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ChangeLog
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==================================================
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.
Add watercolumn example for SPH.
Add example script to test different kernel functions.
Add README to examples SPH.
Fix conflict.
Fix eigen3 inclusions.
Add one more example for sph.
Split all capillary function into smaller one.
Add YADE_SPH macroses to fix FTBFS, when SPH disabled
Minor fix (replace #ifdef by #endif)
Add an opportunity to change liquid volume during simulation.
Disable temporarly Cs calculation in SPH.
Fix interaction removal in VeiscoElPM
Store an information about active liquid contacts.
Add -= operator to OpenMPAccumulator.
Fix compilation with clang, when openmp is switched off.
Add OpenMPVector for thread-safe vector work.
Minor fix in installation section of documentation.
Export current value from PIDController.
Add a note in installation section of docs.
Do not link libloki and boost_date_time.
Fix scrolling direction for libQGLviewer > 2.5.0
One more minor fix in zooming.
Implement Liquid Migration model (experimental).
Replace LIQCONTROL by LIQMIGRATION.
Fix compilation with clang.
Set capillary parameters to 0. instead of -1.
Fix Id export in ymport.textClumps
Remove YADE_DEPREC_DOF_LIST prepocessor.
Add blockedMovement parameter to state of body
Add conveyor example.
Minor fix in documentation/installation.
Add mask parameter to NewtonIntegrator
Replace png-pictures by xpm.
Fix the beginning camera position in GUI.
Remove integrateInertia=False from packs.py.
Add discretization parameter to appendClumped.
Do not use getTorqueUnsynced and forces.getForceUnsynced in clumps
Make addForceTorqueFromMembers more readable.
Revert last change in Newtonintegrator.
One more revert in NewtonIntegrator.
Bruno Chareyre (60):
avoid crash when Vh==NULL in FlowEngine. The sphere is ignored in the flow problem, otherwise FlowEngine runs as usual.
Merge branch 'master' of github.com:yade/trunk
remove redundant "from yade import *" in example scripts, as it mess-up scopes
small change in PFV checkTest
fix a bug in ISCollider that would create interactions with unbounded bodies
remove deprecated code linked to queuing requestErase'd interactions in an older version of the collider
Merge pull request #39 from lsibille/master
Merge pull request #38 from Kubeu/patch-4
Merge pull request #37 from Kubeu/patch-3
Merge pull request #36 from Kubeu/patch-2
Better behavior of QGLViewer for shift+select and moving bodies (fixes LP bug 806469)
let libparmetis be used as an alternative of libmetis
Add hideBody/showBody to selectively display bodies in the 3D view
Merge pull request #40 from burak-er/master
Parallel InsertionSortCollider
fix compilation issues for ENABLE_OPENMP=OFF
some renaming and code cleaning in PFV code
some renaming and code cleaning in PFV code (part2)
PFV: First step in refactoring templates
dummy engine for showing how to derive from FlowEngine + a preliminary version of DFNFlow
make FlowEngine a template yade class
Periodic version of flow engine in separate source files
PFV: simplify (c++ wise) value assignement to Info types. More refactoring. Final step of code cleaning.
fix a bug in PFV code (fictious vetices not defined correctly)
minor changes in FlowEngine
remove a useless data member
fix compile error due to dirty hack (cpp's included by another cpp)
Added documentation for changing the velocity gradient of periodic cell
TriaxialStressController: reference sample sizes can be modified by users (was previously read-only)
ignore *~ files in git status
update biblio references
Hack YADE_CLASS macro to make it work with c++ templates (introduces a macro for pyClass name different from c++ class name)
new YADE_CLASS_PYCLASS_... macro, missing in previous commit
update bibliographic reference in a script
introduce CellInfo::getInfo() for more generic interpolation between triangulations
better detection of changes in Cell::velGrad
fix the example script periodic-simple-shear.py
- introduce SoluteFlowEngine (from Thomas Sweijen) - move Flow classes to a separate folder
fix include paths after moving files to pkg/pfv
fix include path pkg/pfv
Bugfixes in PeriodicFlowEngine, as discussed with Donia
remove useless FlowBoundingSphere.cpp
fix https://bugs.launchpad.net/yade/+bug/1301443
undef flag, so SoluteFlow doesn't break compilation on buildbot.
