference papers
small update in the publication page
fix and sort some bib references + change the title of the conference section
+1 journal paper
+1 conference paper
+1 journal paper and fix alphabetic ordering of a few items
FlowEngine safely impose flux at every iteration without remeshing + documentation
implement blockHook for PeriodicFlowEngine as well
Add .mailmap file defining git alias for multiple adress emails
sphinx '..only::' directive removing some parts that break in latex
integrate Ning's FEMxDEM doc in yade's doc
add references in relation with FEMxDEM + couple fixes in *.bib
remove FEMxDEM readme, replace by FEMxDEM.rst for inclusion in doc
remove '..only:' from sphinx files - not yet supported on older sphinx then breaking the html build | update bib's
Update introduction.rst
Chao Yuan (7):
move computePoreThroatRadius() to 2PFlow
-move initialization() to 2PF
-fix inconsistency in invasionSingleCell and getMaxImbibitionPC; clean code; remove savePhaseVTK in Unsat
-remove cleanInterfaceWithinPore() in Unsat.
fix inconsistency of side boundary cell pressure of closeBC drainage.
Add some comments on FlowEngine(by bruno).
Fix error in computing cell->info.solidLine
Christian Jakob (10):
fix force and torque vtk output for boxes
temporary fix for pfv vtk output when vertex ids were not zero-based
fix fusion detection for hertz model in capillary law
reduce error message spam for capillary law
remove unused testing function in capillary law
fix previous commit for case (fusionDetection && hertz model) in capillary law (re-initiate bodiesMenisciiList at first real contact) and add some comments
improve/fix documentation about clumps
insert link to user manual in documentation of NewtonIntegrator
update DEM background doc for clumps
some code cleaning in clump methods
Francois Kneib (1):
Add the Yubuntu (live-usb with Xubuntu and Yade) alternative for installation.
Jan Stránský (10):
PolyhedraMat and PolyhedraPhys are now inherited from FrictMat and FrictPhys, modified related examples Added Ig2_Sphere_Polyhedra_ScGeom
Added examples for Ig2_Sphere_Polyhedra_ScGeom, added ymport.ele function
Added documentation of Ig2_Sphere_Polyhedra_ScGeom
Allowed Polyhedra-Wall interaction if Wall.sense==0
fixed Cpm for Sphere-Box interactions
added export.textPolyhedra function
added Elias2014 article to yade-articles.bib
add attrs parameter to export.textPolyhedra
modified Clump::updateProprties to handel non-spherical bodies, added associated example
box inertia computation correction
Jerome Duriez (19):
Sign convention change for fCap, to be consistent with global framework. Plus other minor changes. As discussed in http://www.mail-archive.com/[email protected]/msg10868.html and http://www.mail-archive.com/[email protected]/msg10877.html
Doc hyperlinks, and erase of commented lines
Many changes towards a more consistent sign convention throughout the code for stresses and strains. Should fix e.g. https://bugs.launchpad.net/yade/+bug/1381282. The goal is to know directly the meaning of a strain or stress value each time one is encountered. Relying on the classical Continuum Mechanics convention (editorial choice...). A global announcement is planned in a couple of days, in case some errors appear in the meantime.
Other changes regarding sign convention. Add of deprecation warnings (existing in the code and at execution) in the doc. Fix of script-session2.py previously broken
See https://bugs.launchpad.net/yade/+bug/1394942 answer # 3
Minor doc fixes
Anecdotic doc change, see http://www.mail-archive.com/[email protected]/msg10972.html
Add of O.thisScene() function to know in which scene we are
Add of sphSph parameter in plotDirections() to take into account only sph-sph interactions in polar histograms. Seems it does not modify really the plots, but it is easier to figure out with the parameter
TSC engine: internal compaction now may consider isotropic tensile cases. See http://www.mail-archive.com/[email protected]/msg11047.html
Removal of parallel loops in capillary Law2: needs maybe more verification, and improvements for fusion detection
Typo in the doc (missing space)
Correction of minor inconsistency between comment and command
Extra parenthesis removed in doc
Doc of capillary law2, concerning fusionDetection, precised (see https://lists.launchpad.net/yade-dev/msg11792.html)
Doc typos
Parallelization of one loop of Law2_ScGeom_CapillaryPhys_Capillarity (see http://www.mail-archive.com/[email protected]/msg11238.html) and some comments
Typo in ScGeom, precision about twist doc (axis) in ScGeom6D
Minor fix of previous commit (hyperlink)
Klaus Thoeni (2):
update references
update some links and typos
Luc Scholtes (3):
changes for DFNFlow + corrections in JCFpm associated with the use of the never erase flag
minor changes in DFN Flow
add references
Luc Sibille (5):
Add 2 article references in yade-articles.bib
correct a proceeding reference
correct reference key in 1 proceeding
fix missing comas after key references
add fragile parameter to CohFrictMat and redefine unpMax CohFrictPhys
Ning GUO (2):
Ning Guo's FEMxDEM package added to trunk
Example REV generation for FEMxDEM
Raphael Maurin (6):
add some references in yade-conference.bib
Switch a private argument to public in HydroforceEngine.