update about openblas+openmp on 12.04
initialize CellInfo members (avoids hardly detectable bugs) + remove artifact facets from loop when cell1==cell2
remove an inacurate reference, introduce another one
fix bad link to capillary files
clean of commented blocks
Merge pull request #43 from bchareyre/pc
fix gravity checkScript (es -> 'et')
enable run/pause from QGLViewer (retun key) + fix compile warning
remove empty file
add FlowEngine::doInterpolate to force interpolation during mesh swap
Add user defined boundary condition to FlowEngine
add authors in files headers
-fix bibliographic link
add missing #ifdef, breaking compilation without LINSOLV + better volume computation
fix compile error in 298f0b6
switch to 1-thread colliding when problem detected in parallel run (fix https://bugs.launchpad.net/yade/+bug/1314736)
Burak Er (1):
added an adaptive Runge Kutta integrator scheme. Also, added an example using this integrator.
Christian Jakob (15):
allow user to set an output folder for PFV-based saveVtk() method
Merge branch 'master' of github.com:yade/trunk
fix compilation bug in InsertionSortCollider.hpp
fix a bug in inertia tensor calculation for clumps if integrateInertia=True
extend/fix replaceByClumps() method for multiple overlapping clump templates
absorb bool integrateInertia from Clump::updateProperties by int discretization
Merge branch 'master' of github.com:yade/trunk
Parallelize replaceByClumps(): drastically reduce generation time of clump replacement if discretization>0
fix bugs in Clump::updateProperties, fixes https://bugs.launchpad.net/yade/+bug/1273172
introduce updateClumpProperties() method in yadeWrapper - can be used e.g. when clumps are imported in yade
update of O.bodies.erase(): it can erase clump members too when erasing a clump
Merge branch 'master' of github.com:yade/trunk
remove typenames from Polyhedra.cpp (fixes compiler error)
let ymport.textClumps() return all ids from members and clumps
fix some indents
Francois (2):
Undo modifications about ViscElMat into Ip2_FrictMat_FrictMat_FrictPhys. The young modulus and poisson ratio have to be set for both materials to perform a contact between a frictMat body and a viscElMat body. Add a comment for that.
Fix 2 bugs linked to the Grids : - in utils.py : remove a factor 2 in the calculation of the bending stiffness kr. - in Grid.cpp : fix a bug that occured in the Sphere-GridConnection contact. The contact was not detected in a very specific case : if the sphere was next to a node and the node goes from a convex (angle>180°) form to a concav (angle<180°) form.
Jan Stransky (13):
added vtk export of polyhedral particles
improvement of previous commit (vtk polyhedra export)
added example of paraview sphere "solid sections" improvement of export.textExt function to support arbitrary quantity export
added O.stopAtTime (question246284)
chenged return type of O.stopAtTime from previous commit
fixed some errors and warnings for documentation build
one more little info inside code
export.VTKExporter: improved comments, fixed bug (thanks Jan Havelka for reporting), updated corresponding example script
code cleanup in ConcretePM, fixed one more bug in export.VTKExporter
added exportContactPoints function to exporter.VTKExporter, updated example script
fixed export.VTKExporter.exportContactPoints for nonexisting interactions
Polyhedra implementation improvement (Contributed by Jan Elias)
modification of utils.calm function (bug 1318513)
Jerome Duriez (15):
Change in the doc of ymport.text/textExt to better reflect the behaviour
A doc sentence for pericell recorder in VTKRecorder
Typo in doc of CohFric Law2 : the shear adhesion is a_s, not a_n
Typos and link syntax in doc of CohFrictPhys
Typo correction in porosity() doc : porosity instead of poro sity (in 2 words)
Use of correct version of requestErase() in JCFpm (https://bugs.launchpad.net/yade/+bug/1273775)
Small changes in JCFpm IP logic : it is now possible to have new contacts that are always cohesive, and "poisson"=0 is possible (=> ks = 0 rather than infinity...)