HydroForceEngine: minor fix + add an averaging function Minor fix : modify some default value of the parameters, remove unecessary parameters. Add a 1D averaging function which evaluate the average depth profiles of the solid volume fraction, the solid velocity, and the drag force. The averaging is weighted by the volume occupied by the particles in the layer considered.
Add new function to compute stress tensor depth profile. Compute and return the stress tensor for each cell of height dz, between two limit points given by the user. The stress tensor computed include contributions from both particles inertia and Love-Weber stress tensor. This last take into account only the part of the branch vector contained in the cell.
Minor fix in getStressProfile. The order of the argument in _utils.cpp was not the right one.
HydroForceEngine: small modifications in the averaging function. Perform the averaging also on the y and z component of the particle velocity, instead of only x before.
T Sweijen (7):
update for dynamic two-phase flow
small correction
add initSolver()
delta t for dynamic two-phase flow
add function to get the pore body radius
add one get functions for pore volume and rename that of inscribed sphere
add one get functions for pore volume and rename that of inscribed sphere
==================================================
yade-1.12.0
Mon, 20 Oct 2014 21:22:00 +0200
Anton Gladky (27):
Remove RELEASE file.
Use toleranceWarning and toleranceCritical for DEM-PFV check.
Fix crash after clumps removing. Closes LP:1354433
Add checkClumpHopper autotest.
Fix crash after removal of the whole clump.
Fix calculation of massR in ViscoelasticPM
Fix cs calculation in ViscoelasticPM
Fix ViscElPM one more time.
Create an array of clump`s memberIds to remove.
Return fictional value from deprecated functions.
Respect returnin value in computeForceTorqueViscEl
Update Schwager2007 URL
Add one more paper
Merge pull request #44 from fifthguy/master
Add firstIterRun parameter to PyRunner.
Use system call "sphinx-build" instead of python module.
Fix compilation error in PeriodicFlow.hpp
Set python versions explicitly.
Move function declarations of _utils.cpp into .hpp
Fix runtime error in debug mode and without openmp.
Drop including "yade/" folder in cpp and hpp files.
Fix docs-generation.
SPH-code refactoring.
Use only vtkCommonCore vtkIOImage vtkIOXML components for VTK.
Use Python 2.7 only
Reintroduce viscosity in SPH-modell.
Add RELEASE file.
Bruno Chareyre (33):
-include UnsaturatedEngine to start Chao's work
fix a few mistakes and make a real (not empty) test function
- replace hand-defined positions by scene's positions
Merge branch 'master' of https://github.com/yade/trunk into chaoUnsat
remove pack.particleSD and variants, unmaintained and deprecated by makeCloud (functions kept temporarily but returning error)
fix https://bugs.launchpad.net/yade/+bug/1362090
fix https://bugs.launchpad.net/yade/+bug/1308074
fix https://bugs.launchpad.net/yade/+bug/1368591 + remove a useless test
remove a temporary fix for https://bugs.launchpad.net/yade/+bug/923929, after better fix in https://github.com/yade/trunk/commit/4ea76ad6e47ac5074a389ad61712a0840e8560a5, thanks Anton
parallel removal of old interactions
replace LOG_ERROR by LOG_WARN for notifying deprecation of GravityEngine
improve falling back to 1-thread in parrallel collider (fix https://bugs.launchpad.net/yade/+bug/1368591)
fix missing brackets resulting in wrong permeability in periodic PFV
point to Bourrier2013 for a partial explanation of the CohesiveFrictional contact law
fix doc regarding requestErase() - https://bugs.launchpad.net/yade/+bug/1370736, thanks Jan
selective blocking of cells of the mesh in FlowEngines (preliminary steps)
remove empty file
PFV: don't skip perm calculation for blocked cells, yet
fix filename
remove cpp with wrong filename
reset id of erased bodies; enabling this: b=Body(); O.bodies.erase(O.bodies.append(b)); O.bodies.append(b)
turn DeprecationWarning (not displayed) into UserWarning (displayed) since the error messages where cryptic
no indexing of blocked cells in PFV
decrease verbosity of blocking PFV cells
DFNFlow unblock cells as fractures reach them + additional attributes in JCFPM
split resetNetwork and resetLinearSystem + add more getter/setter
split TwoPhaseFlowEngine in hpp/cpp for inclusion in child engines
#ifdef guard for openmp function
don't overwrite imposed fluid pressure when initializing the values (more flexible) + a function returning barycenter + improved "locate" for interpolation
increased flexibility of imposing fluid pressure in FlowEngine's
specialized getter/setter's for TwoPhaseFlowEngine + no re-indexing of cells in UnsatEngine
better #def/#ifdef logic for TwoPhaseFlowEngine
rename cellCenter->cellBarycenter (missing in prev. commit)
Chao Yuan (86):
- my first work on drainage simulation
Commit the first working code for drainage
- make the FAR constant more flexible (a parameter in addBoundaries)
-add poreRadius
-a test commit to escape big mess...
Merge github.com:yade/trunk into chaoUnsat
-add saveLatticeNode functions for generating axial-normal slice with "0" and "1"
-add isWaterReservoir, isAirReservoir.
-add another version for drainage.
-delete unnecessary recursion for invadeSingleCell2()
Merge github.com:yade/trunk into chaoUnsat
Merge github.com:yade/trunk into chaoUnsat
-add UnsatCellInfo, UnsatVertexInfo
clean code
-add temp function for pore connection
Merge github.com:yade/trunk into chaoUnsat
-update boundary attributes
-a backup for laptop
-add UnsatVertexInfo(void) for future use
-test commit
-test commit
Merge remote-tracking branch 'origin/chaoUnsat' into chaoUnsat
Merge github.com:yade/trunk into chaoUnsat
-clean code
add capillaryCellVolume in cellinfo, optimize getSaturation()
-replace cell->info().p with isAir/WaterReservoir
-add solidLine in cell info. partly code for force.
clean code, fix mistake on Facet_Force.
a test version of computing fluid force.
fix solidLine[i][j] when facetNFictious case(1).
-fix noCache.
-fix solidLine[i][j] when facetNFictious case(2).
-clean code.
fix reservoir attr. change boundcells.isWaterReservoir=true when finish drainage.
clean code.
add temp test func.
add cell->info().trapCapP; fix pressure calculation for trapped phase.
clean code.
Merge github.com:yade/trunk into chaoUnsat
clean code.add action()
add getSaturation2() for mode 2.
Merge github.com:yade/trunk into chaoUnsat
borrow saveVTK from FlowEngine
normalize two invade modes.
make computeForce optional;a bakcup
a temporary save, change waterReservoir=bound[2], add invadeBounday option
-make invade from boundary optional.(default false)
-fix Line_Solid_Pore() in Network.
Merge github.com:yade/trunk into chaoUnsat
-big change, inherit from FlowEngine.
remove old files
clean code
fix force calculation.
add compute specific interficial area, lots of bugs...
fix computeCellInterfacialArea with fictious vertex
-test. no big change.
Merge github.com:yade/trunk into chaoUnsat
Merge github.com:yade/trunk into chaoUnsat
Merge github.com:yade/trunk into chaoUnsat
-fix ‘python’ declared bug
-clean some info in debug
-fix core dump in computerForcePoreForceWithCache, currentTes shoule be solver->T[solver->currentTes],NOT solver->T[currentTes]
Merge github.com:yade/trunk into chaoUnsat
Merge github.com:yade/trunk into chaoUnsat
-update with PFV
-use bndCondValue to mark reservoir.