Small improvement in JCFPM doc about the cracks file, and typo in user.rst
Mistake in hyperlink previous commit
Copy paste mistake in State and typo UniaxialStrainer doc
Proposal of correction of UniaxialStrainer, in relation with https://bugs.launchpad.net/yade/+bug/1300167
Add of an external reference, about the "derivation" of bodyStressTensor
Correction of copy-paste mistake in doc of Bound
Hyperlink about sortAxis in InsertionSortCollider doc
Minor changes (not affecting results) in these scripts towards an easier understanding
Klaus Thoeni (2):
Correct shear stiffness averaging for Ip2_FrictMat_FrictMat_ViscoFrictPhys
new simple contact law with normal viscose damping which allows to specify kn and ks/kn in Ip2
Kubeu (3):
Added Antons hint to first install external depencies of Yade before following installation instructions
small typo fix
typofix
Luc Sibille (10):
add test on alphaKtw to allow nil value of twisting stiffness
engine to compute a fluid flow with the lattice Boltzmann method LBM
Definition of the basic elements used by the LBM engine
definition of the compilation option ENABLE_LBMFLOW to make the compilation of the LBM engine optional, this option is disable by default
remove all LBM file
Merge remote-tracking branch 'upstream/master'
definition of the LBM engine inside a lbm directory, with license GPLv2
definition of the compilation option ENABLE_LBMFLOW to make the compilation of the LBM engine optional, this option is disable by default
A buoyancy example for the DEM-LBM coupling
Merge branch 'master' of github.com:yade/trunk
==================================================
yade-1.07.0
Fri, 10 Jan 2014 21:23:33 +0100
Anton Gladky (37):
Remove RELEASE file.
Add -ftrack-macro-expansion=0, if gcc>=4.8
Provide VTK6-support.
Use ADD_DEFINITIONS instead of adding those directly in CXX_FLAGS.
Remove information about yade-stable from Readme.
Add BicyclePedalEngine as a new kinematic motion.
Add -save-temps if GCC-4.8 is used.
Split Grid into Grid and Grid_GUI.
Add information about missing packages in documentation and external PPA. Closes: LP:1250928
Add notice about using libqglviewer-qt4-dev instead of libqglviewer-dev on older Ubuntu versions.
Add script to create PPA-packages. (Not finished)
Use othermirror for some ubuntu versions.
Add stl-gts example.
Add qt.View() to clumps-example.
Add one more check-script to check the functionality of ViscoElastic PM.
Consider massMultiply-parameter, calculating parameters in ViscoElasticPM.
Add functions to save and load clumps.
Set the higher pripority in sys.path to self-compiled modules. Closes LP:1254708
Fix volume calculation. Closes LP:1261415
Set the higher pripority in sys.path to self-compiled modules in yade-batch.
Update scripts for PPA.
Add configuration files, needed for PPA.
Minor update of PPA scripts.
Update information about yadedaily prebuilt packages.
Add support for qglviewer>=2.5.0.
Open GUI in packs/packs.py after 1 step to show all elements.
Raise warning, if no spheres are produced by regular* commands.
Update information about daily-packages.
Set one more paramter -ftemplate-depth-512 for clang
Prevent attraction forces in ViscPM due to viscosity
Add some more steps to checkWeight-script.
Minor formatting in references.
Remove cout accidentally added in a prev. commit.
Minor change of setFromTwoVectors in utils.py.
Rename createtar.py to buildppa.py.
Minor fix in docs.
Add RELEASE-file.
Bruno Chareyre (17):
a function to increase the size of a single sphere (~>Thomas swelling)
easier manipulation of state files in TesselationWrapper
restore the python wrapping of utils.growParticles() as it was before fb02a74 (changed by mistake, sorry Christian)
give unique identifiers to trangulation's cells
FlowEngine::nCells retruns the number of finite cells; FlowEngine::getVertices returns the vertices of a cell defined by its id
make cmake output more consistent when missing dependency for LinSolv
Fix the behavior of FlowEngine.updateTriangulation=True
FlowEngine: increment a counter correctly
small changes in the installation section regarding suitesparse and related libs
installation.rst: smallfix in indentation
remove a not necessary sorting in FlowEngine, as it triggers a critical bug in the STL (http://gcc.gnu.org/bugzilla/show_bug.cgi?id=58800)
correct target values of the DEM-PFV checktest
Fix paths to online and packaged documentation (fix url error with GUI's hyperlinks)
DEM Background chapter: a note on the semantic strain vs. displacement for contact kinematics
Merge branch 'master' of github.com:yade/trunk
fix undefined "key" in triax-tutorial/script-session1.py
+1 published paper
Christian Jakob (1):
small fix in an example script tetra/oneTetra.py
Francois (3):
Fix missing REGISTER_CLASS_INDEX(...) into ViscElPhys. This macro is essential for a right law dispatch !
Corrected a minor mistake in code comments : k=2*r*E
Allow the contact between (coh)frictMat and viscElMat as frictPhys. Almost everything was done by inheritance, just had to convert stiffnesses to modulus and modulus to stiffnesses to ensure material compatibility. Note that for the moment the timeStepper cannot handle this kind of simulations -> will be fixed soon.