-fix reservoirs determination; fix invade(), Pw can be negative (mode1)
-change invade rule, use bndCondValue to determine invasion. reservoirInfo depends on bndCondValue; merge isInvadeBoundary.(mode1)
-change invade rule for mode2. merge some functions
-fix getWindowsSaturations.
-add pore radius checking funcs(tmp)
-rename variables for computePoreRadius(); clean code.
-clean code
Merge github.com:yade/trunk into chaoUnsat
Merge github.com:yade/trunk into chaoUnsat
-add debugOut to test isInvadeBoundary=True isPhaseTrapped=True
-insert debugOut. (core dump fixed by ulimit -s 16000)
Merge github.com:yade/trunk into chaoUnsat
This is TwoPhaseFlowEngine (alpha version) yeah!
Merge github.com:yade/trunk into chaoUnsat
-merge TwoPhaseFlowEngine, add more cell infos.
Merge branch 'master' of github.com:yade/trunk
-add savePhaseVtk. rename function.
-remove check cell.index
Merge branch 'master' of github.com:yade/trunk
comment #define TWOPHASEFLOW
Christian Jakob (6):
insert updatePorosity option in TriaxialStressController
fix long line in github doc
small fix of a warning in NewtonIntegrator
minor fix in doc introduction.rst
include fluid stiffness for TSC for undrained flow condition
fix fluidStiffness for TSC when FlowEngine is deactivated
Dominik Boemer (1):
Add check-script for ViscoElasticPM.
Francois (1):
Correct contact tracking bugs for grids. They essencially came from the new logic of laws that have to return booleans.
Jan Stransky (7):
Added force and torque export to VTKRecorder (question #252413)
fixed typo in utils.polyhedron function
enable periodic simulations with Polhedron and Tetra
rename PolyhedraVolumetricLaw -> Law2_PolyhedraGeom_PolyhedraPhys_Veolumetric
deleted vtk output of force for boxes (bug #1376734)
added Polyhedra::GetSurfaces function
Added volumePower attribute to Law2_PolyhedraGeom_PolyhedraPhys_Volumetric, Polyhedra code small cleanup
Janek Kozicki (2):
Fix bug in 'inspect' that made editing values annoying.
Merge doc/sphinx/references.bib into doc/references.bib
Jerome Duriez (3):
Re-write of "Yade on GitHub" wiki page in sphinx doc.
Anecdotic commit to keep a track (in code comment) of a useful link for JCFpm paraview analysis
Removal of very last wiki-link github-related in rst files
Raphael Maurin (1):
New force engine to couple Yade with a 1D RANS code. Add a new force engine applying the main hydrodynamical forces in function of a 1D average fluid velocity vector which depends only on the depth. The engine is calculating at each time step the drag, lift and buoyant forces for each particle. Complete the references for the documentation associated to the engine.
T Sweijen (1):
Merge two-phase flow engine
Thinkpad (1):
-a test commit from laptop
cyuan (7):
a small change for check reservoir boundingCells.
-add temp function for generating sample windows, calculating responding saturation...
-add savePhaseVtk
Merge github.com:yade/trunk into chaoUnsat
Merge github.com:yade/trunk into chaoUnsat
-replace abs, max, min by std::abs, std::max, std::min
Merge github.com:yade/trunk into chaoUnsat
cyuanLaptop (1):
-change debugOut
fifthguy (1):
Fixed a bug that appeared when running the uniaxial-post.py script from examples. Edited py/post2d.py to capture exception while importing Vector3 from minieigen.
jduriez (12):
Correction of an error using psd() with monodisperse packings (false = False in python). Add of an explanatory message
Few changes in capillary doc: assumption of null wetting angle, hyperlinks, and some comments in source code
One forgotten change during previous commit about TriaxialStressController <-> 3DTriaxialEngine ? https://github.com/yade/trunk/commit/77bc6d75b780bcbad5bdadc5bb3645badb009cd9
Adding mention of different save files kinds. Tried to comment differences, please correct if I was wrong
Typos and precisions in capillary doc
porosity() function infers now a volume value for non-periodic cases, rather than throwing an error. Positiv volume values eventually passed as argument override this inferred value
porosity doc changed according to previous commit
getStress() considers now an adequate volume value for non-periodic case (values passed as parameters may still also be taken into account)
Re-introducing change from https://github.com/yade/trunk/commit/ab91b3cf8654f6d563dede10184e784a8ce84219, reverted since, without reason
Improvement of https://github.com/yade/trunk/commit/05599b23808991dbfef6b85400c7ddd32be594e0 regarding volume computation in getStress for non periodic cases
Typo in CapillaryPhys doc
Parallelization of interaction loops in Law2_..._Capillarity (which is in fact not a LawFunctor handled by InteractionLoop). Moreover adopting the FOREACH iterator for the non-parallel flavour.
==================================================
yade-1.11.0
Mon, 4 Aug 2014 18:54:00 +0200
Alexander Eulitz (9):
small corrections of messed up indentations
another indentation fixed
rearranged compilation and installing procedure so that hints for multicore compilation are placed directly after the make command
typo fix
fixed --cores implementation and improved arg-parse argument documentation.
improved doc of betan and betas
replacing damping coefficient betan and betas by damping ratio betan and betas
rearranged indentation of examplarily folder structure for yade complation
Added hint about make errors during compilation when user does not posses root priviledges.
Anton Gladky (58):
Delete RELEASE file.
Add YADE_PTR_DYN_CAST to define dynamic_cast.
Remove all "using namespace std;"
Fix compilation with disabled openmp.
Roll back last 2 commits.
Remove most of "using namespace std;"
Replace math.h by cmath in includes.
Remove some more "using namespace std;"
Remove "using namespace std;" everywhere. Tests are failing.
Replace abs by std::abs.
Clean up in header inclusions.
First stage of C++11 implementing.
Add missing header.
Remove isIndexable and isFactorable.
Use boost::shared_ptr for C++11 as well.
Drop Qt3 workaround
Enable LBM by default.
Enable C++11 by default.
Do not consider Eigen3 like a feature.
Capitalize feature list.
Use double precision for VTKREcorder.
Do not use -DTYPEOF, use explicit decltype
Move definitions of YADE_PTR_CAST YADE_CAST YADE_PTR_DYN_CAST into Math.hpp
Remove -std=c++0x definition for pygts.
Join [CohFrict]Mat, Phys and Ip2_.
Move Ip2_*_MindlinCapillaryPhys into HertzMindlin
Move Ip2_*_CapillaryPhys. into CapillaryPhys.
Move Ip2_FrictMat_* into FrictPhys
Move all NormalInelastic files into NormalInelasticPM
Join all InelastCohFrict files into InelastCohFrictPM.
Join all KinemC*Engine.* into KinemC__Engine.*
Set C++11 only for CXX-files, not C
Update LICENSE file, does not need exception any more
Cut off some header inclusions.
Disable reusing of removed body ids.
Fix compilation.
Replace nullptr by reset().
Join all Bo1_* into Bo1_Aabb
Remove some more .cpp-files.
Move many Gl1_* into Gl1_Primitives.
Remove some more small cpp-files.
Remove some warnings.
Remove LBMbody.cpp and LBMlink.cpp.
Remove Indexable.cpp
Exclude Indexable.cpp from CMakeLists.txt
Redirect --test output into stdout
Modify slightly description of save-loadVars
Change stderr to stdout in greeting message.
Update Vaclav`s occupation in sphinx-doc
Cut long line in HertzMindlin.hpp
Move some YADE_PLUGINS into common.cpp
Fix most of compilation warnings.
Return false in BubbleMat, if no penetration.
Fix and enable DEM-PFV-check.py.
Replace L3eom by SCgeom in stl and gts examples.
Use global interpreter lock (GIL) in OpenGLRenderer.
Update mtTkinter version.
Remove NEWS file (outdated).