Jan Stransky (4):
Modified error message if not yade.runtime.hasDisplay (bug #1241817)
fixed SyntaxError from previous commit
uncomment and modify utils.forcesOnCoordPlane function
corrected mistake in examples/test/triax.py
Jerome Duriez (15):
- Introducing (uncommenting in fact) tens/shearBreakRel variables in JCFpmState : relative part of broken interactions per body (instead of absolute number). - Few changes in some doc of JCFpm variables.
Quite important changes in JCFpm code
Modifying JCFpm example scripts so that they still work after previous commit
Re-put some commented lines, after discussion of this thread (https://lists.launchpad.net/yade-dev/msg10185.html), thanks Anton. The comments solution is (at the moment ?) finally still used to avoid putting a new variable in VTKRecorder..
A script example for JCFpm : two rock parts with one joint in the middle, like in laboratory experiments
Some forgotten corrections in some example scripts, so that they still work after changes of today in JCFpm
Some corrections in the JCFpm doc (hyperlinks...)
(Hopefully) Fixing some rst links in DEM Background doc
Some changes in the doc of getStress() function, to be consistent with the source code (https://answers.launchpad.net/yade/+question/239919)
Merge branch 'master' of github.com:yade/trunk
Idem as previous commit
Restoring the 2d version of growParticle previously erased by mistake..
Some hyperlinks in JCFpm doc corrected
Typos and hyperlinks corrected in Peri3dController doc
Correction of a link in TesselationWrapper() doc
Klaus Thoeni (1):
add CGAL link and delete libgmp3 from install list
Raphael Maurin (1):
Change in the calculation of the normal and tangential stiffness and damping. The change affects only the behavior when one of the two parameters is zero, e.g. for two particles with different stiffness k1 and k2, the contact stiffness will always be k = k1*k2/(k1+k2). Before it gave the same except when k2 = 0 (respectively k1 = 0), where it gave k = k1 (resp. k=k2). This is done to ensure continuity in the behavior when one of the two parameter tend to zero. Add a function contactParameterCalculation in Ip2_ViscElMat_ViscElMat_ViscElPhys to avoid code duplication.
==================================================
yade-1.05.0
Mon, Oct 28 19:49:48 2013 +0200
Anton Gladky (19):
Add system-component of boost to be linked.
Fix typo in equations in getViscoelasticFromSpheresInteraction (documentation). Thanks to Medack (TU Freiberg).
Explicitly link BZip2-library
Explicitly link ZLIB-library
Update installation docs, add libbz2-dev zlib1g-dev.
Fix LudingPM.
Rename variables in LudingPM (Theta->Delta).
Fix k2-calculation in LudingPM.
Update script for LudingPM.
Split gui/qt4/GLViewer.cpp.
Remove pkg/dem/DomainLimiter.*
Recover DomainLimiter (LawTester should be moved somewhere).
Remove some warnings.
Update numpy_boost.hpp from svn.
Remove executes bit on py, cpp and h-files.
Split Shop.cpp on Shop_01.cpp and Shop_02.cpp
Fix compilation.
Remove stable-PPA reference from documentation.
Replace all libboost-*-dev by libboost-all-dev.
Christian Jakob (19):
complete description of clump methods in users manual
fix a bug in inertia tensor approximation scheme
fix some links in users manual and Scene doc
fix description of default material in users manual
fixing/updating refs and links in users manual - part 1
removed SpherePadder description from users manual
fixing/updating refs and links in users manual - part 2 (finished)
adapt buoyancy example with new O.forces.addF() method and make it look nicer
update in Clump::updateProperties: included new bool integrateInertia and int discretization and adapt clump(), appendClumpend(), addToClump(), releaseFromClump(), replaceByClumps() and growParticles()
create links to some example scripts in wrapper
increase initialization speed of examples/packs/packs.py (fix https://bugs.launchpad.net/yade/+bug/1229783)
try to fix (still broken) refs in users manual
Merge branch 'master' of github.com:yade/trunk
make getRoundness() more flexible: empty excludeList is no more needed as input argument; adapt replaceByClumps-example.py and associated part in users manual
small fix in users manual
fix a link in TesselationWrapper
fix a link in TesselationWrapper (second try)
fix buoyancy example for clumps
removed typenames from Polyhedra.cpp, make gcc < version 4.7 happy
Donia (4):
Save the relative velocities of particles.