Bruno Chareyre (9):
Revert "Revert "Set minimal required Eigen3 version 3.2.1"" / Thanks Anton for uploading the backport
replace abs by std::abs (complement of https://github.com/yade/trunk/commit/1997c194c0aa759cae101a3dd0a559fcf049b29f)
+2 conf papers
Law2 return bool - fix https://bugs.launchpad.net/yade/+bug/1324190
add missing 'return bool' in some Law2's
Revert "implement more accurate porosity calculation..." (temporary required in order to revert 915fd94606af6 without conflict)"
Revert "fix typos and indents; cut long lines.. - please no formatting commits (+there is nothing wrong in long lines). Please reapply the documentation part."
make growParticles fatser for clumps
use Shop::growParticles in TriaxialStressController (fix https://bugs.launchpad.net/yade/+bug/1351275)
Christian Jakob (5):
fix typos and indents; cut long lines in TriaxialStressController; bit more documentation of stressMask
implement more accurate porosity calculation for clumps in TriaxialStressController; inserted updateClumpProperties command in Triax tutorial
Merge branch 'master' of github.com:yade/trunk
make PFV compatible with clumps (clumps are treated as spheres with equivalent radius - valid for nearly spherical clumps)
reapply 9e512fd50083
Francois (1):
Simplify the contact detection in Ig2_GridConnection_GridConnection_GridCoGridCoGeom.
Jan Stransky (3):
fixed bug in export.VTKExporter.exportInteractions (question #250922)
modification of utils.UnstructuredMesh, added utils.polyhedron
fixed bug in MASK_ARBITRARY feature
Jerome Duriez (7):
Correction of some broken sphinx links: yade._utils => yade.utils
Removal of a double :
Improvement of previous commit: there was no extra : but a missing blank line
Export principal stresses and directions in VTKRecorder
Some shortening in VTKRecorder, mainly according to http://www.mail-archive.com/[email protected]/msg10370.html
Revert sign convention in bstresses in VTKRecorder (tension=positiv now)
Slight modif in JCFpm doc. To better describe the logic of the code.
Kubeu (1):
replaced "root" from last commit
Nolan Dyck (2):
Update BubbleMat.hpp and BubbleMat.cpp
Update bubble example script.
==================================================
yade-1.10.0
Wed, 25 Jun 2014 19:35:00 +0200
Anton Gladky (47):
Delete Release file.
Add orientation parameter to ymport.textClumps
Resize ForceContainer after each body insert
Added assert to get*Unsynced function
Better fix for ForceContainer-size-change
Remove extra/floating_point_utilities_v3
Remove some 'using namespace boost'
Remove some more `using namespace boost`.
Remove all remaining `using namespace boost`
Fix compilation in DEBIG-mode.
Link against libboost_date. Fix LP:1322274
Set the mask to a clump the same as the first member of it.
Revert removal of embedded floating_point_utilities_v3.
Add particleconserve parameter to LiqControl.
Replace features by CONFIGURED_FEATS.
Prevent first empty item in features.
Add checkLiquidMigration autotest.
Better check for DEM-PFV-check.py
Add missing header.
Add --as-needed flag to yade-lib.
Comment some lines, where defined unused variables.
Minor fix in documentation of viscoelastic.
At every sync check, whether ForceContainer is large enough.
Disable parallel code in conditionalyEraseNonReal
Skip interactions, where one of body isClump
Fix doc-compilation for IPython >=2
Enable vectorization in eigen3-lib
Do not use Eigen3 in parallel mode.
Recommend minimal Eigen3 version 3.2.1.
Set minimal required Eigen3 version 3.2.1
Add NOVECTORIZE option
Prevent adding liqVol-parameters into VTK-files
Prevent crash in liqVolIterBody
Disable vectorization by default.
Replace Quaternion.Identity by Quaternion((1,0,0),0)
In state pos_set and ori_set use passing by value.
Add addLiqInter function to set liquid "properly"
Liquid migration model, code refactoring.
Add script to changes commit`s author`s names.
Fix typo in installation.
PFV code refactoring.
Fix typo in previous commit.
Fix templates names.
Clean in ymport.stl
Remove service-messages in CMakeLists
Add missed #pragma once
Add RELEASE file.
Bruno Chareyre (11):
CohFritMat documentation
document Ip2_CohFrictMat more
make the parallel collider warning more explicit regarding turning collider.ompThreads=1
CohesiveFrictional contacts: make them elastic only if strength<0 (previous condition was <=0) + Lingran's elastic energy of contact moments
fix fluidForce=0 after remeshing + allow constant positions for DFNFlowEngine
make FlowEngine::setPositionsBuffer virtual
missing declaration of function
fix default attribute in DFNFlow
CohesiveFrictionalContactLaw does not warn about incremental formulation of rolling/twisting moments when the moments are elastic
fix bug in FlowEngine::updateBCs() (reported by Luc Scholtes, thanks)
Revert "Set minimal required Eigen3 version 3.2.1"
Christian Jakob (2):
remove relicts of Dem3Dof and code cleaning
increase maximum length of char filename in saveVtk method for FlowEngine
Francois (1):
Update the documentation for Law2_ScGridCoGeom_NormalInelasticityPhys. At this moment it's not done, but it will be fixed and come with a reference article during 2014.
Jan Stransky (4):
Body::groupMask may be optionally boost::python::long_, subsequently modified code where necessary
fixed bug in yade.export.exportFacetsAsMesh (thanks Jan Havelka for reporting)
added mask_t type for bitmask variables to be int or optionally std::bitset of fixed (yet arbitrary) size. Added bitset to/from python long conversion. Added MASK_ARBITRARY cmake option. Subsequent changes in other files
corrected git warning in CMakeLists.txt
Jerome Duriez (6):
Correction of mispelling in example script name of one Law2
Minor changes in JCFpm
Important change in Kinem.. engines. Both changes in position and velocities of boundary bodies were still existing, while now changes in position should be handled by NewtonIntegrator
JCFpm : doc of JCFpmPhys.FnMax precised (minor change). And formulation of kn for onJoint interactions according to JCFpmPhys.crossSection (rather than mean of surfaces) to be consistent with the whole formulation ("major" change : this may impact the results of previous scripts depending on psd and how much the mechanical behaviour of joint is important)
Doc of VTKRecorder.skipFacetIntr precised so that it better corresponds to code
Extra s in previous commit removed..
Klaus Thoeni (4):
remove old code
improve output and remove first iteration in calculation velocity estimation
add definition for functor order
set number of iterations to be run correctly (thanks Alex)
==================================================
yade-1.09.0
Sun, 18 May 2014 17:32:07 +0200
Alexander Eulitz (1):
corrected a little bug in description of yadedaily-installation and added example and folder structure for compilation
Anton Gladky (97):
Remove RELEASE-file.
Fix setting of wall's color.
+1 reference.
Replace some bazaar-links by github.
Update installation instructions.
Update INSTALL file.
Fix version definition for IPython>1.0.0
Fix warning for IPython > 1.0.0
Add radiusTopInner, radiusBottomInner to facetCone and facetCylinder.
Increase number of steps in checkWeight.py
Prevent returning a reference to local temp object.
Prevent binding a reference member to a temp. value.
Remove notice on the main page about daily packages on Launchpad.
Some more changes on the main page.
Add Lambert formulation into capillary models.
Use enum instead of string to keep capyllar type.
Update config of mini-dinstall.
Do not ignore k* and c* parameters if mass==0
Add billiard example script.
Introduce YADE_ODEINT feature
Implement binary-arch only builds for yadedaily.
Fix split delimiter
Fix library name for new openblas.
Output some additional messages, when DEBUG mode is enabled.
Fix compilation with libqglviewer>=2.5.1
Fix compilation with libqglviewer>=2.5.1
Add informational message, if VTK6 is found.
Disable some debug-messages, because they break compilation.
Check, whether manipulatedFrame exist, if not - create it.
Set mouse parameters, only if frame is created.
Better fix for QGLviewer next version.
Fix compilation.
Move all force and torque calculation into separate function
Move capillary functions out of ViscEl-classes.
Implement Soulie capillary model.
Add an example to test different capillary models.
Deprecate getViscoelasticFromSpheresInteraction.
Update examples and test-scripts due to deprecating of getViscoelasticFromSpheresInteraction.
Update Warning about last changes.
Use MatchMaker to set tc, et and en in ViscEl model
Update URL in getViscoelastic
Fix compilation in ViscElCap.
Minor description update.
Replace isnan by isfinite to let the numbers be 0.
Remove last capillar-parameters from ViscEl.
Remove massMultiply paramter
Fix compilation.
Implement experimental SPH-model
Add gradients and laplacian of the kernel functions.
Implement some more kernel functions.
Remove duplicated code.
Normalize parameters of kernel functions.
Produce meaningful error message.
Add Cs parameters to particles, visualize them in VTK.
Export in VTK some more SPH-parameters.
Get a coordination number from body.
Use bool return type for force calculation.