Compute edgesSurfaces if viscousShear is true.
Save the interactions only between spheres into a vector.
get the shear and normal viscous stress in each interaction.
Jan Stransky (10):
marginal modifications
Merge branch 'master' of github.com:yade/trunk
Added periodic cell VTK export (to VTKRecorder and export.VTKExporter)
Merge branch 'master' of github.com:yade/trunk
added forgotten example file
fixed bug in export.VTKExporter from one previous commits
Merge branch 'master' of github.com:yade/trunk
Polyhedra implementation + examples (Contributed by Jan Elias).
adding examples with tetrehadron modeled by new Polyhedron class
CombinedKinematicEngine will not call its 'dead' subengines (question #237437)
Jerome Duriez (6):
Correction of typo in comment
Proposal of new (similar but more compact) examples using JCFpm classes. A choice can be made one day after some feedback ?
Some changes in JCFpm documentation (add of external references, and removal of cross reference towards the CFpm model which does not exist anymore). In cpp, some commented lines to add (in the future ?) some post-pro features that could maybe break current saves of (existing ??) current users
Commiting changes discussed briefly in https://lists.launchpad.net/yade-dev/msg09979.html. Mainly written by L. Scholtes, they allow to vizualize with paraview some features of JCFpm classes. It adds then 2 recorders, "jcfpm" and "cracks", that are separated mainly for historical reasons.. They are anyway now documented
Add of pylab.ion() in plotNumInteractionsHistogram() and plotDirections() so that yade does not hang anymore after launch of these functions (even after closing the plot window, here). Still thanks to Vaclav ! (http://stackoverflow.com/questions/9753885/pylab-matplotlib-show-waits-until-window-closes)
Anecdotic changes in an example script
Klaus Thoeni (2):
resolve problem with mask in GridConnection
ignore local kdevelope specific files on git
==================================================
yade-1.00.0
Sun, Sep 29 23:10:48 2013 +0200
Anton Gladky (64):
Remove release file.
Add documentation, how to render particle with ParaView`s PointSprite plugin.
Fix spelling errors.
Add Changelog.
Add different capillar models into ViscoElasticPM.
Add links to equations, consider not only monodisperse particles.
Fix s parameter for Willet-formulation of capillar.
Add one more critical-calculation to capillar model.
Cleanings in viscoelastic capillar modell.
Move capillar calculation into another function not to overload VPM.
Modify Weigart`s model.
Update equations for Weigart`s capillar model.
Update capillar equations and names of schemas.
Move references to a references.bib.
Add comment on liquid bridges.
Fix some warnings (clang).
Fix compilation.
Implement rotational resistance in ViscoElasticPM.
Add massMultiply-parameter to ViscoElasticPM to have an opportunity to set kn, kt, cn and ct without multiplication on mass.
Implement Rabinovich`s capillar model.
Fix wrong calculation of the average rotational resistance.
Split ViscoelasticPM on capillar and dry parts.
Prevent devision by 0 in capillar Rabinovich model.
Prepare for flowengine compilation.
Merge libplugins, libsupport and libcore in libyade.
Fix FindCholmod.cmake.
Fix compilation of FlowBoundingSphere.ipp
Replace Cholmod-Feature by LinSolv.
Minor fix in CMakeList (FlowEnginge).
Implement PID controller to have a servo-engine.
Fix tests due to failing clumps-autotests.
Use combinedengine for ServoPIDController.
Fix hopefully clumps-autotests.
Add LudingPM.
Merge branch 'ndyck'
Add an example for LudingPM.
Use libyade again. Revert Bruno`s revert.
Fix configuration issue with CHUNKSIZE>0.
Drop RockPM.
Remove ParticleSizeDistrbutionRPMRecorder.
Remove CohesiveStateRPMRecorder.
Show PFVflow and LinSolv in disabled features, if they are disabled.
Include loki-library dirs and link against them. Fixes compilation on HPC TU Freiberg.
Set LinSolv and PFVFLOW ON by default.
Add recommended build-dependency for LinSolv and PFVFlow into documentation.
Replace ifndef/define-constructions by "#pragma once" in lib/triangulation, where it is possible.
Minor fix in capillary models in ViscoelasticPM.
Add [Pournin2001] into the description of ViscoelasticPM.
Minor fix in calculation s_crit in ViscoelasticPM.
Add information about github-hosting into the main page.
Add a notification to the screen, whether the current build is debugbuild.
Remove explicit linking of libstdcxx.
Use skipScripts variable to skip some scripts on check-tests.
Skip temporarly DEM-PFV-check.py to let daily-builds packages be built.
Remove kde-files from the trunk.
Minor fix in installation section of documentation.
Remove Fedora list package from documentation. The list is unsupported.
Add Antypov2011 reference and some links in Hertz-Mindlin model.
Fix some compilation warnings (GCC).
Replace libqglviewer-qt4-dev on libqglviewer-dev in installation section.
Fix errors in ForceContainer, detected by clang.
Fix compilation error.
Add export into LIGGGHTS-format.
1.00.0
Bruno Chareyre (68):
+1 journal article
Add the color of the periodic cell a registered attribute.
- fix a bug that would let the capillary tables empty when postLoad was not triggered
Add function getCapillaryStress(), equivalent of getStress() but for capillary forces
-code cleaning
fix a latex equation
FlowEngine: exclude corner cases when listing constrictions sizes along the void path
+1 article
-fix url of an article
+4 journal papers
+1 journal article
- add "LINSOLV" source code for DEM-PFV coupling with direct sparse solvers
add strainRate attribute to TriaxialStressController + fix bug in example script
Revert "Merge libplugins, libsupport and libcore in libyade." Cause: the new cmake system breaks buildbot and does not work for chunkSize>0
- add getSceneAsString() to pass scenes between instances without going through the hard drive
fix CMakeList for chunkSize>=1
- enable load/save from/to python strings with O.sceneToString and O.stringToScene (for communication between parallel instances of yade)
-fix the return type of stringToScene()
clean the flow code (part 1)
cleaning the flow code (smallfix of part 1)
cleaning the flow code (part2)
cleaning the flow code (part3 and last)
-first example script for the fluid coupling with the DEM-PFV method
- new conference and journal papers
fixed reference
+1 PhD thesis
- more documentation of TesselationWrapper, with a section in user manual and pointer to published equations.
git ignore changes to .gitignore
undo previous change in gitignore, not the right way to fix
Turn a LOG_DEBUG into LOG_ERROR/return, to escape segfault. (ref: https://bugs.launchpad.net/bugs/1208878)
Add an optional argument to O.forces.f() and O.forces.t() to get correct forces on clumps.
doc improvement and more cross-links for TesselationWrapper and FlowEngine
-enable user defined forces on bodies applying permanently (with updated user manual)
+1 conference paper
-workaround https://bugs.launchpad.net/yade/+bug/1183402#3, allowing startup imports with optional argument example: $yade -lscipy.interpolate
-fix '-l' command line option (no import lib was crashing)
fix uninitialized member of ForceContainer
fix compile warnings (unused variables)
- smallfixes in documentation
fix FlowEngine docstring
fix duplicate bib reference
small fix in bib entries
remove duplicate bib reference
commit small fix and update in bib files
make default FlowEngine::permeabilityFactor less absurd (crashing by default sucks)
regression (check-)test for FlowEngine
remove Dem3Dof form Yade (also eudoxos module, mostly based on Dem3Dof)
- remove Dem3Dof from documentation
remove eudoxos from build system (+ remove from VTKRecorder, that was left behind)
remove Dem3Dof from a docstring
remove Dem3Dof from alias
various fixes and improvements in checkTests
- increase verbosity of DEM-PFV checkTest
remove some debugging code left in chekList.py
make sure FlowEngine has been compiled before trying the checkTest DEM-PFV, as suggested by Klaus
make the DEM-PFV checktest fully determinist with a data file for initial positions
new attributes in FlowEngine to access low level cholmod/metis data
\#include <cholmod.h> in FlowEngine.cpp (why is it not needed on lucid?!)
add #ifdef LINSOLV guards in appropriate places in case someone (e.g. buildbot) compiles without cholmod
one more #ifdef LINSOLV guard
add a cmake path for metis.h on wheezy
Return a warning at startup if X rendering is unavailable despite gui is required.
User manual: correct the meaning of body.dynamic + remove utils. prefixes
Typo fix in prog.rst
Fix sphinx warning (no :gui: role)
yadeSphinx.py: remove eudoxos module from the build list
-remove empty section of doc: External modules
revert 3d7ca8577 (doc/current hyperlink), see also https://lists.launchpad.net/yade-dev/msg10035.html.
Chiara Modenese (1):
Prevent the normal force become negative when viscous damping is applied.
Christian Jakob (23):